Biology Commons^™

Using Student-Generated Uv-Induced Escherichia Coli Mutants In A Directed Inquiry Undergraduate Genetics Laboratory, Frank G. Healy, Kevin D. Livingstone

Biology Faculty Research

We report a thematic sequence of directed inquiry-based labs taking students from bacterial mutagenesis and phenotypic identification of their own self-created mutant, through identification of mutated genes by biochemical testing, to verification of mutant alleles by complementation, and finally to mutant allele characterization by DNA sequence analysis. The lab utilizes UV mutagenesis with wild-type Escherichia coli and a UV-sensitive isogenic derivative optimized for undergraduate use. The labs take advantage of the simplicity of E. coli in a realistic genetic investigation using safe UV irradiation methods for creation and characterization of novel mutants. Assessment data collected over three offerings of the …

The Role Of Oxidative Stress In Setting Thermal Tolerance Limits In Mytilus, Lars Tomanek

Biological Sciences

No abstract provided.

Nonylphenol In Marine Organisms In North American Estuaries: Trophic Chain Accumulation And Proteomic Responses, Lars Tomanek, J. M. Diehl, S. E. Johnson, K. Xia, S. J. Teh

Biological Sciences

No abstract provided.

Widespread Over-Expression Of The X Chromosome In Sterile F-1 Hybrid Mice, Jeffrey M. Good, Thomas Giger, Matthew D. Dean, Michael W. Nachman

Biological Sciences Faculty Publications

The X chromosome often plays a central role in hybrid male sterility between species, but it is unclear if this reflects underlying regulatory incompatibilities. Here we combine phenotypic data with genome-wide expression data to directly associate aberrant expression patterns with hybrid male sterility between two species of mice. We used a reciprocal cross in which F-1 males are sterile in one direction and fertile in the other direction, allowing us to associate expression differences with sterility rather than with other hybrid phenotypes. We found evidence of extensive over-expression of the X chromosome during spermatogenesis in sterile but not in fertile …

Gender Dimorphism In The Exercise-Naïve Murine Skeletal Muscle Proteome, Lauren Ann Metskas, Mohini Kulp, Stylianos P. Scordilis

Biological Sciences: Faculty Publications

Skeletal muscle is a plastic tissue with known gender dimorphism, especially at the metabolic level. A proteomic comparison of male and female murine biceps brachii was undertaken, resolving an average of 600 protein spots of MW 15–150 kDa and pI 5–8. Twenty-six unique full-length proteins spanning 11 KOG groups demonstrated statistically significant (p<0.05) abundance differences between genders; the majority of these proteins have metabolic functions. Identified glycolytic enzymes demonstrated decreased abundance in females, while abundance differences in identified oxidative phosphorylation enzymes were specific to the proteins rather than to the functional group as a whole. Certain cytoskeletal and stress proteins showed specific expression differences, and all three phosphorylation states of creatine kinase showed significant decreased abundance in females. Expression differences were significant but many were subtle (≤ 2-fold), and known hormonally-regulated proteins were not identified. We conclude that while gender dimorphism is present in non-exercised murine skeletal muscle, the proteome comparison of male and female biceps brachii in exercise-naive mice indicates subtle differences rather than a large or obviously hormonal dimorphism.

Bio-Inspired Materials And Devices For Chemical And Biological Defense, James J. Valdes, Erica R. Valdes

Defense and Technology Papers

This report addresses materials for synthetic matrices of chemical and biological defense using a conceptual platform known as the abiotic networked threat system (ANTS). This system is based on lessons learned from biology, incorporating abiotic homologues to biological recognition events and metabolic pathways to provide programmable capabilities to sense and respond to environmental threats.

Conidia But Not Yeast Cells Of The Fungal Pathogen Histoplasma Capsulatum Trigger A Type I Interferon Innate Immune Response In Murine Macrophages, Diane O. Inglis, Charlotte A. Berkes, Davina R. Hocking Murray, Anita Sil

Biology Faculty Publications

Histoplasma capsulatum is the most common cause of fungal respiratory infections and can lead to progressive disseminated infections, particularly in immunocompromised patients. Infection occurs upon inhalation of the aerosolized spores, known as conidia. Once inside the host, conidia are phagocytosed by alveolar macrophages. The conidia subsequently germinate and produce a budding yeast-like form that colonizes host macrophages and can disseminate throughout host organs and tissues. Even though conidia are the predominant infectious particle for H. capsulatum and are the first cell type encountered by the host during infection, very little is known at a molecular level about conidia or about …

