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Always Read The Introduction: Integrating Regulatory And Coding Sequence Evolution In Yeast, Annette M. Evangelisti

Biology ETDs

We analyze duplicate genes in a yeast, Saccharomyces cerevisiae with the aim of determining a genes history and to observe that gene in its genomic context. In Chapter 2 we show that the fate of a duplicate gene pair is in part determined by its genome location. Moreover, we show that for two classes of duplicate genes, resulting from either small-scale duplication or whole-genome duplication, this fate can often be assessed by measuring the patterns of asymmetry in the sequence divergence of the genes in question. In Chapter 3 we study duplicate genes in the context of their local environments …

High-Throughput Genomic/Proteomic Studies: Finding Structure And Meaning By Similarity, George Sidney Davidson

Biology ETDs

The post-genomic challenge was to develop high-throughput technologies for measuring genome scale mRNA expression levels. Analyses of these data rely on computers in an unprecedented way to make the results accessible to researchers. My research in this area enabled the first compendium of microarray experiments for a multi-cellular eukaryote, Caenorhabditis elegans. Prior to this research approximately 6% of the C. elegans genome had been studied, and little was known about global expression patterns in this organism. Here I cluster data from 553 different microarray experiments and show that the results are stable, statistically significant and highly enriched for specific biological …

Female Perception Of Testeronized Male Facial Images: Evidence Of A Co-Evolutionary Tradeoff Responsive To Conditions For Both Competition And Cooperation, Melissa L. Franklin

Biology ETDs

Theorists and researchers who examine the evolutionary ecology of mating dynamics consider two primary forces, intrasexual and intersexual, as important pressures of selection. Bilateral symmetry and, more controversially, hormone markers in many species, impart information that has been found to influence some aspects of intersexual selection. Both symmetry, as a sign of developmental stability, and hormone markers (i.e., testosteronized traits as cues of immunocompetence) have been classically treated as signals of genetic fitness (Moller & Swaddle, 1997; Hamilton & Zuk, 1982), although neither are consistently shown to correlate with increased mating success. Indeed, results between studies on either trait independently …

Increased Abundance And First Breeding Record Of The Neotropic Cormorant (Phalacrocorax Brasilianus) On The Alluvial Plain Of Mississippi, Katie C. Hanson, Travis L. Devault, Stephen J. Dinsmore

United States Department of Agriculture Wildlife Services: Staff Publications

Phalacrocorax brasilianus (Neotropic Cormorant) has been observed with increasing frequency in the alluvial plain (Delta region) of Mississippi. In the past 6 years, 22 individuals have been observed in 20 separate sightings during spring and summer. These sightings have occurred at breeding colonies of other colonial waterbirds and commercial aquaculture facilities of Ictalurus punctatus (Channel Catfish). Two sexually mature Neotropic Cormorants have been collected at a colonial waterbird breeding colony near the Mississippi River in the western Delta region among flocks of Phalacrocorax auritus (Double-crested Cormorants). Twice during the summer of 2008, confirmed nesting of Neotropic Cormorants were documented in …

Upper Thermal Tolerances Of Early Life Stages Of Freshwater Mussels, Tamara J. Pandolfo, W. Gregory Cope, Consuelo Arellano, Robert B. Bringolf, M. Christopher Barnhart

College of Natural and Applied Sciences

Freshwater mussels (order Unioniformes) fulfill an essential role in benthic aquatic communities, but also are among the most sensitive and rapidly declining faunal groups in North America. Rising water temperatures, caused by global climate change, industrial discharges, drought, or land development, could further challenge imperiled unionid communities. The aim of our study was to determine the upper thermal tolerances of the larval (glochidia) and juvenile life stages of freshwater mussels. Glochidia of 8 species of mussels were tested: Lampsilis siliquoidea, Potamilus alatus, Ligumia recta, Ellipsaria lineolata, Lasmigona complanata, Megalonaias nervosa, Alasmidonta varicosa, and Villosa delumbis. Seven of these species also …

Microarray Analysis Of A Salamander Hopeful Monster Reveals Transcriptional Signatures Of Paedomorphic Brain Development, Robert B. Page, Meredith A. Boley, Jeramiah J. Smith, Srikrishna Putta, Stephen R. Voss

Biology Faculty Publications

Background

The Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis.

