Assessing Stream Channel Restoration: The Phased Recovery Framework, Jacob M. Dyste

Graduate Student Theses, Dissertations, & Professional Papers

Channel reconfiguration projects command a large portion of stream restoration resources, while long-term monitoring and research is severely underfunded and rarely implemented. This has led to a limited knowledge base about ecological response and efficacy. Although channel reconfiguration projects are being implemented to restore biological function to lotic systems, the document responses are highly variable and little evidence has shown these projects are reaching their target goals. I predicted the inconsistent response to these projects is the result of disturbance-induced successional processes and catchment-scale water quality impairment. To address how these endogenous and exogenous factors influence stream response to channel …

Are Maximum Ground Forces And Leg Compression In Phase? A Test Of The Classical Spring Mass Model Of Running Gaits, Seth Donahue

Graduate Student Theses, Dissertations, & Professional Papers

The mechanical understanding of human running has classically been described as a spring-mass system, with subsequent models predicting the movements of the body’s center of mass and the forces applied by the leg against the ground. A central requirement of any spring system is the phasic relationship between the length of the elastic elements and the forces applied to these structures. Specifically, elastic elements compress under load and extend as the load is released. We tested whether this model applies to individuals with specialization for extreme performance in human gait. Recent work from elite level sprint runners suggest that their …

Limited Evidence For Co2-Related Growth Enhancement In Northern Rocky Mountain Pinus Contorta Populations: Trends In Growth And Intrinsic Water-Use Efficiency Across Climate Gradients, Charlotte C. Reed

Graduate Student Theses, Dissertations, & Professional Papers

Forests sequester large amounts of carbon annually; however, the degree to which enhanced forest productivity is due to more conducive climate or CO₂ fertilization remains uncertain. Increasing atmospheric CO₂ may enhance photosynthesis and/or decrease stomatal conductance thereby enhancing intrinsic water use efficiency (iWUE). While increasing iWUE has been observed in most trees globally, this increase does not necessarily translate into greater growth. This study aims to evaluate whether responses of radial growth and iWUE to increasing CO₂ vary across climatic gradients. To investigate interactions between climate and CO₂ and their impacts on tree physiology and growth, …

Growth Response Of Whitebark Pine (Pinus Albicaulis) Regeneration To Thinning And Prescribed Burn Release Treatments, Molly L. Mcclintock Retzlaff

Graduate Student Theses, Dissertations, & Professional Papers

Whitebark pine (Pinus albicaulis Engelm.) plays a prominent role throughout high-elevation ecosystems in the northern Rocky Mountains. It is an important food source for many birds and mammals, as well as a major player in high-elevation watershed maintenance, both slowing snowmelt and stabilizing soils. Whitebark pine is vanishing from the landscape due to three main factors – white pine blister rust (Cronartium ribicola) invasions, mountain pine beetle (Dendroctonus ponderosae) outbreaks, and successional replacement by more shade-tolerant tree species historically controlled by wildfire. In the past century, human activity such as fire suppression has altered these …

Integrated Stress And Community Perceptions: Toward An Understanding Of Human-Cougar Tolerance, Lara Brenner

Graduate Student Theses, Dissertations, & Professional Papers

Evidence suggests that cougars (Puma concolor) are beginning to recolonize their traditional range in the Midwestern and Eastern US, returning to a landscape and a social environment that have changed drastically in a century of absence. Any hope of the cougar’s persistence depends on both human tolerance of their presence and on cougar tolerance of disrupted habitat. In this thesis, we took advantage of diverse cougar policy in place in the Western US to explore variation in human attitudes and acceptability of cougars and in the cougar stress response. We validated a process to identify and extract cortisol …

The Health, Fitness, And Anthropometric Characteristics Of Firefighters On The North Coast Of California, Gil Spitz

Cal Poly Humboldt theses and projects

ABSTRACT

THE HEALTH, FITNESS AND ANTHROPOMETRIC CHARACTERISTICS OF FIREFIGHTERS ON THE NORTH COAST OF CALIFORNIA

Gil Spitz

Limited research has been conducted on the health-related physical fitness level of rural firefighters on the northern coast of California. The geographic isolation of rural firefighters creates unique challenges, including staffing shortages placing individual firefighters under unusual physiological stress.

PURPOSE: The purpose of this study was to examine the health-related physical fitness status of rural firefighters.