Repression Of Wnt Signaling By A Fer-Type Nonreceptor Tyrosine Kinase, Aaron P. Putzke

Biology Faculty Scholarship

The Wnt signaling pathway must be properly modulated to ensure an appropriate output: pathological conditions result from either insufficient or excessive levels of Wnt signal. For example, hyperactivation of the Wnt pathway is associated with various cancers and subnormal Wnt signaling can lead to increased invasiveness of tumor cells. We found that the Caenorhabditis elegans ortholog of the Fer nonreceptor tyrosine kinase, FRK-1, limits Wnt signaling by preventing the adhesion complex-associated β-catenin, HMP-2, from participating in Wnt-dependent specification of the endoderm during embryogenesis. Removal of FRK-1 function results in relocalization of HMP-2 to the nucleus of epidermal cells, and allows …

The Biopax Community Standard For Pathway Data Sharing, E. Demir, M. P. Cary, S. Paley, K. Fukuda, C. Lemer, I. Vastrik, G. Wu, P. D’Eustachio, C. Schaefer, J. Luciano, F. Schacherer, I. Martinez-Flores, Z. Hu, V. Jimenez-Jacinto, G. Joshi-Tope, K. Kandasamy, A. C. Lopez-Fuentes, H. Mi, E. Pichler, I. Rodchenkov, A. Splendiani, S. Tkachev, J. Zucker, G. Gopinath, H. Rajasimha, R. Ramakrishnan, I. Shah, M. Syed, N. Anwar, O. Babur, M. Blinov, E. Brauner, D. Corwin, S. Donaldson, F. Gibbons, R. Goldberg, R. Hornbeck, A. Luna, P. Murray-Rust, E. Neumann, O. Reubenacker, M. Samwald, M. Van Iersel, S. Wimalaratne, K. Allen, B. Braun, M. Whirl-Carrillo, K. H. Cheung, Kam D. Dahlquist, A. Finney, M. Gillespie, E. Glass, L. Gong, M. Honig, O. Hubaut, D. Kane, S. Krupa, M. Kutmon, J. Leonard, D. Marks, D. Merberg, V. Petri, A. Pico, D. Ravenscroft, L. Ren, N. Shah, M. Sunshine, R. Tang, R. Whaley, S. Letovksi, K. H. Buetow, A. Rzhetsky, V. Schachter, B. S. Sobral, U. Dogrusoz, S. Mcweeney, M. Aladjem, E. Birney, J. Collado-Vides, S. Goto, M. Hucka, N. Le Novère, N. Maltsev, A. Pandey, P. Thomas, E. Wingender, P. D. Karp, C. Sander, G. D. Bader

Biology Faculty Works

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic …

Nona-Arginine Facilitates Delivery Of Quantum Dots Into Cells Via Multiple Pathways, Yi Xu, Betty Revon Liu, Han Jung Lee, Katie Shannon, Jeffrey G. Winiarz, Tien-Chun Wang, Huey-Jenn Chiang, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

Semiconductor quantum dots (QDs) have recently been used to deliver and monitor biomolecules, such as drugs and proteins. However, QDs alone have a low efficiency of transport across the plasma membrane. In order to increase the efficiency, we used synthetic nona-arginine (SR9), a cell-penetrating peptide, to facilitate uptake. We found that SR9 increased the cellular uptake of QDs in a noncovalent binding manner between QDs and SR9. Further, we investigated mechanisms of QD/SR9 cellular internalization. Low temperature and metabolic inhibitors markedly inhibited the uptake of QD/SR9, indicating that internalization is an energy-dependent process. Results from both the pathway inhibitors and …

Selection For Non-Amyloidogenic Mutants Of Islet Amyloid Polypeptide (Iapp) Identifies An Extended Region For Amyloidogenicity, Ayano Fox, Thibaut Snollaerts, Camille Errecart Casanova, Anastasia Calciano, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-residue polypeptide IAPP, as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type II diabetes. While IAPP has been known to be the primary component of type II diabetes amyloid, the molecular interactions responsible for this aggregation have not been identified. To identify the aggregation-prone region(s), we constructed a library of randomly generated point mutants of IAPP. This mutant IAPP library was expressed in E. coli as genetic fusions to the reporter protein enhanced green fluorescent protein (EGFP). Because IAPP aggregates rapidly, both …