Results

Transcript abundances from whole brain …

Probiotic Therapy - Recruiting Old Friends To Fight New Foes, Roy D. Sleator

Department of Biological Sciences Publications

Against a backdrop of increasing antibiotic resistance, and the emergence of new and evolving pathogens, clinicians are increasingly forced to consider alternative therapies - probiotics are one such alternative.

The Interpretation Of Habitat Preference Metrics Under Use–Availability Designs, Hawthorne L. Beyer, Daniel T. Haydon, Juan M. Morales, Jacqueline L. Frair, Mark Hebblewhite, Michael Mitchell, Jason Matthiopoulos

Biological Sciences Faculty Publications

Models of habitat preference are widely used to quantify animal–habitat relationships, to describe and predict differential space use by animals, and to identify habitat that is important to an animal (i.e. that is assumed to influence fitness). Quantifying habitat preference involves the statistical comparison of samples of habitat use and availability. Preference is therefore contingent upon both of these samples. The inferences that can be made from use versus availability designs are influenced by subjectivity in defining what is available to the animal, the problem of quantifying the accessibility of available resources and the framework in which preference is modelled. …

Resolving Issues Of Imprecise And Habitat-Biased Locations In Ecological Analyses Using Gps Telemetry Data, Jacqueline L. Frair, John Fieberg, Mark Hebblewhite, Francesca Cagnacci, Nicholas J. Decesare, Luca Pedrotti

Biological Sciences Faculty Publications

Global positioning system (GPS) technologies collect unprecedented volumes of animal location data, providing ever greater insight into animal behaviour. Despite a certain degree of inherent imprecision and bias in GPS locations, little synthesis regarding the predominant causes of these errors, their implications for ecological analysis or solutions exists. Terrestrial deployments report 37 per cent or less non-random data loss and location precision 30 m or less on average, with canopy closure having the predominant effect, and animal behaviour interacting with local habitat conditions to affect errors in unpredictable ways. Home-range estimates appear generally robust to contemporary levels of location imprecision …

Distinguishing Technology From Biology: A Critical Review Of The Use Of Gps Telemetry Data In Ecology, Mark Hebblewhite, Daniel T. Haydon

Biological Sciences Faculty Publications

In the past decade, ecologists have witnessed vast improvements in our ability to collect animal movement data through animal-borne technology, such as through GPS or ARGOS systems. However, more data does not necessarily yield greater knowledge in understanding animal ecology and conservation. In this paper, we provide a review of the major benefits, problems and potential misuses of GPS/Argos technology to animal ecology and conservation. Benefits are obvious, and include the ability to collect fine-scale spatio-temporal location data on many previously impossible to study animals, such as ocean-going fish, migratory songbirds and long-distance migratory mammals. These benefits come with significant …

Correlation And Studies Of Habitat Selection: Problem, Red Herring Or Opportunity?, John Fieberg, Jason Matthiopoulos, Mark Hebblewhite, Mark S. Boyce, Jacqueline L. Frair

Biological Sciences Faculty Publications

With the advent of new technologies, animal locations are being collected at ever finer spatio-temporal scales. We review analytical methods for dealing with correlated data in the context of resource selection, including post hoc variance inflation techniques, ‘two-stage’ approaches based on models fit to each individual, generalized estimating equations and hierarchical mixed-effects models. These methods are applicable to a wide range of correlated data problems, but can be difficult to apply and remain especially challenging for use–availability sampling designs because the correlation structure for combinations of used and available points are not likely to follow common parametric forms. We also …

Habitat–Performance Relationships: Finding The Right Metric At A Given Spatial Scale, Jean-Michel Gaillard, Mark Hebblewhite, Anne Loison, Mark Fuller, Roger Powell, Mathieu Basille, Bram Van Moorter

