Digital Commons Network^™

The Effect Of Postural Alterations On Metabolic Cost In Running On Incline Slopes, Nikaela K. Hemminger

Cal Poly Humboldt theses and projects

In spite of an intuitive relationship between running technique and performance, the influence of specific techniques on metabolic cost remains unclear. While recent studies suggest that postural lean affects metabolic cost during level ground running, little information exists regarding the influence of postural lean on the metabolic cost of running on an incline slope. Purpose: This study sought to investigate the effect of postural lean on metabolic cost, kinematics, and muscle activation of running across a range of incline slopes. Methods: Sixteen healthy adult runners (21±2 years, 8M/8F) of different competitive standards participated in twelve running trials on a motorized …

The Desert's Canary: A Narrative Examination Of The Socio-Political Role Of The Threatened Desert Tortoise, Halle Rayn Kohn

Cal Poly Humboldt theses and projects

Through story, personal experience is connected to broader meaning. The stories that individuals tell about a flagship species contribute not only to the animal’s role in conservation, but also to collective human imagination and culture. The purpose of this research is to reveal the roles (social, cultural, political, and ecological) that the desert tortoise plays in the California Desert, and to uncover how these roles are demonstrated through conservationist’s narratives. This study utilizes mixed qualitative methods with the goal of discovering why the Mojave Desert Tortoise (Gopherus agassizii), an iconic and threatened species, has particular significance within the …

Using Functional Infrared Thermal Imaging To Measure Stress Responses, Julia Tenaya Kandus

Cal Poly Humboldt theses and projects

The stress response reflects a coordinated pattern of physiological changes that serves the adaptive function of increasing an organism’s ability to cope with situations that require action or defense. The changes in blood flow associated with the stress response may be detectable using the relatively new research technique of functional infrared thermal imaging (fITI). The present study was designed to determine the time-course and topography of temperature changes in human faces during the experience of a stressor. Infrared images were taken from 29 female participants while they completed the mental arithmetic component of the Trier Social Stress Test (TSST). Continuously …

Test Of Bpa's Estrogenic Effects On Brain Aromatase Expression, Neural Activity, And Locomotive Behavior In Zebrafish Larvae, Ryan J. Mcauley

Cal Poly Humboldt theses and projects

Bisphenol A (BPA) is a well-known endocrine disrupting chemical that mimics the effects of estrogens. Aromatase B (Cyp19a1b) is a brain-specific enzyme that converts testosterone to estrogen and is highly upregulated in response to estrogen receptor activation localized to radial glial cells. During embryonic zebrafish development, there is a small window of time denoted by an increase in neurogenesis and estrogen receptor activity. Previous studies have demonstrated that a low dose BPA exposure (0.1µM) during this window causes hyperlocomotion in larval zebrafish, yet no further explanation for this behavior change has been described. The purpose of this study was to …

Seasonal Home Range Variation And Spatial Ecology Of Peregrine Falcons (Falco Peregrinus) In Coastal Humboldt County, Ca, Elizabeth-Noelle F. Morata

Cal Poly Humboldt theses and projects

Peregrine falcons (Falco peregrinus) are renowned for their migratory habits, with ‘peregrinus’ often translated as ‘wanderer’ or ‘pilgrim’. However, their migratory habits may differ by population and some peregrine may falcons forgo migration when climate and resources remain stable. To examine peregrine falcon home range and space use, I fitted GPS-satellite transmitters to nine breeding adults in coastal northern California, an area with a mild climate and abundant waterbird populations. I used kernel density estimates and time-local convex hulls to examine seasonal home ranges and within-home range habitat use. All nine peregrine falcons remained resident in …

The Influence Of Microclimate And Local Adaptation For A Climate-Sensitive Species (Aplodontia Rufa), Jennie K. Jones Scherbinski

Cal Poly Humboldt theses and projects

Climate change models and analyses predict a disproportionate impact on climatically sensitive species such as the mountain beaver (Aplodontia rufa). Mountain beavers have physiological constraints that limit their distribution to cool, moist climates. While mountain beavers have persisted through past periods of climate change, increasing temperature since the last glacial maximum is believed to have had a strong influence in reducing their range. This is particularly true for the Point Arena subspecies (A. r. nigra, “PAMB”), found towards the southwestern edge of their range on the coast of California. Here, I examined the climatic niche of …

Treatment Wetland Remediation Via In Situ Solids Digestion Using Novel Blue Frog Circulators, Kyle T. Sipes

Cal Poly Humboldt theses and projects

After 33 years of operation with little maintenance, the treatment wetlands at the Arcata Wastewater Treatment Facility (AWTF) suffer from reduced treatment capacity and internal loading issues, leading to reduced performance in recent years. The next NPDES permit for the facility will regulate discharge ammonia concentrations, and internal ammonia loads, associated with accumulated solids in the system, may lead to future regulation violations.

