Integrative Biology Commons^™

The Mechanism Of Biotremor Production In The Veiled Chameleon (Chamaeleo Calyptratus), Samuel Tegge

Masters Theses & Specialist Projects

Vibratory communication has evolved in numerous animal groups, including insects, spiders, fishes, mammals, and was recently discovered in veiled chameleons (Chamaeleo calyptratus). I examined the mechanism by which C. calyptratus produce these biotremors. Muscle activity data were gathered during simulated anti-predator responses via electromyography (EMG) with simultaneous recordings of biotremor production using an accelerometer. I correlated EMG data with the accelerometer data to implicate the muscles responsible for the production of the biotremors. Mixed-effect linear regression models described the mechanism, and a model selection framework determined which model fit the data best. I then used an analysis of variance to …

Using Multi‐Response Models To Investigate Pathogen Coinfections Across Scales: Insights From Emerging Diseases Of Amphibians, William E. Stutz, Andrew R. Blaustein, Cheryl J. Briggs, Jason T. Hoverman, Jason R. Rohr, Pieter T. J. Johnson

Integrative Biology Faculty and Staff Publications

1. Associations among parasites affect many aspects of host–parasite dynamics, but a lack of analytical tools has limited investigations of parasite correlations in observational data that are often nested across spatial and biological scales.
2. Here we illustrate how hierarchical, multiresponse modelling can characterize parasite associations by allowing for hierarchical structuring, offering estimates of uncertainty and incorporating correlational model structures. After introducing the general approach, we apply this framework to investigate coinfections among four amphibian parasites (the trematodes Ribeiroia ondatrae and Echinostoma spp., the chytrid fungus Batrachochytrium dendrobatidis and ranaviruses) and among >2,000 individual hosts, 90 study sites and five amphibian host …

Olfactory Learning Capabilities Of Paraphrynus Laevifrons, John Perez

Honors Program: Senior Projects (Public)

Amblypygids, a species of nocturnal arachnids from the tropics and subtropics are incredibly intelligent and are able to not only navigate through difficult tropical terrain but also, it is believed, possess olfactory learning capabilities that aid in navigation and recollection of environments. It is hypothesized that through sensitive olfactory receptors on their antenniform legs and highly developed mushroom bodies, Amblypygi can not only learn smells but also learn to associate smells with certain stimuli such as a crevice to take refuge in. To test this hypothesis, Paraphrynus laevifrons, a species of amplypygid was subjected to four different learning treatment groups …

Do Host‐Associated Gut Microbiota Mediate The Effect Of An Herbicide On Disease Risk In Frogs?, Sarah A. Knutie, Caitlin R. Gabor, Kevin D. Kohl, Jason R. Rohr

Integrative Biology Faculty and Staff Publications

1. Environmental stressors, such as pollutants, can increase disease risk in wildlife. For example, the herbicide atrazine affects host defences (e.g. resistance and tolerance) of the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), but the mechanisms for these associations are not entirely clear. Given that pollutants can alter the gut microbiota of hosts, which in turn can affect their health and immune systems, one potential mechanism by which pollutants could increase infection risk is by influencing host‐associated microbiota.
2. Here, we test whether early‐life exposure to the estimated environmental concentration (EEC; 200 μg/L) of atrazine affects the gut bacterial composition of …

Agrochemicals Increase Risk Of Human Schistosomiasis By Supporting Higher Densities Of Intermediate Hosts, Neal T. Halstead, Christopher M. Hoover, Arathi Arakala, David J. Civitello, Guilio A. De Leo, Manoj Gambhir, Steve A. Johnson, Nicolas Jouanard, Kristin A. Loerns, Karena Nguyen, Jason R. Rohr

Integrative Biology Faculty and Staff Publications

Schistosomiasis is a snail-borne parasitic disease that ranks among the most important water-based diseases of humans in developing countries. Increased prevalence and spread of human schistosomiasis to non-endemic areas has been consistently linked with water resource management related to agricultural expansion. However, the role of agrochemical pollution in human schistosome transmission remains unexplored, despite strong evidence of agrochemicals increasing snail-borne diseases of wildlife and a projected 2- to 5-fold increase in global agrochemical use by 2050. Using a field mesocosm experiment, we show that environmentally relevant concentrations of fertilizer, a herbicide, and an insecticide, individually and as mixtures, increase densities …

How The Egg Rolls: A Morphological Analysis Of Egg Shape In The Context Of Displacement Dynamics, Ian R. Hays

