Biology Commons^™

Supercomplex-Associated Cox26 Protein Binds To Cytochrome C Oxidase, Valentina Strecker, Zibirnisa Kadeer, Juliana Heidler, Cristina-Maria Cruciat, Heike Angerer, Heiko Giese, Kathy Pfeiffer, Rosemary A. Stuart, Ilka Wittig

Biological Sciences Faculty Research and Publications

Here we identified a hydrophobic 6.4 kDa protein, Cox26, as a novel component of yeast mitochondrial supercomplex comprising respiratory complexes III and IV. Multi-dimensional native and denaturing electrophoretic techniques were used to identify proteins interacting with Cox26. The majority of the Cox26 protein was found non-covalently bound to the complex IV moiety of the III–IV supercomplexes. A population of Cox26 was observed to exist in a disulfide bond partnership with the Cox2 subunit of complex IV. No pronounced growth phenotype for Cox26 deficiency was observed, indicating that Cox26 may not play a critical role in the COX enzymology, and we …

Phylogenetics And Diversification Of Whirligig Beetles (Coleoptera, Gyrinidae), Grey Thomas Gustafson

Biology ETDs

Whirligig beetles are a family of aquatic beetles with an estimated 1,000 species distributed globally. Phylogenetic analysis incorporating molecular data has only recently been conducted on the family and many genera have never received modern taxonomic revision. The first chapter of the dissertation provides a taxonomic revision of the Southeast Asian whirligig beetle genus Porrorhynchus, finding the genus to contain 5 species, and no support for the numerous proposed subspecies. For the second chapter a phylogenetic analysis utilizing the most novel phylogenetic reconstructions methods incorporating the new Fossilized Birth-Death macroevolutionary model implemented in the program MrBayes 3.2.6 was conducted on …

Energetics Across Ecological Scales, John M. Grady

Biology ETDs

Energy is a common currency of ecological interactions. In this dissertation, I consider ecological energetics at different temporal, spatial and organizational scales. In my first chapter, I examine the energetics and thermoregulation of an enigmatic taxon: dinosaurs. From fossil evidence and assessment of living vertebrates I conclude that many non-avian dinosaurs were likely thermally intermediate, or 'mesothermic'. In my second chapter I detail the empirical evidence gathered to buttress my claim of dinosaur mesothermy. In my third chapter, I show how ecosystem rates of carbon flux, gross primary production and total biomass can be linked to individual body size. In …

Coevolving Histories Inside And Out: Phylogenetics, Comparative Parasitology, And Host Affinities Of Chipmunk Sucking Lice And Pinworms, Kayce C. Bell

Biology ETDs

Diversification of parasite species, in light of their host association, is an area ripe for testing hypotheses of evolution when one species requires another for survival. The 23 species of western North American chipmunks (genus Tamias) host two species of ectoparasitic sucking lice (Anoplura) and two species of endoparasitic pinworms (Nematoda). I used a phylogenetic approach to investigate the evolutionary histories of the parasites in light of the hosts and the landscape. In comparing the parasites, I found that the two pinworm species have similar diversification patterns, linked to hosts, but those processes occurred on different time scales. As another …

Altitudinal Gradients Do Not Predict Plant-Symbiont Responses To Experimental Warming, Melanie R. Kazenel

Biology ETDs

Fungal symbionts, ubiquitous inhabitants of above- and belowground plant tissues, can play important roles in increasing plant tolerance to abiotic and biotic stress. Disruption of plant-fungal interactions may therefore have important consequences for plant responses to climate change. Both altitudinal gradients and warming experiments can be useful tools for understanding responses of symbioses to climate shifts, but the degree to which altitudinal patterns will predict species responses to warming has received little attention for plant-symbiont interactions. This study combined surveys along replicated altitudinal gradients with a long-term warming experiment at the Rocky Mountain Biological Laboratory (RMBL) in Colorado, USA to …

Mammals Of The Greater Gila Region, Amanda K. Jones

Biology ETDs

The Greater Gila Region is an important area for study of mammals due to its unique physiographic history, leading to high elevational relief and many associated habitats. Due to the variety of habitats, the Gila is home to a very diverse assemblage of mammal fauna: 100 native species, 95 of which are extant in the region. This paper documents these species' current and historic distributions, taxonomy, habitat affinities, current phylogeographic studies, reproductive timing, and any other pertinent information. In addition, novel phylogeographic studies for four selected species were performed to fill in gaps in previous studies where Gila sampling was …

