Digital Commons Network^™

Uncovering Over 150 Years Of Herbarium Specimen Data To Examine The Impacts Of Climate Change On Alpine Plant Phenology In The Southern Rocky Mountains, Erin Berkowitz

Museum Studies Theses

Due to generalized botanical collecting practices, herbarium specimens provide important long term data dating back hundreds of years. The historical data preserved in herbaria can be used to study biological responses to climate change, such as changes in plant phenology, across various habitats including understudied alpine ecosystems. This study will use historical data from over one hundred years of plant collecting, along with updated collecting and community science efforts, to investigate how climate change is influencing alpine plant phenology in the Southern Rocky Mountains. These records will be analyzed alongside historical climate data to explore phenological sensitivities to climate change, …

Structural Analysis Of Dj-1 Glyoxalase Activity By Mix-And-Inject Serial Synchrotron Crystallography, Coleman Dolamore

Department of Biochemistry: Dissertations, Theses, and Student Research

Observing enzyme structures while they are catalyzing a reaction has been a major goal of both enzymology and structural biology for decades. With the advent of time-resolved serial X-ray crystallography using X-ray free electron lasers (XFELs) and synchrotron sources, enzyme reactions can be monitored in real time in crystallo. Here, we use two different approaches to study related enzymes involved in methylglyoxal detoxification. For human DJ-1, we used pink beam mix-and-inject serial crystallography (MISC) at the Advanced Photon Source (BioCARS 14-ID) to probe the controversial mechanism of DJ-1’s action on methylglyoxal by using serial Laue diffraction. The high flux …

Data-Driven Drug Repurposing For Immune System-Related Diseases, Sabyasachi Mohanty

Department of Biochemistry: Dissertations, Theses, and Student Research

In this research, we explore a data-driven approach for drug repurposing to enhance the immunomodulatory effect by integrating pattern-based search and genome-scale metabolic modeling. This research helps to find a solution to the preexisting problems of drug discovery which includes expenses and a high amount of time consumption. By leveraging the pre-existing data of the approved drugs to identify the major metabolic pathway changes, we can find new drugs with similar effects with less off-target effects.

The focus on the immune system modulating drugs is due to the high prevalence of immune system-involved diseases and the growing demand for effective …

Interleukin 24 Induces Apoptosis Through Glycogen Synthase Kinase-3 Beta Inactivation In Prostate Cancer Cells, Sual J. Lopez, Moira Sauane

Theses and Dissertations

Interleukin 24 (IL-24) is a tumor-suppressing protein currently in clinical trials. IL-24 induces cancer-specific apoptosis by activating endoplasmic reticulum (ER) stress and mitochondria dysfunction. We have previously demonstrated that IL-24 leads to apoptosis in cancer cells by protein kinase A (PKA) activation in human breast cancer cells. To further understand the mechanism by which IL-24 induces apoptosis, I analyzed the role of glycogen synthase kinase-3 (GSK3), a highly conserved and normally active serine/threonine kinase in cancer cells and downstream target of PKA. The work reported here provides direct evidence that GSK3 was inhibited following IL-24 treatment in human prostate cancer …

Elucidation Of Potential Antimicrobial Properties Of Chalcones, Caleb Howell

Theses

The rise of antibiotic-resistant bacteria is a growing concern for the medical and biological community. Increased use of antibiotics has led to increased development of bacterial tolerances. This phenomenon, driven by the principles of evolution, has been exacerbated by the improper antibiotic use of these antibiotics. Often, individuals stop taking antibiotics once symptoms subside, mistakenly believing the infection is cured. This practice allows bacteria or fungi to develop resistance.

