Duke University

NSF Awards · FY 2026 · 2026-08

Precise control of laser light is critical for many areas of science, including quantum computing with atoms and ions. Quantum computers could solve outstanding problems in material science, chemistry, and physics. However, in order to build useful quantum computers the research community needs several tools such as improved photonics devices that can be integrated into quantum computer prototypes. Some modern photonics devices for controlling laser light are already fabricated in the same facilities that are used to make silicon computer chips, leveraging nanometer-sized features on small silicon chips to control the propagation of light. Advances in this approach can lead to high performance devices in compact packages that could replace current bulky and fragile optics systems used for quantum computer prototypes today. One of the challenges is that quantum computing operations with atoms require both high power and precise laser frequency control. This project will evaluate the use of state-of-the-art photonic technologies for quantum computing with trapped ions. When successful, the integration of photonic devices could expand current quantum computers from 100 to 1000 qubits and enable transformative advances in science and engineering. This project involves students at all levels – from K-12 summer programs to community college internships. The research emphasizes interdisciplinary engineering, and the student involvement will expand quantum education and promote the field to the next generation of scientists and engineers. Thin-film lithium niobate (TFLN) offers high electro-optic nonlinearity and tight optical confinement, making it a strong candidate for miniaturized photonic components such as those needed for trapped ion quantum computing. However, its behavior under visible light — especially the photorefractive (PR) instabilities that can distort control signals — remains poorly understood and is a core focus of this research. This CAREER project explores the integration of TFLN photonic devices into quantum systems to enable compact, fast, and precise control of laser light. The three main research goals are: (1) understanding PR in TFLN, (2) assessing its impact on ion-based quantum control, and (3) building the first trap-integrated TFLN modulator. The research goals address a critical challenge in scaling trapped-ion quantum computers by integrating optical modulators directly into surface electrode ion traps using TFLN, an emerging and highly promising photonic platform. This approach leverages the ability to fabricate trap electrodes directly atop lithium niobate modulators, offering a compact and potentially scalable solution. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2026 · 2026-07

The vision of quantum information science and technology (QIST) is to process information with quantum interactions, performing computational logic with improved efficiency via the unique non-local correlations---entanglement---permeating many-body quantum systems. As such, entanglement is a critical resource for all applications of quantum devices, promoting them to be exponentially more complex than the sum of their individual parts. While the technology of quantum computing is rapidly progressing, practical insight into correspondingly large-scale entanglement has remained challenging, especially in the context of more than a few qubits (or qudits, modes, etc.) and in the presence of realistic noisy experimental environments. This program responds to this challenge by leveraging quantum fields as a guide to new theory and calculation techniques that specifically focus on the scalable entanglement structures found in our fundamental descriptions of the particles and forces of Nature. Beyond critical resource characterization, this research is positioned to connect with distributed quantum sensing, to impact our designs of quantum simulations relevant to collider experiments, and to guide hardware specifications of modular quantum architectures for scientific applications in subatomic physics. The study of mixed-state entanglement structure between detectors at spacelike separations in the free scalar field vacuum has introduced new computational tools to the many-body QIST toolbox, e.g., improving quantification of entanglement distribution requirements in quantum simulations and determining optimal entanglement sensing protocols. This program extends the partnership between fields and many-body entanglement insights by considering more complex field states: interacting vacuums with and without local symmetries, those inherent in current quantum computational architectures, and the real-time evolution of key dynamical processes. Capturing the interplay of quantum correlations in these directions will leverage non-Gaussian techniques and tensor networks with carefully controlled computational precision. In doing so, this program aims to discover new properties of many-body quantum information along our path to entanglement-informed design of quantum field simulations. Students involved in the research program will advance our ability to simultaneously think abstractly in the mathematical foundations of quantum information and think physically in collaboration with natural entanglement to codesign quantum simulations at scales relevant to the next decade and future of quantum technology. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2026-06

ABSTRACT Optimizing the safe and effective use of therapeutics in pregnancy and childhood is a critical public health need. These populations have historically been understudied in clinical research and lack evidence-based dosing guidance for most therapeutics. The Integrated National Network for Obstetric and Pediatric AdVAncement in Therapeutic Education (INNOVATE) T32 program will directly address this gap through specialized training in obstetric and pediatric clinical pharmacology. The program will offer a rigorous, interdisciplinary research training experience anchored in three core scientific domains relevant to obstetric and pediatric clinical pharmacology: 1) Pharmacokinetics/Pharmacodynamics and Clinical Trials, 2) Pharmacoepidemiology and Data Science, and 3) Translational Research. The INNOVATE T32 Program will leverage existing training opportunities through the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Clinical Pharmacology Training Network (CPTN), and will capitalize on the robust infrastructure, expertise, and collaborative environment across four outstanding institutions: Duke University, Indiana University, University of North Carolina at Chapel Hill, and the University of Utah. The national scope of the program enhances its impact by fostering cross-institutional collaboration, peer learning, and access to unique research environments. The program will also utilize the extensive research and training resources available through the Pediatric Trials Network (PTN) and the Maternal and Pediatric Precision in Therapeutics (MPRINT) Hub, providing trainees with unparalleled access to cutting-edge data, tools, and multidisciplinary mentorship. We anticipate supporting four post-doctoral fellows each year, with each fellow receiving two years of funding through the program. Each post- doctoral fellow will develop a research project under the guidance of accomplished faculty mentors, while also engaging in structured career development activities to support their growth as independent investigators. The training of each fellow will be guided by an Individual Development Plan. The post-doctoral fellows will participate in the monthly INNOVATE Forum, a virtual platform that promotes peer interaction, professional development, and focused discussions on topics such as scientific rigor, reproducibility, and responsible conduct of research. Didactic and experiential learning will be complemented by individualized mentorship, interdisciplinary exposure, and frequent evaluation to ensure progress. Program outcomes and effectiveness will be continuously monitored and refined with input from an External Advisory Board composed of national leaders in pediatric and obstetric therapeutics, clinical pharmacology, and regulatory science. Through the completion of a robust research project and structured mentorship, the INNOVATE T32 program will prepare post-doctoral fellows to pursue impactful careers focused on advancing therapeutic development and precision dosing in pregnancy and childhood.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY. Introduction: RNA editing introduces nucleotide base substitutions post- transcriptionally, expanding the transcriptome and proteome without the need for additional gene programs. RNA editing relies on precise, spatiotemporal interactions between RNA-editing enzymes and RNA substrates, yet the features of RNA that guide these interactions, and the impact of editing events on protein-RNA interactions, remain poorly understood. In this proposal, I will examine how RNA sequence and structure establish RNA editing sites, and how RNA editing changes RNA sequence and structure to tune RNA-protein interactions within the cell. I hypothesize that RNA editing tailors RNA-protein interactions to drive local protein synthesis. Research: In Aim 1, I will identify novel sites of RNA editing across the transcriptome of the giant, single cell, Physarum polycephalum. I will examine the RNA structures and sequences associated with these sites of modification and implement a machine learning approach to predict new sites of RNA editing that will have general applications beyond Physarum. In Aim 2, I will quantitatively assess the spatial organization of RNA editing, and how these events alter the composition and function of protein-RNA assemblies to drive changes in local protein synthesis. The overall outcome will be a mechanistic understanding of how cells govern RNA editing, and the role of RNA editing in organizing the cytoplasm. Training: I will complete my training with Prof. Amy Gladfelter at Duke University. During the training period, I will work with innovative collaborators to acquire new skills that will enable me to identify RNA editing across the genome using bioinformatics, probe and manipulate RNA structure, and implement machine learning approaches for the prediction of novel editing sites. These skillsets will accelerate discovery during the remainder of my training and form the core expertise of my independent lab. Specifically, I will learn powerful strategies to (1) identify signatures of RNA within sequencing data with Fred Dietrich at Duke University: (2) map RNA structure with Alain Laederach at UNC Chapel Hill; and (3) develop machine learning approaches for novel RNA editing site prediction with Rohit Singh at Duke University. Environment: Prof. Gladfelter is a supportive and inspiring mentor who fosters creativity and collaboration. Duke university, and the greater Research Triangle in which it is a part, is a hub for world-class RNA biology and will provide valuable opportunities to learn from experienced scientists. This K99/R00 award will enable me to pursue exciting new research directions beyond my core skillsets, form strong collaborations with leading labs, and immerse myself in new disciplines through a variety of courses, seminars, workshops, and conferences. Impact on Public Health: RNA-based technologies have gained attention as emerging genetic therapies due to their ability to modify the transcriptome without altering the genome. My work aims to uncover fundamental mechanisms of RNA editing and identify novel editing strategies. Through my work, I hope to aid in the development of RNA editing therapies and clinical interventions for genetic disease that result from Single-Nucleotide-Polymorphisms.

