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Advancing Peptide-Based Vaccines Against Candida: A Comparative Perspective On Liposomal And Synthetic Formulations, Hong Xin

School of Graduate Studies Faculty Publications

The growing threat of multidrug-resistant fungal pathogens, especially Candida auris, has underscored the need for effective antifungal vaccines. This commentary highlights recent advances in peptide-based vaccination using the SNAP (Spontaneous Nanoliposome Antigen Presentation) platform, focusing on the FM-SNAP vaccine, a bivalent liposomal formulation targeting the surface-expressed peptides fructose bisphosphate aldolase (Fba) and methionine synthase (Met6). Compared to earlier constructs such as MP12, FM-SNAP achieves superior immunogenicity and long-lasting protection at lower antigen doses. It elicits balanced Th1/Th2 cytokine responses and demonstrates durable efficacy in both immunocompetent and complement-deficient mouse models. The platform's compatibility with clinically approved adjuvants (MPLA and QS-21), …

Mhc Gene Analysis And Immune Variation In Lepidodactylus Lugubris (The Mourning Gecko), Helen T. Vu

2025 Fall Honors Capstones Projects - Archive

The major histocompatibility complex (MHC) plays a central role in vertebrate immune defense by enabling pathogen recognition and initiating adaptive immune responses. While MHC diversity has been extensively studied in sexually reproducing species, comparatively little is known about its evolution in asexual lineages. The parthenogenetic gecko Lepidodactylus lugubris provides a unique opportunity to investigate how clonality and hybrid origins influence immune gene diversity. By leveraging whole-genome data, this study overcomes the limitations of previous transcriptome-based analyses and provides a more comprehensive view of MHC diversity in a clonal vertebrate. As the first step towards understanding MHC evolution in parthenogenetic lizards, …

Use Of Modified Z-Domain Peptides To Specifically Label The Constant Region Of Immunoglobulin G And Vegf, Madeline Allen

Department of Chemistry: Dissertations, Theses, and Student Research

Antibodies are increasingly being used in medicinal therapies due to their ability to specifically bind to a target antigen. This fundamental behavior of antibodies has been used as a key component in drug development to address common problems with traditional drug molecules such as off-targeting, fast drug clearance, and low efficacy. This thesis provides some background into how antibodies can be used as potential treatments for a few diseases. Chapter 1 begins with an overview of the human immune system, and the role antibodies play within it. Then, the variety of ways in which antibodies can be used as medicinal …

Ybx1-Mediated Activation Of Srebp2 Drives Sorafenib Resistance Via Cholesterol Biosynthesis In Hepatocellular Carcinoma, Veerababu Nagati, Dennis Kwabiah, Yamile Abuchard, Ana Ayala Pazzi, Shaibir Hussain, Salique H. Shaham, Manish Tripathi

Research Colloquium

Background: Hepatocellular carcinoma (HCC) is an aggressive, largely chemo-resistant cancer with a poor prognosis and is the leading cause of cancer-related deaths worldwide. Currently, there is no effective systemic chemotherapy for HCC. Sorafenib is a multikinase inhibitor commonly used as the first-line treatment for advanced HCC. However, acquired drug resistance significantly limits its clinical effectiveness. The Y-box binding protein (YBX1) is an oncogenic RNA-binding protein found to be upregulated in sorafenib-resistant HCC cells and tissues.

Methods: HCC model SK Hep1, YBX1 overexpression, and knockdown cells were prepared by transient transfection with puromycin selection, and stable cell lines were established through …

A Single-Dose Long-Lasting Live-Attenuated Chimeric Vaccine Candidate Against The Emerging Tick-Borne Kyasanur Forest Disease, Young-Min Lee

Funded Research Records

No abstract provided.

