Investigating the role of BECN2 CCD interactions in canonical and non-canonical autophagy

Autophagy is a conserved cell-survival pathway wherein old, damaged or harmful cellular components are surrounded by a double membrane vesicle called the autophagosome for lysosomal degradation and recycling. All eukaryotes have a conserved BECN homolog, a key coiled-coil domain (CCD)-containing autophagy protein. Mammals are unique as they have two BECN homologs, BECN1 and BECN2, both of which have the same domain architecture and function in autophagy. BECN2 has been shown to also function in non-canonical autophagy. My research focused primarily on investigating selected interactions of the BECN2 CCD. We investigated interactions of the BECN2 CCD with two CCD-containing proteins known to bind to BECN1: UVRAG, an important autophagy protein, and TAB2, a protein important for inflammatory responses. We show that the BECN2 and UVRAG CCDs interact, but were unable to purify stable complexes for structural studies. In comparison, the CCDs of BECN2 and TAB2 bind with an affinity tighter than that of BECN2 homodimerization, forming a well-folded elongated heterodimer. These preliminary results provide information regarding interactions that enable BECN2 to regulate autophagy, in a manner analogous to BECN1. We also show that, unlike BECN1, BECN2 facilitates non-canonical autophagy involving ATG9A-bearing vesicles, via interactions with the STX6 SNARE domain. We show that the STX6 SNARE domain binds to BECN2 residues 181-250 (BECN2(181-250)) within the BECN2 CCD. The STX6 SNARE is disordered in the absence of interacting partners but becomes helical when in complex with BECN2. The BECN2(181-250):STX6 SNARE complex is also more stable than either the BECN2(181-250) or the BECN2 CCD homodimer. We determined the 2.65 ? X-ray crystal structure of the STX6 SNARE bound to BECN2, showing that the complex is a heterotrimeric helical bundle, consisting of one helix comprising BECN2(181-250) and two STX6 SNAREs that are anti-parallel to each other. The heterotrimer interface is stabilized by 15 layers of three residues, each contributed by a different helix, of which, six layers are entirely hydrophobic, including two consisting of three leucines each. We verified the importance of these hydrophobic layers using point mutations and affinity pulldowns, showing that mutations of the hydrophobic layers either significantly or completely disrupt the interaction between BECN2(181-250) and STX6 SNARE domain. This 3-helix bundle likely represents an intermediate during the formation of the full SNARE complex, thereby providing mechanistic insights into the process by which ATG9A-bearing vesicles transport lipids to the growing phagophore. Together these studies help explain the role of the BECN2 CCD in canonical and non-canonical autophagy, providing clues as to why mammals have two BECN paralogs

An assessment of barriers to nurse practitioners? utilizing pharmacogenetic testing for depression

As a leading cause of disability worldwide, depression is considered a chronic disease. Medication management is the first-line treatment for moderate to severe major depressive disorder. Medications are selected based on provider experience and preference with a trial-and- error? approach. These medications may take several weeks to reach therapeutic dosing. If it is not tolerated or ineffective for treating the disease, then the medication regimen is changed, requiring a minimum of 4-6 weeks to determine efficacy. This trial-and-error approach to depression treatment can lead to patients living with persistently debilitating depressive symptoms for months, increased healthcare costs due to continued need to seek medical follow-up, or patients discontinuing care due to lack of efficacy early in treatment attempts. In a post-market release study regarding the efficacy of antidepressant use, results indicated that 11% of the United States population takes an antidepressant. Depressed patients that do not benefit from the first antidepressant they are prescribed is 60% (Alemi et al., 2021). Pharmacogenomic testing (PGT) is beneficial in disease management by determining individual genotype responses to specific medications. Incorporating PGT into routine care for depression can lessen the time it takes to reach disease remission as well as avoid any adverse medication effects. Despite the known benefits of PGT, it continues to have a slow adoption rate in clinical practice. Nurse Practitioners (NPs) surveyed aided the co-investigator in assessing current rates of NPs utilizing PGT as well as identifying barriers to use. Understanding limits for using PGT can contribute to developing targeted education in hopes of enhancing the uptake of PGT for managing depression into routine clinical practice. use. Understanding limits for using PGT can contribute to developing targeted education in hopes of enhancing the uptake of PGT for managing depression into routine clinical practice

Identification and mapping of QTL associated with crown rust resistance in recombinant inbred lines of oat (Avena sativa L.)