NIH Research Projects · FY 2026 · 2026-06

.PROJECT SUMMARY—NEWGARD/ZHANG ./ Over the past 20 years, our laboratory has used tools available in the Duke Molecular Physiology Institute (DMPI) metabolomics core laboratory to identify strong associations between branched-chain amino acids (BCAA) and a cluster of related metabolites with chronic cardiometabolic diseases. In part through our studies, it is now well- established that BCAA and related metabolites are predictive of incident diabetes and intervention outcomes and highly responsive to therapeutic interventions. Our mechanistic studies in animal models have established causal connections between BCAA and disease-related phenotypes such as insulin resistance, hepatic steatosis, and cardiac protein synthesis. The current proposal is based on a set of recent discoveries in this realm that provide novelty, innovation, and translational relevance for our work: 1) We found that largely unrecognized intermediates in the BCAA catabolic pathway, the branched-chain hydroxyacids (BCHA), are generated from branched-chain ketoacids (BCKA) in skeletal muscle via the action of an NADH-requiring dehydrogenase activity, and then shuttled to the liver where they are reconverted to BCKA to engage with branched-chain ketoacid dehydrogenase (BCKDH). 2) Using a stable isotope labeled BCHA, [U-13C] 2-OHIV, we determined that BCHA catabolism to distal mitochondrial metabolites is higher in livers of female compared to male rats; 3) We have identified two enzymes in liver capable of catalyzing the BCHA to BCKA reaction that are distinct from the enzyme that catalyzes BCKA to BCHA in muscle, with one of these having dramatically different activities in male compared to female livers, possibly explaining the enhanced propensity for BCHA catabolism in females; 4) The rate of BCHA catabolism in female rats links to increases in hepatic threonine (Thr) levels and lowering of liver fat relative to male rats. We propose that BCHA catabolism, Thr, and liver fat are linked by the Thr catabolic product 2-ketobutryate (2-KB), an alternate BCDKH substrate, and by an anti- steatotic effect of Thr. On this backdrop of new findings, we propose the following specific aims: 1) To investigate the impact of sex, genetics, and nutritional status on regulation of lipid and BCAA metabolism in the liver; 2) To investigate the mechanism(s) underlying preferential hepatic catabolism of BCHA in female animals; 3) To investigate sex-dependent regulatory links between Thr, BCHA metabolism, and liver fat. This work will define mechanisms connecting sex-dependent differences in BCAA catabolism with metabolic disease risk, thereby contributing to development of new therapeutic strategies to benefit both sexes.

NSF Awards · FY 2026 · 2026-06

Across the tree of life, cells are able to sort and deliver protein components to the appropriate cell locations, thus ensuring healthy biological function and development. In large cells such as developing oocytes and neurons, the transport of proteins such as messenger RNA (mRNA) is especially important in controlling how genes express in space and time, with defects often leading to neurological and developmental dysfunctions. While microscopy and imaging experiments of these proteins have undergone significant advances, the mathematical theory and quantitative methods for interpreting this complex experimental data are lacking. This project aims to establish a rigorous mathematical framework for analyzing complex data from living cells and for learning mechanisms of mRNA transport and organization. The project will advance dynamical systems and data-driven modeling techniques with the goal of testing biological hypotheses and making predictions about the dynamics of proteins in living cells. In addition, the project will improve the training of students interested in interdisciplinary research by incorporating regional undergraduates in summer and semester research projects. A network of local mathematical modeling competitions will also engage mathematics and STEM students and make instructional resources more accessible. This research aims to establish a framework for inferring underlying protein dynamics from microscopy images and for predicting mechanisms that govern the spatio-temporal organization of mRNA in cells. Challenges include the limited spatial resolution of experiments performed in living cells and difficulties associated with coupling the relevant timescales of protein cargo and filament dynamics. The project will build new reaction-diffusion mathematical models for the interaction of mRNA and binding proteins in biomolecular condensates, which package the RNA in healthy transport and development. Novel parameter inference and identifiability techniques will be developed to connect these models with microscopy data. Methods from pattern formation and stochastic modeling will be leveraged to investigate the formation of protein assemblies and their heterogeneity. In addition, the interaction of mRNA and cytoskeleton filaments will be investigated using state-switching models, informed by machine learning and model selection techniques. From the standpoint of biotechnology, the project studies the formation of RNA complex and develops machine-learning-based computational tools that includes spatio-temporal information for accurate understanding of dynamic biological systems. These advances have the potential to impact our biological understanding of embryonic patterning and development, with implications for neurological function and disorders. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2026-06

