Digital Commons Network^™

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …

Structural Characterization Of The P1+ Intermediate State Of The P-Cluster Of Nitrogenase, Stephen M. Keable, Oleg A. Zadvornyy, Lewis E. Johnson, Bojana Ginovska, Andrew J. Rasmussen, Karamatullah Danyal, Brian J. Eilers, Gregory A. Prussia, Axl X. Levan, Simone Raugei, Lance C. Seefeldt, John W. Peters

Chemistry and Biochemistry Faculty Publications

Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N₂) to ammonia (NH₃) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum–iron protein (MoFe protein) that contains the iron–molybdenum cofactor (FeMo-co) sites where N₂ is reduced to NH₃. The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the …

Utah State University Commencement, 2018 – Main Campus, Utah State University

Commencement Programs

131st Annual Commencement of Utah State University.

Tremblings, May 2018, Western Aspen Alliance

Tremblings

Wyoming's High Desert: Aspen habitat presents challenges

Kevin Spence

The high elevation desert of southwest Wyoming occurs between 6,040 ft. and 9,550 ft. Isolated “high points” in the area are dryland oases supporting high aquatic and terrestrial wildlife species richness, as vegetative diversity provides essential life stage habitat needs for numerous species. Although aspen makes up the smallest percentage of all vegetation types on this landscape, I consider aspen stands and their associate understories the most ecologically important in this ecosystem. Just a few benefits these aspen stands provide include: solid dam building material for beaver pond complexes providing riparian …

Calculating Redshift Via Astronomical Spectroscopy, Joshua Glatt

Physics Capstone Projects

The Doppler effect is a well-known physical phenomenon which results in a change of a wave’s frequency or wavelength due to the motion of its source. Celestial objects in space (stars, galaxies, etc.) also experience a Doppler effect on their emitted electromagnetic radiation called redshift. In this study, redshifts were observed in the spectrographic observations of various celestial objects. This was done using a high-resolution near ultra-violet spectrometer in conjunction with a 14-inch Celestron Schmidt-Cassegrain telescope. The spectrometer was used to measure the absorption spectrum of the bodies and then these absorption spectrums were compared against the Hydrogen emission spectrum. …

Association Learning Via Deep Neural Networks, Trevor J. Landeen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Deep learning has been making headlines in recent years and is often portrayed as an emerging technology on a meteoric rise towards fully sentient artificial intelligence. In reality, deep learning is the most recent renaissance of a 70 year old technology and is far from possessing true intelligence. The renewed interest is motivated by recent successes in challenging problems, the accessibility made possible by hardware developments, and dataset availability.

The predecessor to deep learning, commonly known as the artificial neural network, is a computational network setup to mimic the biological neural structure found in brains. However, unlike human brains, artificial …

The Use Of Microfluidics And Dielectrophoresis For Separation, Concentration, And Identification Of Bacteria, Cynthia Hanson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Typical bacterial analysis involves culturing and visualizing colonies on an array of agar plates. The growth patterns and colors among the array are used to identify the bacteria. For fast growing bacteria such as Escherichia coli, analysis will take one to two days. However, slow growing bacteria such as mycobacteria can take weeks to identify. In addition, there are some species of bacteria that are viable but nonculturable. This lengthy analysis time is unacceptable for life-threatening infections and emergency situations. It is clear that to decrease the analysis of the bacteria, the culturing and growth steps must be avoided. …

Investigations Of Polyhydroxyalkanoate Secretion And Production Using Sustainable Carbon Sources, Chad L. Nielsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Polyhydroxyalkanoates (PHAs) are a type of biologically-produced plastic known for their biocompatibility and biodegradability. They have the potential to replace petroleum-based plastics as an environmentally-friendly alternative. This is beneficial because the release of plastics into environments such as the ocean and the buildup of plastics in landfills are major concerns facing society today. Currently, however, PHAs are significantly more expensive than their petroleum-based counterparts. This is largely due to the cost of carbon sources and of extracting the bioplastics from bacteria. The goal of these studies was to examine replacing traditional carbon sources used in PHA production like sugar and …

Breeding Season Ecology And Demography Of Lesser Scaup (Aythya Affinis) At Red Rock Lakes National Wildlife Refuge, Jeffrey M. Warren

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

It is hypothesized that individuals make reproductive decisions based on current assessments of their physiological condition and environmental conditions. For female lesser scaup (Aythya affinis), breeding occurs after an energetically costly spring migration. Increasing fat reserves (i.e., ‘body condition’) prior to breeding allows a female to produce a larger clutch of eggs, but time spent gaining body condition is costly in terms of time allowed to raise ducklings before freezing conditions in the fall. In Chapter 2 I explored rate of pre-breeding body condition gain in female lesser scaup, and how that rate influenced clutch size. Spring phenology, …