Biological Sciences Faculty Publications

The field of habitat ecology has been muddled by imprecise terminology regarding what constitutes habitat, and how importance is measured through use, selection, avoidance and other bio-statistical terminology. Added to the confusion is the idea that habitat is scale-specific. Despite these conceptual difficulties, ecologists have made advances in understanding ‘how habitats are important to animals’, and data from animal-borne global positioning system (GPS) units have the potential to help this clarification. Here, we propose a new conceptual framework to connect habitats with measures of animal performance itself—towards assessing habitat–performance relationship (HPR). Long-term studies will be needed to estimate consequences of …

How Do Polar Marine Ecosystems Respond To Rapid Climate Change?, Oscar Schofield, Hugh W. Ducklow, Douglas G. Martinson, Michael P. Meredith, Mark A. Moline, William R. Fraser

Biological Sciences

Climate change will alter marine ecosystems; however, the complexity of the food webs, combined with chronic undersampling, constrains efforts to predict their future and to optimally manage and protect marine resources. Sustained observations at the West Antarctic Peninsula show that in this region, rapid environmental change has coincided with shifts in the food web, from its base up to apex predators. New strategies will be required to gain further insight into how the marine climate system has influenced such changes and how it will do so in the future. Robotic networks, satellites, ships, and instruments mounted on animals and ice …

Utilization Of Phylogenetic Systematics, Molecular Evolution, And Comparative Transcriptomics To Address Aspects Of Nematode And Bacterial Evolution, Scott M. Peat

Theses and Dissertations

Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co-phylogenetic, and …

Candidate Genes For Chromosomes 6 And 10: Quantitative Trait Loci For Age-Related Retinal Degeneration In Mice, D.G. Ogando, Kam D. Dahlquist, M. Alizadeh, K. Kunchithapautham, J. Li, N. Yu, M.M. Lavail, B. Rohrer, D. Vollrath, M. Danciger

Biology Faculty Works

Purpose: In a previous study, several quantitative trait loci (QTL) that influence age-related degeneration (ageRD) were identified in a cross between the albino strains B6(Cg)-Tyr(c-2J)/J (B6a) and BALB/cByJ (C). The Chromosome (Chr) 6 and Chr 10 QTL were the strongest and most highly significant loci and both involved B6a protective alleles. The QTL were responsible for 21% and 9% of the variance in phenotypes, respectively. We focused on these two QTL to identify candidate genes. Methods: DNA microarrays were used for the two mouse strains at four and eight months of age to identify genes that are differentially regulated and …

Tooth Chipping Can Reveal The Diet And Bite Forces Of Fossil Hominins, Paul J. Constantino, James Jin-Wu Lee, Herzl Chai, Bernhard Zipfel, Charles Ziscovici, Brian R. Lawn, Peter W. Lucas

Biological Sciences Faculty Research

Mammalian tooth enamel is often chipped, providing clear evidence for localized contacts with large hard food objects. Here, we apply a simple fracture equation to estimate peak bite forces directly from chip size. Many fossil hominins exhibit antemortem chips on their posterior teeth, indicating their use of high bite forces. The inference that these species must have consumed large hard foods such as seeds is supported by the occurrence of similar chips among known modern-day seed predators such as orangutans and peccaries. The existence of tooth chip signatures also provides a way of identifying the consumption of rarely eaten foods …

Behavioural Display Systems Across Nine Anolis Lizard Species: Sexual Dimorphisms In Structure And Function, Michele A. Johnson, J. Wade

Biology Faculty Research

Relationships between structure and function are a primary focus in biology, yet they are most often considered within individual species. Sexually dimorphic communication behaviours and the morphology of associated structures can vary widely, even among closely related species, and these traits provide an ideal opportunity to investigate the evolution of structure-function patterns. Using nine Anolis lizard species, we addressed a series of questions regarding sex differences in and the evolution of relationships between extension of the throat fan (dewlap) and morphology of the muscles and cartilage controlling it. The main results indicated that within species, males displayed the dewlap more …