Abstract Pancreas Ductal AdenoCarcinoma (PDAC) is a highly lethal cancer and progress towards improving patient outcomes over the past decade has been limited. Early detection and surgery to remove early-stage PDAC before it has spread beyond the pancreas is the only treatment with the potential to yield long-term patient survival. However, resecting PDAC tumors requires a highly morbid surgery that can limit or delay other forms of treatment if the disease recurs, thus identifying the patients most appropriate for surgery is critical. The current clinical approach of using imaging features and the CA19-9 blood test is insufficient, as evidenced by the fact that the majority of patients eligible for curative resection experience disease recurrence and will succumb to their disease within five years. We propose that occult residual disease, either present at the surgical margin or circulating in patient blood, could predict a patient’s risk of PDAC recurrence after surgery. Nearly all PDAC tumors have an oncogenic point mutation in the gene KRAS, which demarks a cell in PDAC patients as being derived from their tumor. However, screening for such mutations has been thwarted by the high error-rate of next generation sequencing. I therefore adopted ultrasensitive Maximum Depth Sequencing (MDS) to screen the diagnostic exon in KRAS for oncogenic mutations and now propose to develop this approach to screen patients eligible for curative resection for occult residual disease in three aims. In AIM 1 I will prospectively profile PDAC resection margins for occult tumor DNA via MDS and then monitor how this predicts patient recurrence risk at the surgical margin. In AIM 2 I will simultaneously profile blood at the time surgery of the same patients for the presence of circulating tumor DNA (ctDNA) by MDS and then evaluate the relationship between ctDNA and risk of metastatic recurrence. In AIM 3, I will multiplex MDS to simultaneously screen for the second most common mutations in PDAC, namely mutations in the tumor suppressor gene TP53, and evaluate the ability of the assay to increase specificity and clinical utility. Completion of these three aims will inform future approaches to identify those PDAC patients most likely to benefit from surgical resection and direct perioperative use of chemotherapy and radiation. The methodology developed by this proposal will provide the foundation for future research in early PDAC detection and use of targeted therapy for early-stage patients. Additionally, this project and associated mentorship team will provide an invaluable resource to help launch my future translational research program focused on improving the use of molecular profiling for PDAC patients.

NSF Awards · FY 2026 · 2026-06

It supports the Research Experiences for Undergraduates (REU) site in physics at the Triangle Universities Nuclear Laboratory (TUNL) and Duke University. TUNL is a research consortium consisting of four major universities in the North Carolina Triangle Area: Duke University, North Carolina Central University, North Carolina State University, and the University of North Carolina at Chapel Hill. The award will support twelve undergraduates for ten weeks of summer research on topics in nuclear and particle physics. Eight students will conduct research at TUNL, and the other four will spend part of their summer at CERN in Geneva, Switzerland working with the Duke high-energy physics group. Each student is assigned a faculty mentor and is integrated into a research group consisting of faculty, postdocs, graduate students, and other undergraduate students. In addition, the students have opportunities to visit the physics departments at the consortium universities to learn about the graduate programs at these institutions and to see the scope of research pursued in each department. Through the implementation of active research, seminars, lab tours, and discussion groups, the students are exposed to various aspects of nuclear and particle physics research and their connections to broader science areas. Lecture and seminar topics are chosen to emphasize the nuclear and particle physics research activities at TUNL and CERN, respectively. The students will have opportunities to interact with world-renowned physicists, learn about the most advanced theoretical concepts in the fields, and work with state-of-the-art technologies used in these research areas. Also, professional development activities in scientific writing and oral presentations constitute an important component of the REU program. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY The objective of this proposal is to investigate the ability of an injectable polypeptide scaffold to improve patient outcomes after peripheral nerve repair. Peripheral nerve injuries (PNI) affect >20 million people in the US alone, with $150 billion in healthcare costs annually, and are a cause of devastating functional disability and chronic pain in those affected. The gold-standard treatment for PNI is primary neurorrhaphy when a tension-free repair approach is feasible; otherwise, secondary options such as autografts, decellularized allografts, or nerve conduits are used. However, regardless of approach, only about half of patients achieve meaningful sensorimotor recovery and the majority of patients continue to experience chronic pain. Lack of success is generally attributed to a poor microenvironment for neuroregeneration which must simultaneously be able to provide neovascularization, low inflammation, cell infiltration, and successful neuroaxonal migration. Current treatment strategies fail to address all these needs. Motivated by this clear clinical need, we will investigate the applicability of partially ordered polypeptides (POPs) to improve outcomes after peripheral nerve repair. POPs are a unique platform of biomaterials that transition from an injectable liquid at room temperature to a physically crosslinked, porous network at body temperature. POPs are highly biocompatible, integrating into the surrounding tissue, initiating remodeling, cell infiltration, and vascularization. Further, their ability to phase transition under the action of body temperature, letting them be injected as a low-viscosity liquid, allows for easy handling and integration in the operating room, and their scalable manufacturing process means that POPs have the capability to be a clinically translatable product. Our central goal will be to demonstrate that POPs is uniquely suited to provide the needed mechanical support and well-vascularized microenvironment essential for successful neuroaxonal regeneration. Our strategy will include tailoring the POPs biomaterial formulation to have the correct porous microarchitecture, mechanical properties, and promotion of beneficial local signaling for peripheral nerve repair applications. We will then investigate the ability of POPs to augment outcomes following peripheral nerve repair in models of rat sciatic nerve injury. Functional and histological testing will be performed and compared to current gold-standard primary neurorrhaphy and commercially available products. If this proposal is successful, it will provide a strong foundation to commence large animal testing and begin scale-up for translation into clinical application. The improvement of surgical outcomes following peripheral nerve repair by application of POPs has the potential for a transformative impact for patients with peripheral nerve injuries by reducing long-term disability and chronic pain.

