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Evaluating And Improving The Serious Game Life With Hereditary Cancer, Jenna K. Peterson Mar 2025

Evaluating And Improving The Serious Game Life With Hereditary Cancer, Jenna K. Peterson

USF Tampa Graduate Theses and Dissertations

Hereditary cancer syndromes increase cancer risks for individuals with pathogenic variants and their family members, yet many at-risk individuals do not pursue genetic testing due to barriers in family communication. Serious games—interactive tools designed to educate through gameplay—offer a promising approach to addressing these barriers by engaging users and creating supportive learning environments. LIFE with Hereditary Cancer is a serious game designed to improve genetic literacy, promote informed decision-making, and encourage family conversations about hereditary cancer risks and genetic testing. This evaluation used a mixed-methods approach to assess participant emotions, perceptions, and experiences with LIFE with Hereditary Cancer and identify …


Efficacy And Safety Of Venetoclax Plus Azacitidine For Patients With Treatment-Naive High-Risk Myelodysplastic Syndromes, Jacqueline S Garcia, Uwe Platzbecker, Olatoyosi Odenike, Shaun Fleming, Chun Yew Fong, Uma Borate, Meagan A Jacoby, Daniel Nowak, Maria R Baer, Pierre Peterlin, Brenda Chyla, Huipei Wang, Grace Ku, David Hoffman, Jalaja Potluri, Guillermo Garcia-Manero Mar 2025

Efficacy And Safety Of Venetoclax Plus Azacitidine For Patients With Treatment-Naive High-Risk Myelodysplastic Syndromes, Jacqueline S Garcia, Uwe Platzbecker, Olatoyosi Odenike, Shaun Fleming, Chun Yew Fong, Uma Borate, Meagan A Jacoby, Daniel Nowak, Maria R Baer, Pierre Peterlin, Brenda Chyla, Huipei Wang, Grace Ku, David Hoffman, Jalaja Potluri, Guillermo Garcia-Manero

Faculty, Staff and Student Publications

Outcomes are poor in patients with higher-risk myelodysplastic syndromes (HR MDS) and frontline treatment options are limited. This phase 1b study investigated safety and efficacy of venetoclax, a selective B-cell lymphoma 2 inhibitor, at the recommended phase 2 dose (RP2D; 400 mg for 14 days per 28-day cycle), in combination with azacitidine (75 mg/m2 for 7 days per 28-day cycle) for treatment-naive HR MDS. Safety was the primary outcome, and complete remission (CR) rate was the primary efficacy outcome. Secondary outcomes included rates of modified overall response (mOR), hematologic improvement (HI), overall survival (OS), and time to next treatment (TTNT). …


Influence Of Inselbergs On Bat Diversity In Afrotropical Ecosystems, Amanda Lee Grunwald Mar 2025

Influence Of Inselbergs On Bat Diversity In Afrotropical Ecosystems, Amanda Lee Grunwald

Dissertations and Theses

Humans are altering biological communities on local to global scales, driving profound changes in biodiversity and ecosystem functioning. However, significant gaps and biases in biodiversity data hinder our understanding of ecosystem interactions, making it challenging to develop effective, data-driven policies to protect remaining biodiversity. Bats, the second most species-rich groups of mammals, have a global distribution, and perform a broad array of vital ecosystem functions. Their diversity peaks in the tropics, where they often constitute more than 50% of mammal species diversity. The Afrotropics host substantial bat diversity, yet have historically been perceived as having lower species richness compared to …


Synthesis Of A Series Of Rare-Earth-Based Multi-Anion Chalcogenide Iodides Re3Si2SeXS8-XI (Re = La, Ce, Pr, And Nd) Using The Flux-Assisted Boron-Chalcogen Mixture Method, Gopabandhu Panigrahi, Habiba Binte Kashem, Gregory Morrison, Hans Conrad Zur Loye Mar 2025