Theses and Dissertations

Very little is known about how morphology effects the motion, stability and the resulting viability of avian eggs. The limited research that exists focuses on the pyriform or ‘pointed’ egg shapes found in the Alcidea family. This unusual shell form is thought to suppress displacement and prevents egg loss on the cliffside nesting habitat of the Uria genera. Unfortunately, these studies never isolated or quantify the specific morphological features (elongation, asymmetry and conicality) of these pyriform eggs, which limits their applicability to other taxa and hampers a robust proof of concept. We isolated each feature as a variable, produced models …

Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 (KEGG map number 02010). We predict these genes encode components of a Branched Chain Amino Acid ATP Binding Cassette (ABC) transporter: 1) Mrub_1325 (DNA coordinates 1357399-1358130 on the reverse strand) encodes the ATP binding domain; 2) Mrub_1326 (DNA coordinates 1358127-1359899 on the reverse strand) encodes the ATP-binding domain and permease domain; 3) Mrub_1327 (DNA coordinates 1359899-1360930 on the reverse strand) encodes a permease domain; and 4)Mrub_1328 (DNA coordinates 1711022-1712185 on the reverse strand) encodes the substrate binding domain. This system is not predicted to …

Repeated Translocation Of A Gene Cassette Drives Sex-Chromosome Turnover In Strawberries, Jacob A. Tennessen, Na Wei, Shannon C.K. Straub, Rajanikanth Govindarajulu, Aaron Liston, Tia-Lynn Ashman

Faculty & Staff Scholarship

Turnovers of sex-determining systems represent important diversifying forces across eukary- otes. Shifts in sex chromosomes—but conservation of the master sex-determining genes— characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxo- nomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heteroga- metic (ZW) inheritance, yet sex maps to three different chromosomes in …

Rest Upregulates Gremlin To Modulate Diffuse Intrinsic Pontine Glioma Vasculature, Shavali Shaik, Bridget Kennis, Shinji Maegawa, Keri Schadler, Yang Yanwen, Javad Nazarian, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive glial tumor that occurs in children. The extremely poor median and 5-year survival in children afflicted with DIPG highlights the need for novel biology-driven therapeutics. Here, we have implicated the chromatin remodeler and regulator of brain development called RE1 Silencing Transcription Factor (REST), in DIPG pathology. We show that REST protein is aberrantly elevated in at least 21% of DIPG tumors compared to normal controls. Its knockdown in DIPG cell lines diminished cell growth and decreased their tumorigenicity in mouse intracranial models. DIPGs are vascularized tumors and interestingly, REST loss in …

The Ecology And Economics Of Restoration: When, What, Where, And How To Restore Ecosystems, Jason R. Rohr, Emily S. Bernhardt, Marc W. Cadotte, William H. Clements

Integrative Biology Faculty and Staff Publications

Restoration ecology has provided a suite of tools for accelerating the recovery of ecosystems damaged by drivers of global change. We review both the ecological and economic concepts developed in restoration ecology, and offer guidance on when, what, where, and how to restore ecosystems. For when to restore, we highlight the value of pursuing restoration early to prevent ecosystems from crossing tipping points and evaluating whether unassisted natural recovery is more cost-effective than active restoration. For what to restore, we encourage developing a restoration plan with stakeholders that will restore structural, compositional, and functional endpoints, and whose goal is a …

A Faculty Professional Development Model That Improves Student Learning, Encourages Active-Learning Instructional Practices, And Works For Faculty At Multiple Institutions, Karen N. Pelletrau, Jennifer K. Knight, Paula P. Lemons, Jill S. Mccourt, John E, Merrill, Ross H. Nehm, Luanna B Prevost, Mark Urban-Lurain, Michelle K. Smith

Integrative Biology Faculty and Staff Publications

Helping faculty develop high-quality instruction that positively affects student learning can be complicated by time limitations, a lack of resources, and inexperience using student data to make iterative improvements. We describe a community of 16 faculty from five institutions who overcame these challenges and collaboratively designed, taught, iteratively revised, and published an instructional unit about the potential effect of mutations on DNA replication, transcription, and translation. The unit was taught to more than 2000 students in 18 courses, and student performance improved from preassessment to postassessment in every classroom. This increase occurred even though faculty varied in their instructional practices …

Resilience In Moving Water: Effects Of Turbulence On The Predatory Impact Of The Lobate Ctenophore Mnemiopsis Leidyi, Cornelia Jaspers, John H. Costello, Kelly R. Sutherland, Brad J. Gemmell, Kelsey N. Lucas, Jennifer Tackett, Kara Dodge, Sean P. Colin