Bioluminescent Escherichia Coli Strains For The Quantitative Detection Of Phosphate And Ammonia In Coastal And Suburban Watersheds, Cristina V. Cardemil , '01, D. R. Smulski, R. A. Larossa, Amy Cheng Vollmer

Biology Faculty Works

Accumulation of phosphate and ammonia in estuarine systems and subsequent dinoflagellate and algal blooms has been implicated in fish kills and in health risks for fishermen. Analytic chemistry kits are used to measure phosphate and ammonia levels in water samples, but their sensitivity is limited due to specificity for inorganic forms of these moieties. An Escherichia coli bioluminescent reporter system measured the bioavailability of inorganic nutrients through fusion of E. coli promoters (phoA or glnAp2) to the luxCDABE operon of Vibrio fischeri carried either on the chromosome or on a multicopy plasmid vector, resulting in emission of light in response …

Maternal Health Behaviours During Pregnancy And Associations With Infant Feeding Factors, Roslyn Tarrant, Katherine Younger, Margaret Sheridan-Pereira, John Kearney

Other resources

Maternal health behaviours during pregnancy and associations with postnatal infant feeding practices

Objectives: To examine modifiable maternal health behaviours during pregnancy, including folic acid use peri-conceptually, smoking and alcohol consumption patterns, and relate these factors to maternal postnatal infant feeding practices.

Materials and Methods: A prospective observational study involved the recruitment of 539 pregnant women from a Dublin maternity hospital. Following application of exclusion criteria, 450 mothers were followed up at 6 weeks and 6 months postpartum. Quantitative data on folic acid use, as well as mothers’ smoking and alcohol consumption patterns during pregnancy were collected from the antenatal questionnaire. …

Discrimination Of Human And Non-Human Sources Of Pollution In Gulf Of Mexico Waters By Microbial Source Tracking Methods And The Investigation Of The Influence Of Environmental Factors On Escherichia Coli Survival, Asja Korajkic

USF Tampa Graduate Theses and Dissertations

Water quality worldwide is assessed by enumeration of fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli, and enterococci) intended to act as surrogates for human enteric pathogens. In environmental waters, this predictive relationship is confounded by many possible sources of FIB with varying implications for human health. Many physico-chemical and biological factors influence the fate of enteric pathogens and FIB in aquatic habitats, but are poorly understood, thus limiting our understanding of the usefulness of FIB as fecal pollution indicators.

These studies explored the field application of a “toolbox” approach to microbial source tracking (MST) intended to discriminate between human …

Evolution Of The Hammerhead Cephalofoil: Shape Change, Space Utilization, And Feeding Biomechanics In Hammerhead Sharks (Sphyrnidae), Kyle Reid Mara

USF Tampa Graduate Theses and Dissertations

The relationship between form and function is often used to elucidate the biological role of a structure. Hammerhead sharks offer a unique opportunity to study form and function through phylogeny. Because sphyrnid sharks display a range of cranial morphologies this group can be used to address questions about the evolution of cranial design and investigate the effects of changes in head morphology on feeding structures and bite force. Geometric morphometrics, volumetric analyses, morphological dissections, and phylogenetic analyses of the cephalofoil were used to gain insight into changes in cranial design through evolutionary history. External morphometrics and internal volumetric analyses indicated …

Predicting The Distribution Of Air Pollution Sensitive Lichens Using Habitat Niche Modeling, Gajendra Shrestha

Theses and Dissertations

Usnea hirta and Xanthoparmelia cumberlandia are commonly used as bio-monitors of air quality. In order to more accurately and efficiently determine the distribution of these two sensitive indicator species, we have developed a probabilistic distribution map as a function of 9 macroclimatic and topographic variables for the White River National Forest, Colorado using Non-Parametric Multiplicative Regression (NPMR) analysis. Furthermore, we also developed a logistic regression (LR) model for X. cumberlandia in order to evaluate the strengths and limitations of the NPMR model. The best model for U. hirta included four variables - solar radiation, average monthly precipitation, average monthly minimum …

Ecological Thresholds In Marine Communities: Theory, Experiments And Management. In Threshold Dynamics In Marine Coastal Systems (Theme Section), Richard W. Osman, Pablo Munguia, Roman Zajac