Synthesis Of A Series Of Rare-Earth-Based Multi-Anion Chalcogenide Iodides Re3Si2SeXS8-XI (Re = La, Ce, Pr, And Nd) Using The Flux-Assisted Boron-Chalcogen Mixture Method, Gopabandhu Panigrahi, Habiba Binte Kashem, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Single crystals and polycrystalline powders of rare earth mixed chalcogenide iodides La3Si2Se1.21S6.79I, Ce3Si2Se1.39S6.61I, Pr3Si2Se1.22S6.78I, and Nd3Si2Se1.18S6.82I were prepared using the reactive flux-assisted boron-chalcogen mixture (BCM) method at 850 °C. All compounds crystallized in the monoclinic crystal system, space group C2/c (space group number 15). The series adopts the La3Si2O8Cl structure type, containing isolated SiQ4 tetrahedra connected by REQ8 (RE = La, Ce, Pr and Nd) polyhedra; this arrangement creates tunnels that are filled by I atoms. The partial substitution of S by Se was carried out to modulate the optical properties. Phase pure samples and uniform solid solutions were obtained …


General Biology 2 Laboratory Manual: In Person Edition, Dmitry Y. Brogun, Azure N. Faucette, Farshad Tamari, Kristin Polizzotto Mar 2025

General Biology 2 Laboratory Manual: In Person Edition, Dmitry Y. Brogun, Azure N. Faucette, Farshad Tamari, Kristin Polizzotto

Open Educational Resources

The completed project is an in-person teaching version of the General Biology II OER (Open Educational Resource) lab manual. This lab manual was initially written by the four of us during the pandemic when all courses were online, but it is now has been adapted for in-person lab activities. We also ensured it aligns with UDL (Universal Design for Learning) and accessibility principles. This adaptation aims to make the lab manual suitable for traditional classroom settings while incorporating diverse teaching practices to accommodate diverse learners.


Evaluating The Meditation Practices And Barriers To Adopting Mindful Medicine Among Physicians, Tiffany Champagne-Langabeer, Chelsea G Ratcliff, Christine Bakos-Block, Francine Vega, Marylou Cardenas-Turanzas, Aila Malik, Radha Korupolu Mar 2025

Evaluating The Meditation Practices And Barriers To Adopting Mindful Medicine Among Physicians, Tiffany Champagne-Langabeer, Chelsea G Ratcliff, Christine Bakos-Block, Francine Vega, Marylou Cardenas-Turanzas, Aila Malik, Radha Korupolu

Faculty, Staff and Student Publications

Background: Chronic pain affects over 25% of U.S. adults and is a leading cause of disability. Mindfulness meditation (MM) is a nonpharmacologic approach to manage pain and improve well-being. Despite mounting evidence supporting its efficacy, MM remains underutilized in medical practice. Understanding physicians' engagement with MM and the barriers they face can inform strategies for integration into clinical care. This study assessed physicians' attitudes toward MM, including barriers to practice and their likelihood of recommending it to patients.

Methods: A cross-sectional survey of U.S. physicians was conducted from April to July 2024. Participants provided information on demographics, health struggles, and …


Structural Basis For Intrinsic Strand Displacement Activity Of Mitochondrial Dna Polymerase, Ashok Nayak, Viktoriia Sokolova, Sirelin Sillamaa, Karl Herbine, Juhan Sedman, Dmitry Temiakov Mar 2025

Structural Basis For Intrinsic Strand Displacement Activity Of Mitochondrial Dna Polymerase, Ashok Nayak, Viktoriia Sokolova, Sirelin Sillamaa, Karl Herbine, Juhan Sedman, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

Members of the Pol A family of DNA polymerases, found across all domains of life, utilize various strategies for DNA strand separation during replication. In higher eukaryotes, mitochondrial DNA polymerase γ relies on the replicative helicase TWINKLE, whereas the yeast ortholog, Mip1, can unwind DNA independently. Using Mip1 as a model, we present a series of high-resolution cryo-EM structures that capture the process of DNA strand displacement. Our data reveal previously unidentified structural elements that facilitate the unwinding of the downstream DNA duplex. Yeast cells harboring Mip1 variants defective in strand displacement exhibit impaired oxidative phosphorylation and loss of mtDNA, …


