Digital Commons Network^™

Capturing Functional Epigenomes For Insight Into Metabolic Diseases., Fiona Allum, Elin Grundberg

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Metabolic diseases such as obesity are known to be driven by both environmental and genetic factors. Although genome-wide association studies of common variants and their impact on complex traits have provided some biological insight into disease etiology, identified genetic variants have been found to contribute only a small proportion to disease heritability, and to map mainly to non-coding regions of the genome. To link variants to function, association studies of cellular traits, such as epigenetic marks, in disease-relevant tissues are commonly applied.

SCOPE OF THE REVIEW: We review large-scale efforts to generate genome-wide maps of coordinated epigenetic marks and …

Dual X-Ray Absorptiometry Has Limited Utility In Detecting Bone Pathology In Children With Hypophosphatasia: A Pooled Post Hoc Analysis Of Asfotase Alfa Clinical Trial Data., Jill H. Simmons, Eric T. Rush, Anna Petryk, Shanggen Zhou, Gabriel Á. Martos-Moreno

Manuscripts, Articles, Book Chapters and Other Papers

Asfotase alfa is an enzyme replacement therapy approved for treatment of patients with pediatric-onset hypophosphatasia (HPP), a rare, inherited, systemic disease causing impaired skeletal mineralization, short stature, and reduced physical function in children. The role of dual X-ray absorptiometry (DXA) in the assessment of children with HPP has been insufficiently explored. This post hoc analysis included pooled DXA data from 2 open-label, multicenter studies in 19 children with HPP. The study population was aged ≥5 to≤6.6 years at enrollment (male: 79%; median age at enrollment: 10.4 y [range: 5.9-16.7]; treatment duration: 6.3 y [range: 0.1-6.6]. Baseline height Z-scores indicated short …

De Novo Variants Of Nr4a2 Are Associated With Neurodevelopmental Disorder And Epilepsy., Sakshi Singh, Aditi Gupta, Michael Zech, Ashley N. Sigafoos, Karl J. Clark, Yasemin Dincer, Matias Wagner, Jennifer B. Humberson, Sarah Green, Koen Van Gassen, Tracy Brandt, Rhonda E. Schnur, Francisca Millan, Yue Si, Volker Mall, Juliane Winkelmann, Ralitza H. Gavrilova, Eric W. Klee, Kendra Engleman, Nicole P. Safina, Rachel Slaugh, Emily M. Bryant, Wen-Hann Tan, Jorge Granadillo, Sunita N. Misra, G Bradley Schaefer, Shelley Towner, Eva H. Brilstra, Bobby P C Koeleman

Manuscripts, Articles, Book Chapters and Other Papers

PURPOSE: This study characterizes the clinical and genetic features of nine unrelated patients with de novo variants in the NR4A2 gene.

METHODS: Variants were identified and de novo origins were confirmed through trio exome sequencing in all but one patient. Targeted RNA sequencing was performed for one variant to confirm its splicing effect. Independent discoveries were shared through GeneMatcher.

RESULTS: Missense and loss-of-function variants in NR4A2 were identified in patients from eight unrelated families. One patient carried a larger deletion including adjacent genes. The cases presented with developmental delay, hypotonia (six cases), and epilepsy (six cases). De novo status was …

One Step Toward Success: Motivation For Reengagement For Out-Of-School Youth, Karen Kwandrans

Education Doctoral

The purpose of this study is to gain understanding, from the perceptions of former out-of-school youth (OSY), as to what motivated reconnection into education or training programs. In addition, the study investigated what recruitment and program approaches they felt were important engagement strategies. A phenomenological design was chosen to capture the lived experience of OSY, aged 20 to 24 years old, who have reconnected at adult literacy and training centers. Nine OSY participated in open-ended interviews. As a result of the rich stories and open discussion, the researcher was able to identify the following four themes that capture the overall …

It Takes A Village: Perspectives From A Multidisciplinary Team To Address The Needs Of Students In School-Based Mental Health Programs, Amanda L. Hopkins

Education Doctoral

Currently, 22% of American children are found to have a diagnosable mental illness that critically affects their social or emotional development. Of those diagnosed, only 7.4% receive treatment services (Child Mind Institute, 2015). In 2003, it was estimated that 43-56% of students with mental health needs dropped out of school (Landrum, Tankersley, & Kauffmen, 2003). This study was conducted with the goal of improving outcomes for children with mental health and significant behavior problems. This study examined the perspectives of a multidisciplinary team composed of individuals with a variety of specialties such as teachers, administrators, social workers, and therapists. Three …

Protective Factors For Secondary Traumatic Stress In Residential Treatment Staff, Stacey Gagliano