These antibiotics have been developed from secondary metabolites. While we have many effective antibiotics we are facing new threats. Chalcones are being looked at for their potential in addressing this issue. …

The Relationship Between Changing Land Cover And Benthic Macroinvertebrate Diversity In Choccolocco Creek, Northeast Alabama, Kindall Brown

Theses

Land cover changes, driven by urbanization, agriculture, and deforestation, significantly affect the physical and chemical characteristics of water bodies at both the watershed and riparian levels. At the larger spatial scale, a stream’s surrounding watershed facilitates lateral inputs into the stream that are essential for biodiversity support, hydrological stability, and water quality. When a stream becomes disconnected from the lateral inputs due to urban or agricultural development, the morphology of the stream is significantly altered. On a smaller spatial scale, the riparian zone can act as a buffer to pollutants. The vegetation surrounding the stream bank promotes stability to the …

Tenure And Promotion Announcement, 2024, University Of Mississippi. Provost

Tenure and Promotion Announcements

No abstract provided.

Orthodontic Load Quantification Leveling A Deep Curve Of Spee With Different Archwire Designs, Ahmed Youssef

Master's Theses (2009 -)

Objective: This study aimed to quantify the effects of different materials, sizes of the continuous archwires in leveling the exaggerated curve of Spee. We used an orthodontic force tester apparatus to measure the forces and moments delivered by the archwires to the brackets attached to the sensors of one quadrant of the arch (from 1st incisor to 2nd molar). The hypothesis is that there is no difference in the load and moments between the incisors when the curve of Spee is leveled with the three different mechanical designs being tested. Methods: An orthodontic force tester (OFT) was used to measure …

The Role Of Obesity In The Development Of Disordered Breathing, Sarah N. Framnes-Deboer

Master's Theses (2009 -)

Obesity is a complex disease that is defined by an excess amount of body fat. Obesity can have physical, neurological, and endocrine effects and detrimental effects on health. Some obese co-morbid conditions, such as type 2 diabetes have known mechanisms, while others, such as sleep disordered breathing do not. Moreover, there are common respiratory diseases associated with obesity, such as obstructive sleep apnea and obesity hypoventilation syndrome. Furthermore, individuals with obesity or obstructive sleep apnea have a blunted hypercapnic ventilatory response (HCVR) (120), which is indicative of impaired chemosensitivity, as HCVR is a measure of how well an individual responds …

Marketplace Summer 2024, Southern Adventist University

MarketPlace - School of Business Newsletter

The Summer 2023 issue of MarketPlace features information on Business department events, Alumni features, and a research competition.

Impact Of Non-Thermal Plasma Generated Using Air And Nitrogen On Functional Properties Of Milk Protein Dispersions, Nikitha Modupalli, Md Mahfuzur Rahman

Food Science Faculty Publications and Presentations

This study focuses on improving the functionalities of milk protein concentrate (MPC) using a nonthermal plasma jet and plasma-activated water (PAW) with atmospheric air and nitrogen as source gases. The 5% and 10% MPC dispersions were directly treated with a plasma jet, and PAW was used to make the MPC dispersions. The dispersions were analyzed for changes in protein structure and functional properties. The treatment altered the secondary structure of MPC protein structure by increasing β-components and changing the order of random coils. The solubility of the PAW-treated 5% protein dispersions doubled due to plasma-induced modification of hydrophilic and covalent …

Spatial And Temporal Variability In Nutritional Physiology Of Pyropia Perforata, Matthew S. Elliott

Capstone Projects and Master's Theses

The red alga, Pyropia perforata, commonly referred to as nori, is ubiquitous in intertidal communities throughout coastal California and offers high nutritional value to marine herbivores. However, California rocky shores are dynamic ecosystems, with dramatic abiotic and biotic shifts resulting in environmental heterogeneity. Research has shown that seaweed nutrient physiology is impacted by environmental heterogeneity, yet there is sparse data on how internal nitrogen and total protein content change as a result of environmental heterogeneity. Here, I studied the impacts of seasonality, geography (spanning 4° of latitude from Northern to Southern California), and the onset of environmental heterogeneity on internal …

Fedgmmat: Federated Generalized Linear Mixed Model Association Tests, Wentao Li, Han Chen, Xiaoqian Jiang, Arif Harmanci

Faculty, Staff and Student Publications

Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for performing high-powered studies. As the sample sizes become more heterogeneous, complex statistical approaches, such as generalized linear mixed effects models, must be used to correct for the confounders that may bias results. On another front, due to the privacy concerns around Protected Health Information (PHI), genetic information is restrictively protected by sharing according to regulations such as Health Insurance Portability and Accountability Act (HIPAA). This limits data sharing …