NIH Research Projects · FY 2026 · 2026-06

Project Summary/Abstract Modifiable multi-level determinants of head and neck cancer (HNC) outcomes have persisted for decades, and groups have differed in survival rates and outcomes. Unfortunately, most HNC studies have focused on individual-level factors to explain outcomes, and there has been a paucity of research to understand the complex, but modifiable multi-level determinants that underline HNC outcomes. To address this research gap and in direct response to PAR-25-095; the Ascertaining Multilevel drivers of hEad and Neck cancer-related health Disparities (AMEND) project will utilize a cellsto- society framework, and robust secondary, longitudinal, and linked datasets (SEERMedicare and SEER-Medicaid), to identify multi-level determinants of head and neck cancer (HNC) outcomes. Advanced statistical techniques will be employed to conduct these analyses, including highly novel, deep-learning, time-to-event causal survival models. To achieve the overall project objective, we will predict multi-level (individual sociodemographic, regional and geographic) determinants of HNC outcomes; use group-based trajectory modelling to map long-term population trajectories in HNC; and quantify the effect and relative contribution of modifiable upstream and downstream factors (e.g. smoking, alcohol and other lifestyle factors, stage of presentation, treatment modality, rural/urban residency) and time-to-event factors in overall and disease-specific mortality among patients with HNC. Importantly, knowledge from our study will provide scientific evidence to guide both policies and multi-level interventions to target drivers of HNC outcomes, which aligns with the administration’s promotion of healthy living, and the Healthy People 2030 objective of dismantling the impact of multilevel determinants of health outcomes.

NIH Research Projects · FY 2026 · 2026-06

ABSTRACT Noncoding genetic variation that alters gene regulation is of paramount importance for health, disease, and evolution. Diseases ranging in incidence from the most common to the most rare all have substantial risk associated with regulatory variation; and most of the genetic differences between closely related species are noncoding. Whole genome sequencing can directly identify that variation but to realize its potential to elucidate the genetic determinants of health and disease, will require accurate annotation of this noncoding variation for functionality. In coding sequence, the genetic code allows variants to be annotated to a rough hierarchy of likely functional effects and pathogenicity. In noncoding sequence such annotation is less clear. Perturbation assays, i.e., assays that modify genetic or epigenetic states and measure the effect of those perturbations on regulatory endpoints, offer a possible path to annotating noncoding variation. However, to fully leverage this data, novel and sophisticated statistical and machine learning approaches are required to extract useful information from those assays, to integrate that information across regulatory endpoints, and to extrapolate findings so that annotation of previously unobserved (unperturbed) variation in diverse cell types is possible. The goal of the Duke Prediction Center is to develop the analytic approaches and tools that will allow for the routine annotation of noncoding variation for functionality and ultimately pathogenicity. Aim 1 is to establish best practices in perturbation assay design and analysis. This will allow IGVF characterization centers design their experiments so that, when coupled with optimized analyses, the data produced will be maximally informative for subsequent predictive modeling. Aim 2 is to develop novel mechanistic machine learning approaches for predicting the functional effect of noncoding variation on function in diverse cell-types. Aim 3 is to identify noncoding genomic regions that are subject to functional constraint which will be leveraged in prioritizing variants for pathogenicity. The expected outcomes of this project will be (i) robust estimates of optimal experimental design parameters and recommendations for analysis tools and best practices for the various assays used within the IGVF consortium, (ii) predicted functional effects of observed variation to be shared through the IGVF variant/phenotype catalog as well as a state-of-the-art machine learning method (and associated tools) that can identify previously-unknown interactions among genomic variants, both observed and novel, and predict their functional impact in diverse cell types, and (iii) a list of regulatory elements subject to functional constraint shared through the IGVF variant/phenotype catalog and a principled prioritization framework (and associated tools) for interpreting variation within patient genomes for pathogenicity. Due to the considerable success of genetics, there are thousands of unknown regulatory causes of disease. Each of those causes is an opportunity to improve treatment, diagnostics, or prevention. This project will be a major advance towards unlocking that potential.

NIH Research Projects · FY 2026 · 2026-06

ABSTRACT Epidermis of the skin undergoes continuous self-renewal through a tightly regulated balance of keratinocyte proliferation and terminal differentiation. Disruption of this balance is characteristic of inflammatory skin disorders such a psoriasis, atopic dermatitis, and neutrophilic dermatoses. The etiologies of these skin disorders are complex and heterogeneous, as are the needs for treatments. Our long-term goal is to elucidate how dysregulation of K63-Ub-mediated signal transduction pathways in keratinocytes contribute to skin inflammation. Towards this end, our recent studies have focused on UBE2N, a ubiquitin conjugase that forms heterodimers with an essential noncatalytic partner, UBE2V1 or UBE2V2, to specifically catalyze K63-Ub of target proteins. We demonstrate that conditional knockout of Ube2n in mouse keratinocytes induces psoriasis- like inflammatory skin lesions with a raised and scaly appearance. Transcriptomic and histological analyses identified a diminished epidermal stem cell compartment, a thickened epidermal spinous layer, and an increased infiltration of myeloid-skewed immune cells. This is correlated with increased expressions of myeloid cell chemokines such as CXCL1 and CXCL2 and IL1 family cytokines in keratinocytes and infiltrating myeloid cells. Oral delivery of the small molecule inhibitor of IRAK1/4, common mediators of the IL1R and TLR signaling pathways, alleviated immune infiltration and epidermal defects of the mutant skin. These data highlight a key role for UBE2N in regulation of epidermal and cutaneous immune homeostasis. In line with these animal data, recent GWS studies demonstrate a causal association between UBE2V1 polymorphism and psoriasis. Together, these data support the hypothesis that UBE2N partners with UBE2V1 to restrain keratinocyte recruitment of myeloid cells through suppression of IL1 and CXCL1/2-mediated inflammatory crosstalk between keratinocytes and myeloid cells. We propose 3 specific aims to: 1) validate the importance of UBE2N catalytic function and the role of UBE2V1 in epidermal homeostasis and cutaneous immune homeostasis, 2) determine the contribution of the IL1 signaling pathway in UBE2N-null skin inflammation, and 3) assess the utility of CXCL1/2 receptor antagonists in mitigating neutrophilic dermatosis. We will utilize conditional genetic animal models along with the cutting-edge techniques of single cell transcriptomics and global proteomics to comprehensively analyze mechanistic aspects of UBE2N/UBE2V1-mediated K63-Ub in cutaneous inflammation and therapeutic targeting. Results of these studies will reveal novel mechanisms of epidermal and cutaneous immune homeostasis, as well as insights for therapeutic development.

NIH Research Projects · FY 2026 · 2026-06

Rod and cone photoreceptors are highly specialized cells responsible for transforming the information reaching the eyes in the form of photons into the language of neuronal activity. Human vision relies primarily on cones, which support high acuity color vision. It is commonly accepted that, like in all other placental mammals, human cones have a conventional morphological organization, including the presence of a single light-sensitive outer segment in each cell. However, our recent ultrastructural analysis of the human retina challenges this concept by revealing the presence of an entirely novel type of cone photoreceptors. We have found that a fraction of human cones contains two fully developed outer segments emanating from the same cell soma (inner segment). We tentatively term these cells “bicornuate cones”. Such a major original observation is rarely made in the mature field of human morphology, which calls to thoroughly characterize this novel type of photoreceptor cells. To propose to accomplish this task in two Specific Aims. In Aim 1, we will conduct high-resolution ultrastructural analysis of these cones using three-dimensional electron tomography. Of particular interest will be to determine the number of centrioles in the inner segment of these cones, which will point out the mechanism by which their “twin” outer segments are formed. In Aim 2, we will identify which visual pigments bicornuate cones express and determine the abundance and spatial distribution of these cells across the retina.