Clinical Applications Of Probiotics: A Comprehensive Review Of Benefits And Challenges, Riyam Wissam Hassan

Maaen Journal for Medical Sciences

Probiotics are beneficial microorganisms that help balance microbes in intestines and promote growth beneficial bacteria, they vary between bacteria, yeasts, and fungi and they are helpful to human health when taken in adequate and suitable amounts. In addition to maintaining intestinal health and help with digestion and absorption, also inhibiting development and preventing spread of harmful microorganisms. It exists in different forms, in the intestines and in the foods, products fermented, and in the pharmaceutical supplements. Because human health depends largely on the interaction between humans and these microorganisms known as probiotics, it has found that these organisms have vital …

Enhancing The Care Of Patients With Bone And Joint Infections Through Educational Interventions, Neel B. Shah, Jessica Seidelman, Katherine Belden, Elizabeth Thottacherry, Allison Lastinger, Priya Nori, Ronald M. Beaulieu, Don Bambino Geno Tai

Division of Infectious Diseases and Environmental Medicine Faculty Papers

Musculoskeletal infections represent a significant proportion of the clinical workload for infectious diseases (ID) providers, often presenting complex diagnostic and therapeutic challenges. Many providers may feel inadequately prepared to manage these conditions, which require a nuanced understanding of microbiology, musculoskeletal anatomy, surgical intervention, and orthopedic hardware. We implemented a pair of educational interventions including an online library of high-yield musculoskeletal ID literature and an educational podcast. © The Author(s) 2025. Published by Oxford University Press on behalf of Infectious Diseases Society of America.

Fisheries Occasional Publication No. 149 - Economic Contribution Of Wild-Catch Fishing In Western Australia, 2024: Beyond Gross Value Of Production, Dipesh Maharjan, Vilaphonh Xayavong, Ben Fraser, Rebecca Thomas

Fisheries Occasional Publications

The wild-catch fishing industry plays a significant role in Western Australia’s economy, particularly in regional communities. This report summarises the economic contribution of the commercial wild-catch fishing sector in 2024, based on REMPLAN’s input-output (I-O) modelling methodology and DPIRD data and analysis. This report focuses on key economic indicators including total economic output, gross value added (GVA), and employment (FTEs).

Key findings:

• Total Economic Output of the wild-catch fishing industry is $1.22 billion (total value of goods and services produced, including intermediate inputs)
• Gross Value Added (GVA) of the wild-catch fishing industry is $487 million (value of profit, wages, salaries …

Bmp Signaling Co-Regulation Of Immune Response And Lipid Metabolism, Katerina K. Yamamoto

Dissertations, Theses, and Capstone Projects

The Bone Morphogenetic Proteins (BMPs) are secreted peptide ligands of the Transforming Growth Factor beta (TGF-β) family, initially identified for their roles in development and differentiation across animal species. They are now increasingly recognized for their roles in physiology and infectious disease. In the nematode Caenorhabditis elegans, the BMP ligand DBL-1 controls fat metabolism and immune response, in addition to its roles in body size regulation and development. DBL-1 regulates classical aspects of innate immunity, including the induction of anti-microbial peptides. We theorized that BMP-dependent regulation of fat metabolism could also promote resilience against microbial pathogens. We found that …

Hubungan Karakteristik Kontak Erat Dengan Pengetahuan, Sikap, Dan Perilaku Pencegahan Tuberkulosis: Studi Potong Lintang Di Puskesmas Kenarilang, Alor, Nusa Tenggara Timur, Hanif Abadi, Ezra Maraben Lily

Jurnal Epidemiologi Kesehatan Indonesia

Indonesia ranks second globally in the number of tuberculosis (TB) cases, accounting for 10% of all global cases. In the working area of Kenarilang Public Health Center, 951 confirmed TB cases were recorded as of October 2024. Close contacts of TB patients are at high risk of infection and may become new sources of transmission if not properly managed. Knowledge, attitudes, and practices (KAP) among close contacts play a crucial role in TB prevention, aligning with the target of TB elimination by 2030. This study aims to determine the relationship between the characteristics of close contacts and their KAP levels …

Crossroads Of Covid-19 And Alzheimer’S: Investigating Sars-Cov-2 Nsp6 And Orf7a In Amyloid-Β42 Toxicity, Jeffrey William Huettemann, Amit Singh

Research from the Berry Summer Thesis Institute, 2025

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in several hundred million contracted cases of coronavirus disease 2019 (COVID-19) and a global pandemic. In some of these cases, previous neurological diseases, such as Alzheimer’s disease (AD), seemed to progress much more rapidly after the COVID-19 infection. Thus, we became interested in studying the effects of SARS-CoV-2 infection on prior neurological disease progressions.