To begin addressing this problem, the City of Arcata entered into a rental agreement with Absolute Aeration to install two Blue Frog circulators in Treatment Wetland 3 (TW3). The goal of this project was to determine if …

Effects Of Manual And Mechanical Ammophila Arenaria Removal Techniques On Coastal Dune Plant Communities And Dune Morphology, Monique R. Silva Crossman

Cal Poly Humboldt theses and projects

The removal of invasive species as part of the restoration process can allow natives organisms to rebound. An ecosystem that incurs damages from invasive species is coastal sand dunes, which are dynamic systems. Some coastal sand dunes on the west coast of the United States have been invaded by Ammophila arenaria. The invasive grass, A. arenaria, is thought to alter and stabilize foredune morphology and reduce populations of native species. The objectives of my research are to examine the effects that manual and mechanical A. arenaria removal techniques have on coastal sand dune morphology and vegetative cover over time. …

Changes In Demography, Distribution, And Diet In Garter Snakes Following Eradication Of A Non-Native Prey Subsidy, Justin A. Demianew Mr.

Cal Poly Humboldt theses and projects

Interactions between non-native and native consumers are often complex and cryptic. I shed light on relationships between non-native brook trout (Salvelinus fontinalis), native amphibians, their shared predator (aquatic garter snake; Thamnophis atratus) and a sympatric amphibian specialist (common garter snake; T. sirtalis) using a treatment-control removal experiment in a sub-alpine system of northern California. Eradication of non-native S. fontinalis resulted in an immediate decrease in T. atratus abundance and survival, whereas their abundance increased in concert with T. sirtalis in an adjacent control basin. Additionally, T. atratus body condition decreased substantially during this time, despite their …

Evaluating Habitat Selection Models To Improve Site Selection In A Population Monitoring Program For Townsend's Big-Eared Bats (Corynorhinus Townsendii), Katrina J. Smith

Cal Poly Humboldt theses and projects

Winter roost (hibernacula) surveys offer a unique opportunity to monitor Townsend’s big-eared bats (Corynorhinus townsendii) while the population is generally closed, using a simple count method to census the population. Existing knowledge of C. townsendii hibernacula facilitates long-term population trend analysis but improving the accuracy of trend estimates requires identification of additional hibernacula to increase the proportion of the population monitored. Over 800 caves are known within Lava Beds National Monument; 322 of these have never been surveyed in the winter and could potentially hold a substantial portion of the C. townsendii population currently missing from the annual …

Framings Of Nature In Planet Earth Ii And Wild Safari Live, Joshua Gross

Cal Poly Humboldt theses and projects

The percentage of the world’s population living in cities continues to grow, while media technologies become ever more ubiquitous. As a result, the mass media’s role in connecting the general public to the natural world will only increase; the wildlife genre of television may have a particularly large role to play in this regard. Unfortunately, previous authors have argued that the over-dramatized depictions of nature in mainstream wildlife programs may serve to disconnect viewers from the natural world. Scholarship has also not kept up with recent developments in wildlife television, with few authors writing about hugely successful programs like Planet …

Sniffing Out Decomposition: Investigating The Reliability Of Human Remains Detection Dogs, Kristen Marie Nawn

Cal Poly Humboldt theses and projects

The purpose of this study was to investigate the reliability of trained Human Remains Detection (HRD) dogs in the field. HRD dogs are trained to locate deceased individuals, typically in conjunction with law enforcement agencies, by using their enhanced olfactory systems to detect scents that humans cannot. Limited research has been conducted on both the strengths and weaknesses of these dogs and their abilities to locate human remains. This study focused on one North Carolina based organization that trains HRD dogs. Data were collected by distributing surveys and by observing regularly scheduled training exercises conducted by the organization. The collected …

Export Of Invertebrate Drift From Fishless Headwater Streams, Jonathan M. Hollis

Cal Poly Humboldt theses and projects

An understanding of ecological linkages between headwater systems and downstream habitats is needed to enhance management practices for aquatic conservation. I quantified and described the export of invertebrate drift from fishless headwater streams to assess its potential importance to downstream populations of coastal cutthroat trout (Oncorhynchus clarki clarki) in the lower Klamath River in northern California. From June 2015 through April 2016, I sampled invertebrate drift in six fishless headwaters in the sub-basins of Tectah, Ah Pah, and Tarup creeks. Concurrently, I collected invertebrate drift and trout diet samples from adjoining fish-bearing streams. Drift export rates were lowest …

