Biology Commons^™

Towards Elucidation Of A Viral Dna Packaging Motor, Chad T. Schwartz

Theses and Dissertations--Pharmacy

Previously, gp16, the ATPase protein of phi29 DNA packaging motor, was an enigma due to its tendency to form multiple oligomeric states. Recently we employed new methodologies to decipher both its stoichiometry and also the mechanism in which the protein functions to hydrolyze ATP and provide the driving force for DNA packaging. The oligomeric states were determined by biochemical and biophysical approaches. Contrary to many reported intriguing models of viral DNA packaging, it was found that phi29 DNA packaging motor permits the translocation of DNA unidirectionally and driven cooperatively by three rings of defined shape. The mechanism for the generation …

Effects Of Streamside Management Zone Timber Harvest On Salamander Communities In Robinson Forest, Thomas Maigret

Theses and Dissertations--Forestry and Natural Resources

Salamanders are critical components of forest ecosystems, in terms of total biomass, as well as for their value as indicators of ecosystem stress. Considering the worldwide decline in amphibian populations, the known effects of timber harvest on salamander populations, and the importance of the forest products industry in Kentucky and elsewhere, the impacts of silvicultural operations on salamander communities cannot be overlooked. The objective was to investigate the effects of three different silvicultural treatments, each involving different streamside management zone (SMZ) characteristics, on salamander communities in ephemeral streams. Data were collected by regular checks of pitfall traps, coverboards, and transect …

Equine Serum Antibody Responses To Streptococcus Equi And Streptococcus Zooepidemicus, Rafaela De Negri

Theses and Dissertations--Veterinary Science

Streptococcus zooepidemicus (Sz) and Streptococcus equi (Se) share 98% DNA sequence homology, but display different pathogenic properties. Infection by one organism does not cross-protect against the other. To better understand pathogenic differences between these organisms and gain information about which proteins are expressed in horses infected experimentally with Se, intrauterine Sz or naturally with respiratory Sz we compared antibody specificities of convalescent sera using ELISA. These comparisons were based on sets of 8 and 14 immunoreactive recombinant proteins of Se strain CF32 and Sz strain NC78, respectively. Sera from donkeys that were previously naturally affected with strangles and later developed …

Individual And Population Responses Of The Caribbean Sponge, Aplysina Cauliformis, To Natural And Anthropogenic Stressors, Cole Gregory Easson

Electronic Theses and Dissertations

Coral reefs are under increasing threat from a diversity of stressors. These reefs have undergone a phase shift from coral-dominated to algal-dominated ecosystems, and in many cases other functional groups such as sponges are now the predominant organisms on many reefs. This dissertation investigated the responses of a combranching sponge, Aplysina cauliformis, to algal contact, eutrophication, hurricanes, and disease. The effects of algal competition, anthropogenic nutrients and a combination of these stressors on A. cauliformis were examined using factorial designed field experiments on Bahamian reefs. These experiments demonstrated a complex interaction between sponge and alga, in which the green alga, …

Enhancing Pcr Amplification Of Dna From Recalcitrant Plant Specimens Using A Trelahose-Based Additive, Tharangamala Samarakoon, Shiao Y. Wang, Mac H. Alford

Faculty Publications

Premise of the study: PCR amplification of DNA extracted from plants is sometimes difficult due to the presence of inhibitory compounds. An effective method to overcome the inhibitory effect of compounds that contaminate DNA from difficult plant specimens is needed.

Methods and Results: The effectiveness of a PCR additive reagent containing trehalose, bovine serum albumin (BSA), and polysorbate‐20 (Tween‐20) (TBT‐PAR) was tested. PCR of DNA extracted from fresh, silica‐dried, and herbarium leaf material of species of Achariaceae, Asteraceae, Lacistemataceae, and Samydaceae that failed using standard techniques were successful with the addition of TBT‐PAR.