Biology and Environmental Science Faculty Publications

There is increasing interest in the resilience of marine and estuarine populations, communities and ecosystems, and their rapid change when stresses reach some threshold or tipping point. Current research on thresholds is altering our understanding of these systems, the processes by which they change, and our approach to their management and restoration. In this Theme Section conceptual, modeling, and empirical studies explore threshold dynamics in marine coastal systems in a variety of habitats and across different scales. The contributions provide a window on present research, highlight some of the issues being debated, and point to some of the potential applications …

Differential Expression Of N-Methyl-D-Aspartate Receptors Of Cynprinidae, Taito Eguchi

Honors Capstone Projects and Theses

No abstract provided.

The Histology And Histochemistry Of Rathke's Glands In The Mississippi Mud Turtle, Kinosternon Subrubrum Hippocrepis, Sarah Jean Webb

Student Theses and Dissertations

Rathke's glands are found in both extinct and extant turtle species, specifically in both megaorders Pleurodira and Cryptodira. The glands are homologous in all turtles and are thought to be the most ancient vertebrate integumentary gland. The anatomy of Rathke's glands in the Mississippi mud turtle, Kinosternon subrubrum hippocrepis, was examined in this study. Light and scanning electron microscopy were utilized, along with histochemical methods, for the examination of the glands. Museum specimens collected from eight counties within Arkansas from 1989-2009 were examined. This species has two pairs of glands, one axillary and one inguinal, which are usually bi-lobed. The …

Demographics And Terrestrial Ecology Of An Amphibian Community In A Large Ephemeral Pond In The Ozark Mountains, Corey Lynn Shaffer

Student Theses and Dissertations

This thesis examines the aquatic and terrestrial ecology of an amphibian community at an ephemeral pond in the Ozark Mountains. Literature on amphibian community assemblage is reviewed, and reasons for species abundance at the pond (hydrology, interspecific interactions, and terrestrial habitat requirements) are inferred. Sixteen species were observed using Stout Pond. Emigration orientation, distance of migration, and terrestrial macrohabitat use are assessed for some species. Emigration was concentrated in the south and southwest toward northeastern hillsides. Species avoided pine forests in the southeast and younger forests in the northwest. On average, species migrated from 80-200 m to reach terrestrial home …

Alternative Processing Of Scrambled Genes Generates Protein Diversity In The Ciliate Chilodonella Uncinata, Laura A. Katz, Alexandra M. Kovner

Biological Sciences: Faculty Publications

In ciliates, chromosomal rearrangements occur during the development of the somatic macronuclear genome from the germline micronuclear genome. These rearrangements are extensive in three ciliate classes-Armophorea, Spirotrichea, and Phyllopharyngea-generating a macronucleus with up to 20,000,000 gene-sized chromosomes. Earlier, we have shown that these three classes also share elevated rates of protein evolution relative to other ciliates. To assess the evolution of germline-limited sequences in the class Phyllopharyngea, we used a combination of traditional and walking PCR to analyze micronuclear copies of multiple genes from two lines of the morphospecies Chilodonella uncinata for which we had previously characterized macronuclear sequences. Analyses …

Notonecta Exhibit Threat-Sensitive, Predator-Induced Dispersal, Shannon J. Mccauley, Locke Rowe

Biological Sciences

Dispersal is a central process determining community structure in heterogeneous landscapes, and species interactions within habitats may be a major determinant of dispersal. Although the effects of species interactions on dispersal within habitats have been well studied, how species interactions affect the movement of individuals between habitats in a landscape has received less attention. We conducted two experiments to assess the extent to which predation risk affects dispersal from an aquatic habitat by a flight-capable semi-aquatic insect (Notonecta undulata). Exposure to non-lethal (caged) fish fed conspecifics increased dispersal rates in N. undulata. Moreover, dispersal rate was positively correlated with the …

Potential Biases In Estimating The Rate Parameter Of Sigmoid Growth Functions, Robert Ricklefs, Suzanne Austin, Tara Robinson, W. Robinson

Biology Department Faculty Works

1. We compare biases in estimates of the rate constant of the logistic and Gompertz functions applied to avian growth using three methods of parameter estimation. The methods differ in how the asymptote is determined, and consist of either floating asymptotes estimated from the full data (floating A) or data truncated at 70% of the adult mass (70%A), or fixing the asymptote at the adult mass (fixed A).2. First, using data for two passerine species exhibiting different growth patterns, we truncated mass measurements at different ages to explore how each method of growth rate estimation responded to simulated differences in …