Experimental Drought And Soil Depth Interactively Influence Fungal Community Composition In Piñon-Juniper Woodland, Eric Olivas

Biology ETDs

Drought can flip ecosystems between states and in the process alter key systems such as plant biomass and carbon balance. Many drought-related studies have focused on plant responses or charismatic megafauna. Less work has addressed drought in the context of aboveground-belowground feedbacks. Impacts of drought are increasing, particularly in arid environments such as the southwestern United States. Major tree species of these regions, such as piñon pine, are adapted to a wetter and more predictable climate than the projected future climate. The effects of drought on piñon and its ectomycorrhizae have been studied observationally and in laboratories. Soil depth has …

A Multidimensional Investigation Of The Niche: Geographic Distributions, Body Size, And Interspecific Interactions Of Late Quaternary North American Canidae, Melissa Irene Pardi

Biology ETDs

A pressing conservation challenge is understanding how organisms will be impacted by climate change. From the paleontological record, we know organisms have options when facing change: they can do nothing, move, or adapt. These responses shape an organism's niche (a foundational concept in biology) that is abiotically constrained, but modified by biotic interactions. The greatest disturbances in recent North American geologic history is the human mediated extinction of megafauna ~11,700 years B.P. and climate change following the last glacial period. We used the fossil record to address ecological questions concerning conservationists; our focus was on Canidae and humans. Species distribution …

Patterns In Richness And Community Structure: From Bacteria To Apex Predators, Ara S. Winter

Biology ETDs

Patterns of community structure and richness provide context for studies from microbial ecology, global macroecology, languages, to Bayesian statistics. Diversity patterns for animals on land and their predictor variables are well studied. However, diversity patterns for bacterial communities and marine macroorganisms are not well studied or understood. Here I examine diversity patterns in caves, on the external surface of Chiroptera (bats), and in marine ecosystems. At the local to regional scale we investigate factors that drive bacterial community patterns in richness and composition in lava cave microbial mats and microbes on bats. Lastly, out of the cave and into the …

Behavioral Responses Of Ringed And Spotted Salamanders To Diet-Related Cues From Predators, Kayla Shelton

Graduate Theses/Dissertations

Multiple species of Ambystoma can sometimes coexist in ponds, often forming a prey guild. In the Ozarks, ringed salamanders (Ambystoma annulatum) can coexist with marbled salamanders (A. opacum) and spotted salamanders (A. maculatum). Ringed and marbled salamanders lay their eggs in ponds in the fall and overwinter as larvae, whereas spotted salamanders breed in the spring. Ringed and marbled salamander larvae can be cannibalistic and can prey upon larvae of the other two species. Larvae should experience increased survival if they can discriminate between predators that have recently consumed another salamander (high risk) versus those that have not (low risk). …

The Explorations Program: Benefits Of Single-Session, Research- Focused Classes For Students And Postdoctoral Instructors, Jeremy L. Hsu, Anna M. Wrona, Sarah E. Brownell, Waheeda Khalfan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present an update to Explorations, a program at Stanford University that allows undergraduates in an introductory biology course to explore specialized topics in the biological sciences while providing graduate students and postdoctoral scholars the unique opportunity to develop and teach single-session, research-focused classes. We provide an assessment of eight iterations of the program, using program attendance, student and instructor evaluations, senior exit surveys, course grades, and completion of undergraduate honors theses to assess the impact of our program on students and instructors. Students rated their experiences highly, and most reported that the program had a positive impact on their …

Endozoochorous Spread Of Nonnative Plant Species By White-Tailed Deer, Odocoileus Virginianus, Andrew Jordan Spychalla

Graduate Theses/Dissertations

Movement of plant seeds can be facilitated by endozoochory in white-tailed deer (Odocoileus virginianus) and elk (Cervus elaphus), but at rates that are unknown in natural systems. Spread of planted forage crops into wildlands, or nonnative invasive weeds into food plots would affect ecosystem processes and management costs. To address endozoochory, collections of fecal pellets from both ungulate species were done at the Current River Conservation Area in Southeastern Missouri. Randomly chosen individual pellets collected from nine food plots were planted in a greenhouse setting. After cold stratification of pellets (2°C at 15 days), pellets were either left whole or …