NIH Research Projects · FY 2026 · 2026-06

ABSTRACT Transposable elements (TEs) make up over half of the human genome and are increasingly recognized as key regulatory sequences of gene expression in development and disease. While cellular intrinsic transcriptional and epigenetic mechanisms controlling TE sequences are well-documented, whether and how TEs response to external microenvironmental signals, particularly mechanical forces, remains unexplored. This represents a critical gap in understanding both TE regulation and genome–environment interactions. Our preliminary data reveal that several TE families, including LTR7 from the primate-specific HERV-H family, function as Mechano-Response Enhancer Elements (MREEs) that regulate gene expression and human pluripotent stem cell fate in response to mechanical stimuli. Additional preliminary findings support our central hypothesis that TEs act as MREEs by modulating human genes and cell fate of human pluripotent stem cells through a mechanism at least partially governed by the key mechano-effector YAP, which regulates TEs’ local epigenetic activity and facilitates their long-range chromatin looping with target genes in response to mechanical changes. To test this model, we propose three specific aims: 1) determine how mechanical signals regulate the local chromatin activity of TE MREEs; 2) elucidate how mechanical cues mediate long-range chromatin interactions between TE MREEs and their distal target genes; 3) delineate the mechanism by which TE MREE modulating human embryonic stem cell fate. Our objective is to rigorously establish the novel concept that TEs function as MREEs, uncover their underlying molecular mechanisms, and assess their biological significance in regulating developmental genes and hESC fate. The expected outcome will not only shift the current paradigm of mechanobiology from protein- coding genes to non-coding regulatory elements such as TE but also improve our understanding of TE regulation and genome-environment interactions in health and disease.

NIH Research Projects · FY 2026 · 2026-05

Abstract The development of effective vaccines against complex pathogens like HIV-1 requires immunogens that elicit broadly neutralizing antibodies (bnAbs). Traditional vaccine development strategies, including live- attenuated or subunit vaccines, and newer approaches leveraging genomic data, have not consistently induced bnAbs against HIV-1. Challenges stem from the unique structural and functional properties of bnAbs, such as improbable somatic mutations, autoreactivity, and long heavy-chain complementarity determining region-3 (HCDR3) loops. While priming immunogens have shown promise in selecting bnAb precursors, the production of mature bnAbs remains elusive, even in models engineered to ensure the presence of the relevant B-cell receptors. Our preliminary findings highlight the critical role of the transition state between unbound and bound antibody-antigen interactions in determining HIV-1 neutralizing antibody affinities. These transient structural states, which influence affinity maturation, neutralization breadth, and viral evolution, are poorly understood. Current methodologies primarily focus on static structural determinants of binding, neglecting the dynamic encounter complexes and intermediates that govern antibody-antigen association. This proposal aims to elucidate the association transition states and related intermediates for V2 apex- and CD4- binding site-directed bnAbs. Using structural and kinetic analyses, we will determine how variations in HIV-1 Env influence these transition states and how bnAbs overcome association barriers posed by Env sequence diversity. By dissecting the residue-level processes involved in antibody-antigen association, we will identify critical factors driving bnAb maturation and viral escape mechanisms. Using this information and large affinity datasets based on antibody clone HIV-1 Envelope interactions, we will develop cutting edge artificial intelligence/machine learning models to design immunogens with favorable affinity gradients for maturing bnAbs. Our work will address significant gaps in the understanding of antibody-antigen association, transitioning from phenomenological models to precise structural definitions of these poorly understood states and will directly use this information to inform immunogen development.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT The development of broadly neutralizing HIV antibodies is a desired outcome for immunotherapies because these antibodies can protect against HIV infection. For broadly neutralizing antibodies (bnAbs) to be protective they must be made in large quantities by specialized B cells called plasma cells. In HIV infection, bnAbs only arise after years of chronic HIV infection as the result of long maturational pathways. Recapitulating this long, arduous process with a limited set of immunogens has been a central challenge in the development of medical countermeasures for HIV. Recently, we have shown progress in this area by inducing broad serum neutralization in mice in which the sequence of a precursor bnAb B cell clonal family has been knocked in. However, little is known about the conditions required for precursor bnAb B cells to evolve and develop into mature bnAb B cells that produce durable antibodies in the blood. Our progress in inducing bnAbs in a knockin mouse model now gives us a reproducible system to test hypotheses about how B cells develop to generate bnAbs in the blood. The overall goal of this grant is to use our reproducible system to elucidate the rules governing prolonged B cell evolution and plasma cell differentiation, both of which are critical components in the generation of neutralizing antibodies in the blood, but which remain poorly understood. We will use high- throughput antibody sequencing to recover antibody sequences of plasma cells from mice immunized with our regimen, produce a selection of these antibodies, and experimentally measure their capacity to neutralize various strains of HIV. This will allow us to determine which plasma cells are responsible for the total neutralization capacity found in the serum. We will also use sequencing to determine the critical evolutionary events that occur during the maturation of bnAbs to determine which immunogens were essential for selecting the specific mutations required for bnAbs to evolve broad neutralization activity. The evolution of bnAb B cells occurs in the germinal center prior to their differentiation into plasma cells. We will use the insight gained from our sequencing and experimental characterization of bnAb B cells to construct computational models of the germinal center. We will use computational analysis to estimate the strength in which mutations are selected by our immunogens and perform simulations using our computational models of the germinal center to test hypotheses about how bnAb maturation and plasma cell differentiation can be accelerated by altering characteristics of immunogens and regimens. Our work will provide insight into how HIV bnAbs develop which will help inform the design of HIV immunotherapies and countermeasures.