Dissertations

Gagliano, Stacey. Protective factors for secondary traumatic stress in residential treatment staff. Unpublished Doctor of Philosophy Dissertation, University of Northern Colorado, 2020. This cross-sectional study examined the relationship between empathy, a problem-focused coping style, compassion satisfaction (CS), staff cohesion, and symptoms of secondary traumatic stress (STS) in residential treatment center (RTC) staff, while controlling for previous direct trauma exposure. A total of 44 participants were recruited from RTCs in a western state and included mental health care providers (clinical staff), direct-care staff, and educational staff. Participants completed a 62-question electronic survey that included several self-report measures evaluating each of the …

The Structure And Symmetry Of The Radial Spoke Protein Complex In Chlamydomonas Flagella, Emiliya Poghosyan, Ioan Iacovache, Lenka Faltova, Alexander Leitner, Pinfen Yang, Dennis R. Diener, Ruedi Aebersold, Benoit Zuber, Takashi Ishikawa

Biological Sciences Faculty Research and Publications

The radial spoke is a key element in a transducer apparatus controlling the motility of eukaryotic cilia. The transduction biomechanics is a long-standing question in cilia biology. The radial spoke has three regions – a spoke head, a bifurcated neck and a stalk. Although the neck and the stalk are asymmetric, twofold symmetry of the head has remained controversial. In this work we used single particle cryo-electron microscopy (cryo-EM) analysis to generate a 3D structure of the whole radial spoke at unprecedented resolution. We show the head region at 15 Å (1.5 nm) resolution and confirm twofold symmetry. Using distance …

Developing Metrics And Protocols For Evaluating Restoration Success For The Little Thompson River, Colorado, Haylie Brown

Master's Theses

In September 2013, the US Colorado Front Range experienced an extreme rainfall event causing mass flooding in the region. Many Front Range rivers were impacted and subsequently restored, especially those adjacent to roadways. Channel restoration practices often lack a standard approach, and evaluating project success is usually lacking. An assessment framework was developed incorporating both ecological and geomorphic variables in addition to project-specific objectives, applied to the Little Thompson River. Topographic and functional traits vegetation surveys were conducted at both the restored reach and an upstream reference reach, with the ultimate goal of contributing to the knowledge of best practices …

Assessing The Effects Of Habitat On Bird Song Propagation, Braelei Hardt

Master's Theses

The Acoustic Adaptation Hypothesis (AAH) posits that animal acoustic signals meant for long-range communication should be adapted to transmit well within the habitats in which they evolved. However, comparative studies investigating predictions of the AAH relating to signal form indicate that support for the hypothesis is not universal. Several studies have employed experimental playback approaches to testing signal transmission which can provide complimentary analyses to comparative studies of signal form in the field. Here, I first summarize these experimental playback tests of the AAH in birds, mammals, insects, and anurans, describing the methodologies used in these tests, and assessing the …

Urban Air Quality Modeling: Evaluating Impacts Of Ecoroofs On Urban Air Quality In Portland, Oregon, Danlyn L. Brennan, Selina Teng

altREU Projects

In this work, the authors present a mathematical model simulating the impact of ecoroof vegetation on air quality in an urban microclimate. An ecoroof is a layer of vegetation established on rooftops to reduce stormwater runoff, mitigate heat, and enhance air quality. Certain plant species in ecoroofs may however have a detrimental effect on air quality, due to their emission of biogenic volatile organic compounds (BVOCs), which include potentially reactive species such as isoprene. These chemical species can interact with urban air pollution, particularly NOx produced by car traffic, to create other harmful pollutants such as ozone and particulate matter …

Restless Hungary, András Máté-Tóth

Occasional Papers on Religion in Eastern Europe

"Nowadays, many people ask what is happening in Hungary. Especially people who came to know and appreciate our country as the happiest barrack in the Eastern bloc and who knew from their own experience that it was an island in the great communist Red Sea, the Archipelago Goulash (alluding to the Archipelago Gulag in the Soviet Union). After the fall of the Berlin Wall in 1989, Hungary was for a while still a pioneer in the transformation to the market economy, to democracy, in short–in the direction of freedom. And now the economic data shows that Hungary is no longer …

Cosm Diversity & Inclusion Newsletter, Georgia Southern University

College of Science & Mathematics: News & Publications (2012-2022)

• Diversity Quote of the Month
• Fact Fuel for Data-driven Conversations
• COSM Community D&I Spotlight
• D&I Campus Connections and Opportunities
• Try This! - Teaching Tips
• This Month's Theme: Why is it important for departments to work on diversity & inclusion?
• Reflective Moment
• Something you'd like to see? We'd love to hear from you.