Targeted-Grazing As A Fuels Reduction Treatment: Evaluation Of Vegetation Dynamics And Utilization Levels, Travis Decker

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Wildfires have caused concern as they have increased in severity and intensity over the last few decades. Land managers have sought management actions to mitigate the risk of wildfire by reducing fuel loads, thus decreasing wildfire intensity. Camp Williams is a National Guard camp near Bluffdale, Utah, where small arms and artillery training occurs. Managers at Camp Williams have created fuel breaks by implementing targeted sheep and goat grazing to remove fine fuel and thin brush. Management objectives set utilization of fine fuels (herbaceous) at 80% by weight. Questions arose regarding the ecological impact of the prescribed grazing rates in …

Motor Affordance For Grasping A Safety Handle, Doug W. Mcdannald

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Observation of objects in our environment can potentiate movement, a fact reflected by increased activity in motor cortical networks when participants simply view a graspable object. This suggests that specific areas in the motor cortex play an important role in processing visual information to rapidly determine an appropriate action. The present study was conducted to test if visual access to a wall-mounted safety handle results in activation of motor cortical networks. We hypothesized that the hand area of the primary motor cortex would be facilitated shortly after visual access to a safety handle versus when no handle was visible. To …

Assessing Variation In Air Quality Perception: A Case Study In Utah, Karen Jayne Mendenhall

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

In recent years, Utah has experienced poor air quality due to pollution-trapping winter inversions and summer ozone pollution. The resulting impacts of poor air quality include health issues, reduced visibility, economic impacts and ecological impacts. Utah’s topography and exploding urban population are factors which increase human exposure to these adverse impacts of air pollution. It is important for State and local governments to understand how people perceive air quality so that clean air campaigns target those who are most likely to foster pro-environmental behaviors. An analysis was conducted using data from a state-wide survey conducted in July 2017. The survey …

Values, Mushfaking, And Literacy In Disability: Applying James Paul Gee’S Discourse Theory To The Deaf And Mental Health Communities, Adrienne Griffiths

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

The disability community has been a historically marginalized group and continues to be. Many advocates for inclusive language feel uncomfortable around the disability community because they are uncertain how to act and speak. There are two forms of language syntaxes that people primarily use to refer to someone with a disability: People-first language and Identity-first language. People-first language identifies someone first, then refers to their disability, such as “person with autism.” The second framework, Identity-first language, includes referring to someone’s disability first, then by another attribute. In other words, “autistic person.”

Both forms of language syntaxes have many reasons as …

Effect Of Wood Chips As A Component Of Soilless Media On Growth And Nutrition Of Food And Ornamental Crops, Kristen Bullough

Undergraduate Honors Capstone Projects

Peat is the central component of the soil-less media mix in all greenhouse crop production but it is expensive because it is harvested in Canada and shipped to greenhouses across North America. Wood chips provide a local, low-cost alternative to peat, but observations by growers indicate potential growth reductions from the addition of wood to peat-based media. Here I report the effects of the addition of wood chips to peat-based media. The study included four treatments: two controls (peat/vermiculite: 50/50 and 75/25) and two treatments with wood chips ' (peat/wood chips: 50/50 and 75/25) with three species (sunflowers, soybeans, and …

Enamel Hypoplasia And Its Relation To Ethnicity And Socioeconomic Status In The 19th Century United States, Amanda Drew Olivas Cook

Undergraduate Honors Capstone Projects

Linear enamel hypoplasia (LEH) is a condition of tooth enamel characterized by linear bands in tooth enamel that result from metabolic stress during the childhood years of enamel formation. The presence of LEH has frequently been used in biological anthropology as a marker of stress experienced during childhood. This paper uses a biocultural approach to investigate the occurrence and severity of LEH defects on the teeth of African American and European American adult male remains in the Terry Anatomical Skeletal Collection. The Terry Collection consists of low socioeconomic status individuals whose remains were unclaimed at St. Louis morgues and hospitals, …

Designing A Synthetic Spider Silk-Based Coating For Urinary Catheters To Reduce The Risk Of Cautis, Alexander Cook

Undergraduate Honors Capstone Projects

Urinary and Intravenous (IV) catheters are two of the most commonly used medical devices for administering vital drugs and obtaining diagnostic samples from patients. Unfortunately, hospital acquired infections (HAIs) occur at alarming rates due to catheter usage. The aim of this project was to design a urinary catheter that would decrease the occurrence of these infections with a catheter coating that utilizes the antimicrobial properties of synthetic spider silk in combination with the antiseptic chlorhexidine. This synthetic spider silk catheter will introduce a novel approach to catheterization in the medical industry.

