Grants

NSF

This project will identify and characterize spatially coupled biochemical processes in methanogenic archaea, microbes that have the unique capability to grow by synthesizing the high-energy fuel methane. 60-99% of the carbon that methanogenic archaea consume is converted to methane gas that can be used to produce heat, electricity, transportation or rocket fuel with clean water as a byproduct. Molecular, biochemical, and computational techniques will be used to investigate how enzymes used by methanogenic archaea work together to efficiently convert low-energy growth substrates to high-energy methane gas. By identifying and characterizing enzyme interactions within cells, the research will reveal how methanogenic archaea control the flow of carbon and electrons to convert abundant, low-energy substrates such as acetate and methanol into methane gas. This knowledge will lead to a better understanding of how methanogenic archaea function in a variety of natural environments, such as in marine, freshwater, and terrestrial subsurface or in human and animal digestive tracts. This work generates knowledge with translational potential that could be used to increase the supply of renewable methane fuel to meet society’s energy needs. This project also supports recruitment and education of undergraduate, graduate, and postdoctoral trainees in anaerobic microbial physiology, molecular biology, and redox biochemistry in preparation for careers in industry, academia, and government to support US bioindustries. Methanogenic archaea (methanogens) have evolved to thrive near the “thermodynamic limit of life” in that they obtain less than 1 mole ATP per mole substrate consumed. The extreme thermodynamic constraint faced by methanogens requires a high degree of metabolic efficiency compared to heterotrophic organisms such as E. coli that obtain more than 36 ATP per mole of glucose substrate. Because of the ancient evolutionary origin of methanogenesis enzymes (predating the Last Unified Common Ancestor, LUCA), determining if and how Wood-Ljungdahl pathway and Wolfe Cycle methanogenesis enzymes interact could shed light on biochemical strategies that have evolved to optimize metabolic efficiency in methanogens and other microbes. Previous work has shown that enzymes in these two pathways form a multi-enzyme complex in the methanogen Methanosarcina acetivorans. It is proposed that highly conserved enzymes such as those in the Wolfe Cycle and Wood-Ljungdahl pathway may have evolved to form large multienzyme complexes resulting in low spatial, kinetic, and chemical entropy that enables highly efficient growth on low-energy substrates. Specifically, the project will test the hypothesis that methanogenic growth kinetics of M. acetivorans are dependent on substrate-specific composition and stoichiometry of multi-enzyme complexes that physically couple the terminal oxidoreductase with carbon-dioxide-fixation enzymes. Molecular, biochemical, and computational techniques, including cryoEM, will be used to detect, characterize, and model methanogenesis enzyme complexes in M. acetivorans. 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.

NIGMS - National Institute of General Medical Sciences

PROJECT SUMMARY Tissue and organ development occurs through coordinated cellular processes driven by the interplay of biochemical, mechanical, and spatial signals. However, the mechanisms by which such signals are integrated to produce functional structures remain poorly understood. In particular, we are only beginning to explore the role of extrinsic mechanical signals such as those originating from the extracellular matrix. The long-term goal of my research is to address this knowledge gap by investigating how mechanoregulatory signals control cell and tissue behavior during development. To this end, during this 5-year project, we will focus on dissecting the mechanisms by which mechanical regulation exerted by the extracellular matrix modulates cellular mechanisms of remodeling and adhesion to achieve tissue-level deformations. We will combine powerful optogenetic manipulations together with molecular/genetic perturbations, biophysical measurements and advanced imaging in in vitro and in vivo. Our approach proposes an integral understanding of the dynamic and complex nature of cell-ECM mechanical communication by studying mechano-regulation from multiple angles, ranging from intrinsic ECM mechanical properties (Gap 1: modulation of active tissue-deformation via ECM viscoelasticity) to a mechanistic understanding of cell-ECM signaling models remodeling (Gap 2: Cell-ECM communication mechanisms promoting active ECM remodeling); and adhesion (Gap 3: Interplay of cell-cell and cell-ECM adhesions driving tissue deformations).This work will provide a more comprehensive understanding of the dynamic and complex nature of cell-ECM mechanical communication, which is an essential component to unravel mechanochemical interactions driving the emergence of cell and tissue organization. Ultimately, the understanding provided by these studies will have important implications in two main fronts, first, to mechanistically understand mechanoregulatory signals leading to abnormal events and treat them as potential mechano-targets; and second, to leverage such signals as a means to engineer functional tissues in a predictable fashion for use in regenerative medicine.