Integrative Biology Faculty and Staff Publications

Despite its delicate morphology, the lobate ctenophore Mnemiopsis leidyi thrives in coastal ecosystems as an influential zooplankton predator. Coastal ecosystems are often characterized as energetic systems with high levels of natural turbulence in the water column. To understand how natural wind‐driven turbulence affects the feeding ecology of M. leidyi, we used a combination of approaches to quantify how naturally and laboratory generated turbulence affects the behavior, feeding processes and feeding impact of M. leidyi. Experiments using laboratory generated turbulence demonstrated that turbulence can reduce M. leidyi feeding rates on copepods and Artemia nauplii by > 50%. However, detailed feeding …

Author Correction: Evolutionary History Of Plant Hosts And Fungal Symbionts Predicts The Strength Of Mycorrhizal Mutualism, Jason D. Hoeksema, James D. Bever, Sounak Chakraborty, V. Bala Chaudhary, Monique Gardes, Catherine A. Gehring, Miranda M. Hart, Elizabeth A. Housworth, Wittaya Kaonongbua, Marc J. Lajeunesse

Integrative Biology Faculty and Staff Publications

In the original published version of the article, the description of the fixed-effect predictor Inoculum Complexity presented in the Methods was incorrect. The incorrect description given was: “single fungal genus, multiple fungal genera, or whole soil inoculum”. The correct description is: “single fungal species, multiple fungal species, or whole soil inoculum”. The error does not affect any of the results presented in the paper. The correction has been made to the HTML and PDF versions of the paper.

The Evolution Of Peristenus (Hymenoptera: Braconidae): Taxonomy, Phylogenetics And Ecological Speciation, Yuanmeng Zhang

Electronic Theses and Dissertations

Parasitoid wasps are ecologically and economically important as biological control agents. However, little is known about the diversity, distribution and biology of most hymenopteran parasitoids due to their small size, morphological conservatism, and complex life styles. The focus of my PhD research was to investigate the evolution and speciation of euphorine braconid wasps, using a combination of multilocus phylogenetics and population genomic techniques combined with traditional taxonomy. The three data chapters of my dissertation are divided into different taxonomic ranks of euphorine braconids, focusing on genera, species, and populations. For chapter 2, I built a multilocus phylogeny of the tribe …

Evolution And Distribution Of Phenotypic Diversity In The Venom Of Mojave Rattlesnakes (Crotalus Scutulatus), Jason Strickland

Electronic Theses and Dissertations

Intraspecific phenotype diversity allows for local adaption and the ability for species to respond to changing environmental conditions, enhancing survivability. Phenotypic variation could be stochastic, genetically based, and/or the result of different environmental conditions. Mojave Rattlesnakes, Crotalus scutulatus, are known to have high intraspecific venom variation, but the geographic extent of the variation and factors influencing venom evolution are poorly understood. Three primary venom types have been described in this species based on the presence (Type A) or absence (Type B) of a neurotoxic phospholipase A2 called Mojave toxin and an inverse relationship with the presence of snake venom metalloproteinases …

Altered Spring Phenology Of North American Freshwater Turtles And The Importance Of Representative Populations, Fredric J. Janzen, Luke A. Hoekstra, Ronald J. Brooks, David M. Carroll, J Whitfield Gibbons, Judith L. Greene, John B. Iverson, Jacqueline D. Litzgus, Edwin D. Michael, Steven G. Parren, Willem M. Roosenburg, Gabriel F. Strain, John K. Tucker, Gordon R. Ultsch

Faculty & Staff Scholarship

Globally, populations of diverse taxa have altered phenology in response to climate change. However, most research has focused on a single population of a given taxon, which may be unrepresentative for comparative analyses, and few long-term studies of phenology in ectothermic amniotes have been published. We test for climate- altered phenology using long-term studies (10–36 years) of nesting behavior in 14 populations representing six genera of freshwater turtles (Chelydra, Chrysemys, Kinosternon, Malaclemys, Sternotherus, and Trachemys). Nesting season initiation oc- curs earlier in more recent years, with 11 of the populations advancing phenology. The onset of nesting for nearly all populations …

Microbial Community Response To Light And Heavy Crude Oil In Freshwater Systems, Timothy M. Butler

Dissertations, Master's Theses and Master's Reports

With increased demand for oil, there is an increased risk for oil spills in many environments. A number of pipelines transport oil near or across freshwater systems including the Great Lakes. Microbes are capable of breaking down oil and have thus been proposed as tools for oil spill response through bioremediation. There is a need to understand the microbial response to diverse oil types in freshwater environments due to the lack of research into this topic. This study’s main objectives are to understand how the freshwater microbial communities respond to oil, and how the bacterial communities may respond to different …