Maternal Vitamin D Deficiency And Early Childhood Health Outcomes Including Autism Development, Kelsey L. Girardelli

Undergraduate Honors Capstone Projects

Many studies have shown that vitamin D deficiency during pregnancy is associated with a variety of adverse maternal and pediatric outcomes. Disease outcomes that have been observed in pregnant women who are vitamin D deficient include increased risk of C-section, preeclampsia, bacterial vaginosis, and gestational diabetes. In children born to deficient mothers, increased rates of childhood asthma, type 1 diabetes, low birthweight, and autism spectrum disorder (ASD) have been observed. Although there is much evidence to support these correlations, much is yet to be understood regarding the etiology of these outcomes. This paper specifically examines the relationships between risk factors …

Evaluation Of Antiviral Agents In Two Mouse Models Of Rna Virus Infections, John Hyrum Mcclatchy

Undergraduate Honors Capstone Projects

The first model we are evaluating is human influenza virus in mice. Influenza virus is a negative sense RNA virus, which the CDC estimates causes between 9.2 million and 35.6 million illnesses each year in the United States.^[1] In the current influenza season, H3N2 viruses have been the predominant subclade of influenza A virus in circulation.^[2] Development of a mouse model for influenza H3N2 virus infection has been difficult. In these studies, we endeavored to mouse-adapt influenza A/Hong Kong/4801/2014 H3N2 virus by serial passaging in AG129 mice. This virus strain was chosen as it overlaps in serotype with …

Crowdsourcing Consciousness: You Think, Therefore I Am, Justin M. Campbell

Undergraduate Honors Capstone Projects

The challenge to understand consciousness is a centuries-old interdisciplinary research program. The search entails fundamental questions about our nature - the desire to understand who we are has been around for nearly as long as experience itself. It is also one of the most important questions we can ask; meaning itself is predicated on having some sort of conscious experiencer for whom something can matter. Given the magnitude and intractability of explaining the paradox of how consciousness can be at once the most obvious thing in the universe, and also the most inaccessible, the endeavor is a tremendous undertaking. Until …

Designing A Synthetic Spider Silk Based Coating For Urinary Catheters To Reduce The Risk Of Cautis, Tess Marie Armbrust

Undergraduate Honors Capstone Projects

Catheter associated urinary tract infections (CAUTis) are a leading cause of morbidity and mortality in patients with life-threatening conditions. Foley catheters are the most common catheter used when a patient requires hospitalization but can become burdened with microbes which lead to CAUTis, the most common source of hospital acquired infection (HAI). The attached bacteria can form biofilms on the catheter which are difficult to treat using oral antibiotics and can lead to chronic infections. Synthetic spider silk as a catheter coating shows great promise because of demonstrated strength, biocompatibility, and antimicrobial properties. In addition, the antiseptic chlorhexidine can enhance the …

The Effect Of Gender And Socioeconomic Status On Concussion Reporting Behavior Among Ncaa Student-Athletes, Joshua Anthony Hansen

Undergraduate Honors Capstone Projects

Concussions are traumatic brain injuries that result from "brain shaking" that can occur during any situation that transmits force to the head. Concussions are defined as a clinical syndrome characterized by immediate and transient post-traumatic impairment of neural functions which lead to a complex grouping of both psychological and physiological symptoms (McCrory, et al., 2013). As knowledge of the long-term implications of these injuries grows, concussions are becoming more of a major health concern worldwide. One subset of concussion classifications, sports-related concussions, is receiving an increasing amount of attention from both scientists and health-care practitioners. It is estimated that more …

Impacts Of Hydroelectric Dams On Aquatic Macroinvertebrate Oviposition Strategies: The Role Of Desiccation, Jesse R. Fleri

Undergraduate Honors Capstone Projects

Previous studies quantifying the density, distribution and diversity of aquatic insects overwhelmingly focus on larval life stages. However, many aquatic insects exhibit selective oviposition behaviors, with a preference for emergent substrates along a river's edge. The practice of hydropeaking creates an artificial intertidal zone that is absent from natural rivers and to which freshwater organisms are not adapted. We hypothesized that this novel disturbance could reduce the availability and temporal persistence of oviposition habitats resulting in egg mortality. To test this hypothesis, we quantified the oviposition behavior of four aquatic insects using a hierarchical field survey of habitat availability and …

The Role Of Trailing Behavior In Conspecific Mating In Thamnophis Elegans And Thamnophis Sirtalis, Eleanor Watson

Undergraduate Honors Capstone Projects

In many gartersnake species, successful mating depends on the ability of males to follow pheromone trails left by females. The populations we investigated (Thamnophis sirtalis and Thamnophis elegans, closely related sympatric species) overwinter together and simultaneously emerge. Although, mating occurs concurrently, there is no evidence of hybridization. Therefore, we sought to investigate the mechanisms that allow male snakes to differentiate between heterospecific and conspecific females to ensure mating success. Behavior studies were conducted by presenting male snakes with extracted scents of conspecific females, heterospecific females, and conspecific males. We measured male preference by number of investigatory tongue flicks …