Characterizing The Effect Of Cjun On The Expression Of Oct4 Variants And How They Correlate With The Expression Of Genes Associated With Potency And Cell Fate Of Murine Embryonic Stem Cells, Kristine Teague

Cal Poly Humboldt theses and projects

cJun is a transcription factor associated with proliferation and growth. Recent evidence has shown it plays a role in cell fate decision making of embryonic stem cells and correlates with changes in Oct4 expression, an important marker for pluripotency. There are multiple Oct4 isoforms that arise from alternative splicing and alternative translation. Oct4A is the variant most frequently associated with pluripotency, while evidence suggests that Oct4B variants have roles in potency as well as stress responses.

We aimed to study the effect of cJun over expression in murine embryonic stem cells on Oct4 gene expression through two methods: transient transfection …

Parameter Uncertainty Analysis For Biofuel Crops

Journal of Spatial Hydrology

Watershed scale models are preferred to quantify long-term impacts of various land use decisions. Numerous models are available for carrying out land use change analyses, however, there are uncertainties associated with the simulation modeling system. Uncertainty in parameters is inevitable and has to be assessed before reporting modeled results to stakeholders. Parameter uncertainty analyses have been carried out in the past for different land use conditions. However, very few studies have been conducted on the parameter uncertainty analysis for biofuel crops. The production of biofuel crops is increasing since 2007 mainly because of the Energy Independence and Security Act (EISA) …

Improving The Bureaucracy: What Leads Government Officials To Use Evidence-Based Reports?, Nicholas Moffitt

Sigma: Journal of Political and International Studies

No abstract provided.

Efficacy Of Oral Administration Of Sodium Iodide To Prevent Bovine Respiratory Disease Complex, B. M. Shoemake, B. L. Vander Ley, B. W. Newcomer, M. C. Heller

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: The prevention of bovine respiratory disease complex (BRD) in beef cattle is important to maintaining health and productivity of calves in feeding operations.

Objective: Determine whether BRD bacterial and viral pathogens are susceptible to the lactoperoxidase/hydrogen peroxide/ iodide (LPO/H₂O₂/I^-) system in vitro and to determine whether the oral administration of sodium iodide (NaI) could achieve sufficient concentrations of iodine (I) in the respiratory secretions of weaned beef calves to inactivate these pathogens in vivo.

Animals: Sixteen weaned, apparently healthy, commercial beef calves from the University of Missouri, College of Veterinary Medicine teaching herd. …

Methods, Systems, And Devices Relating To Force Control Surgical Systems, Shane M. Farritor, Thomas Frederick, Kearney Lackas, Joe Bartels, Jacob Greenburg

Department of Mechanical and Materials Engineering: Faculty Publications

The various embodiments herein relate to robotic surgical systems and devices that use force and/or torque sensors to measure forces applied at various components of the system or device. Certain implementations include robotic surgical devices having one or more force/torque sensors that detect or measure one or more forces applied at or on one or more arms. Other embodiments relate to systems having a robotic surgical device that has one or more sensors and an external controller that has one or more motors such that the sensors transmit information that is used at the controller to actuate the motors to …

Characterization Of Neofabraea Actinidiae And N. Brasiliensis As Causal Agents Of Apple Bull’S-Eye Rot In Southern Brazil, Amauri Bogo, Carla C. Comparin, Rosa M. Valdebenito Sanhueza, Patricia Ritschel, Ricardo T. Casa, Fábio N. Silva, Sydney E. Everhart

Department of Plant Pathology: Faculty Publications

The causal agents of apple bull’s-eye rot in southern Brazil have recently been described as Neofabraea actinidiae and N. brasiliensis. Isolates of both species were evaluated for response of mycelial growth index (MGI) to different temperatures, enzyme production, mycelial growth inhibition and effective concentrations (EC₅₀ and EC₁₀₀) of the fungicides triflumizole, pyrimethanil and thiophanate methyl, as well as aggressiveness on fruits of ‘Fuji’ hybrid and ‘Pink Lady’. There was significantly lower mycelium growth in N. brasiliensis compared with N. actinidiae at all temperatures tested. Neither species grew at 3 and 32°C. There were minor differences in …