Upper Thermal Limits Of Freshwater Mussels (Bivalvia, Unionoida) In Ramped Temperature Exposures, Kathryn Rae Cottrell Martin

Graduate Theses/Dissertations

The purpose of this study was to determine the upper thermal limits of unionids. Three species of juvenile freshwater mussels were tested in lab experiments mimicking a diel pattern of temperature change (increasing 6 h, peak 2 h, and decreasing 8 h). The peak temperature fatal to half of the exposed population (LT50) was tested with respect to species, population, age, and seasonal acclimation. Mortality was monitored for 2 weeks after exposure. The smallest size classes were tested in a thermal cycler instrument, a novel application for testing mussels. LT50s for juveniles less than 3 weeks old were within 2-3°;C …

Phycotoxin Loads In Bottlenose Dolphins (Tursiops Truncatus) From The Indian River Lagoon Estuary System And Coastal Altlantic Waters, Florida: 2002-2011, Jeremy Alan Browning

Theses and Dissertations

Harmful algal blooms (HABs) are dramatic increases of algae that produce phycotoxins, and these toxins lead to subsequent neurological dysfunction with symptomatic illness leading, in extreme cases, to mass mortalities of marine mammals. This presents a conservation challenge since the frequency and severity of HABs are increasing on a global scale. Two HAB species that impact marine mammals residing in and utilizing an eastern Florida estuary and surrounding coastal Atlantic waters are Karenia brevis (K. brevis) and Pyrodinium bahamense (Pyrodinium); these HAB species produce the neurotoxins brevetoxin (PbTx) and saxitoxin (STX), respectively. These toxins are present at times in high …

Early-Onset Alzheimer’S: Should You Worry?, Troy Rohn

Biology Faculty Publications and Presentations

You have forgotten where you put your car keys, or you can’t seem to remember the name of your colleague you saw in the grocery store the other day. You fear the worst, that maybe these are signs of Alzheimer’s disease.

Interactions Between Hiv-1 Tat And Tumor Suppressor P53, Kristen Lane Spotts

Theses and Dissertations

The most well studied cancer-related gene in history, p53, is responsible for protecting the integrity of the genome. A variety of different stresses are detected by p53 and its regulators, allowing for numerous post-translational modifications that activate p53. After activation p53 can then regulate transcription of a myriad downstream targets, resulting in either cell cycle arrest or apoptosis. One of the stress signals that activates p53 is viral infection in part through the induction of type-1 interferon. However some viruses, like the DNA tumor viruses have evolved factors capable of binding to p53 and inhibiting its ability to regulate its …

A New Method For Ecoacoustics? Toward The Extraction And Evaluation Of Ecologically-Meaningful Soundscape Components Using Sparse Coding Methods, Alice Eldridge, Michael Casey, Paola Moscoso, Mika Peck

Dartmouth Scholarship

Passive acoustic monitoring is emerging as a promising non-invasive proxy for ecological complexity with potential as a tool for remote assessment and monitoring (Sueur & Farina, 2015). Rather than attempting to recognise species-specific calls, either manually or automatically, there is a growing interest in evaluating the global acoustic environment. Positioned within the conceptual framework of ecoacoustics, a growing number of indices have been proposed which aim to capture community- level dynamics by (e.g., Pieretti, Farina & Morri, 2011; Farina, 2014; Sueur et al.,2008b) by providing statistical summaries of the frequency or time domain signal. Although promising, the ecological relevance and …

Individual Movement Rates Are Sufficient To Determine And Maintain Dynamic Spatial Positioning Within Uca Pugilator Herds, Eilea R. Knotts

Theses and Dissertations

Spatial location within aggregations (i.e. periphery, central) is of biological significance to gregarious animals. Because these positions are a potential consequence of consistent individual behavioral differences, or personality, a better understanding of potential mechanisms concerning personality is central to predicting an individuals’ location. To determine the effects of individual personality on the dynamic spatial positioning of Uca pugilator while herding, field data collection and agent-based modeling were employed. Individuals were assayed to establish their personalities and returned to the field for observation as a means of identifying location preference within selfish herds. There was a significant difference between the extreme …