To modulate this condition, we used Drosophila melanogaster as a genetic model system. We had previously developed the Alzheimer’s Disease Fly Model with expression of human amyloid beta 42 (Aβ42) peptide, which is responsible for extracellular Aβ-42 …

Host, Microbiome, And Parasite: How Apicomplexan Microorganisms Interact With Gut Microbiota, Senia Bu, Andrew T. Ozga

Mako: NSU Undergraduate Student Journal

The gut microbiome, a complex ecosystem of microorganisms residing in the human gastrointestinal tract, plays a crucial role in maintaining overall health. It functions in immune system regulation, digestion, and protection against pathogens. Apicomplexan parasites, such as Toxoplasma gondii, Plasmodium spp., and Cryptosporidium spp., are major pathogens that can significantly disrupt the gut microbiota, leading to alterations in microbial composition and function. This review explores the bidirectional interactions between Apicomplexan parasites and the gut microbiome, focusing on how these parasites influence microbial diversity, immune responses, and host metabolism. It examines the mechanisms by which infection-induced inflammation, altered …

Fabrication Of Protein-Based Nanomicelle Against Inflamed Synoviocytes In Rheumatoid Arthritis, Madhumithra Thangadurai

Theses and Dissertations

Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by persistent synovial inflammation, progressive cartilage and bone destruction, and systemic complications. 1% of the global population are affected by RA, when their immune system targets synovial tissues, leading to joint pain, swelling, and functional disability. Standard treatments, such as disease-modifying antirheumatic drugs (DMARDs) like methotrexate (MTX), are limited by systemic toxicity and inconsistent patient responses, highlighting the need for improved therapies. This research work explores protein-glycosaminoglycan nanomicelles engineered using Zein with Chondroitin or carboxymethylated Dextran Sulfate as targeted drug delivery vehicles for RA.

MTX was encapsulated within these nanomicelles to …

Histologic And Immune Characterization Of Cutaneous Immune-Related Adverse Events Induced By Immune Checkpoint Inhibitors, Omar Pacha, Anisha B Patel, Jonathan L Curry, Cara L Haymaker, Nejla Ozirmak Lermi, Dzifa Yawa Duose, Ken Chen, Joud Hajjar, Aung Naing

Faculty, Staff and Student Publications

Background: Although immune checkpoint inhibitors (ICIs) are efficacious, they often cause immune-related adverse events (irAEs), most commonly cutaneous irAEs (CirAEs). The mechanisms underlying CirAEs remain unclear.

Methods: Attempting to better understand their mechanisms and histology we conducted a prospective study of 15 patients with advanced cancers treated with ICIs who developed grade 2 or higher CirAEs. Clinical and histologic characterization of biopsy specimens of CirAEs was performed. Histologic analysis of patient biopsy specimens were subdivided by epidermal reaction patterns that included spongiotic, lichenoid, and interface dermatitis patterns. A targeted RNA expression assay was used to identify immune markers in CirAE …

In Vitro Assessment Of The Antihistomonal Activity Of Methyl Jasmonate And Jasmonic Acid, Mckayla B. Williams

Poultry Science Undergraduate Honors Theses

Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis in gallinaceous birds. There are currently no approved prevention or treatment options available for histomonosis control in the United States. Mortality in affected turkey flocks can exceed 80% which highlights the urgent need for research investigating novel strategies to mitigate histomonosis in the field. The objective of this study was to evaluate the in vitro antihistomonal and antibacterial effects of of methyl jasmonate (MeJA) and jasmonic acid (JA), two plant-derived compounds, in a xenic culture of H. meleagridis. Assays were conducted using cultured H. meleagridis (PHL strain) treated …

Analysis Of The Scleroderma / Systemic Sclerosis Etiopathology Using The University Of California At Davis (Ucd)-Ssc Chicken Line, Angeline E. Rodriguez