A Meta-Analysis Of The Human Uses Of Pteridophytic Species In Tennessee, Diana Sevier

Honors Theses

Pteridophytes are an ancient lineage of plants, composed of ferns and fern allies, which are spread across the globe. There is also a long record of humans using pteridophytes to their benefit, which includes the broad categories of medicine, ornamentation, food, phytoremediation, and agriculture. Understanding these concepts, the goal of this thesis was to conduct a meta-analysis which pulled together data from many resources on the 94 Tennessee pteridophyte species to create a repository of human use information, as well as to examine, analyze, and comment on the trends present within and between taxonomic groups of pteridophytes. The methods used …

Colleague To Banner Migration: Data Conversion Guide For Institutional Research, Laura Osborn

Masters Theses & Doctoral Dissertations

When the SDBOR decided to migrate their current student information system into a shared system with HR and Finance, adjustments needed to be made to accommodate for current Banner settings and work around tables that were already populated with HRFIS data. The change in data type of the student identifier from that of a 7-digit numeric field to a 9- digit alpha-numeric field poses problems for running aggregate data calculations. Additional complications include having some information such as first-generation status that was not migrated between the systems, and cases such as college coding where tables that were designed for student …

Phenotypic Characterization Of Arabidopsis Thaliana Lines Overexpressing Avp1 And Miox4 In Response To Abiotic Stresses, Nirman Nepal, Jessica P. Yactayo‐Chang, Ricky Gable, Austin Wilkie, Jazmin Martin, Chineche L. Aniemena, Roberto Gaxiola, Argelia Lorence

Arkansas Biosciences Institute

Premise AVP1 (H+-pyrophosphatase) and MIOX4 (myo-inositol oxygenase) are genes that, when overexpressed individually, enhance the growth and abiotic stress tolerance of Arabidopsis thaliana plants. We propose that pyramiding AVP1 and MIOX4 genes will further improve stress tolerance under water-limited and salt-stress conditions. Methods MIOX4 and AVP1 reciprocal crosses were developed and phenomic approaches used to investigate the possible synergy between these genes. Results Under normal and stress conditions, the crosses had higher foliar ascorbate content than the wild-type and parental lines. Under water-limited conditions, the crosses also displayed an enhanced growth rate and biomass compared with the control. The observed …

Plant Science Decadal Vision 2020–2030: Reimagining The Potential Of Plants For A Healthy And Sustainable Future, Natalie Henkhaus, Madelaine Bartlett, David Gang, Rebecca Grumet, Ingrid Jordon‐Thaden, Argelia Lorence, Eric Lyons, Samantha Miller, Seth Murray, Andrew Nelson, Chelsea Specht, Brett Tyler, Thomas Wentworth, David Ackerly, David Baltensperger, Philip Benfey, James Birchler, Sreekala Chellamma, Roslyn Crowder, Michael Donoghue, Jose Pablo Dundore‐Arias, Jacqueline Fletcher, Valerie Fraser, Kelly Gillespie, Lonnie Guralnick, Elizabeth Haswell, Mitchell Hunter, Shawn Kaeppler, Stefan Kepinski, Fay‐Wei Li, Sally Mackenzie, Lucinda Mcdade, David Stern

Arkansas Biosciences Institute

Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far-reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the …

Building Community-Based Approaches To Systemic Reform In Mathematical Biology Education, Olcay Akman, Carrie Diaz Eaton, Dan Hrozencik, Kristin P. Jenkins, Katerina V. Thompson

All Faculty Scholarship

Starting in the early 2000’s, several reports were released recognizing the convergence of mathematics, biology and computer science, and calling for a rethinking of how undergraduates are prepared for careers in research and the science and technology workforce. This call for change requires careful consideration of the mathematical biology education system to identify key components and leverage points for change. This paper demonstrates the wide range of resources and approaches available to the mathematical biology education community to create systemic change by highlighting the efforts of four community-based education reform organizations. A closer look at these organizations provides an opportunity …

Adapting Biotoxin Monitoring For The Future: An Opportunity For A Harmful Algae Bloom (Hab) Network In Casco Bay, Maine, Zachary B. Gordon

All Theses And Dissertations

Harmful Algae Blooms (HABs) related to marine biotoxins have considerable impacts on coastal communities and have been increasing in size and frequency globally. Maine is recognized as a leader in biotoxin management as it relates to bivalve shellfish, but it has been unclear how current management practices effect the growth of shellfish aquaculture and how they will adapt to future conditions. This research uses a collaborative approach to analyze the current state of biotoxin management in Maine. First, the current management practices in Maine were compared and contrasted with five other states dealing with similar issues. Then, the perspectives of …