Ultrapotent Broadly Neutralizing Human-Llama Bispecific Antibodies Against Hiv-1, Jianliang Xu, Tongqing Zhou, Krisha Mckee, Baoshan Zhang, Cuiping Liu, Alexandra F Nazzari, Amarendra Pegu, Chen-Hsiang Shen, Jordan E Becker, Michael F Bender, Payton Chan, Anita Changela, Ridhi Chaudhary, Xuejun Chen, Tal Einav, Young Do Kwon, Bob C Lin, Mark K Louder, Jonah S Merriam, Nicholas C Morano, Sijy O'Dell, Adam S Olia, Reda Rawi, Ryan S Roark, Tyler Stephens, I-Ting Teng, Emily Tourtellott-Fogt, Shuishu Wang, Eun Sung Yang, Lawrence Shapiro, Yaroslav Tsybovsky, Nicole A Doria-Rose, Rafael Casellas, Peter D Kwong

Faculty, Staff and Student Publications

Broadly neutralizing antibodies are proposed as therapeutic and prophylactic agents against HIV‐1, but their potency and breadth are less than optimal. This study describes the immunization of a llama with the prefusion‐stabilized HIV‐1 envelope (Env) trimer, BG505 DS‐SOSIP, and the identification and improvement of potent neutralizing nanobodies recognizing the CD4‐binding site (CD4bs) of vulnerability. Two of the vaccine‐elicited CD4bs‐targeting nanobodies, G36 and R27, when engineered into a triple tandem format with llama IgG2a‐hinge region and human IgG1‐constant region (G36×3‐IgG2a and R27×3‐IgG2a), neutralized 96% of a multiclade 208‐strain panel at geometric mean IC80s of 0.314 and 0.033 µg mL−1, respectively. Cryo‐EM …

Identification Of Immune-Associated Biomarkers Of Diabetes Nephropathy Tubulointerstitial Injury Based On Machine Learning: A Bioinformatics Multi-Chip Integrated Analysis, Lin Wang, Jiaming Su, Zhongjie Liu, Shaowei Ding, Yaotan Li, Baoluo Hou, Yuxin Hu, Zhaoxi Dong, Jingyi Tang, Hongfang Liu, Weijing Liu

Faculty, Staff and Student Publications

BACKGROUND: Diabetic nephropathy (DN) is a major microvascular complication of diabetes and has become the leading cause of end-stage renal disease worldwide. A considerable number of DN patients have experienced irreversible end-stage renal disease progression due to the inability to diagnose the disease early. Therefore, reliable biomarkers that are helpful for early diagnosis and treatment are identified. The migration of immune cells to the kidney is considered to be a key step in the progression of DN-related vascular injury. Therefore, finding markers in this process may be more helpful for the early diagnosis and progression prediction of DN.

METHODS: The …

Phase 1 Dose Escalation Study Of The Mdm2 Inhibitor Milademetan As Monotherapy And In Combination With Azacitidine In Patients With Myeloid Malignancies, Courtney D Dinardo, Rebecca Olin, Eunice S Wang, Barry Skikne, Joseph Rosenthal, Prasanna Kumar, Hiroyuki Sumi, Yoshiyuki Hizukuri, Ying Hong, Parul Patel, Takahiko Seki, Tao Duan, Arnaud Lesegretain, Michael Andreeff

Faculty, Staff and Student Publications

BACKGROUND: Mouse double minute-2 homolog (MDM2) plays a key role in downregulating p53 activity in hematologic malignancies, and its overexpression is associated with poor outcomes.

METHODS: This phase 1 study assessed the safety and efficacy of different dosing regimens of the MDM2 inhibitor milademetan as monotherapy and in combination with azacitidine (AZA) in patients with relapsed or refractory acute myeloid leukemia or high-risk myelodysplastic syndromes.