METHODS: 20 male firefighters (mean±sd, age = 32±7 yr, height = 180±5 cm, body mass = 96±16 kg, fire service = 9±7 yr) on the …

Habitat Use And Movement Patterns Of Two Redwood Forest Salamanders, Aneides Vagrans And Ensatina Eschscholtzii, With An Examination Of The Efficacy Of Pit Tags For Marking Small Plethodontids, Christian Brown

Cal Poly Humboldt theses and projects

The habitat use and movements of small, secretive salamanders are generally poorly understood, in part due to the difficulty associated with marking and recapturing such animals. This study was designed to test the efficacy, both in the laboratory and in the field, of using passive integrated transponder (PIT) tags to mark and track two small-bodied plethodontid salamander species native to coastal northwestern California, Aneides vagrans, the Wandering Salamander, and Ensatina eschscholtzii, the Ensatina Salamander.

Aneides vagrans inhabits tree crowns. Using cover objects and visual encounter surveys, I searched for A. vagrans in the angiosperm understory canopy at least twice …

In The Face Of Drought: Do Fuel Treatments Promote Resistance To Multi-Year Drought In A Mixed-Conifer Forest Of Northern California?, Michael Vernon

Cal Poly Humboldt theses and projects

Climate change is predicted to increase the frequency, duration, and severity of drought events across many bioregions. Forest managers have two active management techniques to promote resistance and resilience to drought: prescribed fire and mechanical thinning. Generally applied to reduce fuels and fire hazard, treated areas may also reduce competition for resources that may improve tree-growth during drought and reduce mortality. The recent severe and prolonged drought in California allowed me to investigate the effects of climate stress and fuel treatments on tree growth responses in a dry mixed-conifer forest ecosystem.

To assess tree-growth responses to fuel treatments during severe …

Effects Of A Post-Activation Potentiation Warm-Up On Submaximal Parallel Back Squat Volume, Rating Of Perceived Exertion, Peak Velocity, And Peak Power, Carlton Wei

Cal Poly Humboldt theses and projects

Resistance training (RT) is effective for improving athletic performance, with specific training loads and volumes dictating the adaptations. A warm-up is necessary to safely and effectively engage in RT: typically with a low intensity aerobic activity, stretching, and movement specific potentiating exercises. Post-activation potentiation (PAP) acutely increases muscular power following a conditioning contraction, though limited research has assessed its use for RT. The purpose of this study was to assess how a PAP warm-up protocol affects volume, rating of perceived exertion (RPE), and peak velocity and power with 75%1RM in the barbell parallel back squat (PBS) exercise across 4 sets. …

Propensity Of Predator Mimicry In Wild Steller's Jays, Trinity C. Tippin

Cal Poly Humboldt theses and projects

Avian vocal mimicry has been described in a variety of contexts, suggesting its function is multifaceted within and across species; however, basic empirical data describing mimetic signal prevalence and context is lacking for numerous species. I examined occurrence and context of mimicked red-shouldered hawk (Buteo lineatus) calls over a 12-month period in a wild population of 49 individually color-marked Steller’s jays (Cyanocitta stelleri) and reviewed the occurrence of the behavior in historic re-sight data. I documented mimicry of red-shouldered hawk calls in 14 of 49 (28.6%) jays during the study. Hawk mimicry occurred more often during …

Seasonal Fish And Invertebrate Communities In Three Northern California Estuaries, Katherine Osborn

Cal Poly Humboldt theses and projects

The majority of Northern California estuaries are small, flooded, river valleys that are largely unstudied due to their small sizes and remote locations. Yet these estuaries serve as important nursery areas for many marine fish species including rockfish, flatfish, smelt, and herring, and they are vital to anadromous species such as Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (O. mykiss). I sampled the summer and winter fish and invertebrate communities of the Big, Mad, and Ten Mile river estuaries. Fish were sampled via beach seine or fyke net and invertebrates were sampled via benthic cores, June 2014-June …

Factors Associated With Continuing Emergence Of Β-Thalassemia Major Despite Prenatal Testing: A Cross-Sectional Survey, Haleama Al Sabbah, Sarah Khan, Abdallah Hamadna, Lamia Abu Ghazaleh, Anwar Dudin, Bashar Adnan Karmi

All Works

© 2017 Al Sabbah et al. Purpose: Health care initiatives focusing on prenatal testing and premarital genetic screening aiming to reduce the incidence of β-thalassemia have emerged during the last decade. In Palestine, 4% of the population are known thalassemia carriers with new cases continuing to appear despite the availability of prenatal testing. This study aims to identify factors that influence the decision to retain or abort fetuses affected by β-thalassemia in Palestine. Methods: Convenience sampling was used to select 32 women (72 fetuses) who were at risk of having a baby with β-thalassemia. A questionnaire on prenatal testing, test …