Foraging Behavior, Taxonomy, And Morphology Of Bees (Hymenoptera: Apoidea), With An Emphasis On Perdita (Hymenoptera: Andrenidae), Zachary M. Portman

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bees are the most important pollinators of flowering plants and are necessary for pollinating both wild plants and many of the crops that produce the food we eat. There are many different species of bees, with about 20,000 species worldwide and 4,000 species in the United States. Even though bees are important pollinators, there is still much we do not know about how many species there are and their biology. In order to better understand the species and their biology, I performed three projects that help fill these gaps by reviewing the species of a poorly known bee group, examining …

Managing For Multiple Objectives In Southwestern Forests: Evaluating The Trade-Offs Between Enhancing Mexican Spotted Owl Nest Habitat And Mitigating Potential Crown Fire, Daniel C. Deane Mckenna

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Forest Inventory and Analysis (FIA), the United States’ forest census, measured sixty-six Mexican spotted owl nest stands in order gain insight into the structure and composition of the nest habitat of this threatened species. I used these data, along with the greater FIA database and the Forest Vegetation Simulator to explore questions surrounding the management of Mexican spotted owl habitat, specifically how to balance the objective of sustaining and enhancing nest habitat in face of increasing forest fire size and severity in the Southwest. My research consisted of three studies. The first study quantified the structure and composition of …

Pruning Strategies For High Density ‘Montmorency' Tart Cherry, Sheriden M. Hansen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The tart cherry (Prunus cerasus) is the most significant fruit tree crop in Utah, accounting for roughly 51% of the total statewide commercial fruit acreage. In order to accommodate harvesting equipment, tart cherries are grown in conventional orchards with large trees spaced up to 5.5 meters apart. New methods of harvest are adapted to smaller trees in tighter spaced high density (HD) orchards. HD orchards bear fruit earlier in the orchard life than conventional orchards, but likely require different pruning and management strategies, which have not yet been determined for tart cherry. Experimental HD orchards were used to …

Evaluating Water Filtration And Disinfection For Household, Using Slow Sand Filters Plus Solar Disinfection, Mariana Demitry

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In this research, a household water treatment system was built and evaluated as a trial for improving the drinking water quality of the Nile River for the low-income communities. The system consisted of household-scale slow sand filters, and transparent polyethylene terephthalate-bottles for solar disinfection. The evaluation of the system depended on the removal/inactivation of some surrogates for the reference pathogens, and turbidity. The reference pathogens are pathogens specified by the World Health Organization to evaluate the efficiency of the household water treatment options. They were chosen to represent the classes of pathogens in water (bacteria, viruses, protozoa). The surrogates used …

In-Situ Educational Research From Concept To Classroom Implementation: A Multiple Paper Dissertation, David Mark Weiss

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

An educational researcher sought to collaborate with a classroom instructor to introduce problem-based learning as a new teaching intervention. First, a classroom instructor was approached to consider how a problem-based learning instructional approach might fit with their existing curriculum plan. The researcher and the classroom teacher used a discussion framework to decide together how to best design a professional learning course meant to prepare the teacher to use the new techniques in their classroom. The teacher took the professional learning course and subsequently designed his own problem-based learning course. That course was then delivered to undergraduate students in a college …

Advancement To The Highest Faculty Ranks In Academic Stem: Explaining The Gender Gap At Usu, Helga Van Miegroet

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Science and technology (S&T) disciplines at universities are still largely dominated by men, and few women are found in the highest employment ranks. Using the faculty data from Utah State University, this thesis explores the factors that help explain the difference in career trajectory between men and women in the S&T colleges. While there were few women in S&T colleges prior to the 1990s, more women have been hired since then, and the lower ranks of the faculty corps are starting to reflect the gender composition of the doctoral degree holders in the different fields. This is not the case …

Using Remotely Piloted Aircraft And Infrared Technology To Detect And Monitor Greater Sage-Grouse, Thomas R. Thompson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In wildlife management, using cutting edge technology and science to monitor greater sage-grouse (Centrocercus urophasianus; sage-grouse) populations, enables land managers to better assess the impact of their management decisions. Having precise counts of sage-grouse lek attendance, and specifically male lek attendance, is an important metric used to evaluate population status and response to conservation actions (Gifford et.al, 2013, Dahlgren et al., 2016). Leks are seasonal breeding sites where males perform a ritualistic courtship dance for females.

Our case study examined if a Remotely Piloted Aircraft (RPA) was effective in detecting, and counting, sage-grouse during the lek season (early …