RESULTS: Seventy-four patients (monotherapy, n = 57; milademetan-AZA combination, n = 17) were treated. The maximum tolerated dose of milademetan was 160 mg once daily given for the first 14-21 days of 28-day cycles as …

A Deep Catalogue Of Protein-Coding Variation In 983,578 Individuals, Kathie Y Sun, Xiaodong Bai, Siying Chen, Suying Bao, Chuanyi Zhang, Manav Kapoor, Joshua Backman, Tyler Joseph, Evan Maxwell, George Mitra, Alexander Gorovits, Adam Mansfield, Boris Boutkov, Sujit Gokhale, Lukas Habegger, Anthony Marcketta, Adam E Locke, Liron Ganel, Alicia Hawes, Michael D Kessler, Deepika Sharma, Jeffrey Staples, Jonas Bovijn, Sahar Gelfman, Alessandro Di Gioia, Veera M Rajagopal, Alexander Lopez, Jennifer Rico Varela, Jesús Alegre-Díaz, Jaime Berumen, Roberto Tapia-Conyer, Pablo Kuri-Morales, Jason Torres, Jonathan Emberson, Rory Collins, Regeneron Genetics Center, Rgc-Me Cohort Partners; Michael Cantor, Michael Cantor, Timothy Thornton, Hyun Min Kang, John D Overton, Alan R Shuldiner, M Laura Cremona, Mona Nafde, Aris Baras, Gonçalo Abecasis, Jonathan Marchini, Jeffrey G Reid, William Salerno, Suganthi Balasubramanian

Faculty, Staff and Student Publications

Rare coding variants that substantially affect function provide insights into the biology of a gene1-3. However, ascertaining the frequency of such variants requires large sample sizes4-8. Here we present a catalogue of human protein-coding variation, derived from exome sequencing of 983,578 individuals across diverse populations. In total, 23% of the Regeneron Genetics Center Million Exome (RGC-ME) data come from individuals of African, East Asian, Indigenous American, Middle Eastern and South Asian ancestry. The catalogue includes more than 10.4 million missense and 1.1 million predicted loss-of-function (pLOF) variants. We identify individuals with rare biallelic pLOF variants in 4,848 genes, 1,751 of …

Targeting Of Cyp2e1 By Mirnas In Alcohol-Induced Intestine Injury, Hyejin Mun, Sungyul Lee, Suyoung Choi, Ji-Hoon Jeong, Seungbeom Ko, Yoo Lim Chun, Benjamin Deaton, Clay T Yeager, Audrey Boyette, Juliana Palmera, London Newman, Ping Zhou, Soona Shin, Dong-Chan Kim, Cari A Sagum, Mark T Bedford, Young-Kook Kim, Jaeyul Kwon, Junyang Jung, Jeong Ho Chang, Je-Hyun Yoon

Faculty, Staff and Student Publications

Although binge alcohol-induced gut leakage has been studied extensively in the context of reactive oxygen species-mediated signaling, it was recently revealed that post-transcriptional regulation plays an essential role as well. Ethanol (EtOH)-inducible cytochrome P450-2E1 (CYP2E1), a key enzyme in EtOH metabolism, promotes alcohol-induced hepatic steatosis and inflammatory liver disease, at least in part by mediating changes in intestinal permeability. For instance, gut leakage and elevated intestinal permeability to endotoxins have been shown to be regulated by enhancing CYP2E1 mRNA and CYP2E1 protein levels. Although it is understood that EtOH promotes CYP2E1 induction and activation, the mechanisms that regulate CYP2E1 expression …

Ghcu, A Molecular Chaperone, Regulates Leaf Curling By Modulating The Distribution Of Kngh1 In Cotton, Yihao Zang, Chenyu Xu, Lishan Yu, Longen Ma, Lisha Xuan, Sunyi Yan, Yayao Zhang, Yiwen Cao, Xiaoran Li, Zhanfeng Si, Jieqiong Deng, Tianzhen Zhang, Yan Hu