Graduate Theses and Dissertations

Scleroderma/Systemic Sclerosis (SSc) is a multifaceted autoimmune disorder affecting approximately 300,000 people in the United States. Main features include vasculitis, immune dysfunction (innate and adaptive), autoantibody production, perivascular leukocyte infiltration, and extensive tissue fibrosis. The University of California, Davis (UCD) SSc chicken line was shown to exhibit all clinical and biological manifestations of human SSc. One early and distinctive clinical sign in both humans and UCD-SSc chickens is Raynaud’s phenomenon (RP), characterized by decreased blood flow in extremities and skin lesions. RP-like lesions develop in combs of UCD-SSc chickens within one- to two-weeks post-hatch, progressing from erythema and edema to …

Computational Frameworks To Unravel The Immune Landscape, Shan He

Dissertations and Theses (Open Access)

Recent advances in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, face challenges such as resistance and immune-related adverse events, partly due to our limited understanding of the immune signaling pathways. While high- throughput genomic data provide unprecedented resolution into these immune pathways, their full potential is limited by the lack of well-annotated, context-specific immune gene sets. To address this need, I developed a workflow to construct immune gene sets by integrating RNA- seq datasets and performing decomposition. Using this approach, I constructed 28 immune- specific gene sets from 83 bulk RNA-seq datasets and 12 Natural Killer (NK) …

Studies Of The Mechanisms Of Reverse Signaling By Cd40l, Barbara M. Nassif Rausseo

Dissertations and Theses (Open Access)

CD40 ligand (CD40L) is a transmembrane protein expressed on activated CD4 T cells, traditionally known for its role in forward signaling by engaging CD40 on antigen- presenting cells to promote immune activation. While this pathway is well characterized, there is evidence that CD40L also mediates reverse signaling, acting as a signaling receptor on T cells which enhances T cell function. However, the extent, consequences, and mechanism of CD40L-mediated reverse signaling in CD4 T cells remain poorly defined. This dissertation investigates the mechanisms and effects of CD40L reverse signaling on T cell function using both primary human T cells and the …

Orchestrated Architecture Dismantling: Borrelia Burgdorferi’S Coordinated Destruction Of Adaptive Immune Responses, Craig A. Land

Electronic Theses and Dissertations

Borrelia burgdorferi represents the most prevalent vector-borne bacteria in North America, affecting ~476,000 Americans annually yet persisting despite robust immune responses. This project reveals spirochetes target adaptive immunity through coordinated lymphatic colonization and precision immune dysregulation.

Using comparative host models (C57BL/6 vs. reservoir Peromyscus leucopus), we demonstrate lymph node colonization within 48-hours, with spirochetes exploiting LYVE-1-positive lymphatic structures as dissemination highways while avoiding the interior of follicular regions. Critically, we identify targeted CD4+ T-cell elimination in germinal center border zones at 21-DPI, precisely when these cells should be coordinating protective immunity. Concurrent upregulation of inhibitory receptor CD32b creates molecular …

A Multicomponent Microneedle Patch For The Delivery Of Meloxicam For Veterinary Applications, Katherine Alejandra Miranda Munoz

Graduate Theses and Dissertations

Veterinary medicine requires innovative drug delivery strategies to enhance therapeutic efficacy while minimizing stress and handling. This dissertation explores the development and application of biodegradable microneedle patches for the transdermal delivery of meloxicam in livestock, offering a minimally invasive alternative to traditional administration methods. The research investigates the fabrication and characterization of microneedles using polyvinyl alcohol, collagen, and chitosan blends, demonstrating their mechanical strength, biocompatibility, and ability to facilitate sustained drug release. In vitro and in vivo evaluations confirm effective skin penetration, dissolution, and localized drug delivery. Pharmacokinetic studies highlight anatomical site-dependent variations in drug absorption, emphasizing the need for …

Ppp2r1a Mutations Portend Improved Survival After Cancer Immunotherapy, Yibo Dai, Anne Knisely, Mitsutake Yano, Minghao Dang, Emily M Hinchcliff, Sanghoon Lee, Annalyn Welp, Manoj Chelvanambi, Matthew Lastrapes, Heng Liu, Zhe Yuan, Chen Wang, Hao Nie, Stephanie Jean, Luis J Montaner, Jiakai Hou, Ami Patel, Shrina Patel, Bryan Fellman, Ying Yuan, Baohua Sun, Renganayaki Krishna Pandurengan, Edwin Roger Parra Cuentas, Joseph Celestino, Yan Liu, Jinsong Liu, R Tyler Hillman, Shannon N Westin, Anil K Sood, Pamela T Soliman, Aaron Shafer, Larissa A Meyer, David M Gershenson, David Vining, Dhakshinamoorthy Ganeshan, Karen Lu, Jennifer A Wargo, Weiyi Peng, Rugang Zhang, Linghua Wang, Amir A Jazaeri

