University of Idaho Library Digital Initiatives
Not a member yet
54971 research outputs found
Sort by
Invader Probe Targeting of Chromosomal DNA
No full textInterest in developing probes capable of targeting chromosomal DNA in cells has grown to meet diagnostic and therapeutic needs. DNA has a stable predicable double-stranded structure that has been the subject of study to identify agents that can specifically bind to the duplex (CHAPTER 1). Success stories from probe technologies such as triplex-forming oligonucleotides, peptide nucleic acids (PNAs), and minor-groove-binding polyamides have been well characterized. However, they suffer limits of detection with experimental conditions requirements (homopurine targets; denaturing steps; low ionic strengths; short target sequences). Newly discovered CRISPR-Cas9 has garnered much attention; however, the approach requires transfection of plasmids encoding CRISPR-Cas9 components. To address these shortcomings, our laboratory has developed Invader probes. Placement of 2'-O-(pyren-1-yl)methyl RNA monomers in +1 interstrand zipper arrangements destabilizes the probe duplex as the intercalating pyrene moieties vie for the same space between two Watson-Crick base pairs. These ‘energetic hotspots’ activate the double-stranded probe and, in concert with the high affinity for complementary DNA (cDNA) displayed by individual probe strands, provide the driving force for recognition of mixed-sequence target sites. The capabilities and features of Invader probes specific detection of chromosomal DNA fluorescent in situ hybridization (FISH) assays at near physiological conditions were statistically analyzed. Based on these results, Optimized Invader probes were synthesized and showed improved efficiency in chromosomal DNA detection (CHAPTER 2). Moreover, the combination of Invader FISH probes with the powerful detection properties of flow cytometry was used to quantify thousands of specifically label isolated nuclei, offering a potential advantage over the laborious microscope evaluation of detection (APPENDIX A).masters, M.S., Chemistry -- University of Idaho - College of Graduate Studies, 2020-0
A Model and Device for High Throughput Measurements of Stem Flexural Stiffness in Grains
No full textThe global issue of crop lodging has significant, negative impacts on crop quality and supply. Crop lodging refers to the structural failure of crops due to external (e.g., rain, wind) and internal loading (e.g., grain weight). To reduce crop lodging, crops with high lodging resistance must be developed through selective breeding. However, numerous confounding factors make it difficult to evaluate lodging resistance accurately and efficiently. Several devices and methods have been developed to evaluate lodging resistance. Unfortunately, most of these devices are low throughput and only allow a limited number of plants to be tested at a time. More rapid evaluations are required to enable more efficient and effective selective breeding processes. This thesis presents a novel device known as the SOCEM (Stiffness of Crops Extrapolation Machine) that can determine the lodging resistance of grain crops in a high throughput manner. The SOCEM is able to evaluate entire experimental plots in just a few minutes. The device utilizes a novel mathematical crop model to account for nonlinearities and interactions within mechanobiological systems. The model is derived and validated using physical and finite-element model experiments and its most effective range is highlighted.masters, M.S., Mechanical Engineering -- University of Idaho - College of Graduate Studies, 2020-0
An Assessment of Grassland Bird Communities, Shrub Use, and Reproduction In the Context of Shrub Encroachment
No full textGrassland communities are declining and are considered an endangered ecosystem in North America. The decline in grassland community’s extent and availability directly influences the grassland bird community. One cause of the decline in grassland communities is the increasing encroachment of shrubs into grasslands. This thesis explores grassland bird in a wet meadow system experiencing shrub encroachment, mainly by black hawthorne (Crataegus douglasii), in Weippe Idaho. In the first chapter, we report how artificial nest temperatures are influenced by distance from shrubs. Shrubs act as a temperature buffer from extreme temperature fluctuations. In the second chapter, we describe the avian community on the Weippe Prairie and report how birds are using the shrubs on site. Shrub use is evaluated by season, time of day, and species.masters, M.S., Natural Resources -- University of Idaho - College of Graduate Studies, 2019-0
Understanding Microhabitat Distribution at the Riverscape: Insights from Coupled Hydrodynamic and Bioenergetic Modeling
