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Showcase Marilyn Reed

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.

Relationship between Sleepiness Symptoms Questionnaire Ratings and Psychomotor Vigilance Test Performance in a Laboratory-Based Sleep Deprivation Study

Relationship between Sleepiness Symptoms Questionnaire Ratings and Psychomotor Vigilance Test Performance in a Laboratory-Based Sleep Deprivation Study

Primary author: Alicja Skwara
Co-author(s): Lillian Skeiky; Hans Van Dongen; Devon Hansen

Primary college/unit: Elson S. Floyd College of Medicine
Campus: Spokane

Abstract:

Sleep deprivation has been demonstrated to adversely impact on cognitive performance and safety. Measuring the impairment caused by sleep deprivation is best done with objective performance assessments such as the psychomotor vigilance test (PVT), but subjective self-report assessments may provide a more practical alternative in real-world settings. The Sleepiness Symptoms Questionnaire (SSQ) is a self-report instrument based on ratings of observable symptoms of sleepiness and motor vehicle driving performance impairment. In a laboratory-based sleep deprivation study, we compared SSQ ratings to performance impairment on a 10min PVT.
Twelve healthy normal sleepers (ages 21-39y, 6 females) participated in a 4-day in-laboratory study. Between a baseline day and a recovery day, participants underwent 38 hours of total sleep deprivation. Participants completed the SSQ and PVT following 6.5, 14.5, 22.5, and 30.5 hours of sleep deprivation, and 6.5 hours after recovery sleep.
As sleep deprivation progressed, the SSQ sleepiness ratings and the number of lapses (reaction times > 500 ms) on the PVT were elevated, peaking after 22.5 hours awake. Both measures returned to baseline levels after recovery sleep. There was a moderate correlation between SSQ ratings and PVT lapses (r=0.44, F1,43=24.1, p<0.001). Subjective sleepiness on the SSQ and objective performance impairment on the PVT reflected expected changes by time awake and time of day during sleep deprivation and following recovery sleep. The moderate correlation we observed suggests that the SSQ may be reasonably reliable for measuring impairment under conditions of acute sleep deprivation.

Rest-Activity Patterns in Adults Receiving Methadone for Medication-Assisted Treatment of Opioid Use Disorder

Rest-Activity Patterns in Adults Receiving Methadone for Medication-Assisted Treatment of Opioid Use Disorder

Primary author: Lillian Skeiky
Co-author(s): Marian Wilson; Matthew Layton; Raymond Quock; Hans Van Dongen; Devon Hansen
Faculty sponsor: Devon A. Hansen, PhD, LMHC

Primary college/unit: Arts and Sciences
Campus: Spokane

Abstract:
Individuals with opioid use disorder (OUD) report significant sleep/wake disturbances, which continue even when they stabilize with medication-assisted treatment. However, the nature of reported sleep/wake disturbances has not been well documented. We compared rest/activity patterns observed with a wrist-worn activity monitor, which provides objective estimates of sleep/wake disturbances, to control groups comprised of nurses working day or night shifts.

Seven adults undergoing methadone treatment for OUD wore a wrist activity monitor continuously for 7 days. Hospital nurses – 7 on a day shift schedule and 7 on a night shift schedule (six 12-hour shifts within a two-week period) – also wore a wrist activity monitor continuously for 14 days. The observed rest/activity patterns were analyzed through cosinor analysis to evaluate circadian rhythmicity, and through analysis of the distribution of inactive periods to estimate sleep continuity.

As expected, nurses working day shifts displayed strong circadian rhythmicity and high sleep continuity. Nurses working night shifts showed dampened circadian rhythmicity, but exhibited high sleep continuity. For the OUD methadone treatment group, the strength of circadian rhythmicity was between that of nurses on day versus night shifts, and this group experienced reduced sleep continuity.

These findings suggest disturbed sleep in individuals receiving methadone for medication-assisted treatment of OUD. This may interfere with their ability to achieve OUD recovery goals, and is worthy of investigation in a laboratory setting. This research was partially supported by the State of Washington via the Alcohol and Drug Abuse Research Program.