Prodrug Activation In Malaria Parasites Mediated By An Imported Erythrocyte Esterase, Acylpeptide Hydrolase (Apeh), Sesh A. Sundararaman, Justin J. Miller, Ellora C. Daley, Kelsey A. O'Brien, Paulina Kasak, Abigail M. Daniels, Rachel L. Edwards, Kenneth M. Heidel, Darean A. Bague, Madeleine A. Wilson, Andrew J. Koelper, Elexi C. Kourtoglou, Alex D. White, Sloan A. August, Georgia A. Apple, Regis W. Rouamba, Anthony J. Durand, John J. Esteb, Florian L. Muller, R. Jeremy Johnson, Geoffrey C. Hoops, Cynthia S. Dowd, Audrey R. Odom John Mar 2025

Prodrug Activation In Malaria Parasites Mediated By An Imported Erythrocyte Esterase, Acylpeptide Hydrolase (Apeh), Sesh A. Sundararaman, Justin J. Miller, Ellora C. Daley, Kelsey A. O'Brien, Paulina Kasak, Abigail M. Daniels, Rachel L. Edwards, Kenneth M. Heidel, Darean A. Bague, Madeleine A. Wilson, Andrew J. Koelper, Elexi C. Kourtoglou, Alex D. White, Sloan A. August, Georgia A. Apple, Regis W. Rouamba, Anthony J. Durand, John J. Esteb, Florian L. Muller, R. Jeremy Johnson, Geoffrey C. Hoops, Cynthia S. Dowd, Audrey R. Odom John

College of Health Professions Faculty Papers

The continued emergence of antimalarial drug resistance highlights the need to develop new antimalarial therapies. Unfortunately, new drug development is often hampered by undesirable drug-like properties of lead compounds. Prodrug approaches temporarily mask undesirable compound features, improving bioavailability and target penetration. We have found that lipophilic diester prodrugs of phosphonic acid antibiotics, such as fosmidomycin (Fsm), exhibit significantly higher antimalarial potency than their parent compounds [R.L. Edwards et al., Sci. Rep. 7, 8400 (2017)]. However, the activating enzymes for these prodrugs were unknown. Here, we show that an erythrocyte enzyme, acylpeptide hydrolase (APEH), is the major activating enzyme of multiple …


Alpha-Frequency Stimulation Strengthens Coupling Between Temporal Fluctuations In Alpha Oscillation Power And Default Mode Network Connectivity, Yijia Ma, Joshua A Brown, Chaowen Chen, Mingzhou Ding, Wei Wu, Wen Li Mar 2025

Alpha-Frequency Stimulation Strengthens Coupling Between Temporal Fluctuations In Alpha Oscillation Power And Default Mode Network Connectivity, Yijia Ma, Joshua A Brown, Chaowen Chen, Mingzhou Ding, Wei Wu, Wen Li

Faculty, Staff and Student Publications

Alpha (8–12 Hz) oscillations and default mode network (DMN) activity dominate the brain's intrinsic activity in the temporal and spatial domains, respectively. They are thought to play crucial roles in the spatiotemporal organization of the complex brain system. Relatedly, both have been implicated, often concurrently, in diverse neuropsychiatric disorders, with accruing electroencephalogram (EEG)/magnetoencephalogram and functional magnetic resonance imaging (fMRI) data linking these two neural activities both at rest and during key cognitive operations. Prominent theories and extant findings thus converge to suggest a mechanistic relationship between alpha oscillations and the DMN. Here, we leveraged simultaneous EEG–fMRI data acquired before and …


Avasimibe Abolishes The Efficacy Of Fluvastatin For The Prevention Of Cancer In A Spontaneous Mouse Model Of Breast Cancer, Anjana Bhardwaj, Alexander Koh, Rhea Bhala, Janvi Sandhu, Zhenlin Ju, Leslie Faye Cando, Jing Wang, Isabelle Bedrosian Mar 2025

Avasimibe Abolishes The Efficacy Of Fluvastatin For The Prevention Of Cancer In A Spontaneous Mouse Model Of Breast Cancer, Anjana Bhardwaj, Alexander Koh, Rhea Bhala, Janvi Sandhu, Zhenlin Ju, Leslie Faye Cando, Jing Wang, Isabelle Bedrosian