No full textUnderstanding and evaluating complex links between anthropogenic and natural processes has become an essential piece in freshwater conservation and management. Characterization and monitoring of streams worldwide has been difficult due to the complex nature of river systems and the organisms that inhabitant them. With recent advances in technology and modeling techniques, the scientific community has begun to improve characterization of processes governing freshwater streams and rivers. To further understanding and management of river systems, we present novel technological and modeling techniques to gain insights into said links and provide guidance related to freshwater and fisheries management where we apply these methods to the Lemhi River of Eastern Idaho. First, we processed and validated a new generation bathymetric light detection and ranging system known as the Experimental Advanced Airborne Research LiDAR-B (EAARL-B). This newly developed aerial system relies on the travel time of light energy pules to measure distance from the sensor which generates high resolution mapping (~1 point/m2) of stream corridors, including the bathymetry, banks, and floodplains at watershed scales (100 km). Next, we used a validated, bare earth filtered, digital surface model supported by the EAARL-B system to develop a series of numerical flow models for the assessment of aquatic habitat as it relates to endangered Chinook salmon. Leveraging the spatially continuous modeled depth and velocities, we coupled flow hydraulics with publicly available empirical data including: Lemhi River Chinook salmon length and mass distributions, drifting macroinvertebrate rates, measured stream temperature, and representative measured discharges to develop a bioenergetics model to assess the impacts of water diversion, stream flow, morphological channel simplification, and stream temperature on juvenile Chinook salmon habitat suitability of the mainstem Lemhi River. We compared three distinct 1 km reaches with variable morphological complexity, a single thread confined channel, a multithread complex reach, and an engineered restoration reach to model juvenile Chinook salmon bioenergetic profitability for two critical time periods, late summer low flow (August) and late fall, fully undiverted, natural flow regime (October). We conclude that morphological complexity, specifically side and off-channel habitat, is essential for supporting juvenile Chinook salmon growth. As temperature begins to decrease in the fall, and mainstem discharges are increased due to water management, the morphologically complex reach provided the greatest amount of suitable habitat to sustain or promote growth for juvenile Chinook salmon.masters, M.S., Environmental Science -- University of Idaho - College of Graduate Studies, 2019-0
Leveraging High-Throughput Sequencing Data to Understand Complex Systems: Effects of Heat Stress Along the Swine Gastrointestinal Microbiome, Inflammation in the Bovine Milk Microbiome, and the Genetics of Human Lactation with Respect to Human Milk Oligosaccharide Synthesis
No full textResearch has become entwined with sequencing of DNA and RNA to contribute to our understanding of life. The progression of sequencing technology from pattern finding; to targeted, quantitative sequencing; to high-throughput sequencing has provided deep surveys into the breadth of variation in life across all ecosystems. This compilation of chapters seeks to leverage the development of high-throughput sequencing to assess changes in the microbiomes of the gastrointestinal tracts (GIT) of heatstressed pigs, the milk microbiome of cows with varying levels of mammary inflammation, and the host genetic variation of milk carbohydrate-related genes in women around the globe. In heatstressed pigs, microbial composition clustered distinctly by location in the GIT (stomach, ileum, colon/feces) and differed in select microbes and diversity metrics. The ma- jor finding was that fecal assessment of bacterial composition may not accurately evaluate membership or function the entire gastrointestinal microbiome. Milk microbial composition differed in cows on two dairies and varied with somatic cell counts (SCC; a proxy for inflam- mation). Bacterial richness and diversity of milk with low SCC (200,000 cells/mL). Multivariate analysis showed that quarters within a cow were more similar in their microbial composition than among all quarters analyzed. The genetic regulation and composition of milk carbohydrates examined variation on a global scale among women. Some of the genes (FUT2, FUT3, ST6GalNAc5 ), which are critical in the synthesis of human milk oligosaccharides (HMO), were found to be under selective pressure. Additionally, novel single nucleotide polymorphisms (SNP) were identified and known ones confirmed and related to the HMO and lactose in human milk. These studies provide just a glimpse into the field of milk and lactation, addressing how the GIT may change with external input, how the milk microbiome may fluctuate due to inflammation, and how genetic regulation likely plays a key role in milk composition. The complexities in the field of lactation have only grown with the advancement of sequencing technologies. However, our ability to leverage new information, particularly related to milk, may be the key to further benefitting mother and neonate.doctoral, Ph.D., Bioinformatics & Computational Biology -- University of Idaho - College of Graduate Studies, 2019-0