Defensive Roles And Factors That Affect The Production Of Monoterpenes In Morella Cerifera, Florence C. Anoruo

Theses and Dissertations

Plants as sessile organisms encounter myriad biotic and abiotic challenges in their habitats. Pathogen and herbivore attack are among the prominent biotic challenges that plants face in their environment. Plants respond to these attacks by using chemical compounds including monoterpenes that are constitutively and inductively produced in some plants, and stored inside glands on their leaves. Among the abiotic factors that influence the production of defense compounds, especially monoterpenes are light intensity and nutrient availability.

The objectives of this dissertation are to 1) comprehend the defensive role of monoterpenes, specifically investigating the associational defense of a non-odorous species (Ilex vomitoria) …

Enhancing The Efficacy Of Thymidylate Synthase Inhibitors By Genetic Modulation Or Pharmacological Inhibition Of Bone Marrow Derived Cells In The Tumor Stroma, Nikeya Lashanna Tisdale

Theses and Dissertations

The impact of tumor associated stromal cells in tumor formation, progression, and response to therapy has led to a paradigm shift in cancer therapy. For many years, tumors were considered as a mass consisting only of actively proliferating cancer cells and therapies were design to target these cells. However, research in the last two decades has shown that tumors are not only comprised of a heterogeneous population of neoplastic cells, but they are also comprised of and infiltrated by a heterogeneous population of non-tumor cells that contribute to tumor progression and potentially affect the efficacy of tumor-directed chemotherapies. Tumors are …

The Cranial Morphology Of The Black-Footed Ferret: A Comparison Of Wild And Captive Specimens, Tyler Antonelli

Theses and Dissertations

The black-footed ferret (Mustela nigripes), a North American mustelid species, was once found abundantly throughout the Midwest until extreme decline in prairie dogs, the black-footed ferrets primary food source, brought the species to near-extinction. This resulted in the development of the Black-Footed Ferret Recovery Program which included bringing the entire species into captivity with the intention of breeding the species back to sufficient numbers to allow for successful reintroduction. While in captivity, many components of the ferrets’ health were accounted for, but the current study aims to address the effects that captivity may have had on the cranial morphology of …

Assessment Of The Probability Of Loggerhead Sea Turtle (Caretta Caretta) Recovery In The Northwest Atlantic Ocean Within 50 Years Of Federal And State Protection In The Us, Michael D. Arendt

Theses and Dissertations

Systematic implementation of sea turtle conservation measures have occurred in the U.S. since the 1970’s. As such, this dissertation assessed the probability that loggerhead sea turtles (Caretta caretta) in the NW Atlantic will meet or exceed recovery criteria in the minimum timeframe (i.e., 50 years) specified by the Recovery Plan. Mathematical modeling (Chapter 1) of a theoretical population resembling an important nesting assemblage in a stochastic environment for 200 years revealed broad (<20k to >106k) fluctuation in annual nest counts without extinction, as well as strong contemporary environmental influence on annual nest counts. Modeling also substantiated the importance of monitoring the …

Editorial: Linking Ecosystem Function To Microbial Diversity, Anne E. Bernhard, John J. Kelly

Biology: Faculty Publications and Other Works

No abstract provided.

Tunable Nano-Delivery System For Cancer Treatment: A New Approach For Targeted Localized Drug Delivery, Rana Falahat

USF Tampa Graduate Theses and Dissertations

Localized drug delivery systems have been widely studied as potential replacements for conventional chemotherapy with the capability of providing sustained and controlled drug release in specific targeted sites. They offer numerous benefits over conventional chemotherapy such as enhancing the stability of embedded drugs and preserving their anticancer activity, providing sustained and controlled drug release in the tumor site, reducing toxicity and diminishing subsequent side effects, minimizing the drug loss, averting the need for frequent administrations, and minimizing the cost of therapy.