NIH Research Projects · FY 2026 · 2026-05

Project Abstract Proper recognition and disposal of aberrant RNA is essential for maintaining immune tolerance while enabling appropriate antiviral defense. This process is tightly regulated by RNA decay enzymes such as the 5′→3′ exonuclease XRN1, whose activity prevents the accumulation of immunostimulatory RNA species that can aberrantly activate RNA-sensing pathways like RIG-I and MDA5. Recent findings have uncovered an unexpected role for the cytosolic enzyme MESH1 in regulating nucleotide metabolism and immune responses to RNA. Originally identified as a metazoan homolog of the bacterial SpoT, MESH1 has been shown by us to degrade NADPH and promote ferroptosis. Our preliminary data now identify 3′-phosphoadenosine 5′- phosphate (PAP) as a novel, physiologically relevant substrate for MESH1. Furthermore, MESH1-deficient macrophages exhibit an exaggerated response to immunostimulatory RNA. One probable explanation is that PAP, a byproduct of cellular sulfation reactions, inhibits the XRN1, leading to the accumulation of immunostimulatory RNAs that aberrantly trigger antiviral signaling. We hypothesize that MESH1 is a critical PAP phosphatase that protects cells from PAP-induced dysregulation of RNA decay and inappropriate immune activation. To test this, we propose two aims: In Aim 1, we will biochemically and structurally define the PAP phosphatase activity of MESH1, including enzymatic kinetics, lithium sensitivity, and co-crystal structures with PAP. We will also compare MESH1 with BPNT1, the Golgi-associated, lithium-sensitive PAP phosphatase, to evaluate their relative capacities to regulate PAP levels in cellular compartments relevant to innate immune sensing. In Aim 2, we will assess how MESH1 and PAP metabolism influence the innate immune response to RNA-based danger signals, including viral infection and synthetic RNA ligands, using genetically modified cells. The work is highly innovative, revealing a previously unrecognized regulatory axis between nucleotide catabolism and innate immunity by forging cooperation among investigators with expertise in MESH1, RNA immunology, and virus-host interactions. The results will uncover a novel layer of immune control with broad implications for infection, inflammation, and autoimmunity, and may ultimately reveal MESH1 as a therapeutic target to enhance antiviral immunity.

NIH Research Projects · FY 2026 · 2026-05

Youth living with HIV (YLWH) experience mental health (MH) challenges that compromise their HIV care. Though the MH gap is well described, integrated MH service delivery to YLWH is rare, both in the United States (U.S.), and lower resourced settings. MH professionals are rarely available in HIV clinics and few youth are willing to engage in outside care. Interventions tailored to the needs of this population are scarce and critically needed. Streamlining the Sauti ya Vijana (SYV, The Voice of Youth) intervention offers a way to bridge the MH gap. SYV is a peer-led, group-based treatment designed with and for YLWH to address their self-reported MH challenges. SYV incorporates components of evidence-based psychotherapeutic models to address the needs youth described in formative interviews. Preliminary data estimated effects towards improved MH, antiretroviral therapy adherence, and a 10% greater increase in viral suppression in the intervention arm compared to standard of care. Our prior research shows similar levels of depressive symptoms among U.S. YLWH and a desire to bring this model to the U.S. context through reciprocal innovation (Dow, Pediatrics 2025). The central hypothesis is that the new integrated “i" SYV will be acceptable, feasible, and effective to improve virologic suppression and improve retention in care. The mechanism of change is that improved MH leads to better medication adherence, viral suppression, and care engagement. The rationale is twofold: 1) MH screening is being initiated in HIV clinical visits, but the MH treatment gap persists; 2) the iSYV stepped-care package could be an effective approach to support integrated MH care for YLWH. Evidence generated in the African context can be obtained more cost-efficiently and applied to inform solutions for American YLWH. The central hypothesis will be tested in a hybrid type-2 effectiveness-implementation trial. The first aim will leverage the Fit to Context Framework, using an iterative Designing for Dissemination and Sustainability approach. SYV peer-group leaders (PYL) with extensive experience delivering SYV will co-design the new iSYV package. The iSYV in-person sessions will be delivered by trained PYLs and be aligned to the Tanzanian differentiated care model: stable youth (those fully suppressed) attend clinic every 6 months; and unstable youth (those with HIV RNA > 50 copies/mL) attend enhanced adherence counseling monthly, similar to U.S. guidelines. Youth with symptoms of MH difficulties on screening (PHQ9-depression, GAD7-anxiety, Trauma-related stress) will join the unstable group. To support engagement between visits, iSYV will explore use of a mHealth gamification strategy. The second aim includes a pilot and a four-arm cluster randomized trial. A large U.S. based implementing partner, Elizabeth Glaser Pediatric AIDS Foundation (EGPAF) will support testing the iSYV care package. The third aim will evaluate implementation determinants and outcomes, including acceptability, feasibility, fidelity, and cost informed by the Consolidated Framework for Implementation Research. The proposal is significant because it is expected to help address the MH gap for YLWH with implications for HIV care in Tanzania as well as the U.S.