Identification And Analysis Of Bacterial Genomic Metabolic Signatures, Nathaniel Bowerman, Nathan L. Tintle, Matthew Dejongh, Aaron A. Best

Faculty Work Comprehensive List

With continued rapid growth in the number and quality of fully sequenced and accurately annotated bacterial genomes, we have unprecedented opportunities to understand metabolic diversity. We selected 101 diverse and representative completely sequenced bacteria and implemented a manual curation effort to identify 846 unique metabolic variants present in these bacteria. The presence or absence of these variants act as a metabolic signature for each of the bacteria, which can then be used to understand similarities and differences between and across bacterial groups. We propose a novel and robust method of summarizing metabolic diversity using metabolic signatures and use this method …

Improved Performance Of Gene Set Analysis On Genome-Wide Transcriptomics Data When Using Gene Activity State Estimates, Thomas Kamp, Micah Adams, Craig Disselkoen, Nathan L. Tintle

Faculty Work Comprehensive List

Gene set analysis methods continue to be a popular and powerful method of evaluating genome-wide transcriptomics data. These approach require a priori grouping of genes into biologically meaningful sets, and then conducting downstream analyses at the set (instead of gene) level of analysis. Gene set analysis methods have been shown to yield more powerful statistical conclusions than single-gene analyses due to both reduced multiple testing penalties and potentially larger observed effects due to the aggregation of effects across multiple genes in the set. Traditionally, gene set analysis methods have been applied directly to normalized, log-transformed, transcriptomics data. Recently, efforts have …

Powerful Method For Including Genotype Uncertainty In Tests Of Hardy-Weinberg Equilibrium, Andrew Beck, Alexander Luedtke, Keli Liu, Nathan L. Tintle

Faculty Work Comprehensive List

The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack calibration in the type I error rate, especially as genotype uncertainty increases. We propose a new approach in the spirit of genomic control that properly calibrates the type I error rate, while yielding improved power to detect deviations from Hardy-Weinberg Equilibrium. We demonstrate the improved performance of our method on both …

Feasibility Of Rainwater Catchment In The Taos Mesa Community In Northern New Mexico, Miranda Rivera

Water Resources Professional Project Reports

INTRODUCTION Lack of water is nothing new for New Mexico’s general population. However, its immediate negative effects are unevenly distributed throughout the state, which is increasingly evident in the context of rising temperatures and decreases in precipitation. Access to clean drinking water is significantly more pressing in rural and off-the-grid communities than in metropolitan areas of New Mexico. On the Taos Mesa in northern New Mexico, these off-the-grid communities continue hauling as the only available method for accessing water today. In these communities, water is not only a vital source of livelihood but also necessary for the continuance of cultural …

Analyzing The Rio Chama Flow Project’S Capacity To Implement Adaptive Management, Avery Olshefski

Water Resources Professional Project Reports

The Rio Chama is the main tributary to the Rio Grande in New Mexico. Several reservoirs were built on the Rio Chama to store water for downstream users, which has led to the river section becoming highly managed, resulting in negative ecological effects. Approximately 400,000 AF per year of water is conveyed through the system without considerable consumptive amounts, 96,200 AF of which were added with the San Juan-Chama trans-basin diversion, creating more water in the system then historically available. Therefore, the flow between the El Vado and Abiquiu Reservoirs has the potential to be optimized in order to provide …

Introducing A Theory Of Neutrosophic Evolution: Degrees Of Evolution, Indeterminacy, And Involution, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

During the process of adaptation of a being (plant, animal, or human), to a new environment or conditions, the being partially evolves, partially devolves (degenerates), and partially is indeterminate i.e. neither evolving nor devolving, therefore unchanged (neutral), or the change is unclear, ambiguous, vague, as in neutrosophic logic. Thank to adaptation, one therefore has: evolution, involution, and indeterminacy (or neutrality), each one of these three neutrosophic components in some degree. The degrees of evolution/indeterminacy/involution are referred to both: the structure of the being (its body parts), and functionality of the being (functionality of each part, or inter-functionality of the parts …

Combination Of Bmp-2 And Relaxin To Induce Osteogenesis In Vivo, Sahitya Injamuri