Conclusions: The addition of TBT‐PAR during routine …

Neutrophil In Viral Infections, Friend Or Foe?, Brandon D. Drescher, Fengwei Bai

Faculty Publications

Polymorphonuclear leukocytes or neutrophils are the first immune cells to the site of injury and microbial infection. Neutrophils are crucial players in controlling bacterial and fungal infections, and in particular secondary infections, by phagocytosis, degranulation and neutrophil extracellular traps (NETs). While neutrophils have been shown to play important roles in viral pathogenesis, there is a lack of detailed investigation. In this article, we will review recent progresses toward understanding the role of neutrophils in viral pathogenesis. (C) 2012 Elsevier B.V. All rights reserved.

A Population Genetic Study Of The Fish Rhinichthys Cataractae In Northeast Iowa Using Microsatellite Genotype Data, Haley Ann Rinehart

Honors Program Theses

Rhinichthys cataractae has a wide distribution across the country and can be found in the majority of temperate habitats across North America (Girard & Angers, 2011). Similar to other species that inhabit northeast Iowa streams, its present-day distribution has been heavily influenced by Pleistocene glaciations (Girard & Angers, 2006). Corresponding to the distinct landscape and glacial history of northeast Iowa, the longnose dace is distributed almost exclusively in the northeast comer of Iowa (Figure 3). Investigation of the genetic diversity of this species will help clarify what steps need to be taken to ensure their survival and success, and may …

Evolutionary Biology For The 21st Century, Jonathan B. Losos, Stevan J. Arnold, Gill Bejerano, E. D. Brodie, David Hibbett, Hopi E. Hoekstra, David P. Mindell, Antónia Monteiro, Craig Moritz, H. Allen Orr, Dmitri A. Petrov, Susanne S. Renner, Robert E. Ricklefs, Pamela S. Soltis, Thomas L. Turner

Biology

Theodosius Dobzhansky famously proclaimed that “nothing makes sense in biology except in the light of evolution." Though Dobzhansky's statement is sometimes dismissed by biologists in other fields as self-promotion, recent advances in many areas of biology have shown it to be prophetic. For example, genomics, which emerged mostly from molecular biology, is now steeped in evolutionary biology. Evolutionary theory helps to explain our origins, our history, and how we function as organisms and interact with other life forms, all of which are crucial to understanding our future (e.g., [1]–[5]). Evolutionary approaches have helped reconstruct the history of …

Effects Of Short-Term Dewatering On Grazer Abundance And Algal Biomass In A Wastewater Treatment Algal Turf Scrubber, Emily Husted

Theses and Dissertations

Finding a new, clean, and sustainable energy source to replace fossil fuels is one of society’s most daunting challenges. Algae biomass is a promising renewable resource for biofuel production due to its efficient conversion of solar energy into chemical energy. Algal turf scrubbers (ATS™) systems mimic natural streams, flowing wastewater over hard substrates designed to encourage attached algae growth. This study focuses on the use of replicated ATS™ systems, because they are low maintenance, are effective for removing nutrient pollutants, model natural stream ecosystems, and can produce large volumes of harvestable algal feedstock for biofuel production. A challenge that occurs …

Biology News, Winter 2013, University Of Northern Iowa. Department Of Biology.

Biology News

Contents:

-- Greetings from the Department of Biology
-- Focus on UNI Biology Alumni
-- Focus on UNI Biology Students
-- Microscopes purchased with Carver Trust Grant
-- Two-headed planarian!
-- UNI Day in the Capitol on February 11, 2013
-- Letter of appreciation......
-- Dr. Kimberly Cline-Brown Receives Excellence in Teaching Award
-- Joan Smothers attends national advising meeting
-- Public speaking engagements for Biology faculty
-- Pre-Vet Club project gives aid to shelter animals
-- Faculty on Professional Development Assignment
-- Tri-Beta
-- Reconnect with the Department of Biology
-- Retiring Faculty
-- New Faculty
-- Floyds receive …

Fluorescence Fluctuation Approaches To The Study Of Adhesion And Signaling., Kristopher Kubow

Selected Works

No abstract provided.