NIH Research Projects · FY 2026 · 2026-05

Summary Genetic studies implicate pathogenic missense mutations in the leucine-rich repeat kinase 2 (LRRK2) gene as a common cause of familial Parkinson's disease (PD). Independently, genome-wide association studies identify LRRK2 promoter variants important in idiopathic PD risk. LRRK2 protein signals within the endolysosomal system through phosphorylating Rab protein substrates, altering their function in different pathways and cell responses. Phosphorylation of the prominently expressed Rab10 substrate is absent in LRRK2 knockout mice, diminishes with LRRK2 kinase inhibition, and is upregulated with pathogenic LRRK2 mutations and LRRK2 activation. Genetic variants in non-coding regions in Rab10 are tied to Alzheimer's disease (AD) resilience, and pRab10 upregulation may be associated with tau aggregation in the brain. Post- mortem studies find most LRRK2 carriers harbor 3R/4R tauopathy and Aß changes, often with Lewy pathology. Evidence in models suggests LRRK2 signaling may promote α-synuclein and tau pathology and related inflammation responses. However, there is a paucity of data from humans related to the role of LRRK2 signaling in disease progression. The main goals of this application are to learn whether LRRK2 signaling changes in PD and AD predict disease severity, discover pathways tied to these changes, and how LRRK2 signaling changes in the brain manifest with progressive pathological depositions of α-synuclein and tau. To accomplish these goals, our work in the last decade has culminated in the development of ultra- sensitive single molecule array assays, capable of assessing, with great specificity and sensitivity, LRRK2 signaling in biobanked tissues and fluids. Our recent results, starting from cross-sections of PD patients and controls, suggest a possible association between high pRab10 levels and worse PD severity. Preliminary results in post-mortem brain tissues have identified possible aberrant pRab10 accumulations in PD and AD. Here we propose to fully leverage deeply phenotyped longitudinal cohorts of PD and AD patients, and neurologically normal controls, to measure LRRK2 signaling changes as they occur with disease progression, in both serum and CSF. These measures will provide some of the first well-powered insights into how LRRK2 signaling changes might predict disease outcomes. Whole blood transcriptomic profiles and genomic data will be interrogated for factors critical in driving LRRK2 signaling. In complement, pathologically staged PD and AD brain tissues will be analyzed for LRRK2 signaling changes, together with powerful mouse models that have predictable progressive tau and α-synuclein pathology. Through the proposed work, the first large-scale effort to understand LRRK2 signaling changes in the progression of PD and AD, we expect to uncover new pathobiological mechanisms that further implicate LRRK2 in idiopathic neurodegenerative diseases, and begin to define idiopathic patient populations more likely to benefit from LRRK2-targeted therapeutic approaches.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT Most patients with diabetes suffer from diabetic bladder dysfunction (DBD). Symptoms vary significantly, but the most common presentation is an overactive bladder (OAB). Mitigating OAB symptoms through strict glycemic control has proven to be clinically ineffective and there are no specialized therapies to treat OAB in patients with diabetes. Until the critical need for novel precision medicine therapies is met, the clinical challenge of treating DBD will continue to escalate. A key pathology contributing to OAB symptoms in patients with diabetes is hyperinnervation of afferent nerves in the bladder urothelia. Such hyperinnervation is attributed in part to an increase in nerve growth factor (NGF). Estrogens release NGF from urothelial cells and our preliminary data demonstrate that selective activation of the novel g-protein coupled estrogen receptor (GPER) also mediates urothelial NGF release. However, there is a significant gap in knowledge regarding how diabetes dysregulates these estrogen-dependent mechanisms. The overall objective of this proposal is to determine how diabetes impacts the development and progression of OAB mediated by estrogen-dependent mechanisms in the bladder and peripheral afferent nerves innervating the bladder. Preliminary data generated in the Akita mouse model of diabetes indicates that both estrogen deprivation and GPER antagonism prevent the development of OAB in diabetic mice. Further assessment revealed that estrogen deprivation not only prevented OAB, but also prevented afferent hyperinnervation of the urothelia. We therefore hypothesize diabetes increases estrogen-mediated NGF release via activation of urothelial GPER, which thereby promotes the growth of urothelia-innervating afferent peripheral nerves, increases pelvic nerve activity, and results in OAB. We will pursue two specific aims to test our hypothesis. Aim 1: Determine the impact of diabetes on estrogen-dependent second messenger systems responsible for urothelial NGF release. Aim 2: Determine precise mechanisms by which diabetes impacts estrogen-dependent innervation of afferent peripheral nerves to the bladder during the (a) development and (b) progression of diabetes-mediated OAB. Completion of these aims will identify novel therapeutic targets which have the potential to revolutionize the clinical management of OAB attributed to diabetes. This proposal represents the next step towards our long-term goal to develop precision medicine treatments for DBD.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY HIV-1 establishes life-long infection that requires continual antiretroviral therapy (ART) to suppress virus replication. Although long-acting ART promises to improve treatment adherence, a therapeutic countermeasure for suppressing HIV-1 infection without lifelong treatment is needed. This type of HIV cure strategy is called a functional cure. In preliminary studies, we designed a series of immunogens that elicit serum nAbs against heterologous viruses in macaques. The nAbs target the second variable region (V2) Apex on HIV-1 envelope, with binding orientations similar to known human V2 Apex broadly nAbs (bnAbs). This B cell targeting countermeasure is the main innovation of our study. Furthermore, we developed an integrase-deficient lentiviral vector (IDLV) that delivers the viral gag gene to elicit specific CD8 T cells. Induction of these CD8 T cells suppressed viremia to undetectable levels in macaques. Our conceptual innovation is to combine both successful countermeasures together to potently and durably control viremia. The objective of this study is to sustainably suppress HIV viremia by combining a CD8 T cell countermeasure that controls viremia with a B cell countermeasure that elicits neutralizing antibodies (nAb) that are active against many heterologous viruses. The proposal has three specific aims. First, to determine the immunogenicity of the combination T cell and V2 Apex nAb-inducing countermeasure in ART-suppressed, SHIV-infected macaques by comparing the neutralization breadth of serum and monoclonal Abs, as well as CD8 T cell cytokine production and inhibition of virus-infected cells among a mock-treated group, the countermeasure treated group, and previous groups of uninfected macaques. Second, to demonstrate sustained viral suppression without ART by the administration of the therapeutic countermeasure in chronically SHIV-infected macaques by assessing changes in CD4 T cells and virus nucleic acid over time following ART cessation. Mechanistic studies will be done in macaques to show CD8 T cell and V2 apex nAb contributions to viral suppression. Third, to determine the impact of ART on the frequency of V2 Apex-specific B cells in people living with HIV-1 (PLWH) using a 10X Genomics BEAM-seq sequencing and AI/ML approach to identify V2 Apex B cells in PLWH before and during ART. The impact of this study is that it will define a therapeutic countermeasure that can permanently suppress viremia, taking the first steps toward a functional cure for the nearly 40 million people currently living with HIV-1.