Crispr Genetic Editing: Paths For Christian Acceptance And Analysis Of In Vivo And In Vitro Efficiency, Mandeep Sandhu

Scripps Senior Theses

With advancements in CRISPR-cas9 broadening the potential paths for clinical usage of genetic editing, conversations about genetic editing have grown to outside simply scientific communities and into mainstream conversations. This study focuses specifically on Christian discourse of genetic editing and locates four major tensions for many Christians when they think about genetic editing: beginning of life, Creator-human relationship, imago Dei, and stewardship. With these major concerns in mind, I identify epigenetics, somatic cell genetic editing, and in vivo genetic editing research as important research paths to pursue as they can potentially produce techniques that more Christian individuals would feel comfortable …

Life On The Edge: Risk Of Predation Drives Selection Of Habitat And Survival Of Neonates In Endangered Sierra Nevada Bighorn Sheep, Shannon Forshee

Graduate Student Theses, Dissertations, & Professional Papers

Long-term viability of endangered populations requires development of effective management strategies that target the population vital rate with the highest potential to influence population trajectories. When adult survival is high and stable, juvenile recruitment is the vital rate with the greatest potential to improve population trajectories. For my thesis I examined how lactating Sierra Nevada Bighorn sheep (Ovis Canadensis sierra) balance forage and predation risk during the neonatal period. I first identified resource selection strategies employed by lactating females to promote survival of neonates and then determined the primary factors affecting survival of neonates. I found lactating females selected for …

A Comparative Study Of Sleep, Diurnal Patterns, And Eye Closure Between The House Mouse (Mus Musculus) And African Spiny Mouse (Acomys Cahirinus), Chanung Wang

Theses and Dissertations--Biology

To understand the function and origins of sleep, sleep needs to be studied across many different species. Although it is well conserved throughout mammals, 95% of papers are restricted to just three species, Homo sapiens, Mus musculus, and Rattus norvegicus. We aimed to characterize sleep and wake in a Murid rodent Acomys cahirinus in greater detail alongside the well-studied laboratory house mouse (Mus musculus) and wild M. musculus using a well validated, non-invasive, piezoelectric system for sleep and activity monitoring. We confirmed A. cahirinus, M. musculus, and wild M. musculus to be primarily …

Increasing Alligator Snapping Turtle Head-Starting Success Through Housing Enrichment And Inoculation Of Hatchlings With Digestive Microbiota, Kristen Erin Sardina

Graduate Theses/Dissertations

Due to historic overharvest and habitat degradation, the alligator snapping turtle (Macrochelys temminckii) has experienced population declines throughout its range. Tishomingo National Fish Hatchery in southern Oklahoma began a captive head-start program for this species in 2000 and has since released over 1,400 turtles in the region. However, there has been a recurring trend of turtles growing faster after release than while in captivity. My research sought to investigate this pattern by determining: 1) the influence of housing enrichment and housing density on juvenile growth rates and stress in indoor enclosures, and 2) the effects of supplementing hatchlings …

Cold Tolerance, Diapause And Winter Survival Of The Brown Marmorated Stink Bug (Halyomorpha Halys), Naomi Sibayan

All Master's Theses

The brown marmorated stink bug, Halyomorpha halys, is native to eastern Asia and is an invasive pest in the United States. Limited research has been done regarding the factors influencing this species’ winter survival within invaded northern regions. Cold tolerance has been previously evaluated in the eastern United States, bot nut within western populations. Winter diapause. Along with any potential links between diapause and cold tolerance remain unstudied. I examined characteristics of cold tolerance, diapause and overwintering sites to evaluate the factors contributing to the winter survival and, ultimately, persistence of this pest within central Washington. This study measured seasonal …

Evaluation And Adaptation Of Live-Cell Interferometry For Applications In Basic, Translational, And Clinical Research, Kevin A. Leslie

Theses and Dissertations

Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug …

Natural And Anthropogenic Drivers Of Tree Evolutionary Dynamics, Brandon M. Lind

Theses and Dissertations

Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence …

Migratory Patterns And Population Genetic Structure In A Declining Wetland-Dependent Songbird, Matthew G. Desaix