Body Size And Social Dominance Influence Breeding Dispersal In Male Pachydiplax Longipennis (Odonata), Shannon Mccauley

Biological Sciences

1. Dispersal behaviour can be affected by an individual's phenotype, by the environmental or social context they experience, and by interactions between these factors. Differential dispersal propensities between individuals may also be an important modifier of functional connectivity between populations. To assess how a key trait, body size, affected both social interactions and dispersal behaviour, this study examined the relationship between body size, antagonistic interactions, and breeding dispersal in male dragonflies (Pachydiplax longipennis) across a seasonal decline in adult body size. 2. During a seasonal peak in male body size in this study, dispersers were smaller than non-dispersers. Later in …

North American Montane Red Foxes: Expansion, Fragmentation, And The Origin Of The Sacramento Valley Red Fox, Benjamin N. Sacks, Mark J. Statham, John D. Perrine, Samantha M. Wisely, Keith B. Aubry

Biological Sciences

Most native red foxes (Vulpes vulpes) in the western contiguous United States appear to be climatically restricted to colder regions in the major mountain ranges and, in some areas, have suffered precipitous declines in abundance that may be linked to warming trends. However, another population of unknown origin has occurred in arid habitats in the Sacramento Valley of California well outside this narrow bioclimatic niche since at least 1880. If native, this population would be ecologically distinct among indigenous North American red foxes. We used mitochondrial and microsatellite markers from historical and modern samples (modes: 1910–1930 and 2000–2008, …

Design And Implementation Of Marine Biology Lessons At The Avila Beach Sea Life Center, Heather L. Price

Biological Sciences

No abstract provided.

The Anorexigenic And Hypertensive Effects Of Nesfatin-1 Are Reversed By Pretreatment With An Oxytocin Receptor Antagonist, Gina L.C. Yosten, Willis K. Samson

Biological Sciences Faculty Research & Creative Works

Nesfatin-1 is an 82-amino acid protein encoded by the nucleobindin2 gene. When injected intracerebroventricularly, nesfatin-1, via a melanocortin 3/4 receptor-dependent mechanism, potently decreased both food and water intakes and elevated mean arterial pressure in a dose-related manner. Because nesfatin-1 colocalized with oxytocin in hypothalamus and because nesfatin-1 had direct depolarizing effects on oxytocin-producing neurons in hypothalamic slice preparations, we hypothesized that the actions of nesfatin-1 required the presence of functional oxytocin receptors. We, therefore, pretreated conscious, unrestrained male rats with the oxytocin receptor antagonist, ornithine vasotocin (OVT), before treatment with nesfatin-1. We found that pretreatment with OVT reversed the effects …

Future Management Of The Metropolitan Recreational Roe's Abalone Fishery., Metropolitan Roe's Abalone Recreational Fishery Working Group.

Fisheries Management Papers

Following the setting of a 40 tonne Total Allowable Recreational Catch (TARC) for the Perth recreational abalone fishery, a working group was formed to examine future management options.

The Metropolitan Roe’s Abalone Recreational Fishery Working Group (“the Working Group”) examined historical management, key principles, amenity of fishing, bag limits, license numbers, season length and timing of the season to assist its deliberations. A questionnaire was also sent out to 1,000 abalone recreational licence holders, with 20 per cent of licensees providing a detailed response.

Behavior And Physiology Of Hermit Crabs During Burial: Shell Abandonment And Lactate Accumulation, Janelle Allison Shives

Loma Linda University Electronic Theses, Dissertations & Projects

Organisms living in the intertidal zone must adapt to environmental and physical stressors. One physical stressor that these organisms may face, and that may require specific behavioral and physiological responses, is burial by sediment. In this thesis I report the results of experiments in which I subjected the intertidal hermit crab, Pagurus samuelis, to burial and analyzed aspects of subsequent behavior and physiology. In the first set of experiments, hermit crabs were buried with the shell aperture facing either up or down, and at one of three depths (2, 4, or 6 cm). The factors hermit crab weight, shell …