Faculty, Staff and Student Publications

The cholesterol biosynthesis pathway is upregulated during breast cancer development and progression. Inhibition of the aberrantly upregulated cholesterol pathway by statins reduces breast tumor incidence and burden by 50% in SV40 C3(1) TAg mice, a mouse model of triple negative breast cancer. We hypothesized that fluvastatin's preventive efficacy could be further enhanced by co-targeting the statin-induced restorative feedback pathways that tightly control the cholesterol pathway and are involved in resistance to statins. Acyl-coenzyme A: cholesterol acyltransferase (


Leveraging Large Language Models For Knowledge-Free Weak Supervision In Clinical Natural Language Processing, Enshuo Hsu, Kirk Roberts Mar 2025

Leveraging Large Language Models For Knowledge-Free Weak Supervision In Clinical Natural Language Processing, Enshuo Hsu, Kirk Roberts

Faculty, Staff and Student Publications

The performance of deep learning-based natural language processing systems is based on large amounts of labeled training data which, in the clinical domain, are not easily available or affordable. Weak supervision and in-context learning offer partial solutions to this issue, particularly using large language models (LLMs), but their performance still trails traditional supervised methods with moderate amounts of gold-standard data. In particular, inferencing with LLMs is computationally heavy. We propose an approach leveraging fine-tuning LLMs and weak supervision with virtually no domain knowledge that still achieves consistently dominant performance. Using a prompt-based approach, the LLM is used to generate weakly-labeled …


A Role For The Actin Cytoskeleton And Plastin-3 In Osteoblast Mineralization And Mechanosensation, Samantha Meagan Chin Mar 2025

A Role For The Actin Cytoskeleton And Plastin-3 In Osteoblast Mineralization And Mechanosensation, Samantha Meagan Chin

Arts & Sciences Graduate Student Theses and Dissertations

The great diversity in actin network architectures and dynamics is exploited by cells to drive fundamental biological processes including cell migration, intracellular trafficking, and cell division. One such system that relies on the actin cytoskeleton to fulfill its physiological function are osteoblasts, which are mesenchymal lineage bone cells that promote bone formation through depositing a collagen scaffold and subsequently promoting mineralization of this matrix. A number of factors are known to drive osteogenic differentiation of pre-osteoblast cells including extracellular matrix cues such as substrate stiffness, which are primarily detected via mechanosensitive machinery linked to the actin cytoskeleton. Disruptions to β-actin, …


Incidence And Correlates Of High-Grade Chemotherapy-Induced Peripheral Neuropathy In Patients With Lung Cancer, Mitchell S Von Itzstein, Sawsan Rashdan, Suzanne E Dahlberg, David E Gerber, Alan B Sandler, Joan H Schiller, David H Johnson, Yating Wang, Zhuoxin Sun, Suresh S Ramalingam Mar 2025

Incidence And Correlates Of High-Grade Chemotherapy-Induced Peripheral Neuropathy In Patients With Lung Cancer, Mitchell S Von Itzstein, Sawsan Rashdan, Suzanne E Dahlberg, David E Gerber, Alan B Sandler, Joan H Schiller, David H Johnson, Yating Wang, Zhuoxin Sun, Suresh S Ramalingam

Faculty, Staff and Student Publications

Background: High-grade chemotherapy-induced peripheral neuropathy (CIPN) represents a dreaded toxicity of cancer treatments. In some cases, it may limit activities of daily living and become permanent. Because many prior studies of CIPN were conducted in breast cancer populations, less is known about CIPN in men. We therefore determined the incidence and correlates of high-grade CIPN in a large cohort of patients with lung cancer.

Methods: We collected data from the ECOG-ACRIN E1594 (comparison of 4 chemotherapy regimens: cisplatin-paclitaxel, cisplatin-gemcitabine, cisplatin-docetaxel, carboplatin-paclitaxel) and E4599 (carboplatin-paclitaxel ± concurrent and maintenance bevacizumab) clinical trials. We identified cases with grade ≥3 CIPN. Multivariable logistic …


Comparative Assessment Of The Impacts Of Wildland–Urban Interface Fire Ash On Growth Of The Diatom Thalassiosira Weissflogii, Talal Alshehri, Amar Yasser Jassim, Bo Cai Ph.D., Tammi L. Richardson, Mohammed Baalousha M.Sc, Ph.D. Mar 2025

Comparative Assessment Of The Impacts Of Wildland–Urban Interface Fire Ash On Growth Of The Diatom Thalassiosira Weissflogii, Talal Alshehri, Amar Yasser Jassim, Bo Cai Ph.D., Tammi L. Richardson, Mohammed Baalousha M.Sc, Ph.D.

