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Transcriptional R-loops in Archaea

Transcriptional R-loops in Archaea

Primary author: Marguerite Smith
Co-author(s): Michael Rolfsmeier; Cynthia Haseltine
Faculty sponsor: Cynthia Haseltine

Primary college/unit: College of Veterinary Medicine
Campus: Pullman

Abstract:

To maintain genome integrity, cells must contend with multiple DNA structures that arise during replication, transcription, and repair. Transcriptionally active regions of the genome are particularly susceptible to DNA damage through the production of R-loop regions, consisting of an RNA:DNA hybrid along with a displaced ssDNA non-template strand, which is particularly susceptible to damage. Failure to dissociate RNA:DNA hybrids can lead to extensive ssDNA regions, stalled transcription machinery, or persistent protein:DNA complexes, all of which are potentially deleterious to the cell. Thus, all organisms must have robust mechanisms to contend with RNA:DNA hybrids within actively transcribed regions of the genome. While transcriptionally associated R-loops have been detected in bacteria and eukaryotes, there have been no reports of their occurrence in archaea. We used the hyperthermophilic crenarchaeon Sulfolobus solfataricus as a model archaeal species to investigate the formation of RNA:DNA hybrids. We established methodology for immunoprecipitation of RNA:DNA hybrids from S. solfataricus and evaluated abundance and persistence of these hybrids for both transcriptionally active and inactive regions of the genome using multiple cell backgrounds. In parallel, we examined topological alterations in the supercoiling state of a plasmid carrying an inducible gene using an in vitro transcription approach. Our molecular characterization of RNA:DNA hybrids in S. solfataricus indicates they are strongly associated with transcriptionally active regions and likely represent R-loop structures. Additionally, variation of production and persistence of these R-loops in strain backgrounds with differential DNA damage responses implicates DSB repair processes in maintaining genome stability during transcriptional activities in S. solfataricus.

Fecal microbiome profiles of neonatal dairy calves with gastrointestinal disease

Fecal microbiome profiles of neonatal dairy calves with gastrointestinal disease

Primary author: Giovana Slanzon
Co-author(s): Lindsay Parrish; Sophie Trombetta; William Sischo; Craig McConnel
Faculty sponsor: Dr. Craig Stephen McConnel

Primary college/unit: College of Veterinary Medicine
Campus: Pullman

Abstract:

Gastrointestinal disease is the most common illness in preweaned dairy calves. Studies have associated fecal microbiome composition with health status, but changes in the microbiome across varying levels of GI disease remain unclear. Our objective was to show a correlation between clinical symptoms and shifts in the microbiome composition. Calves (n=360) were enrolled in a sampling scheme of repeat fecal collections throughout 5-15 d of age. Daily evaluations assessed health status based on clinical signs and treatments. Calves with fecal scores of 3 (loose) or 4 (watery) were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to their behavior and appetite. Calves with fecal scores <3 and no clinical illness were classified as healthy. Sixty-one fecal samples from healthy calves and 30 samples from diarrheic calves were selected to represent different breeds and ages. The V3-V4 region of the 16S rRNA gene was sequenced and analyzed using DADA2 pipeline. The ASV table was used to compare the taxonomic profiles, differences were identified by LEfSe (p2). Healthy calves had greater enrichment of the families Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Eubacteriaceae, Ruminococcaceae, Erysipelotrichaceae. In BS calves Listeriaceae, Clostridiaceae and Lachnospiraceae were more enriched. DS calves had enriched Lactobacillaceae, Streptococcaceae and Enterobacteriaceae in their microbiome. Breed differences included the association of Bacteroidaceae, Eubacteriaceae, Erysipelotrichaceae and Fusobacteriaceae with healthy Jersey calves. Bifidobacteriaceae was more enriched in healthy Holstein calves. On the other hand, Enterobacteriaceae was associated with DS Holstein calves. For DS Jersey calves, the order Lactobacillales was enriched.

Division I Athletics: What is Marketed to Recruits during the Recruiting Process?