Crown rust caused by Puccinia coronata f.sp. avenae is the most destructive fungal disease threatening oat production worldwide. Therefore, a search for novel sources of genetic resistance is considered essential to combat the evolving races of pathogen. The objectives of this study were to develop two recombinant inbred line mapping populations carrying novel sources of crown rust resistance and identify the genomic regions associated with crown rust resistance. 108 and 112 F5:6 RILs developed from each of the bi-parental crosses were evaluated for disease incidence in field and greenhouse under randomized complete block experimental designs with two replications. Genotyping and linkage analysis of markers associated with RILs revealed a major QTL underlying disease resistance in each population respectively. The two QTL identified in this study showed consistency across all the tested locations and the markers associated with the QTL appear to be useful for marker-assisted selection in oat breeding programs

Graph two-sample test via empirical likelihood

In the past two decades, there has been a notable surge in network data. This proliferation has spurred significant advancements in methods for analyzing networks across various disciplines, including computer science, information sciences, biology, bioinformatics, physics, economics, sociology, and health science. Graph two-sample hypothesis testing, aimed at discerning differences between two populations of networks, arises naturally in diverse scenarios. In this paper, we delve into the essential yet intricate task of testing for equivalence between two networks. There are many testing procedures available. For instance, the t-test based on subgraph counts is one of the methods. In this paper, we propose a new test method by using the empirical likelihood. We run extensive simulations to evaluate the performance of the proposed method and apply it a real-world network. Based on the simulation experiments and real data application, the empirical likelihood test consistently outperforms existing subgraph count tests

Implementing Industry 4.0: a study of socio-technical readiness among manufacturers in Minnesota and North Dakota

The implementation of Industry 4.0 has become increasingly prevalent in the manufacturing industry since its inception. With the introduction of these newer technologies, changes in personnel and organizational structures occur. The purposeful joint optimization of social and technical factors of organizations is imperative to the successful adoption of Industry 4.0. Thus, the socio-technical system theory addresses a holistic design of human, technology, and organization subsystems of the manufacturing process and their interdependencies. This dissertation investigates the progress made towards implementing Industry 4.0 by small, medium, and large manufacturers in Minnesota and North Dakota. The outcomes of two surveys conducted among a group in Minnesota and North Dakota are analyzed and the results are compared to national and international data. This research identifies potential challenges, as well as, advantages in the current socio-economic landscape for manufacturers that may be either impeding or encouraging the development of a competitive and sustainable manufacturing business. As well, the implementation of flexible work arrangements in the modern work environment has increased in recent years. The first survey posed questions based on a socio-technical theory framework, Industry 4.0, and productivity outcomes. Insights were provided as to how regional manufacturers were utilizing the socio-technical design framework to integrate Industry 4.0 into the organizational design and extract value, such as increased productivity. The joint optimization of social and technical factors within an organization is necessary for the successful adoption of hybrid work environments. The outcomes of the second survey conducted among a group of small, medium, and large manufacturers in Minnesota and North Dakota were assessed the level of socio-technical readiness among regional manufacturers. The survey posed questions based on socio-technical design, digital maturity, organizational learning, responsible autonomy, leadership, communication strategies, and reduced work week schedules. Insights were provided as to how these critical factors support sustainability initiatives, such as reduced work week schedules. As a result of the surveys, a socio-technical strengths, weaknesses, opportunities, and threats (SWOT) analysis framework to complete was proposed to guide the organization through the Industry 4.0 implementation process, assess opportunities for the reduction of work hours, and facilitate the strategic enterprise-wide buy-in from employees and diverse stakeholders

Computational Methods for Bulk and Single-cell Chromatin Interaction Data

Chromatin interactions occur when the physical regions of chromatin in close proximity interact with each other inside the nucleus. Analyzing chromatin interactions plays a crucial role in deciphering the spatial organization of the genome. Identifying the significant interactions and their functionalities reveals great insights on gene expressions, gene regulations and genetic diseases such as cancer. In addition, single cell chromatin interaction data is important to understand the chromatin structure changes, diversity among individual cells, and the genomics differences between different cell types. In recent years, Hi-C, chromosome conformation capture with high throughput sequencing, has gained widespread popularity for its ability to map genome-wide chromatin interactions in a single experiment and it is capable of extracting both single cell and bulk chromatin interaction data. With the evolution of experimental methods like Hi-C, computational tools are essential to efficiently and accurately process the vast amount of genomic data. Since the experiment costs are notably higher, optimized computational tools and methods are needed to extract most possible information from the data. Moreover, processing single cell Hi-C data imposes number of challenges due to its sparseness and limited interaction counts. So the development of computational methods and tools to process data from both single cell Hi-C and bulk Hi-C technologies are focused in this work and those are proven to be enhancing the efficiency and accuracy of Hi-C data processing pipelines. In this dissertation, each chapter consists of a single individual method or a tool to enhance chromatin interaction processing pipelines and the final chapter focuses on the interplay between epigenetic data and chromatin interactions data. The studies that are focused on building computational methods include increasing data read accuracy for bulk Hi-C, identifying statistically significant interactions at single cell Hi-C data, and imputation of single cell Hi-C data to improve quality and quantity of raw reads. It is anticipated that the utilization of the tools and methods outlined in these studies will significantly enhance the workflows of future research on chromatin organization and its correlation with cellular functions and genetic diseases