Dusty, Dense, Bright, Dark, Narrow, and Broad: the Rings in our Solar System and a Few of the Things They Can Tell Us
No full textThe observations of planetary rings acquired by the Cassini and Voyager missions and from the Earth have launched large advancements in our knowledge of planetary ring formation, evolution, and dynamics. Today, the study of the ring systems around our giant planets has evolved further into using the rings themselves as a tool to learn about their home planetary systems. In Chapter moonlets we use two of the narrow rings of Uranus to probe for unseen nearby small moons who gravitationally interact with the rings and produce wake-like structures. These small moons both provide a possible solution for the confinement of their neighboring narrow rings and may represent a subset of the upper end of the ring particle size distribution. In Chapter eta we detect the effects of a resonant induced radial mode in the Uranian eta ring. The amplitude of the radial oscillations observed in the eta ring allow us to estimate the mass of the perturbing moon Cressida. This is the first such measurement of small inner Uranian moon's mass and density. In Chapter roche we track the presence and strength of periodic brightness variations in Saturn's dusty Roche Division and find that they are most likely caused by the seasonally varying planetary period oscillations of Saturn's magnetic field. This is just one of many ways in which the rings of Saturn have been found to be interacting with their magnetospheric environment.doctoral, Ph.D., Physics -- University of Idaho - College of Graduate Studies, 2019-1
THE SURVIVAL OF PINUS PONDEROSA SAPLINGS TO INCREASING LEVELS OF FIRE BEHAVIOR AND IMPACTS ON POST-FIRE GROWTH
No full textImproved predictions of tree species mortality and growth metrics following fires are important to assess fire impacts on forest succession, and ultimately forest growth and yield. In recent studies, North American conifers do not exhibit a binary response to fire where the tree either lives or dies; rather, there is a ‘toxicological dose-response’ relationship between fire behavior and the resultant mortality or recovery of the trees. Prior studies have not been conclusive due to potential pseudo-replication in the experimental design and time-limited observations. We explored whether dose-response relationships are observed in ponderosa pine (Pinus ponderosa) saplings exposed to surface fires of increasing fire behavior (as quantified by Fire Radiative Energy – FRE). We confirmed equivalent dose-response relationships to the prior studies. We further found that post-fire growth and mortality in ponderosa pine saplings corresponded to the amount of FRE applied and that, as with lodgepole pine (Pinus contorta), a low FRE dose could be applied that did not yield mortality in any of the replicates (r=10). These results suggest that land management agencies could use planned burns to protect similar fire-adapted tree species while eliminating unwanted species. Incorporation of these results into earth-system models and growth and yield models could help reduce uncertainties associated with the impacts of fire on timber growth, forest resilience, carbon dynamics, and ecosystem economics.masters, M.S., Natural Resources -- University of Idaho - College of Graduate Studies, 2019-0
EVALUATING STRUCTURAL BREAKS AND THE DRIVERS OF STRUCTURAL CHANGE IN LIVE CATTLE BASIS
No full textLive cattle basis witnessed incredible volatility in recent years leading to questions of structural change and the possibility of decreased hedging effectiveness. If fundamental drivers of live cattle cash and futures prices have changed, cattle feeders and beef packers alike may need to re-evaluate their business, marketing, and hedging plans. Structural breaks can be identified and confirmed using statistical methods while the drivers of those structural breaks can be evaluated using forecast models. This research finds evidence that both live cattle basis and live cattle basis variability witnessed structural change near the beginning of 2014. Furthermore, results suggest that changes to the live cattle supply chain including regional cash market thinness and a trend towards higher quality beef are among the most important factors driving structural change.masters, M.S., Agricultural Economics and Rural Sociology (Applied Economics) -- University of Idaho - College of Graduate Studies, 2019-0