Faculty Publications

Fires at the wildland–urban interface (WUI) result in the release of ash into the atmosphere that can be transported for long distances and deposited on land and in oceans. Wildfire ash has the potential to increase phytoplankton biomass in the open ocean by providing both major nutrients and trace metals. However, fires that originate at the WUI contain potentially toxic concentrations of metals such as Ti, Cr, Cu, Pb, and Zn, especially in coastal oceans close to WUI fires, where ash deposition rates are high. Here, we investigated the impact of fire ash from different sources originating from vegetation, structures, …


Benzothiadiazole Maintains Redox Balance And Promotes Defense Against Sitobion Avenae (F.) In Wheat By Fine-Tuning The Antioxidant System, Secondary Metabolism, And Osmolyte Accumulation., Fayyaz Ahmed, Samina Tanwir, Jam Nazeer Ahmad, Aysha Kiran, Faiz Ahmad Joyia Mar 2025

Benzothiadiazole Maintains Redox Balance And Promotes Defense Against Sitobion Avenae (F.) In Wheat By Fine-Tuning The Antioxidant System, Secondary Metabolism, And Osmolyte Accumulation., Fayyaz Ahmed, Samina Tanwir, Jam Nazeer Ahmad, Aysha Kiran, Faiz Ahmad Joyia

Turkish Journal of Botany

Aphids are destructive cereal pests causing serious yield losses in the wheat crop. Since wheat is a staple food for more than 75% of the human population, therefore, proper management of insect pests is crucial to enhance its productivity and ensure food security. Aphid herbivory induces highly coordinated defense responses in plants at the cellular and molecular level. This innate plant defense system is activated by a signal transduction pathway mediated by plant hormones like Salicyclic acid (SA). In the present investigation an attempt was made to explore the impacts of Benzothiadiazole (BTH), an analogue of SA on wheat plants …


Immunotherapy-Related Neurotoxicity In The Central Nervous System Of Children With Cancer, Jiasen He, Jeremy Connors, Andrew Meador, Shuo Xu, Heather Meador, Hong Jiang, Juan Fueyo, Candelaria Gomez-Manzano, Gregory K Friedman, Wafik Zaky, Zsila Sadighi, John M Slopis, Ali H Ahmad Mar 2025

Immunotherapy-Related Neurotoxicity In The Central Nervous System Of Children With Cancer, Jiasen He, Jeremy Connors, Andrew Meador, Shuo Xu, Heather Meador, Hong Jiang, Juan Fueyo, Candelaria Gomez-Manzano, Gregory K Friedman, Wafik Zaky, Zsila Sadighi, John M Slopis, Ali H Ahmad

Faculty, Staff and Student Publications

Significant gaps remain in our understanding of immunotherapy-related neurotoxicity in pediatric patients, largely because much of our knowledge comes from studies in adults. Accurately identifying the adverse effects of immunotherapy in children is also challenging, owing to variations in terminology and grading systems. Moreover, the manifestation of immunotherapy-related neurotoxicity differs greatly across different diseases, various modalities, dosages, and delivery methods. Combining immunotherapy with other treatments might improve outcomes but introduces new complexities and potential for increased toxicities. Additionally, pediatric patients with intracranial malignancy have unique responses to immunotherapies and distinct neurotoxicity compared to those with extracranial malignancy. Consequently, we must …


Pituitary Adenylate Cyclase Activating Polypeptide And Its Receptor As Novel Therapeutic Targets For Opioid Induced Hyperalgesia, Elizaveta Mangutov Mar 2025

Pituitary Adenylate Cyclase Activating Polypeptide And Its Receptor As Novel Therapeutic Targets For Opioid Induced Hyperalgesia, Elizaveta Mangutov

Arts & Sciences Graduate Student Theses and Dissertations

Opioids are commonly prescribed for the treatment of pain and headache disorders. However, chronic opioid use can result in a paradoxical increased sensitivity to pain as well as an extension of pain area known as opioid-induced hyperalgesia (OIH). One field OIH has been clearly identified is migraine, known as medication overuse headache (MOH). While opioids may provide acute relief, chronic use results in increased migraine pain severity and progression of migraine from an episodic to chronic state. The primary treatment is opioid cessation, which is difficult to implement as patients are reluctant to stop treatment they believe is helping them, …