Division I Athletics: What is Marketed to Recruits during the Recruiting Process?

Primary author: Taylor Shewchuk
Co-author(s): Brian Elzie
Faculty sponsor: Yong-chae Rhee

Primary college/unit: College of Education
Campus: Pullman

Abstract:

The purpose of this study was to identify what aspects collegiate coaches find most important to market to prospective athletes during the recruitment period. Previous research has examined sport-specific decision factors and overall National Collegiate Athletic Association (NCAA) factors, but not school-specific factors. To investigate this topic, a survey was circulated to all head coaches and recruitment coordinators at a division I, power five conference school located in a small town in the northwestern United States. In-depth interviews with seven coaches and recruitment coordinators followed. Five main factors were determined to be important marketing points (both positive and negative) for coaches at this specific university. Implications for this university are addressed, as well as how the university can build off of these five factors turn previous deterrents into marketable aspects for recruits.

Hot Rocks: Fractures in Methodological Analysis in the Pacific Northwest

Hot Rocks: Fractures in Methodological Analysis in the Pacific Northwest

Primary author: Kate Shantry
Faculty sponsor: Colin Grier

Primary college/unit: Arts and Sciences
Campus: Pullman

Abstract:

Heating stones, or hot rocks, are one of the most common artifact types found at archaeological sites. Ancestral people in traditional cultures heated rocks as an essential tool throughout time. This study is intended to help field archaeologists differentiate slow-cooled versus fast-cooled culturally-heated rocks. In the Pacific Northwest, researchers can use this data to consider behavior related to boiling stone technology in tightly coiled baskets and bentwood boxes. This work is designed to create criteria that can be used for identifying boiling stones with low-magnification in the field. My methods use macro and microscopic analyses of experimentally boiled rocks to create criteria to classify certain heated rocks as boiling stones, one of the most common cooking methods used on the Northwest Coast.

Textures in Uranium-10wt% Molybdenum Alloy Nuclear Fuels

Textures in Uranium-10wt% Molybdenum Alloy Nuclear Fuels

Primary author: Benjamin Schuessler
Faculty sponsor: David P. Field

Primary college/unit: Voiland College of Engineering and Architecture
Campus: Pullman

Abstract:

Uranium – 10wt% Molybdenum (U10Mo) is currently being considered as a next generation nuclear fuel for advanced research reactors. Its usage of low-enriched uranium (LEU) is preferable over the high-enriched (HEU) counterpart as it facilitates the demand to reduce the overall stockpile of HEU materials. However, manufacturing of the U10Mo fuels can be difficult. Varying processing conditions can alter the material in ways that can be detrimental to the overall fuel performance. Studying the effect of manufacturing processes on the microstructure-properties and -performance of the U10Mo is critical to the reliable usage of the fuel for future reactor research. This study focuses on how rolling and annealing of the U10Mo fuel plates affect how the orientations of the crystals inside the material are arranged, otherwise known as crystallographic texture. Mechanical properties can depend on the texture of the material, and by knowing the texture, one can extrapolate how the material will behave under various loading and operating conditions. U10Mo plates were rolled down to various thicknesses and annealed, then characterized using electron backscatter diffraction (EBSD) to gather crystal orientation information. After rolling, the U10Mo exhibit typical rolling textures seen in body-centered cubic metals and after annealing, the U10Mo showed a “randomized” texture. These textures tell a story of how the mechanical properties of the U10Mo evolve throughout the manufacturing process and provide valuable insight into how to adjust the manufacturing procedures to maximize the microstructure-properties and -performance of the fuel.