Elucidating The Role Of Highly Homologous Nicotiana Benthamiana Ubiquitin E2 Gene Family Members In Plant Immunity Through An Improved Virus‑Induced Gene Silencing Approach, Bangjun Zhou, Lirong Zeng

Department of Plant Pathology: Faculty Publications

Background: Virus-induced gene silencing (VIGS) has been used in many plant species as an attractive post transcriptional gene silencing (PTGS) method for studying gene function either individually or at large-scale in a high-throughput manner. However, the specificity and efficiency for knocking down members of a highly homologous gene family have remained to date a significant challenge in VIGS due to silencing of off-targets. Results: Here we present an improved method for the selection and evaluation of gene fragments used for VIGS to specifically and efficiently knock down members of a highly homologous gene family. Using this method, we knocked down …

The Tomato U-Box Type E3 Ligase Pub13 Acts With Group Iii Ubiquitin E2 Enzymes To Modulate Fls2-Mediated Immune Signaling, Bangjun Zhou, Lirong Zeng

Department of Plant Pathology: Faculty Publications

In Arabidopsis and rice, the ubiquitin ligase PUB13-mediated protein degradation plays a significant role in plant pattern-triggered immunity (PTI) and flowering time control. The Arabidopsis PUB13 has been shown to attenuate the pattern recognition receptor FLS2-mediated immune signaling by ubiquitinating FLS2 and consequently promoting its degradation by the 26S proteasome. Nevertheless, the cognate ubiquitin-conjugating enzymes (E2) with which PUB13 acts to modulate FLS2-mediated PTI are unknown. To address this question, we investigate here the tomato (Solanum lycopersicum) homolog of PUB13, SlPUB13 by utilizing the recently characterized complete set of tomato E2s. Of the 13 groups of tomato E2s, …

Proteomic Analysis Of Ubiquitinated Proteins In Rice (Oryza Sativa) After Treatment With Pathogen-Associated Molecular Pattern (Pamp) Elicitors, Xiao-Lin Chen, Xin Xie, Liye Wu, Caiyun Liu, Lirong Zeng, Xueping Zhou, Feng Luo, Guo-Liang Wang, Wende Liu

Department of Plant Pathology: Faculty Publications

Reversible protein ubiquitination plays essential roles in regulating cellular processes. Although many reports have described the functions of ubiquitination in plant defense responses, few have focused on global changes in the ubiquitome. To better understand the regulatory roles of ubiquitination in rice pattern-triggered immunity (PTI), we investigated the ubiquitome of rice seedlings after treatment with two pathogen-associated molecular patterns, the fungal-derived chitin or the bacterialderived flg22, using label-free quantitative proteomics. In chitin-treated samples, 144 and 167 lysine-ubiquitination sites in 121 and 162 proteins showed increased and decreased ubiquitination, respectively. In flg22-treated samples, 151 and 179 lysine-ubiquitination sites in 118 and …

Photosystem Ii Subunit S Overexpression Increases The Efficiency Of Water Use In A Field-Grown Crop, Katarzyna Glowacka, Johannes Kromdijk, Katherine Kucera, Jiayang Xie, Amanda P. Cavanagh, Lauriebeth Leonelli, Andrew D. B. Leakey, Donald R. Ort, Krishna K. Niyogi, Stephen P. Long

Department of Biochemistry: Faculty Publications

Insufficient water availability for crop production is a mounting barrier to achieving the 70% increase in food production that will be needed by 2050. One solution is to develop crops that require less water per unit mass of production. Water vapor transpires from leaves through stomata, which also facilitate the influx of CO2 during photosynthetic assimilation. Here, we hypothesize that Photosystem II Subunit S (PsbS) expression affects a chloroplastderived signal for stomatal opening in response to light, which can be used to improve wateruse efficiency. Transgenic tobacco plants with a range of PsbS expression, from undetectable to 3.7 …

Simulation Of Stimulation: Cytokine Dosage And Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation, Matteo Barberis, Tomáš Helikar, Paul Verbruggen

Department of Biochemistry: Faculty Publications

Triggering an appropriate protective response against invading agents is crucial to the effectiveness of human innate and adaptive immunity. Pathogen recognition and elimination requires integration of a myriad of signals from many different immune cells. For example, T cell functioning is not qualitatively, but quantitatively determined by cellular and humoral signals. Tipping the balance of signals, such that one of these is favored or gains advantage on another one, may impact the plasticity of T cells. This may lead to switching their phenotypes and, ultimately, modulating the balance between proliferating and memory T cells to sustain an appropriate immune response. …