Pituitary Adenylate Cyclase Activating Polypeptide And Its Receptor As Novel Therapeutic Targets For Opioid Induced Hyperalgesia, Elizaveta Mangutov Mar 2025

Pituitary Adenylate Cyclase Activating Polypeptide And Its Receptor As Novel Therapeutic Targets For Opioid Induced Hyperalgesia, Elizaveta Mangutov

Arts & Sciences Graduate Student Theses and Dissertations

Opioids are commonly prescribed for the treatment of pain and headache disorders. However, chronic opioid use can result in a paradoxical increased sensitivity to pain as well as an extension of pain area known as opioid-induced hyperalgesia (OIH). One field OIH has been clearly identified is migraine, known as medication overuse headache (MOH). While opioids may provide acute relief, chronic use results in increased migraine pain severity and progression of migraine from an episodic to chronic state. The primary treatment is opioid cessation, which is difficult to implement as patients are reluctant to stop treatment they believe is helping them, …


Mechanisms Of Macrophage Metabolic Activation And Paracrine Wnt Signaling In The Pathogenesis Of Systemic Sclerosis, Emily Ann Morris Mar 2025

Mechanisms Of Macrophage Metabolic Activation And Paracrine Wnt Signaling In The Pathogenesis Of Systemic Sclerosis, Emily Ann Morris

Dartmouth College Ph.D Dissertations

Systemic sclerosis (SSc) is a chronic autoimmune disease of unknown etiology. We have previously shown that macrophages (MØs) play a critical role in its pathogenesis; however, the mechanisms driving MØ activation in SSc remain poorly understood. This dissertation investigates the molecular signaling pathways and biochemical mechanisms underlying profibrotic MØ activity in SSc.

First, I identify a novel MØ-specific effect of mycophenolate mofetil (MMF), the standard-of-care treatment for SSc. While MMF is a well characterized lymphostatic, my findings demonstrate that its active metabolite, mycophenolic acid (MPA), is also capable of directly inhibiting myeloid viability and profibrotic MØ activation by suppressing de …


A Role For The Actin Cytoskeleton And Plastin-3 In Osteoblast Mineralization And Mechanosensation, Samantha Meagan Chin Mar 2025

A Role For The Actin Cytoskeleton And Plastin-3 In Osteoblast Mineralization And Mechanosensation, Samantha Meagan Chin

Arts & Sciences Graduate Student Theses and Dissertations

The great diversity in actin network architectures and dynamics is exploited by cells to drive fundamental biological processes including cell migration, intracellular trafficking, and cell division. One such system that relies on the actin cytoskeleton to fulfill its physiological function are osteoblasts, which are mesenchymal lineage bone cells that promote bone formation through depositing a collagen scaffold and subsequently promoting mineralization of this matrix. A number of factors are known to drive osteogenic differentiation of pre-osteoblast cells including extracellular matrix cues such as substrate stiffness, which are primarily detected via mechanosensitive machinery linked to the actin cytoskeleton. Disruptions to β-actin, …


Phage Therapy: A Fresh Look At Last Century's Candidate For Fighting Bacteria, Savannah Del Cid Mar 2025

Phage Therapy: A Fresh Look At Last Century's Candidate For Fighting Bacteria, Savannah Del Cid

Osmosis Magazine

Humanity has fought infectious bacteria for ages, but it wasn't until recently that humans began to distil chemicals from nature to fight bacteria, which we know as antibiotics. At first, bacteria were easily treated with antibiotics, such as the well-known penicillin. However, the improper and overuse of antibiotics over the decades has created the perfect environment for mutated bacteria to thrive despite antibiotic treatments. This has become a major concern for doctors and patients because the need to utilize methods beyond the pharmaceutical has not become widely apparent until now.


Osmosis Magazine - Fall 2018 Mar 2025

Osmosis Magazine - Fall 2018

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.