Soluble Epoxide Hydrolase Inhibition: A Novel Therapeutic Strategy In Alcoholic Liver Disease., Jeffrey Barr Warner

Electronic Theses and Dissertations

Emerging evidence suggests that soluble epoxide hydrolase (sEH) inhibition is a valuable therapeutic strategy for the treatment of numerous diseases. sEH rapidly degrades cytochrome P450-produced epoxygenated lipids (epoxy-fatty acids, epFAs), which generally exert beneficial effects on several cellular processes. sEH hydrolysis of epoxy-fatty acids produces dihydroxy-fatty acids which are typically less biologically active than their parent epoxide. sEH inhibition has shown efficacy in treating numerous pathologies associated with non-alcoholic liver disease, yet no efforts to date have tested the efficacy of sEH inhibition in alcoholic liver disease (ALD). Herein, we measured the levels of sEH expression and epFAs in human …

Trust In Primary Care Providers: Perspectives From Deaf People., Greir Ander Huck Flynn

Electronic Theses and Dissertations

Trust is an integral part of the patient-provider relationship, responsible for influencing several key aspects of healthcare behaviors and patient perceptions of health outcomes. Though the topic has previously been discussed by scholars, little evidence exists to support the application of our understanding of trust in culturally Deaf populations. As such, this dissertation seeks to lay the necessary groundwork for further investigations on the topic by first understanding the nature of trust in patient-provider relationships from the perspectives of culturally Deaf people. The dissertation is comprised of five chapters. The first chapter provides an introduction to salient terms and concepts …

A Novel Role For Rassf1a In The Regulation Of Ras Activation., Desmond Ramón Harrell Stewart

Electronic Theses and Dissertations

Ras is the most frequently activated oncogene in human cancer. It is not only the most frequently mutated oncogene, but is also rendered hyperactive in the wild-type form by aberrant regulation. Ras drives transformation and contributes to tumor aggressiveness by activating multiple downstream mitogenic effectors. Ras also possesses the paradoxical ability to induce apoptosis and senescence. Ras-induced apoptosis is not well understood, but has been largely attributed to the RASSF tumor suppressors, particularly RASSF1A. RASSF1A mediates Ras-induced apoptosis by activating pro-apoptotic proteins such as the MST kinases and BAX. RASSF1A is among the most frequently inactivated tumor suppressors in human …

Epithelial Responses To Porphyromonas Gingivalis In The Community Context., Zackary Ray Fitzsimonds

Electronic Theses and Dissertations

Porphyromonas gingivalis, a keystone pathogen for periodontal disease, initiates a complex molecular dialogue with gingival epithelial cells, leading ultimately to disruption of host signaling pathways. Dysbiotic host responses are also thought to contribute to the initiation and progression of oral squamous cell carcinomas. Recently, the homeostatic commensal Streptococcus gordonii has been shown to antagonize P. gingivalis-induced epithelial cell signaling events in host cells, such as proliferation and migration. The aim of this study was to characterize pathways that P. gingivalis targets to disturb host signaling, with a specific focus on pathways that S. gordonii can restore to homeostatic …

A Structural Study Of Correlated Materials: Incipient Mott Insulators And Low-Dimensional Systesm., Alaa Alfailakawi

Electronic Theses and Dissertations

Current theories of high-temperature superconductivity suggest that electrons must organize into Cooper pairs in order for a material to exhibit a superconducting phase. Electrons in insulators experience significant repulsive interactions that tend to keep electrons localized at atomic positions. In contrast, electrons in metals are delocalized, interact weakly, and are free to conduct electricity. Therefore, the formation of Cooper pairs should have different mechanisms for metals compared to insulators. This contrast raises the debate about the origin of high-temperature superconductivity in iron-based material, whether it depends on the strong or weak coupling. Many iron-based materials are metallic in the normal …

Incarceration Experiences Of Older African American Adults Living With Hiv - A Constructivist Grounded Theory Study., Verena Schmidt

Electronic Theses and Dissertations

Two epidemics disproportionally impact older (50 years and over) African Americans compared to the general U.S. population: Incarceration and HIV/AIDS. Those aged 50 and older constitute the fastest growing age group of persons who are incarcerated in the United States. It is estimated that by the year 2030 about one third of the incarcerated population in the U.S. will be aged 55 years and older. While areas of “Incarceration, racial disparities and HIV” as well as “Aging and HIV” have been well studied and discussed in the literature, little is known about the lived incarceration experiences of African American persons …

Bst2 Isoforms: Distribution And Potential Use In Cancer Therapeutics, Ahmed Muhsin