Acaricidal Activity Of Eugenol Based Compounds Against Scabies Mites, Cielo Pasay, Kate Mounsey, Graeme Stevenson, Rohan Davis, Larry G. Arlian, Marjorie Morgan, Diann Vyszenski-Moher, Kathy Andrews, James Mccarthy

Biological Sciences Faculty Publications

Background

Human scabies is a debilitating skin disease caused by the “itch mite” Sarcoptes scabiei. Ordinary scabies is commonly treated with topical creams such as permethrin, while crusted scabies is treated with topical creams in combination with oral ivermectin. Recent reports of acaricide tolerance in scabies endemic communities in Northern Australia have prompted efforts to better understand resistance mechanisms and to identify potential new acaricides. In this study, we screened three essential oils and four pure compounds based on eugenol for acaricidal properties.

Methodology/Principal Findings

Herbivore And Fungal Pathogen Exclusion Aects The Seed Production Of Four Common Grassland Species, Timothy L. Dickson, Charles E. Mitchell

Biology Faculty Publications

Insect herbivores and fungal pathogens can independently affect plant fitness, and may have interactive effects. However, few studies have experimentally quantified the joint effects of insects and fungal pathogens on seed production in non-agricultural populations. We examined the factorial effects of insect herbivore exclusion (via insecticide) and fungal pathogen exclusion (via fungicide) on the population-level seed production of four common graminoid species (Andropogon gerardii, Schizachyrium scoparium, Poa pratensis, and Carex siccata) over two growing seasons in Minnesota, USA. We detected no interactive effects of herbivores and pathogens on seed production. However, the seed production of …

Invasive Predators Deplete Genetic Diversity Of Island Lizards, Amandine Gasc, M. C. Duryea, Robert M. Cox, Andrew Kern, Ryan Calsbeek

Dartmouth Scholarship

Invasive species can dramatically impact natural populations, especially those living on islands. Though numerous examples illustrate the ecological impact of invasive predators, no study has examined the genetic consequences for native populations subject to invasion. Here we capitalize on a natural experiment in which a long-term study of the brown anole lizard (Anolis sagrei) was interrupted by rat invasion. An island population that was devastated by rats recovered numerically following rat extermination. However, population genetic analyses at six microsatellite loci suggested a possible loss of genetic diversity due to invasion when compared to an uninvaded island studied over …

Pismo Beach Fecal Contamination Source Identification Study: Final Report, Christopher L. Kitts, Michael W. Black, Mark M. Moline, Marie Yeung, Alice K. Hamrick, Ian C. Robbins, Andrew A. Schaffner, Nathania I. Boutet

Biological Sciences

No abstract provided.

A Detailed Phylogenetic Analysis Of Fiv In The United States, Eric A. Weaver

School of Biological Sciences: Faculty Publications

Background: Feline immunodeficiency virus (FIV) is a lentivirus associated with AIDS-like illnesses in cats and has been used as a model for the study of human immunodeficiency virus (HIV). A feature of HIV and FIV infection is the continually increasing divergence among viral isolates between different individuals, as well as within the same individuals.

Methodology/Principal Findings: The goal of this study was to determine the phylogenetic patterns of viral isolates obtained within the United States (U.S.) by focusing on the variable, V3-V4, region of the FIV envelope gene.

Conclusions/Significance: Data indicate that FIV, from within the U.S., localize to four …

The Identity Of Zachaenus Roseus Cope, 1890 (Anura: Species Inquirenda), Esteban O. Lavilla, J. J. Nuñez, F. E. Rabanal, José A. Langone, Rafael O. De Sá

Biology Faculty Publications

Zachaenus roseus Cope, 1890, has puzzled systematists working in southern South America. A single individual, the holotype, has ever been collected and this specimen is in extremely poor preservation condition. Herein, the precise location of the type locality of Z. roseus is determined based on a historical review of the literature. Furthermore, following a careful comparison with all species that inhabit the southern austral forest, and that could potentially correspond to Zachaenus roseus, we conclude that this taxon is placed in the synonymy of Eupsophus calcaratus (Günther, 1881)

Model Detection Based Upon Amino Acid Properties, Kit J. Menlove

Theses and Dissertations

Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. Homology detection is one of the most …