Masters Theses

"Bone grafts are a common procedure for treating craniofacial injuries such as trauma, surgery, and reconstruction. Autografts and allografts have limitations which encourages the use of synthetic bone grafts. While synthetic bone grafts, such as hydroxyapatite (HA) microspheres, are advantageous for their cost and reproducibility, they lack the cells and growth factors needed for proper osteoinduction. Bone morphogenetic protein-2 (BMP-2) has been shown to increase the osteoinduction of grafts but the effective dose is above physiological levels and causes undesired effects on the body. Relaxin has been shown to enhance BMP-2's ability to induce bone formation in vitro and thus …

Loss Of Outer Membrane Porins In Clonally Related Clinical Isolates Of Klebsiella Pneumoniae Modifies The Bacteria; Resulting In Altered Resistance To Phagocytosis By Macrophages, Debra Nickole Brunson

UNF Graduate Theses and Dissertations

Klebsiella pneumoniae is an opportunistic pathogen responsible for lobar pneumoniae, liver abscess, and septicemia. Clinical isolates are found to be extended spectrum beta lactamase positive with differential expression of the two classical porins, OmpK35 and OmpK36. Porin loss is associated with increased minimum inhibitory concentrations of beta lactam, cephalosporin, and carbapenem antibiotics that target the peptidoglycan. However, little is known about how porin loss affects other aspects of the cell envelope. The focus of this study was to characterize clinical isolates exhibiting differential porin expression and determine if the cumulative changes altered the resistance to phagocytosis by macrophages. The results …

A Multibiomarker Analysis Of Pollutant Effects On Atlantic Stingray Populations In Florida’S St. Johns River, John Whalen

UNF Graduate Theses and Dissertations

The goal of this study was to examine the potential health effects of organochlorine (OC) and polycyclic aromatic hydrocarbon (PAH) exposure on Atlantic stingray populations in Florida’s St. Johns River (SJR). Special emphasis was placed on identifying OC- and/or PAH-related effects in stingrays from areas of the lower (LSJR) and middle (MSJR) basins shown to possess elevated levels of these compounds, as well as characterizing baseline levels of pollutant exposure in the SJR shipping channel, which may be subjected to dredging in the near future, potentially resuspending and redistributing contaminated sediments and increasing pollutant-associated effects. To accomplish this, we measured …

Transcriptional Regulation Of Skeletal Muscle Atrophy-Induced Gene Expression By Muscle Ring Finger-1 And Myogenic Regulatory Factors, Karina Marie Kakareka

UNF Graduate Theses and Dissertations

Skeletal muscle wasting occurs as a corollary of numerous physiological conditions, including denervation, immobilization, and aging. The E3 ubiquitin ligases MuRF1 and MAFbx are induced under nearly all atrophy conditions and are believed to play a key role in protein degradation. Data in this thesis provides interesting new evidence that MuRF1 may also act as a transcriptional modulator of atrophy-induced genes or atrogenes. The transcriptional regulation of MuRF1 and MAFbx were characterized using a reporter gene system and exhibited repressed activity in C₂C₁₂ cells overexpressing MuRF1. Furthermore, ectopic expression of the myogenic regulatory factors (MRFs), MyoD and …

Mercury Accumulation And Effects In The Brain Of Atlantic Sharpnose Sharks (Rhiszoprionodon Terranovae), Samantha L. Ehnert

UNF Graduate Theses and Dissertations

Sharks often bioaccumulate mercury (Hg) concentrations in their muscle to levels that threaten the health of human consumers. However, few published studies have examined if the high Hg levels seen in shark muscle also occur in the shark brain, or if Hg accumulation affects shark neurophysiology. Therefore, this study examined if shark brains accumulate significant levels of Hg, if Hg accumulation occurs in certain subcomponents of the brain, and if Hg accumulation is associated with oxidative stress effects on the shark central nervous system, with special focus on the Atlantic sharpnose shark (Rhizoprionodon terraenovae). Sharks were collected along …

Prosociality And Risk: How Risky Decision-Making In Young Adults Relates To Altruistic Tendencies, Empathic Concern, And Prosocial Peer Affiliation, Sarah J. Beard

UNF Graduate Theses and Dissertations

Adolescence involves an increase in risky decisions, such as reckless driving and illicit substance use, but prosocial characteristics and peer affiliation have yet to be investigated as protective factors. The present study assessed altruistic tendencies, prosocial peer affiliation (PPA), and empathic concern as predictors and moderators of risk-taking, including both self-reported health risks and riskiness in a behavioral task. Young adults from ages 20 to 25 (M = 22.55, SD = 1.38) completed a battery of behavioral tasks (including the Balloon Analogue Risk Task and the Dictator Game) and questionnaires on Amazon MTurk, measuring risk-taking (drunk driving, texting while …