Raced, Sexed, and Erased, Jews in Contemporary Visual Entertainment

Raced, Sexed, and Erased, Jews in Contemporary Visual Entertainment

Primary author: Carol Siegel

Primary college/unit: Arts and Sciences
Campus: Vancouver

Abstract:

My project, “Raced, Sexed, and Erased, Jews in Contemporary Visual Entertainment,” is an intersectional study currently under peer review at Indiana University Press. The book rebuts the claim that Jews are now racially unmarked white people by providing a history of the intertwined racialization and sexualization of Jews through film and television narratives. The chapters are: One, “Sexual Perversity and the Jewish Therapist Figure,” which compares the films Nymphomaniac and A Dangerous Method; Two, “Imaginary Histories of Americanized Jews in Love,” which analyzes the impact of racialization and sexualization on Jewish efforts to assimilate into mainstream American culture in the films Hester Street, Once Upon a Time in America, Casino and Radio Days; Chapter Three, “Sex, Rage, and Revenge,” discusses films about World War II that eroticize Jewish resistance to fascism and focuses on Black Book and Inglourious Basterds; Chapter Four, “Not So Nice Jewish Girls,” compares the television series Transparent and Broad City; Chapter Five, “Holocaust Erasure and Jewish Identity Erasure,” explores the resemblance of the film Call Me By Your Name to the documentaries Crazy Love and Capturing the Friedmans and the fictional film The Last Embrace, all of which avoid any consideration of the Holocaust and its effects on the sexualities of Jews from WWII on; Chapter Six, “Monstrous Jewish Sexualities as Minoritarian Cinema,” responds to the frequently made accusation that the Coen brothers’ films are anti-Semitic by looking at their double-address narrative strategies. The conclusion suggests ways to combat the erasure of Jewish racialization in media.

Elucidating mechanisms that cause potato glycoalkaloids to spike

Elucidating mechanisms that cause potato glycoalkaloids to spike

Primary author: Moe Hnin Si
Co-author(s): Sen Lin; Roy Navarre

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: WSU-IAREC, Prosser, WA

Abstract:

Developing new potatoes with increased amounts of phytonutrients and low amounts of neurotoxic glycoalkaloids (GLKs) benefits for producers and consumers of potato. Light-induced accumulation of GLKs and concurrent greening tubers is a major problem in rejecting greening tubers from markets, which some have estimated can cause up to 15% -17% of the crop to be culled. Metabolite levels are genetically determined, but several factors such as environmental cues or tuber color can affect their final content. Transcriptomic and metabolomic approaches were applied to monitor levels of GLKs, chlorophyll, and carotenoids, and 32 target genes (biosynthetic genes and/or regulators) in potatoes exposed to light. Levels of GLKs were markedly spiked in eight white and two color flesh genotypes among the 20 studied (10 white and 10 color), exceeding the accepted limit of 20mg/100g FW. Other genotypes had less spiking of GLKs. Metabolic analysis across different genotypes showed color potato with higher amounts of carotenoids had less GLK spiking and revealed a possible mechanism of metabolite sharing by trading of isoprenoid intermediates between the cytosol and the plastid. Only four genotypes among those tested showed a positive correlation between greening and GLKs levels, implying that potatoes showing greening do not necessarily have higher GLKs content. We assessed the relative importance of transcriptional control at GLK regulatory points by assessing gene-gene, gene-metabolite and metabolite-metabolite correlations. These findings provide insights into mechanisms that control levels of GLKs and suggest potato breeding programs may benefit from evaluating spiking potential of breeding lines.

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.

Community Organizing: A Novel Approach to Identifying Healthcare Needs

Community Organizing: A Novel Approach to Identifying Healthcare Needs

Primary author: Katie Schmidt
Co-author(s): Carly Celebrezze; Kelly Anne Hennessey; Andrew Liechty; Courtney Roberts
Faculty sponsor: Dr. Luis Manriquez

Primary college/unit: Elson S. Floyd College of Medicine
Campus: Spokane

Abstract:
The Spokane Alliance is a non-partisan organization of religious institutions, educators, unions and other civic non-profits organizing for the common good in Spokane, Washington. The Healthcare Research Action Team (HRAT) was formed in response to Alliance members attesting that healthcare is a significant stressor in their lives.

The HRAT, led by medical students from WSU and UW, conducted a health needs assessment of its 31 member organizations. Listening sessions were held with 13 Spokane Alliance organizations in 2018 to qualitatively ascertain healthcare needs among community members.

111 Spokane community members participated. Three themes emerged as common issues: healthcare system complexity, affordability, and mental health needs.

Forty-six stories were shared regarding healthcare system complexity. Members stated they had difficulty navigating both the healthcare and insurance systems. They also expressed frustration with the lack of communication between providers and confusion related to healthcare paperwork.

Twenty-six Spokane Alliance members shared about issues with healthcare affordability, regardless of their health insurance status. Eight members stated they experienced challenges accessing mental health services and stigma surrounding mental health needs.

Community organizing methods can yield rich qualitative data on healthcare needs. The issues identified by Spokane Alliance members indicate a need for improvements in healthcare system navigability, affordability, and access to mental health services in Spokane. Since this needs assessment was conducted, the WSU mobile medicine program has launched its first mobile medical unit, which is equipped to provide primary care and reproductive health services, informed, in part, by the results of this needs assessment.