Nucleoredoxin Regulates Wnt Signaling During Pituitary Stem Cell Differentiation, Michelle L. Brinkmeier, Leonard Y M Cheung, Sean P. O'Connell, Diana K. Gutierrez, Eve C. Rhoads, Sally A. Camper, Shannon W. Davis Mar 2025

Nucleoredoxin Regulates Wnt Signaling During Pituitary Stem Cell Differentiation, Michelle L. Brinkmeier, Leonard Y M Cheung, Sean P. O'Connell, Diana K. Gutierrez, Eve C. Rhoads, Sally A. Camper, Shannon W. Davis

Faculty Publications

Nucleoredoxin (Nxn) encodes a multi-functional enzyme with oxidoreductase activity that regulates many different signaling pathways and cellular processes in a redox-dependent manner. Rare NXN mutations are reported in individuals with recessive Robinow syndrome, which involves mesomelic skeletal dysplasia, short stature, craniofacial dysmorphisms, and incompletely penetrant heart and palate defects. Here we report that Nxn is expressed in the ventral diencephalon and developing pituitary gland, and that Nxn deficient mice have pituitary dysmorphology and craniofacial abnormalities that include defects in the skull base and cleft palate. Nxn mutant mice exhibit reduced WNT signaling and reduced differentiation of pituitary stem …


Scupa: Single-Cell Unified Polarization Assessment Of Immune Cells Using The Single-Cell Foundation Model, Wendao Liu, Zhongming Zhao Mar 2025

Scupa: Single-Cell Unified Polarization Assessment Of Immune Cells Using The Single-Cell Foundation Model, Wendao Liu, Zhongming Zhao

Faculty, Staff and Student Publications

MOTIVATION: Immune cells undergo cytokine-driven polarization in response to diverse stimuli, altering their transcriptional profiles and functional states. This dynamic process is central to immune responses in health and diseases, yet a systematic approach to assess cytokine-driven polarization in single-cell RNA sequencing data has been lacking.

RESULTS: To address this gap, we developed single-cell unified polarization assessment (Scupa), the first computational method for comprehensive immune cell polarization assessment. Scupa leverages data from the Immune Dictionary, which characterizes cytokine-driven polarization states across 14 immune cell types. By integrating cell embeddings from the single-cell foundation model Universal Cell Embeddings, Scupa effectively identifies …


Culturable Microbial Communities In Root Nodules Of Red Alder (Alnus Rubra Bong.) And Scotch Broom (Cytisus Scoparius L.): Patterns Of Diversity And Composition, Felisha (Fay) Rene Pooler Mar 2025

Culturable Microbial Communities In Root Nodules Of Red Alder (Alnus Rubra Bong.) And Scotch Broom (Cytisus Scoparius L.): Patterns Of Diversity And Composition, Felisha (Fay) Rene Pooler

Dissertations and Theses

Endophytes are a hyper diverse group of bacterial or fungal organisms residing within plant tissues without causing visible symptoms of disease. While their overall diversity and ecological functions are not well-understood, some endophytes can provide a range of important benefits to their host such as enhanced growth and increased tolerance to environmental stress. Nitrogen-fixing bacteria residing within nodules--specialized structures on the roots of legumes and actinorhizal plants--play an integral role in the plant microbiome by facilitating nitrogen availability in nutrient-poor environments. Remarkably, the patterns of diversity including both bacterial and fungal endophytes in root nodules are virtually known, except in …


5-Hydroxymethylcytosine Sequencing Of Plasma Cell-Free Dna Identifies Epigenomic Features In Prostate Cancer Patients Receiving Androgen Deprivation Therapies, Qianxia Li, Chiang-Ching Huang, Shane Huang, Yijun Tian, Jinyong Huang, Amirreza Bitaraf, Xiaowei Dong, Marja T. Nevalainen, Manishkumar Patel, Jodie Wong, Jingsong Zhang, Brandon J Manley, Jong Y. Park, Manish Kohli, Elizabeth M. Gore, Deepak Kilari, Liang Wang Mar 2025

5-Hydroxymethylcytosine Sequencing Of Plasma Cell-Free Dna Identifies Epigenomic Features In Prostate Cancer Patients Receiving Androgen Deprivation Therapies, Qianxia Li, Chiang-Ching Huang, Shane Huang, Yijun Tian, Jinyong Huang, Amirreza Bitaraf, Xiaowei Dong, Marja T. Nevalainen, Manishkumar Patel, Jodie Wong, Jingsong Zhang, Brandon J Manley, Jong Y. Park, Manish Kohli, Elizabeth M. Gore, Deepak Kilari, Liang Wang

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

BACKGROUND: We evaluated whether 5hmC signatures in cell-free DNA (cfDNA) are associated with treatment failure to androgen-deprivation therapies (ADT) among men with hormone-naive prostate cancer.