Faculty, Staff and Student Publications

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial …

Genetic Analysis Of Seven Patients With Inherited Ichthyosis And Nagashima-Type Palmoplantar Keratoderma, Jing Zhang, Yue Yao, Ya Tan, Hua-Ying Hu, Lin-Xi Zeng, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Inherited ichthyosis comprises a series of heterogeneous dermal conditions; it mainly manifests as widespread hyperkeratosis, xerosis and scaling of the skin. At times, overlapping symptoms require differential diagnosis between ichthyosis and several other similar disorders. The present study reports seven patients with confirmed or suspected to be associated with ichthyosis by conducting a thorough clinical and genetic investigation. Genetic testing was conducted using whole-exome sequencing, with Sanger sequencing as the validation method. The MEGA7 program was used to analyze the conservation of amino acid residues affected by the detected missense variants. The enrolled patients exhibited ichthyosis-like but distinct clinical manifestations. …

Machine Learning Identifies Prognostic Subtypes Of The Tumor Microenvironment Of Nsclc, Duo Yu, Michael J Kane, Eugene J Koay, Ignacio I Wistuba, Brian P Hobbs

Faculty, Staff and Student Publications

The tumor microenvironment (TME) plays a fundamental role in tumorigenesis, tumor progression, and anti-cancer immunity potential of emerging cancer therapeutics. Understanding inter-patient TME heterogeneity, however, remains a challenge to efficient drug development. This article applies recent advances in machine learning (ML) for survival analysis to a retrospective study of NSCLC patients who received definitive surgical resection and immune pathology following surgery. ML methods are compared for their effectiveness in identifying prognostic subtypes. Six survival models, including Cox regression and five survival machine learning methods, were calibrated and applied to predict survival for NSCLC patients based on PD-L1 expression, CD3 expression, …

Mutation Order In Acute Myeloid Leukemia Identifies Uncommon Patterns Of Evolution And Illuminates Phenotypic Heterogeneity, Matthew Schwede, Katharina Jahn, Jack Kuipers, Linde A Miles, Robert L Bowman, Troy Robinson, Ken Furudate, Hidetaka Uryu, Tomoyuki Tanaka, Yuya Sasaki, Asiri Ediriwickrema, Brooks Benard, Andrew J Gentles, Ross Levine, Niko Beerenwinkel, Koichi Takahashi, Ravindra Majeti

Faculty, Staff and Student Publications

Acute myeloid leukemia (AML) has a poor prognosis and a heterogeneous mutation landscape. Although common mutations are well-studied, little research has characterized how the sequence of mutations relates to clinical features. Using published, single-cell DNA sequencing data from three institutions, we compared clonal evolution patterns in AML to patient characteristics, disease phenotype, and outcomes. Mutation trees, which represent the order of select mutations, were created for 207 patients from targeted panel sequencing data using 1 639 162 cells, 823 mutations, and 275 samples. In 224 distinct orderings of mutated genes, mutations related to DNA methylation typically preceded those related to …

Van Raalte Hall, Hope’S Former Campus Center; Hope’S First International Graduates: Class Of 1879, Wyatt Wilcox, Douglas Braat

Archives and Special Collections Quarterly

Van Raalte Hall, Hope’s Former Campus Center

Column: From the Director of Archives and Special Collections

Hope’s First International Graduates: Class of 1879

A Closer Look: Understanding Endometriosis And Pelvic Health Through The Lens Of Occupational Therapy, Brenda Vergara

Occupational Therapy Student Capstones

No abstract provided.

A Day In The Life Of A Sci, Jeffrey Garcia

Occupational Therapy Student Capstones

No abstract provided.

Exploring The Role Of Occupational Therapy In The Criminal Justice System At The County Level, Marisa Given

Occupational Therapy Student Capstones

No abstract provided.

Imposter Syndrome Management And Strategies For Ot Graduate Students, Lauren Magat

Occupational Therapy Student Capstones

No abstract provided.

Integrating Social Connectedness Within Community Programs, Staphany Jimenez

Occupational Therapy Student Capstones

No abstract provided.

Promotes Children’S Wellbeing In The First Year Of Life And Parental Confidence Through Evidence-Based Knowledge, Jocelyn Ong Najera

Occupational Therapy Student Capstones

No abstract provided.

Occupational Therapy’S Role In Concussion Recovery For The Adult Population, Nikki Atis

Occupational Therapy Student Capstones

No abstract provided.