Dehydration In Southern Toads (Anaxyrus Terrestris): Metabolic Costs And Effects Of Temperature Selection, Claire E. Forster

Scripps Senior Theses

Southern toads (Anaxyrus terrestris) are ectothermic terrestrial amphibians. As such they are sensitive to thermal and hydric variability. The interactive effect of hydration state and body temperature is not well understood. The aim of this study is to determine if the costs of dehydration vary at different temperatures and if so, whether toads will select different temperatures to minimize these costs. Costs of dehydration were evaluated by measuring metabolic rate at 100% and 85% hydration state, at 30 and 20 ^oC. Temperature selection of toads at 100% and 85% hydration state was measured using a thermal gradient. …

Salamander Hox Clusters Contain Repetitive Dna And Expanded Non-Coding Regions: A Typical Hox Structure For Non-Mammalian Tetrapod Vertebrates?, Stephen Randal Voss, Srikrishna Putta, John A. Walker, Jeremiah J. Smith, Nobuyasu Maki, Panagiotis A. Tsonis

Biology Faculty Publications

Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the …

A New Social Gene In Dictyostelium Discoideum, Chtb, Lorenzo A. Santorelli, Adam Kuspa, Gad Shaulsky, David C. Queller, Joan E. Strassmann

Biology Faculty Research

BACKGROUND:

Competitive social interactions are ubiquitous in nature, but their genetic basis is difficult to determine. Much can be learned from single gene knockouts in a eukaryote microbe. The mutants can be competed with the parent to discern the social impact of that specific gene. Dictyostelium discoideum is a social amoeba that exhibits cooperative behavior in the construction of a multicellular fruiting body. It is a good model organism to study the genetic basis of cooperation since it has a sequenced genome and it is amenable to genetic manipulation. When two strains of D. discoideum are mixed, a cheater strain …

“Culling The Herd”: Eugenics And The Conservation Movement In The United States, 1900–1940, Garland E. Allen

Biology Faculty Research

While from a late twentieth- and early twenty-first century perspective, the ideologies of eugenics (controlled reproduction to eliminate the genetically unfit and promote the reproduction of the genetically fit) and environmental conservation and preservation, may seem incompatible, they were promoted simultaneously by a number of figures in the progressive era in the decades between 1900 and 1950. Common to the two movements were the desire to preserve the ‘‘best’’ in both the germ plasm of the human population and natural environments (including not only natural resources, but also undisturbed nature preserves such as state and national parks and forests). In …

Greater Sexual Reproduction Contributes To Differences In Demography Of Invasive Plants And Their Noninvasive Relatives, Jean H. Burns, Eleanor A. Pardini, Michele R. Schutzenhofer, Y Anny Chung, Katie J. Seidler, Tiffany M. Knight

Biology Faculty Research

An understanding of the demographic processes contributing to invasions would improve our mechanistic understanding of the invasion process and improve the efficiency of prevention and control efforts. However, field comparisons of the demography of invasive and noninvasive species have not previously been conducted. We compared the in situ demography of 17 introduced plant species in St. Louis, Missouri, USA, to contrast the demographic patterns of invasive species with their less invasive relatives across a broad sample of angiosperms. Using herbarium records to estimate spread rates, we found higher maximum spread rates in the landscape for species classified a priori as …

Maternal Depletion Of Piwi, A Component Of The Rnai System, Impacts Heterochromatin Formation In Drosophila, Tingting Gu, Sarah C.R. Elgin

Biology Faculty Research

A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains, and how that chromatin state is faithfully transmitted. Stable heterochromatin is necessary to silence transposable elements (TEs) and maintain genome integrity. Both the RNAi system and heterochromatin components HP1 (Swi6) and H3K9me2/3 are required for initial establishment of heterochromatin structures in S. pombe. Here we utilize both loss of function alleles and the newly developed Drosophila melanogaster transgenic shRNA lines to deplete proteins of interest at specific development stages to dissect their roles in heterochromatin assembly in early zygotes and in maintenance of the silencing …