Faculty, Staff and Student Publications

Immune checkpoint blockade (ICB) therapy is effective against many cancers, although resistance remains a major issue and new strategies are needed to improve clinical outcomes1-5. Here we studied ICB response in a cohort of patients with ovarian clear cell carcinoma-a cancer type that poses considerable clinical challenges and lacks effective therapies6-8. We observed significantly prolonged overall survival and progression-free survival in patients with tumours with PPP2R1A mutations. Importantly, our findings were validated in additional ICB-treated patient cohorts across multiple cancer types. Translational analyses from tumour biopsies demonstrated enhanced IFNγ signalling, and the presence of tertiary lymphoid structures at the baseline, …

Adiponectin-Regulated Macrophage Responses In Aspergillus Fumigatus Infection: Mechanisms Of Uptake And Killing, Sri Harshini Goli

All-Inclusive List of Electronic Theses and Dissertations

Invasive aspergillosis (IA), caused by Aspergillus fumigatus, is a life-threatening infection in immunocompromised individuals, necessitating novel host-directed therapies. Macrophages are pivotal in antifungal defense, yet their function can be dysregulated; the influence of the adipokine adiponectin (APN) on this process is not fully understood. This thesis investigated the role of APN signaling in alveolar macrophage (AM) and bone marrow-derived macrophage (BMDM) responses to A. fumigatus and assessed the therapeutic potential of the APN receptor agonist, AdipoRon. Initial studies revealed that genetic deficiency in APN or its receptors renders AMs intrinsically pro-inflammatory and significantly impaired fungicidal activity against A. fumigatus. Subsequent …

The Inside Scoop: Elucidating The Three-Way Relationship Between Schistosoma Mansoni, The Gut, And Vaccines, Mariam A. Mhanna

Biomedical Sciences Theses & Dissertations

Schistosomiasis is a neglected tropical disease that affects over 250 million people worldwide. This blood fluke infection burdens communities and areas with limited to no access to clean fresh water. When a host is exposed to cercariae, the infectious agent, in a body of water, it matures in the host’s circulation into adult female and male worms. Copulated adult worms migrate to the mesentery, in the case of Schistosoma mansoni, and produce eggs that can cross the intestinal barrier and get excreted in the feces to continue the lifecycle. The effects of S. mansoni infection on the host …

In Silico Prediction Of Cytotoxic T-Cell Epitopes From Helicobacter Pylori Virulence Factors Using An Immunoinformatics Approach, Demy Valerie Chacon, Kiana Alika Co, Daphne Noreen Enriquez, Aubrey Love Labarda, Reanne Eden Manongsong, Edward Kevin B. Bragais

Biology Faculty Publications

Background: Helicobacter pylori infects approximately half of the global population, leading to gastric and duodenal ulcers. Despite the availability of antibiotics, challenges such as patient reluctance, high treatment costs, and antibiotic resistance limit their effectiveness, making vaccination a promising alternative. This study used immunoinformatics to identify candidate epitopes for a multiepitope vaccine construct against H. pylori.

Material and methods: The protein variability server was utilized for conservation analysis. The epitopes were screened for antigenicity, allergenicity, toxicity, cross-reactivity, and population coverage. Selected epitopes were docked with their corresponding human leukocyte antigen (HLA) alleles, and thermodynamic quantities were determined. Five virulence …

Ecoimmunology Of Dirty Physella Acuta Snails, Kevin Arthur Mcquirk

Biology ETDs

Research on Physella acuta, an invasive freshwater snail, reveals insights into its parasitology, fitness, and molecular biology. Morphological and molecular analyses revealed two distinct mitogenomic lineages, local (B) and invasive (A) strains of native P. acuta, both having comparable trematode infection rates, suggesting that the low infection rates observed from A in invaded regions result from "enemy release" rather than immune incompatibility. Fitness assessments showed that while lineages A and B performed similarly under laboratory conditions, rewilding experiments revealed significantly higher fitness in lineage A. Transcriptomic profiling supported these differences, with A snails showing greater immune-related gene expression and …