METHODS: We collected a total of 139 serial plasma samples from 55 prostate cancer patients receiving ADT at 3 time points including baseline (before initiating ADT, n = 55); 3 months (after initiating ADT, n = 55); and disease progression (n = 15) within 24 months or 24 months if no progression was detected (n = 14). We used selective chemical labeling sequencing to quantify 5hmC abundance across the genome and Kaplan-Meier analysis to assess …


Fusionpub, A Therapeutic Landscape Of Human Fusion Genes, Himansu Kumar, Abayomi Adegunlehin, Zikang Chen, Pora Kim Mar 2025

Fusionpub, A Therapeutic Landscape Of Human Fusion Genes, Himansu Kumar, Abayomi Adegunlehin, Zikang Chen, Pora Kim

Faculty, Staff and Student Publications

To advance the development of fusion protein-targeting therapeutics, it is crucial to understand how patients with fusion oncoproteins have been treated and what small molecules have been studied. To fill this gap, we developed FusionPub, a knowledgebase of the therapeutic landscape of human fusion genes. We searched PubMed abstracts for 107K human fusion genes with 14K drugs. We also searched PubMed abstracts for 18K human fusion proteins, considering all gene synonyms of individual partner genes with 14K drugs. After manual curation, we found 17 342 records from 9623 PubMed abstracts. For these fusion genes and drugs, we provide a summary …


Addressing Health Disparities In Hematologic Malignancies: From Genes To Outreach, Christopher R Flowers, Rachel W Anantha, Veronica Leautaud, Pinkal Desai, Chancellor E Donald, Michelle A T Hildebrandt, Jean L Koff, Rulla M Tamimi, Wendy Cozen, Chijioke Nze, Ari M Melnick Mar 2025

Addressing Health Disparities In Hematologic Malignancies: From Genes To Outreach, Christopher R Flowers, Rachel W Anantha, Veronica Leautaud, Pinkal Desai, Chancellor E Donald, Michelle A T Hildebrandt, Jean L Koff, Rulla M Tamimi, Wendy Cozen, Chijioke Nze, Ari M Melnick

Faculty, Staff and Student Publications

This review underscores our shared responsibility to champion multidimensional strategies rooted in basic and translational science, community involvement, and societal responsiveness for a meaningful impact. Unifying themes include the need to enhance collaborative infrastructure to engage laboratory researchers, epidemiologists, data scientists, clinicians, patients, community leaders, and policymakers; patient-level support services; outreach, education, and navigation for patients at the community level; recruitment and retention of underrepresented groups in the healthcare and research workforce; and funding for these efforts.


Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Hao Min Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss Mar 2025

Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Hao Min Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss

Faculty Publications

Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 in Caenorhabditis elegans, increases the growth of spontaneously regenerating axons. Inhibition of G3BP1 by expression of its acidic or “B-domain” accelerates axon regeneration after nerve injury, bringing a potential therapeutic strategy for peripheral nerve repair. Here, we asked whether G3BP1 inhibition is a viable strategy to promote regeneration in injured mammalian central nervous system (CNS) where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in the transected spinal cord provided with a permissive peripheral nerve graft (PNG) as well as in …


Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Haomin Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss Mar 2025

Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Haomin Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss

Faculty Publications

Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 in Caenorhabditis elegans, increases the growth of spontaneously regenerating axons. Inhibition of G3BP1 by expression of its acidic or “B-domain” accelerates axon regeneration after nerve injury, bringing a potential therapeutic strategy for peripheral nerve repair. Here, we asked whether G3BP1 inhibition is a viable strategy to promote regeneration in injured mammalian central nervous system (CNS) where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in the transected spinal cord provided with a permissive peripheral nerve graft (PNG) as well as …