Sturgis And Kay Mckeever Papers, Zach S. Henderson Library Special Collections

Finding Aids

This collection consists of the papers of Georgia Southern University biology professor Sturgis McKeever and other materials related to the McKeever family, particularly his wife, Kay McKeever, and his brothers Ivan and Kermit McKeever. The materials span 1935–2005 and are predominantly professional in nature, including numerous research reprints and publications on animal species across North America, correspondence between McKeever and other researchers, and handwritten graphs, charts, and research notes. The collection also contains photographic materials, including photographic slides and negatives documenting his research. The recent accrual expands the collection to include personal correspondence between Sturgis and Kay McKeever, as well …

A Bacterial Symbiont Is Converted From An Inedible Producer Of Beneficial Molecules Into Food By A Single Mutation In The Gaca Gene, Pierre Stallforth, Debra A. Brock, Alexandra M. Cantley, Xiangjun Tian, David C. Queller, Joan E. Strassmann, Jon Clardy

Biology Faculty Research

Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria's host is a "farmer" clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer's spore production and …

Gastropods In Lower Snake River And Three Of Its Tributaries And The Effects Of Competition With The New Zealand Mud Snails (Potamopyrgus Antipodarum), Michele Larson

EWU Masters Thesis Collection

"The purpose of this study was to determine the distribution of New Zealand mud snails (Potamopyrgus antipodarum) in the lower Snake River and three tributaries and to determine if this invasive snail is competing with native gastropods. Potamopyrgus antipodarum is a successful invader in much of the Western United States and has been shown to impact nutrient cycling and community structure in invaded ecosystems. This study is divided into two chapters: the first chapter focuses on the current density and genera richness of native gastropods and the distribution of P. antipodarum in the Lower Snake River and three tributaries near …

Sensory Exploitation And Condition Indication May Explain Red Pelvic Spines In The Brook Stickleback Culaea Inconstans, Andrew Hodgson

EWU Masters Thesis Collection

"Background: Sensory bias models of the evolution of sexually selected traits predict that trait preferences evolve in a nonsexual context such as prey selection. Indicator models predict that sexually selected traits indicate mate condition. I investigated the potential for sensory exploitation and condition indication models to explain the evolution of what appears to be a recently evolved sexually selected trait. Question: Did red pelvic spine coloration in male Turnbull National Wildlife Refuge (TNWR) brook stickleback (Cu!aea inconstans) evolve to exploit a preexisting sensory bias for red prey, thus helping males draw females to the nest? Or, did it evolve as …

Presenting Fake Figures: A Tool To Teach Effective Scientific Figure Design, Verónica A. Segarra, Stephanie Pulford, Susan Walsh

Faculty Publications

No abstract provided.

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 …

Structure, Dynamics, And Evolution Of The Intrinsically Disordered P53 Transactivation Domain, Wade Michael Borcherds

USF Tampa Graduate Theses and Dissertations

in numerous disease states, including cancers and neurodegenerative diseases. All proteins are dynamic in nature, occupying a range of conformational flexibilities. This inherent flexibility is required for their function, with ordered proteins and IDPs representing the least flexible, and most flexible, respectively. As such IDPs possess little to no stable tertiary or secondary structure, they instead form broad ensembles of heterogeneous structures, which fluctuate over multiple time scales. Although IDPs often lack stable secondary structure they can assume a more stable structure in the presence of their binding partners in a coupled folding binding reaction.

The phenomenon of the dynamic …

Understanding Amphibian Decline: The Role Of Pesticides And The Pathogenic Chytrid Fungus On Amphibians And Aquatic Communities, Taegan A. Mcmahon

USF Tampa Graduate Theses and Dissertations

Amphibians are the most threatened taxon on the planet. Declines have been associated with over-exploitation, habitat loss, pollution, and pathogenic diseases, but of these factors, pollution and disease have been relatively under-studied. Here, I investigated: 1) the impacts of commonly used pesticides on aquatic communities, 2) the effect of these pesticides on amphibian susceptibility to the pathogenic chytrid fungus, Batrachochytrium dendrobatidis (Bd), and 3) whether there are non-amphibian hosts of Bd and 4) how to best quantify the survival of Bd through ontogeny of the host.