CropSyst regional parameterization and calibration over Columbia River Basin

CropSyst regional parameterization and calibration over Columbia River Basin

Primary author: Fabio Scarpare
Co-author(s): Claudio Stockle; Roger Nelson; Kirti Rajagopalan; Mingliang Liu; Jennifer Adam
Faculty sponsor: Jennifer Adam

Primary college/unit: Voiland College of Engineering and Architecture
Campus: Pullman

Abstract:

Crop water demand is key for policy and resource decision-making questions, including the processing of new irrigation water rights, examining water availability for both out-of-stream and instream uses. Conventional model calibration methods, which concentrate on a model’s performance at plot scale, cannot be used for large-scale regional simulation. Therefore, this study aims to describe a low-data approach used for developing detailed crop parameterization data required for regional level application. CropSyst was parameterized and calibrated based on its sensitivity analysis for the main agricultural irrigated lands in the Columbia River Basin; for most of Oregon, eastern Washington, southern Idaho, and western Montana States. Twenty-five crop types among cereal, forage, fruits and vegetables were selected by using the USDA Crop Data Layer 2018 in each sub-region. Thirty-six years of daily meteorological variables were used to drive the simulations. The calibration was performed by first adjusting the growing season (defined as planting to maturity). Next, the phenological development stages between planting and maturity (end of vegetative growth, flowering, beginning of yield formation, senescence and full senescence if reached) with the green canopy cover development were adjusted. Yield calibration was the last step performed, which was based on model`s sensitivity analysis. Scientific papers and irrigation field trials performed by several Research Extension Centers with less than ten years old developed in the same region were used as main sources for model evaluation. The simulation results were satisfactory and similar to those observed in the literature data, which enable its use across the Pacific Northwest.

Impact of glucose consumption on hibernation phenotype of adipose tissue in brown bears

Impact of glucose consumption on hibernation phenotype of adipose tissue in brown bears

Primary author: Michael Saxton
Faculty sponsor: Joanna Kelley

Primary college/unit: Arts and Sciences
Campus: Pullman

Abstract:

To survive the cold environments and winter food shortage for which they are adapted, brown bears undergo seasonal shifts from maximizing energy gain and storage in summer and fall, to conserving energy in winter hibernation. During hibernation, bears experience a mild decrease in body temperature but up to a 75% reduction in basal metabolic rate, as well as reduced heart rate, respiration rate, and insulin sensitivity. On arousal from hibernation, the bears return to active season physiology, which includes a reversal of the insulin resistance. Fluctuations in weight and high overall adiposity, like those seen in bears, are contributing factors to cardiovascular disease and diabetes in humans. In this study bears were fed dextrose during hibernation to determine the effect of glucose consumption on hibernation and insulin sensitivity. We collected serum from the bears and evaluated the effect of that serum on gene transcription in bear adipose cells grown in vitro. We found a strong cell by serum interaction, with cells collected in hibernation and grown with pre-dextrose hibernation serum showing a starkly different gene expression profile than those grown with either active season or post-dextrose hibernation serum. Though cells treated with post-dextrose hibernation serum closely matched the expression profile of cells grown with active serum, proteomic analysis of serum showed that post-dextrose serum more closely matched hibernation serum. Therefore one of these limited changes in serum proteins after consumption of dextrose leads to near complete reversal of the hibernation phenotype in brown bear adipose tissue.

Resolving the conflicting Hf and Nd isotope records of early Earth crust-mantle evolution

Resolving the conflicting Hf and Nd isotope records of early Earth crust-mantle evolution

Primary author: Ross Salerno
Faculty sponsor: Jeff Vervoort

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

The timing and nature of the formation and growth of Earth’s continents has sparked debate for decades. Fundamentally, two end-member models have been proposed. One favors rapid and early di¬fferentiation of continental crust and a complimentary depleted mantle, while the other proposes and early basaltic proto-crust with true continental crust and depleted mantle forming many hundreds of millions of years later. Radiogenic isotope systems (e.g., Nd and Hf) are crucial in this debate, as they provide constraints on the timing of the Bulk Silicate Earth differentiation. Our attention focuses on the isotopic record – particularly from the Earth’s oldest rocks – to help understand the timing of crustal growth. Two fundamentally different stories appear between the Hf and Nd records of these oldest samples. Hf isotope data, now based primarily on zircon Hf and corresponding U-Pb ages, have chondritic Hf compositions through ~ 3.8 Ga – no evidence for crust or depleted mantle. The Nd isotope data, in contrast, appears to show a characteristic depleted mantle signature for these same rocks. The Hf and Nd compositions we report from the Pilbara Craton (3.5-3.3 Ga) agree – both are chondritic. These rocks preserve no evidence of a depleted mantle or significant crustal reservoir on Earth at that time. In the examples where both systems are closed [Pilbara], the Hf and Nd isotope records agree and there is no Hf-Nd paradox.