The aim of this study is to develop a localized drug delivery system with niosomes embedded in a chitosan …

From Tolerance To Transmission: Linking Within-Individual To Community-Level Disease Processes, Sarah Catherine Burgan

USF Tampa Graduate Theses and Dissertations

Hosts have two main strategies for coping with infections: resistance and tolerance. Resistance is aimed at preventing or eliminating parasites, whereas the goal of tolerance is to maintain performance regardless of parasite burden. The balance between resistance and tolerance within a host may mediate host competence, or the propensity of a host to infect other hosts or vectors. Hosts with high tolerance and low resistance to an infection, for instance, may be highly competent and possess the greatest potential to act as superspreaders. These superspreading hosts will contribute disproportionately to transmission, thus posing the greatest risk to other hosts within …

Dynamic Status Signal Reflects Outcome Of Social Interactions, But Not Energetic Stress, Keith A. Tarvin, L Jin Wong, David C. Lumpkin, Gabrielle M. Schroeder, Dominic D'Andrea, Sophie Meade, Pearl Rivers, Troy G. Murphy

Biology Faculty Research

Social defeat induces stress-responses in a wide array of vertebrates and can generate winner-loser effects. Dynamic condition-dependent signaling systems that reflect preparation for subsequent agonistic interactions, and thereby mediate winner-loser effects, should be more sensitive to competitive history than to non-social sources of stress. Bill color of female American goldfinches (Spinus tristus) is a dynamic condition-dependent ornament that functions as a signal of competitive status and mediates intrasexual agonistic social interactions. We tested the “social experience signaling hypothesis” in female goldfinches by (1) manipulating a non-social energetic stressor by experimentally elevating flight costs via wing-clipping in free-ranging birds, …

Examining Students’ Expectations For Laboratory Learning In A Majors’ Introductory Biology Course, Matthew Crewse

Ursidae: The Undergraduate Research Journal at the University of Northern Colorado

No abstract provided.

Cellular And Molecular Features Of Developmentally Programmed Genome Rearrangement In A Vertebrate (Sea Lamprey: Petromyzon Marinus), Vladimir A. Timoshevskiy, Joseph R. Herdy, Melissa C. Keinath, Jeramiah J. Smith

Biology Faculty Publications

The sea lamprey (Petromyzon marinus) represents one of the few vertebrate species known to undergo large-scale programmatic elimination of genomic DNA over the course of its normal development. Programmed genome rearrangements (PGRs) result in the reproducible loss of ~20% of the genome from somatic cell lineages during early embryogenesis. Studies of PGR hold the potential to provide novel insights related to the maintenance of genome stability during the cell cycle and coordination between mechanisms responsible for the accurate distribution of chromosomes into daughter cells, yet little is known regarding the mechanistic basis or cellular context of PGR in …

Botanical Therapeutics In The Modern World, Vyacheslav Dushenkov, Brittany L. Graf, Mary Ann Lila

Publications and Research

Plants are the source of a broad spectrum of biologically active phytochemicals. For effective defense against pathogens and abiotic stress, plants have developed complicated chemical strategies with different mechanisms of action. By harnessing these phytochemicals, humans have used plants for medicinal purposes for over 30,000 years, and they remain a valuable source for the development of modern therapeutics. Plant-derived materials are utilized as pharmaceuticals, botanical drugs, dietary supplements (nutraceuticals), functional food ingredients, and cosmeceuticals. The Global Institute for Bioexploration (GIBEX), an international conglomerate of researchers, is involved in multiple botanical therapeutics discovery and development programs.

Range-Wide Patterns Of Geographic Variation In Songs Of Golden-Crowned Sparrows (Zonotrichia Atricapilla), Daizaburo Shizuka, M Ross Lein, Glen Chilton

School of Biological Sciences: Faculty Publications

Discrete geographic variation, or dialects, in songs of songbirds arise as a consequence of complex interactions between ecology and song learning. Four of the five species of Zonotrichia sparrows, including the model species White-crowned Sparrow (Z. leucophrys), have been studied with respect to the causes and consequences of geographic variation in song. Within White-crowned Sparrows, subspecies that migrate farther have larger range size of dialects. Here, we assessed geographic patterns of song variation in the fifth species of this genus, the Golden-crowned Sparrow (Z. atricapilla). We analyzed field-recorded songs from 2 sampling periods (1996–1998 and 2006–2013) …