In my first research chapter, I quantified the effects of environmentally relevant concentrations of …

Phenotypic Characterization Of The Pancreatic-Derived Factor (Pander) Knockout Mouse On Pure C57bl/6 Background, Shari Moak

USF Tampa Graduate Theses and Dissertations

PANcreatic-DERived Factor (PANDER), or FAM3B, is a 235-amino acid protein strongly expressed within and secreted from the endocrine pancreas. Research surrounding PANDER has revealed a large role for the protein in maintaining glucose homeostasis, as evidenced by several Ad-PANDER overexpressing murine models, our lab's pancreas-specific PANDER transgenic overexpressor, and most recently our mixed genetic C57/129J PANDER knockout (PANKO) mouse. However, PANDER's overall role in glycemic regulation and glucose homeostasis has yet to be studied in a purebred C57BL/6J PANDER knockout model. Here we present the first phenotypic characterization of our global PANDER knockout mouse on a C57BL/6J background (PANKO-C57) where …

Resistance And Tolerance To Trematode Parasites In Larval Anurans, Brittany Sears

USF Tampa Graduate Theses and Dissertations

Nearly every species on the planet has at least one parasite, which, by definition, incurs a

cost in the host. Therefore, organisms must resist parasites - preventing or reducing infections -

or tolerate parasites - reducing the costs of infection - in order to maintain their fitness despite

the presence of parasites. Here, I investigated: 1) whether parasitic, larval trematodes (cercariae)

can detect the least resistant tadpole host species, 2) a hypothetical framework for how host life

history impacts the utilization of inflammation and thus, resistance and tolerance, 3) whether a

common anesthesia technique used in experimental infections immunocompromises tadpoles, …

Use Of Stable Isotope And Trace Metal Signatures To Track The Emigration Of Female Blue Crabs, Callinectes Sapidus, From Tampa Bay, Sky Barrington Williams

USF Tampa Graduate Theses and Dissertations

The blue crab, Callinectes sapidus, supports a successful fishery in the Atlantic Ocean and throughout the Gulf of Mexico, with a total landing of 8,158,788 lb. and a total value of $10,562,128 for the state of Florida during 2012 (FWC 2012 Annual Landings Summary). An accurate and comprehensive understanding of the blue crab's life history and seasonal migration behavior is essential in defining effective management strategies for the fishery. Tag recapture studies and ultrasonic tracking methods for studying blue crab migrations are costly in terms of time and resources. In this study an alternative approach, microchemical natural tagging, was …

Innate Immune Responses To Respiratory Syncytial Virus: Age-Associated Changes, Terianne Maiko Wong

USF Tampa Graduate Theses and Dissertations

Respiratory syncytial virus (RSV) infection causes ~64 million cases of respiratory disease and 200,000 deaths annually worldwide, yet there is no broadly effective prophylactic or treatment regimen. RSV can produce acute respiratory illness in patients of all ages but strikes the age extremes, infants and the elderly, with highest frequency presumably due to innate immune deficiencies. A higher morbidity and mortality has been reported for the elderly above 65 years of age, which has been attributed to immune senescence. Efforts to generate an effective vaccine have thus far been unsuccessful.

The innate immune system provides the first line of defense …

Growth And Herbivory Of The Black Mangrove, Avicennia Germinans, Along A Salinity Gradient, Danielle Neveu

USF Tampa Graduate Theses and Dissertations

Coastal communities will be most affected by global climate change and are important to study to understand current and future ecological processes. The current model for global climate change predicts a change in rainfall, which will alter the salinity of coastal systems. Given the presence of eutrophication in many coastal waters, it is important to understand the effects that this increase in nutrients, coupled with changes in salinity, will have on these communities. This study was conducted to understand the effect of salinity increase on the growth and herbivory of the black mangrove, Avicennia germinans, in the presence of …