Recent Advances In The Climate Change Biology Literature: Describing The Whole Elephant, A. Townsend Peterson, Shaily Menon, Xingong Li

Peer Reviewed Publications

Climate change biology is seeing a wave of new contributions, which are reviewed herein. Contributions treat shifts in phenology and distribution, and both document past and forecast future effects. However, many of the current wave of contributions are observational and correlational, and few are experimental in nature, and too often a conceptual framework in which to contextualize the results is lacking. An additional gap is the lack of effective cross-linking among areas of research, for example, connection of sea-level rise and climate change implications for distributions of species, or evolutionary adaptation studies with distributional shift studies. Although numerous important contributions …

Endocannabinoid Signalling: Has It Got Rhythm?, Linda K. Vaughn, Gerene Denning, Kara L. Stuhr, Harriet De Wit, Matthew N. Hill, Cecilia J. Hillard

Biomedical Sciences Faculty Research and Publications

Endogenous cannabinoid signalling is widespread throughout the body, and considerable evidence supports its modulatory role in many fundamental physiological processes. The daily and seasonal cycles of the relationship of the earth and sun profoundly affect the terrestrial environment. Terrestrial species have adapted to these cycles in many ways, most well studied are circadian rhythms and hibernation. The purpose of this review was to examine literature support for three hypotheses: (i) endocannabinoid signalling exhibits brain region-specific circadian rhythms; (ii) endocannabinoid signalling modulates the rhythm of circadian processes in mammals; and (iii) changes in endocannabinoid signalling contribute to the state of hibernation. …

Evaluating Captive-Breeding Techniques And Reintroduction Success Of The California Condor (Gymnogyps Californianus), Amy C. Utt

Loma Linda University Electronic Theses, Dissertations & Projects

In this dissertation, I present two original research studies on the behavior and survival of the critically endangered California Condor (Gymnogyps californianus). I also provide a comprehensive review of the role of captive-rearing to the conservation of birds.

The first study examined the behavioral differences of puppet- and parent-reared condor juveniles reared in captivity. This study further defined and examined the behaviors of adult conspecific mentors and their interactions with juveniles. Dominance hierarchy analyses for two cohorts of juveniles and their adult mentors indicated the establishment of a linear hierarchy. Although puppet-reared juveniles engaged in fewer social behaviors in …

A Sea Change For Aquatic Sustainability : Meeting The Challenge Of Fish Resources Management And Aquatic Sustainability In The 21st Century, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Documenting Lineages From My ‘Littlest Ancestor’ To My Deep Ancestral Roots, Emily F. Schmitt Lavin

Biology Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Growth Rate Of Mugil Cephalus From Two Isolated Ponds In Huntington Beach State Park, South Carolina, Matthew Vincent

Honors Theses

Measurement of growth of the euryhaline teleost Mugil cephalus is quite common in open ocean settings, but growth rates of M. cephalus in isolated areas is non-existent. Two isolated ponds in Huntington Beach State, Horry County, South Carolina were selected to study the growth rate of M. cephalus; Sandpiper Pond with virtual no hydrologic connection to the ocean and Jetty Pond with adequate hydrologic connection to the ocean were the sites of sample collection. Scales from M. cephalus in both ponds were collected then aged by two readers, where agreeing ages were kept in the dataset. A von Bertalanffy growth …

Cell Culture Models Of Genetic Variation, Joshua T. Witten

Arts & Sciences Graduate Student Theses and Dissertations

Studying genetic variation presents a dilemma. While the genetic variation of greatest interest is that causing variation in traits and disease risk in natural populations, natural populations have characteristics that make them challenging to study. In this work, I have assessed the use of cell culture methods as a solution to some of these challenges. In particular, I studied genetic variation in the budding yeast Saccharomyces cerevisiae that was generated by selection in the lab as a model for natural genetic variation. I have found that even simplistic selection programs in the laboratory, including the use of chemical mutagenesis to …