Dissertations and Theses (Open Access)

Identifying a cancer-specific cellular target is one of the key factors that can pave a “bench to the bedside” path of a target therapy. Bone marrow stromal cell antigen 2 (BST2) is a raft-associated type II transmembrane protein with an unusual topology. Analyses showed a variable degree of BST2 expression in most organs. Two research groups identified different BST2 isoforms of BST2 generated by posttranscriptional modification. In this research, I studied the long BST2 isoform’s distribution in breast tissue and B cell lines using the novel monoclonal antibody (MAb) LA5, an anti-BST2-long MAb. This approach revealed the expression of the …

Identification Of Trim24 Domain Essentiality In Primary Trim24coe Carcinosarcoma Cell Lines, Cem Dede

Dissertations and Theses (Open Access)

Regulation of transcriptional control is a critical feature for organismal development and survival. Because of its effects on chromatin-controlled expression, disruptions of this delicately tuned mechanism are an important factor in development of tumorigenesis. Therefore, there is a growing interest in targeting these control mechanisms for their potential therapeutic values.

Our lab previously discovered the epigenetic regulator function of Tripartite motif protein 24 (TRIM24) through its H3K4me0 and H3K23ac dual histone signature reader function, its negative regulatory effect on the p53 tumor suppressor, in addition to its shown oncogenic driving capacity on immortalized mammary epithelial cells when overexpressed. Although TRIM24 …

Aging Lowers Pex5 Levels In Cortical Neurons In Male And Female Mouse Brains, Ndidi-Ese Uzor

Dissertations and Theses (Open Access)

Peroxisomes are small organelles with critical functions: lipid synthesis, breakdown of reactive oxygen species by antioxidant enzymes, and amino acid degradation. In the brain, peroxisomal lipids make up the myelin sheath. Brain peroxisomal dysfunction leads to lipid disruption or neurological consequences if key peroxisomal proteins are absent. Still, it is unclear how peroxisomes are affected in neurodegenerative diseases and in normal brain aging. This work examines peroxisomal markers in three settings: 1) in a neuronal and 2) animal model of Huntington disease (HD), where mutant huntingtin (mHtt), the causative protein in Huntington disease pathogenesis is expressed, and 3) in the …

Gear Specific Catch Rates And Population Dynamics Of Channel Catfish In The Mississippi River, Colby Gainer

Graduate Theses/Dissertations

Perpetual anthropogenic alterations have imposed deleterious effects on aquatic ecosystems. In the Mississippi River, channelization, dams, and loss of floodplain connectivity have all been reputed as detrimental. Dynamic rate functions (i.e., recruitment, growth, and mortality) are the driving forces behind fish populations. Understanding population dynamics is important for guiding management decisions. Knowledge of vital rates can provide pivotal information that will determine spatiotemporal population-level changes within the system. In the Mississippi River, Channel Catfish are a commercially and recreationally important species. However, limited population demographic information currently exists in the Upper Mississippi River. We sought to determine the most effective …

Socialism's Specter: The Effect Of Persuasion On Implicit Attitudes Towards Socialism, Amber Yanez

Graduate Theses/Dissertations

Anti-socialist propaganda and media have swayed individuals to skepticism and fear about socialism. The propaganda, however, does not reflect necessarily the truth about socialism, in its persuasion against it. Media often uses persuasion techniques to influence opinions and beliefs. The primary focus of this study was to assess whether persuasion could be used to persuade participants’ implicit attitudes towards socialism. Participants were persuaded with pro-socialism content, anti-socialism content, and neutral content; and then completed an Implicit Association Test. It was hypothesized that the participants in the pro-socialism condition would have an implicit bias towards socialism, the participants in the anti-socialism …

Synthesis, Characterization, And Biological Studies Of Novel Organoantimony(V) Cyanoximates, Kevin Anthony Pinks

Graduate Theses/Dissertations

The requirement of new antimicrobial treatments has become an urgent field recently. Multi-drug resistant (MDR) bacteria are now resistant to common antibiotics. To antagonize such bacteria 8 novel organoantimony(V) cyanoximates were synthesized to be characterized and submitted for biological activity studies. Eight organoantimony(V) cyanoximates were characterized by elemental analysis, thermal analysis, IR-, ¹³C{¹H} NMR, some with UV-visible spectroscopy, and single crystal X-ray analysis. Antimicrobial Disk studies indicated Sb(Ph)₄(ACO) and Sb(Ph)₄(ECO) had significant antimicrobial effect against all three strains: two gram-negative a) Escherichia coli strain S17 and b) Pseudomonas aeruginosa strain PAO1, alongside a …