Exploration, Expansion, And Optimization Of Bacteriophage Virus-Like Particle Vaccines, Andzoa N. Jamus

Biomedical Sciences ETDs

Bacteriophage virus-like particles are highly immunogenic, self-assembling platforms used for various vaccines. This work shows efforts to explore new vaccine candidates against Chlamydia trachomatis, targeting proteins that play critical roles in attachment and entry into the host cell, as well as in pathogenesis and bacteria proliferation. This work also shows the optimization of previously identified candidates, by investigating how altering routes of immunization can change the antibody profiles elicited, both systemically and locally. Finally, this work shows the establishment of various Chlamydia infection models in an effort to expand the ways in which vaccine efficacy can be investigated, particularly …

Immune Regulation In Fungal Airway Inflammation And Host Defense, Ruoning Wang

Biomedical Sciences ETDs

Asthma is a chronic inflammatory disease of the lungs characterized by complex pathophysiological mechanisms and diverse endotypes, primarily categorized as T helper type 2 cell (Th2)-high and Th2-low asthma. Despite significant advances in understanding asthma pathogenesis, the mechanisms governing the pulmonary immune system’s response to external challenges have not been fully understood. To address these gaps, this comprehensive project was designed to investigate the interplay between fungal infections and specific CD4⁺ T cell populations in asthma. Our findings suggest that fungal infections can contribute to neutrophilic asthma by promoting the migration of platelet-myeloid aggregates into the lungs. We also …

Exploring Immune System Through Computational Modeling: A Comprehensive Study Of Lymph Nodes And Immune Response Scaling, Vaccine Efficacy, And Large-Scale Extreme First Passage Time, Jannatul Ferdous

Computer Science ETDs

The adaptive immune response is a complex defense mechanism that develops over time to recognize and eliminate pathogens with remarkable precision and durability. This dissertation investigates the dynamics, scaling, and efficiency of the adaptive immune response through a synthesis of computational modeling, mathematical analysis, and agent-based simulations. First, we analyze the topology of the lymphatic network and investigate the T cell search time to find the lymph node that is containing the matching dendritic cell. Second we show how the scaling of lymph node number and volume with body mass, leads to scale-invariant search times for T cells locating antigen-bearing …

A New Species Of Viscachataenia (Cestoda: Anoplocephalidae) From The Southern Mountain Viscacha, Lagidium Viscacia (Hystricomorpha: Chinchillidae), In Bolivia, Terry R. Haverkost, Scott L. Gardner

MANTER: Journal of Parasite Biodiversity

Anoplocephalid cestodes collected from the southern mountain viscacha, Lagidium viscacia, in Boliva in 1986 are here examined, and a new species of Viscachataenia is described. The new species has numerous body measurements that are larger than the existing species, V. quadrata, but the eggs and corresponding structures of the new species are all smaller than those of V. quadrata.

Feasibility Of Manufacturing And Antitumor Activity Of Til For Advanced Endometrial Cancers, Yongliang Zhang, Kathleen N Moore, Amir A Jazaeri, Judy Fang, Ilabahen Patel, Andrew Yuhas, Patrick Innamarato, Nathan Gilbert, Joseph W Dean, Behzad Damirchi, Joe Yglesias, Rongsu Qi, Michelle R Simpson-Abelson, Erwin Cammaart, Sean R R Hall, Hequn Yin

Faculty, Staff and Student Publications

Lifileucel, a tumor-infiltrating lymphocyte (TIL) cell therapy approved for advanced melanoma, demonstrates promise for treating other solid tumors, including endometrial cancer (EC). The current study evaluates the feasibility of manufacturing TILs from EC tumors using Iovance’s proprietary 22-day Gen2 manufacturing process. Key parameters, including TIL yield, viability, immune phenotype, T-cell receptor clonality, and cytotoxic activity, were assessed. Of the 11 EC tumor samples processed at research scale, 10 (91%) successfully generated >1 × 109 viable TIL cells, with a median yield of 1.1 × 1010 cells and a median viability of 82.8%. Of the four EC tumor samples processed at …