NIH Research Projects · FY 2026 · 2026-05

ABSTRACT Diffuse gliomas are the most common primary brain cancer in adults, with the most aggressive and common form glioblastoma (GBM) having a median survival of only 15 months. Despite advances, current clinical imaging protocols lack the precision to track microscopic tumor infiltration that later becomes recurrence. This can result in poorly defined treatment margins that do not address the full extent of the tumor and can compromise patient safety. Determining the precise site of future recurrence on preoperative imaging could allow improved treatments such as boosted radiation dose to regions at risk for recurrence. Deformable image registration (DIR) enables the alignment of longitudinal MRI scans to achieve this task, but existing DIR approaches suffer from limited accuracy and unreliable verification, hindering clinical adoption. This project aims to develop a verifiable and accurate DIR method for diffuse gliomas by incorporating AI-based blood vessel segmentation and bifurcation matching into a new high-precision DIR approach. I hypothesize that incorporating blood vessel bifurcations as stable anatomical markers into the registration process will permit sub-millimeter accuracy in non-linear image registration. This level of accuracy will permit refined and precise treatment margins and support advanced imaging methods to accurately track tumor growth over time. Using the hierarchical nature of blood vessel trees, I will establish correspondence between blood vessels segmented from pre-operative and post-recurrence MRI scans of the same GBM patient. The DIR method will synthesize these matching vessel points with image features extracted from multi-sequence MRI data to precisely describe the anatomical transformation that occurred between the scans. This can then be used to pinpoint the recurrence origin on the pre-operative time point, allowing for future treatments targeting this site. In addition to GBM, I will adapt and optimize the developed method for slower-growing, low-grade diffuse glioma cases. By quantifying the deformation between low-grade scans with accurate DIR, I can detect small changes in tumor size and shape that can indicate disease progression. I will compare this approach to visual observation to demonstrate its clinical utility. Finally, I will utilize the developed vessel-matching tools to establish the most comprehensive DIR accuracy baseline across diffuse glioma grades to date, supporting further algorithm development and clinical implementation. This research will provide robust, verifiable DIR methods tailored for GBM and low-grade diffuse gliomas, addressing a critical gap in neuro-oncology imaging. By improving registration accuracy, this project can improve the precision of GBM treatment planning, enhance recurrence detection, detect tumor progression, and ultimately improve patient outcomes.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT The association between alcohol misuse and suicide risk among youth has been widely established; however, how these two high-risk behaviors relate to one another in the short-term is relatively unexplored. Given that young adulthood is marked by precipitous rise in heavy drinking and STBs, understanding the proximal relationship between alcohol misuse and STBs is critical. Research examining risk for suicide and alcohol misuse has focused largely on long-term risk, with limited empirical investigations of short-term predictors of suicide or alcohol misuse among youth in vulnerable periods or the common mechanisms and contexts that may explain the relationship. Executive functioning (EF) deficits and interpersonal stressors are posited to be related to increased alcohol misuse and STBs among youth; however, no study has examined these constructs in real time as they relate to both alcohol misuse and STBs. Further, interpersonal stress has been found to negatively affect EF capabilities; yet, no research to date has examined whether EF, particularly in the context of interpersonal stress, is related alcohol misuse and STBs among youth. To this end, the proposed career development award seeks to address an important gap in current research by examining EF deficits, interpersonal stress and the relationship between alcohol misuse and STBs in real time. Participants (N = 90) presenting to two Emergency Departments with recent STBs and alcohol misuse will complete an initial assessment followed by a 30-day ecological momentary assessment (EMA) protocol. The proposed training plan closely aligns with the research goals of this project, and includes (1) achieving expertise in alcohol research; (2) acquiring necessary skills in EMA and applying of advanced analytic approaches to intensive longitudinal data; (3) developing proficiency in the administration and interpretation of ambulatory and stress- induced assessment of EF; and (4) progress towards scientific independence. The mentorship team has expertise in research in youth alcohol misuse with translational implications (Dr. David Goldston), EMA data collection among high-risk youth (Drs. Richard Liu and Evan Kleiman), multi-level modeling for intensive longitudinal data (Drs. Evan Kleiman and David Yanez) and stress-induced and ambulatory assessment of executive function (Drs. Laura Germine and Richard Liu). This application has important clinical implications, as findings from this study may identify intervention targets (e.g. stress-sensitive EF capabilities) for reducing risk for both alcohol misuse and STBs, as well as particular short-term contexts in which both high-risk behaviors are imminently likely (e.g. following interpersonal stress). Thus, the proposed study has potential to inform future research studies examining state-sensitive mechanisms underlying alcohol misuse and STB risk among youth.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY Understanding how proteins interact within the cell to perform specific functions is a central goal of modern biology and crucial for understanding the diverse roles these molecules play in biomedicine. Single-particle cryo-electron tomography (SP-cryo-ET) is currently the only technology capable of visualizing macromolecules in their native environment at high resolution. Despite recent advances in sample preparation, data acquisition, and image processing, structural analysis by SP-cryo-ET is still largely confined to naturally abundant targets—such as ribosomes or ordered supramolecular assemblies—or to resolutions that are insufficient to reveal molecular-level interactions. Furthermore, the complexity and high computational demands of SP-cryo-ET workflows for data processing have restricted access to the technology for structural biologists. These challenges present a significant barrier to fully unlocking the potential of SP-cryo-ET in advancing our understanding of how proteins interact within cells to carry out specific functions and the essential roles they play in biology and disease. Building on recent progress made by our group, the goal of this project is to develop methods to address remaining bottlenecks in the SP-cryo-ET workflow that will result in broader applicability and improved access. Our long-term goal is to enable the routine visualization of a wide range of biomedically important targets in the cellular context at near-atomic resolution. By working closely with a network of experimental collaborators, we will ensure that our method development efforts are driven by diverse and impactful biological projects. Ultimately, our tools will help expand the applicability of SP-cryo-ET and accelerate its adoption, empowering structural biologists to tackle new questions regarding molecular interactions and cellular mechanisms.

NIH Research Projects · FY 2026 · 2026-05

ABSTRACT Aspergillus fumigatus is the most common cause of invasive fungal infections worldwide, with cases continuing to rise due to a growing immunocompromised population. Antifungal therapeutics are currently limited to just 3 drug classes with limited efficacy, and the development of effective treatments is hindered by an incomplete understanding of the strategies this organism employs to resist drugs and persist in the host environment. Agricultural use of fungicides rapidly selects for cross-resistance to antifungal drugs used to treat infections in patients, and the mechanisms contributing to the emergence of antimicrobial resistance is a critical knowledge gap in the field that my dissertation project seeks to address. In order to better understand pathogenic adaptations, we can look to evolutionary mechanisms A. fumigatus may have developed to persist in its complex environmental niche. I discovered that exposure to FK506, a compound produced by soil-dwelling Streptomyces bacteria that has both antifungal and immunosuppressive activity, rapidly selects for unstable full-chromosome disomies in this normally haploid fungus. These disomies confer resistance to both FK506 and clinically-used azole antifungals. I used RNA sequencing to pinpoint upregulation of the neosartoricin biosynthetic gene cluster as one potential tolerance mechanism shared between Chr. 4 and Chr. 7 aneuploids and demonstrated that increasing expression of the transcriptional regulator of this cluster confers FK506 tolerance in a euploid background. Building on these recent discoveries, I hypothesize that full-chromosome disomy leads to transient antifungal resistance via dynamic transcriptional rewiring in A. fumigatus. This proposal will investigate unstable responses that facilitate antifungal resistance, uncovering novel genes and pathways implicated in these adaptive responses. In Aim 1, I will use biochemical and molecular genetic approaches to study target genes and processes conserved between Chr. 4 and Chr. 7 aneuploids in the response to FK506, revealing novel mechanisms of tolerance. Aim 2 will focus on unstable voriconazole resistance, employing different clinical and environmental isolates to identify distinct and conserved resistance mechanisms and investigating transcriptional changes in known and unknown azole resistance genes resulting from aneuploidy. These studies will shed light on a novel phenomenon that serves as a flexible, mutation-independent means to adapt to a range of stresses, ultimately informing our understanding of this organism’s ability to persist during human infections.