Sweat Lodge on Campus: Examining Barriers of Communication of a Project between Native Students and the University of Idaho
No full textThe University of Idaho is a land grant university which is located on traditional Nez Perce lands. Located in the city of Moscow, Idaho the university is located with indigenous tribes surrounding it in all directions. Over the past several decades the university has worked to create relationships with the surrounding tribes through collaborative projects. Through these relationships the university has demonstrated a desire to recruit indigenous students and makes continued efforts to improve retention rates among these students. The most recent of these efforts is a collaborative project to set aside space for a sweat lodge for the university indigenous community. In this paper I seek to examine this recent process for possible barriers in communication which if addressed could work towards strengthening the relationships between the U of I and its surrounding native communities as well as its own community of native students and faculty while working to continue the goals of native student recruitment and retention.masters, M.A., Anthropology -- University of Idaho - College of Graduate Studies, 2019-0
A Study on Microstructure and Properties of Fe-xCr alloys and Fe-9Cr Based ODS Alloys Processed via Spark Plasma Sintering
No full textFe-Cr based oxide dispersion strengthened (ODS) alloys are potential candidates for usage as nuclear fuel cladding material for the upcoming Generation-IV nuclear reactor, especially in liquid sodium cooled fast reactors. These high performance materials have many advantages since they possess remarkable mechanical strength at high temperature and outstanding irradiation resistance. Particularly, ODS steels known as nanostructured ferritic alloys have negligible swelling under irradiation, and equally excellent creep properties because of nano-reinforcements i.e. the nanometric oxides present in the matrix. Traditionally, ODS processing combines mechanical alloying (MA) followed by hot consolidation via hot extrusion and hot isostatic pressing. In the present study, the ODS alloys are produced by a combined route of MA and Spark Plasma Sintering (SPS). After consolidation, the effects of processing parameters including milling parameters and sintering parameters, on the microstructure characteristics and mechanical properties of the milled powder and consolidated alloys are investigated. Once the suitable parameters are decided for the maximum compaction state for Fe-9Cr alloy, Fe-Cr alloys were produced with varying Cr content to understand the effect of Cr on the process of MA and SPS. Secondly, the effect of bimodal distribution obtained by various MA time has been observed after consolidation process. Finally, having understood the basic fundamentals of processing of Fe-Cr alloys, Fe-9Cr ODS was produced with addition of W and Ti and oxide particles as dispersoid phase. During the process of MA, the oxides get dissolved in the matrix and during consolidation process these oxides get precipitated as nanophases in the matrix thus resulting in the higher strength. In general, yttria (Y2O3) has been used as the oxide which is added to the Fe-Cr alloy system. Recently some work has been done on the addition of lanthana (La2O3). In this study, we have introduced a new oxide (CeO2) in the same amount (wt%) compared to Y2O3 and La2O3 to understand the effect of CeO2 on the ODS alloy. Powder and consolidated alloys characterization were performed using Scanning electron microscopy (SEM), Electron backscatter diffraction (EBSD) and Transmission electron microscopy (TEM). The mechanical properties were evaluated using microhardness testing and mini-compression testing. Corrosion tests were conducted at room temperature in various to understand the nature of the oxide layer formed on the Fe-Cr and Fe-9Cr ODS materials. Mechanical alloying created high density of dislocations, vacancies in the powder and facilitated the nucleation of NCs. It resulted in faster densification behavior by initiating sintering at lower temperatures by lowering the activation energy for both grain boundary and volume diffusion. Maximum densification (around 98%) occurred at temperatures 1000 oC for a sintering time of 45 min at 80 MPa pressure for 10 hr ball milled powder. Due to the combined strengthening mechanisms of work hardening, grain refinement, dispersion strengthening and solid solution strengthening, superior strength was achieved for the materials. On addition of alloying elements and the rare earth oxides, the presence of second phase particles like Cr0.875Ti0.125 is observed along with Ti-Cr-O-RE type precipitates which imparts high strength to the matrix both at room temperature an at elevated temperatures.doctoral, Ph.D., Chemical and Materials Science Engineering -- University of Idaho - College of Graduate Studies, 2019-0