Distribution of paycheck protection program funding during the COVID-19 pandemic

This thesis investigates the distribution of Paycheck Protection Program (PPP) loans, focusing on racial disparities in loan allocation and the differential effects on rural businesses. Employing a Cragg-Hurdle regression model, I extend previous methodologies to explore the influence of a community's racial composition on PPP loan distribution, particularly in the previously unexamined third tranche. I also assess the program comprehensively. My results reveal that majority-minority communities, particularly those with a higher Black population share, received drastically more funding in the third tranche compared to earlier rounds. Additionally, I analyze the impact of nontraditional lenders and policy changes introduced by the Biden-Harris Administration, uncovering nuanced variations in loan distribution concerning urban and rural demographics. Ultimately, my findings indicate substantial shifts in racial disparities in PPP loan distribution across the third tranche and the entire program, underscoring the necessity for an updated understanding of this issue in the existing literature

Dietary Impacts on Mitochondrial Respiration of Gestating Heifers and Fetal Offspring

Two projects were conducted to evaluate dietary impacts on mitochondrial respiration of gestating heifers and fetal offspring. Our first hypothesis was that maternal vitamin and mineral supplementation during gestation improves the liver, muscle, and jejunum mitochondrial function of F1 and F2 offspring. In project 1, vitamin and mineral supplementation was provided to the F0 generation of dams from breeding to calving to isolate the effects of nutrition during pregnancy on future generations. Our second hypothesis was that altering limit-fed diets' forage: concentrate ratio would influence mitochondrial respiration in maternal and fetal jejunum and liver. In project 2, replacement heifers were fed high-concentrate and high-forage diets to evaluate the dietary impacts on fetal cellular metabolism of key metabolic organs. In both project 1 and 2, modulations of metabolism occurred in key metabolic organs of gestating heifers

An analysis of intersecting factors influencing first-generation college student enrollment

This study examined the impact of college visits on first-generation college students (FGCS). Specifically, I analyzed data from a midsized university in the upper Midwest to understand the the intersecting effect of variables on FGCS?s choices for attending college. I tested four hypotheses by conducting logistic regression models using the focal variables of the number of campus visits, estimated family contribution, race, high school grade point average, and gender. Results showed that visiting campus, a student?s race, being female, and grade point average significantly impacted their likelihood of enrolling at this university. FGCS who were Black/African American or Hispanic/Latino were substantially less likely to enroll compared to FGCS who were White. When looking at race and college visits, increased college visits indicated higher chances for enrollment for most FGCS; however, Black/African American students? chance of enrolling decreased with additional campus visits

The Landing Park of the Mid-American Steel: Bridging the Past and Future Through Soundscape Analysis

Good soundscape quality in parks can only be provided with a thorough understanding of the complex relationships among sound, environment, and individuals. This study explores visitors' perceptions of the urban park soundscape to relieve stress. The study employed a mixed-methods approach consisting of an objective sound walk survey, a questionnaire survey, and a landscape design approach to improve sound quality in urban parks. Approximately 234 park visitor responses were obtained from online questionnaire surveys administered in the Fargo, North Dakota, region. Objective sound measurements were conducted at 53 survey spots on four different days, two days in the morning and the other two in the afternoon, corresponding to the questionnaire. The findings unveil that acoustic comfort evaluation, besides visual comfort evaluation of landscape, also plays a vital role in users? acceptability of the urban park environment. The soundwalk survey collected visitors' perceptions and evaluation of the urban park soundscape. At the same time, the qualitative questionnaire survey explored visitors' experiences and preferences regarding the soundscape for stress relief and preferred locations to visit inside the park. The literature review and study results showed that visitors perceived the urban park soundscape as essential for promoting stress relief and relaxation. Visitors preferred natural sounds, such as bird songs and water sounds, over human-made sounds, such as traffic and construction noise, as they were more calming and pleasant. The study also found that visitors had varying preferences for the intensity and complexity of the soundscape, with some preferring a quiet and straightforward soundscape. In contrast, others enjoyed a more diverse and complex soundscape, where an above-average decibel range of anthropogenic sounds did not deter the park users' willingness to stay. The results suggest that urban park designers should consider the soundscape as a crucial element in promoting stress relief and well-being for park visitors. Furthermore, these results are applied to the Mid-American Steel site in Fargo, North Dakota, a post-industrial site with a strong historical background. This site has potential features for urban park development and civic facilities to make a good connection between downtown Fargo and the bank of Red River. The major challenge of this location is the rail track, which has passed through the site and, in this design, reduces decibel levels of rail track using a gradient of priorities based on park programming