Theses and Dissertations

Understanding migratory connectivity is essential for assessing the drivers behind population dynamics and for implementing effective management in migratory species. Genetic markers provide a means to describe migratory connectivity, as well as incorporate population genetic analyses, however genetic markers can be uninformative for species with weak genetic structure. In this study, we evaluate range-wide population genetic structure and migratory connectivity in the prothonotary warbler, Protonotaria citrea, a wetland-dependent neotropical migratory songbird, using high-resolution genetic markers. We reveal regional genetic structure between sampling sites in the Mississippi River Valley and the Atlantic Seaboard with overall weak genetic differentiation among populations …

The Three Creeks Allotment Consolidation: Changing Western Federal Grazing Paradigms, Taylor Payne

Human–Wildlife Interactions

The federal government owns approximately 47% of all land in the western United States. In the state of Utah, about 64% of the land base is managed by the federal Bureau of Land Management (BLM) and the U.S. Forest Service (USFS). The government has historically issued permits to owners of private lands to allow the owners to graze their livestock on public lands. The permits (allotments) are generally of 10-year duration and allow for an annual season of use. In some cases, continued and repeated historical annual grazing practices may not be ideal for permit holders and their communities nor …

Establishing Relationships Among Environmental Stressors, Host Immune Status, And Wasting Disease Susceptibility In The Dominant Seagrass Species Thalassia Testudinum, Paige Joy Duffin

UNF Graduate Theses and Dissertations

A growing body of evidence supports the observation that marine disease outbreaks, especially those caused by opportunistic pathogens, are increasing in frequency and severity. One genus of such pathogens, Labyrinthula, has been identified as the causative agent of seagrass wasting disease, an epidemic that has historically plagued seagrass beds around the world. It is suspected that pathogenicity is intimately linked to the ability of the host to initiate defense responses, but a lack of compelling evidence prevents any meaningful application of preliminary observations. This body of work investigated the roles of host genotype, host immune status, and environmental stressors …

Gill Structure & Function In Parasitic And Non-Parasitic Lampreys: The Effects Of Metamorphosis And Freshwater-Seawater Transfer, Julia Sunga

Theses and Dissertations (Comprehensive)

Lamprey (Petromyzontiformes) are a phylogenetically ancient group of jawless fishes that begin their lives as filter-feeding larvae (ammocoetes) before undergoing a complex metamorphosis into juvenile lamprey that involves major changes to their internal and external body plan. Some parasitic species, such as the sea lamprey (Petromyzon marinus), migrate to sea following metamorphosis, where they use their oral discs and rasping tongue to attach to and ingest vast quantities of blood from fishes. Thus, sea lamprey have to counter the simultaneous challenges of hyposmoregulation in sea water and the generation of large quantities of ammonia due to the …

Molecular Characterization Of The Mummichog (Fundulus Heteroclitus) Ovarian Steroidogenic Pathway And Implications For Exogenous Estrogen Effects During Follicular Development, Thiviya Kanagasabesan

Theses and Dissertations (Comprehensive)

This study investigated ovarian development in Fundulus heteroclitus (mummichog), through molecular characterization of key mediators in the ovarian steroidogenic pathway; these included ovarian StAR (steroidogenic acute regulatory protein), cytochrome P450 enzymes, estrogen receptors (ERα, ERβ1 and ERβ2), and gonadotropin receptors (FSHr and LHr); additionally, hepatic vitellogenin (VTG1) and ERs, and brain P450 aromatase (P450arom; CYP19b) were studied. Fish were staged into cortical alveolus, vitellogenic, early mature, late mature, and ovulating stages of maturation; blood (plasma), ovary (tissue and isolated ovarian follicles per stage), liver, and brains were collected. Testosterone (T), 17β-estradiol (E₂) and maturation inducing steroid (MIS), measured …

The Influence Of Water Chemistry And Gill Physiology On The Uptake Of The Lampricide Tfm By Lake Sturgeon (Acipenser Fulvescens), Scott Leslie James Hepditch

Theses and Dissertations (Comprehensive)

Application of 3-trifluoromethyl-4-nitrophenol (TFM) to control invasive sea lamprey (Petromyzon marinus) within the Laurentian Great Lakes seldom causes non-target mortality. However, under certain conditions, TFM can harm species such as the lake sturgeon (Acipenser fulvescens). Lake sturgeon less than 100mm in length are particularly vulnerable to TFM-induced mortality, and are more sensitive to TFM toxicity with increasing water alkalinity as compared to sea lamprey. The objectives of this study were to evaluate the influence of pH and alkalinity on the uptake of TFM by juvenile sturgeon using radio-labeled TFM (¹⁴C-TFM). An additional objective was …