Energy and Comfort Perceptions in University Housing

Energy and Comfort Perceptions in University Housing

Primary author: Shelby Ruiz
Co-author(s): Julia Day

Primary college/unit: Voiland College of Engineering and Architecture
Campus: Pullman

Abstract:

For many universities with quickly aging residential facilities and unpredictable building occupants, making wise infrastructure upgrades can become challenging, and operational costs can increase. Building operations, such as lighting, cooling, and heating, use nearly three quarters of its consumed energy to operate and maintain an indoor environment. The College Board estimates that approximately 40% of full-time public-college students live on campus during their time at university, making residential building occupants a significant variable in this overall energy consumption. If strategic energy-efficiency plans are implemented for these universities, energy cost savings of up to 30% are possible.
This project implemented a mixed methods study to investigate adaptive comfort opportunities in university-owned and managed residential buildings to better understand the human-building interface, resulting energy use implications in buildings, and potential areas for interface and design improvements. An online survey and interviews were implemented to understand occupants’ perceptions of thermal and visual comfort, as well as respective adaptive opportunities and corresponding behaviors (e.g. opening/closing windows). The survey integrates a novel photovoice approach to visually catalog and understand the different types of interfaces available to occupants; this qualitative method is commonly used in community-based participatory research to document the reality of the participants. In addition, individual building utility metrics were analyzed to determine which residences are the most energy consuming and costly to operate; this data may help inform priorities for capital upgrades Next steps of this research include the development of a proposal of an energy-saving campaign for university facilities.

Peering into Potato-Virus Interactions in the Era of Omics

Peering into Potato-Virus Interactions in the Era of Omics

Primary author: Manasseh Richard
Co-author(s): Madhu Kappagantu; Lindani Moyo; Hanu R. Pappu
Faculty sponsor: Prof. Hanu R. Pappu

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Potato is an important staple food crop worldwide. The tuber is especially prized for its high nutritional value, while also offering vital economic benefits. In the U.S., the Pacific Northwest produces nearly 60% of the nation’s potato annually, and potato industry in WA state alone is worth several billions of dollars. However, potato production is curtailed by several viruses, with the most devastating being Potato virus Y (PVY). At least nine biological variants of PVY are known to attack potato. These include relatively newer recombinant types named PVYNTN and PVYNWilga, which induce tuber necrosis in susceptible cultivars. So far, the underlying host-virus interactions have been studied by analysis of gene expression, while the metabolic level, which often correlates poorly with gene expression but directly mediates these phenotypic outcomes, is poorly studied. To assess how PVYNTN and PVYNWilga infections affect potato metabolism, we used GC-MS to obtain comprehensive metabolic profiles of two cultivars inoculated with these recombinants of PVY. A total of 447 peaks were detected, 115 of which were known metabolites that categorized into amino acids, sugars and sugar derivatives, esters and lactones, organic acids, alcohols, ketones and phenols, and sulfur-nitrogen compounds. Using a mix of univariate and multivariate methods, we showed that PVYNTN and PVYNWilga elicit significantly different metabolic alterations in potato. Multivariate receiver-operator characteristic (ROC) curves predicted Dioctyl phthalate, Sedoheptulose, Glycine, 1-Monopalmitin, Ribulose-5-phosphate, Trehalose, Glycerol 3-phosphate, Alpha-Tocopherol, 5-Methoxytryptamine, Sorbitol, Glucose-6-phosphate, Galactinol, L-Malic acid, and Threonic acid as potential metabolite biomarkers of PVYNTN and PVYNWilga infection in potato.