Behavioral And Physiological Assessment Of Zoo-Housed Heterosexual Gorilla (Gorilla Gorilla Gorilla) Troops With Multiple Silverbacks, Kaylin S. Tennant

UNF Graduate Theses and Dissertations

Based on recognized life history traits and ecology, zoos strive to house their gorillas (Gorilla gorilla gorilla) in mixed-sex groups with one mature male or silverback, multiple females, and their offspring. However, successful captive breeding programs and a nearly 50:50 birth sex ratio has created the need to house surplus males in solitary conditions or all-male groups. It is commonly believed that male western gorillas will not tolerate one another in the presence of females; however, multi-male, mixed-sex groups have been observed in the wild. For this reason, some zoos have begun experimenting with this scenario. At the …

Anti-Proliferative Effect Of Hibernating American Bullfrog, Lithobates Catesbeianus, Blood Plasma On The Thp-1 Cells, Sean L. Robbins

Dissertations and Theses @ UNI

Hibernation is a remarkable process that allows an organism to go dormant for long periods of time during the winter, when food is scarce and living conditions can be lethal. Much is unknown about the physiology behind hibernation, and most research comes from mammalian models. For example, it is known that during hibernation many of the cells in the body are impeded from going though mitosis but the mechanism that caused this was unknown. It was recently discovered that 13-lined ground squirrels (Ictidomys tridecemlineatus) and woodchucks (Marmota monax) have a protein, alpha-2-macroglobulin, in their blood plasma, …

Effects Of Group Selection With Yellow Birch (Betula Alleghaniensis) Retention On The Understory And Sapling Layer In Northern Hardwood Forests, Megan A. Petras O'Neil

Dissertations, Master's Theses and Master's Reports

Gap partitioning theory predicts that changes in microenvironment conditions found within a forest opening promote diversity in forest ecosystems. Under this theory we would expect to see variations in tree and understory diversity throughout and surrounding a forest opening. In order to test this theory, we examined manmade openings with legacy-tree retention in a northern hardwood forest located in the Upper Peninsula of Michigan. This work is part of an ongoing study that was started in 2003 with the creation of 49 openings centered on a reserve dominant or co-dominant yellow birch (Betula alleghaniensis Britt.). The primary objective of …

Impacts To Biodiversity And Ecosystem Services From Bioenergy Development: A Pan American Experience, Colin Phifer

Dissertations, Master's Theses and Master's Reports

As part of a broader project that evaluated the social and ecological sustainability of bioenergy, I studied the effects of bioenergy associated land-use change and management on native bees and birds in two bioenergy-producing countries, the United States and Argentina. In Argentina, I worked in Entre Ríos province where eucalyptus (Eucalyptus spp.) plantations are being planted. These fast-growing trees are replacing pasture and annual crops, the current dominant land use. I surveyed for native bees and birds in pastures/annual crops and large-scale eucalyptus plantations, as well as mixed-use farms and native espinal savannas. Both birds and bees declined in …

Feasibility & Discovery Using Fox System To Generate Gain-Of-Function Mutations With Hybrid Poplars, James Rauschendorfer

Dissertations, Master's Theses and Master's Reports

The Full-length complementary DNA OvereXpression (FOX) system is an approach to generating gain-of-function (GF) plants predominantly used for studying Arabidopsis. This approach inserts T-DNAs containing random full-length complementary DNA (fl-cDNA) with upstream promoter and downstream terminator into the host plant genome. Studies using this method report the success generating overexpression populations with high mutation rates. We choose to investigate the feasibility and effectiveness of this method using poplars. We suspected using a succulent xylem specific fl-cDNAs library would enrich the transformant poplars with mutants affected in traits specific to woody tissue development. We observed a characteristically high mutation rate …

Characterization Of Genic Microsatellite Markers (Est-Ssrs) In The Endangered Oak Species Quercus Georgiana M.A.Curtis, Priyanka Dipak Kadav

Dissertations, Master's Theses and Master's Reports

Quercus is important ecologically and economically because it provides food and habitat for wildlife, wood and paper products for humans. Oaks are endangered due to various factors like shifting climates, habitat loss, drought, pathogens and genetic swamping. Quercus georgiana (M.A. Curtis) is an endangered and restricted oak species which is remaining only in the southeastern part of the US. Efforts are required to conserve this endangered species from extinction. Conservation of this species can be done through these methods: ex-situ conservation (arboretum and botanical garden) and in-situ conservation strategies which protect the species in its natural habitat. For this conservation …