Computational Systems Biology Approach For The Study Of Rheumatoid Arthritis: From A Molecular Map To A Dynamical Model, Vidisha Singh, Marek Ostaszewski, George D. Kalliolias, Gilles Chiocchia, Robert Olaso, Elisabeth Petit-Teixeira, Tomáš Helikar, Anna Niarakis

Department of Biochemistry: Faculty Publications

In this work we present a systematic effort to summarize current biological pathway knowledge concerning Rheumatoid Arthritis (RA). We are constructing a detailed molecular map based on exhaustive literature scanning, strict curation criteria, re-evaluation of previously published attempts and most importantly experts’ advice. The RA map will be web-published in the coming months in the form of an interactive map, using the MINERVA platform, allowing for easy access, navigation and search of all molecular pathways implicated in RA, serving thus, as an on line knowledgebase for the disease. Moreover the map could be used as a template for Omics data …

The Colomoto Interactive Notebook: Accessible And Reproducible Computational Analyses For Qualitative Biological Networks, Aurelien Naldi, Celine Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loic Pauleve

Department of Biochemistry: Faculty Publications

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together,many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users’ learning curve of these technologies. The framework …

A Mechanistic Computational Model Reveals That Plasticity Of Cd4+ T Cell Differentiation Is A Function Of Cytokine Composition And Dosage, Bhanwar Lal Puniya, Robert G. Todd, Akram Mohammed, Deborah M. Brown, Matteo Barberis, Tomáš Helikar

Department of Biochemistry: Faculty Publications

CD4+ T cells provide cell-mediated immunity in response to various antigens. During an immune response, naïve CD4+ T cells differentiate into specialized effector T helper (Th1, Th2, and Th17) cells and induced regulatory (iTreg) cells based on a cytokine milieu. In recent studies, complex phenotypes resembling more than one classical T cell lineage have been experimentally observed. Herein, we sought to characterize the capacity of T cell differentiation in response to the complex extracellular environment. We constructed a comprehensive mechanistic (logical) computational model of the signal transduction that regulates T cell differentiation. The model’s dynamics were characterized and analyzed under …

Reactive Oxygen Species In Chronic Obstructive Pulmonary Disease, Samia Boukhenouna, Mark A. Wilson, Karim Bahmed, Beata Kosmider

Department of Biochemistry: Faculty Publications

Chronic obstructive pulmonary disease (COPD) includes chronic bronchitis and emphysema. Environmental exposure, primarily cigarette smoking, can cause high oxidative stress and is the main factor of COPD development. Cigarette smoke also contributes to the imbalance of oxidant/antioxidant due to exogenous reactive oxygen species (ROS). Moreover, endogenously released ROS during the inflammatory process and mitochondrial dysfunction may contribute to this disease progression. ROS and reactive nitrogen species (RNS) can oxidize different biomolecules such as DNA, proteins, and lipids leading to epithelial cell injury and death. Various detoxifying enzymes and antioxidant defense systems can be involved in ROS removal. In this review, …

Genes For Membrane Transport Proteins: Not So Rare In Viruses, Timo Greiner, Anna Moroni, James L. Van Etten, Gerhard Thiel

James Van Etten Publications

Some viruses have genes encoding proteins with membrane transport functions. It is unknown if these types of proteins are rare or are common in viruses. In particular, the evolutionary origin of some of the viral genes is obscure, where other viral proteins have homologs in prokaryotic and eukaryotic organisms. We searched virus genomes in databases looking for transmembrane proteins with possible transport function. This effort led to the detection of 18 different types of putative membrane transport proteins indicating that they are not a rarity in viral genomes. The most abundant proteins are K+ channels. Their predicted structures vary between …

Size-Dependent Catalysis Of Chlorovirus Population Growth By A Messy Feeding Predator, John Delong, Zeina Al-Ameeli, Shelby Lyon, James L. Van Etten, David Dunigan

James Van Etten Publications

Many chloroviruses replicate in endosymbiotic zoochlorellae that are protected from infection by their symbiotic host. To reach the high virus concentrations that often occur in natural systems, a mechanism is needed to release zoochlorellae from their hosts. We demonstrate that the ciliate predator Didinium nasutum foraging on zoochlorellae-bearing Paramecium bursaria can release live zoochlorellae from the ruptured prey cell that can then be infected by chloroviruses. The catalysis process is very effective, yielding roughly 95% of the theoretical infectious virus yield as determined by sonication of P. bursaria. Chlorovirus activation is more effective with smaller Didinia, as larger …