NSF

The Pacific Ocean is a key region for coupled atmosphere-ocean phenomena that influence global climate across different timescales. Currently, seasonal-to-interannual climate predictions predominantly rely on forecasting El Niño-Southern Oscillation (ENSO) while there are emerging efforts on Pacific-rim decadal predictions based on forecasting phases of Pacific Decadal Variability (PDV). In turn global climate change projections hinge on predicting forced changes in the tropical Pacific. On this, however, there is substantial disagreement between models which favor a reduced zonal sea surface temperature gradient and observations which show an increase. The discrepancy reduces confidence in models’ future projections; the differences are critical for associated regional climate change, tropical cyclone behavior and climate sensitivity. By integrating observational analyses, theoretical demonstrations, and model experiments, this research will significantly advance our fundamental understanding of key aspects of Pacific dynamics. The gained understanding is essential for reconciling why climate models struggle to simulate historical trends in the tropical Pacific Ocean and how the models can be improved so as to provide more reliable and accurate predictions and projections of regional climate change and the rate of global warming. The lead investigator is an early career researcher and this work will advance her career focused on the ocean’s role in climate variability and change. This project aims to explain why the patterns of thermocline depth and mixed layer temperature change are meridionally broader for PDV than interannual ENSO and why the climate change patterns are again more meridionally confined and generally distinct from those of PDV. In this context, the research aims to comprehensively investigate the dynamics of contrasting pattern formation of thermocline and mixed layer temperature in the Pacific Ocean across interannual, decadal, and climate change timescales by understanding the different ocean dynamics, surface heat flux and cloud-radiation-sea surface temperature feedbacks involved. Of particular interest is to determine why the climate change signal does not amplify via Bjerknes feedbacks into a pattern more akin to ENSO or PDV and, instead, remains stable. In addition, the study will quantify the connections across timescales of the tropical Pacific Ocean and the Southern Ocean and determine the role of the latter in influencing the climate change pattern in the tropics. 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

The main objective of the project is to study geometric flows, more precisely equations in which one evolves a geometric object (for example a metric or a surface in the Euclidean space) in time, expecting it will improve its properties in time, for example become more symmetric, starting resembling familiar objects, such as spheres or cylinders. These geometric equations usually develop singularities in a finite amount of time, after which one cannot expect to have a nice solution to the considered geometric flow. One would like to understand more closely what happens at those singular times, and what the singularities look like. This should help one find a way to define a solution past the singularities. After repeating this finitely many times, one should get in the end very familiar geometric objects, and this could help, for example, to understand and classify all possible topologies of the initial geometric object. The PI expects that new students and postdocs, besides current ones will be trained, and that they will benefit from the research activity. The PI also plans to co-organize workshops in various topics in Geometric Analysis. This project is to study singularity formation in asymptotic sense, and to classify singularities in nonlinear parabolic equations which come from differential geometry problems, such as the evolution of a hypersurface in the Euclidean space by functions of its principal curvatures, and the Ricci flow. The first part of the project is to understand the formation of cylindrical singularities which are expected to be generis and their stability. This includes understanding the dynamics of nondegenerate and degenerate neckpinch singularities, more precisely the denseness and stability of nondegenerate neckpinch singularities in the Ricci flow and the mean curvature flow. The PI plans to understand the formation of cylindrical singularities in the asymptotic sense in both, the Ricci flow and the mean curvature flow. The second part of the project is the classification of ancient solutions to nonlinear geometric flows, such as, the Ricci flow and the mean curvature flow, since ancient solutions appear as singularity models in both flows. The PI will combine the PDE techniques and geometric estimates to study ancient solutions of such flows. The PI plans to classify ancient closed noncollapsed solutions to higher dimensional Ricci flow (cases n= 2,3 have been solved), under suitable conditions. More precisely, the PI would like to classify four dimensional noncollapsed Ricci flow ancient solutions whose asymptotic shrinker is a round cylinder or a bubble sheet. One motivation for this classification comes from showing an analogue of the Mean Convex Neighborhood Theorem for the Ricci flow. This could potentially help one to perform surgery in the Ricci flow in dimension four without assuming global curvature conditions initially. The PI will also try to understand mean curvature flow ancient solutions whose tangent flows at negative infinity are generalized cylinders. 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

Stochastic ordinary differential equations on random graphs provide a general framework for modelling a range of important applications, including electrical power grids, communication or social networks, machine learning algorithms, epidemiology disease spread, neuroscience, and material models in statistical physics. This project will develop new characterizations of how interactions among large networks of individual particles or agents lead to important larger scale macroscopic phenomena. Examples range from the billions of neurons in the brain that can form macroscopic oscillations that are observable through electrocardiograms (ECG), to individual populations that may incur large outbreaks in disease spread. The project will formulate new classes of macroscopic models that incorporate the microscopic effects of network delays, and local connectivity. It will also involve the training of graduate and undergraduate students in this research area. This project aims to rigorously establish new macroscopic autonomous McKean-Vlasov equations (Fokker Planck type, hydrodynamic limits) for large systems of stochastically interacting particles on random graphs. A key mathematical contribution will be the introduction of new non-standard empirical measures that encode sufficient information regarding the microscopic state of the system. The structure of these measures are a key novelty that enables the derivation, and convergence to, autonomous McKean-Vlasov equations. The project will also establish new formulas for rare events through rigorous large deviations principles. These formulas will characterize how microscopic fluctuations can lead to large scale macroscopic changes. The results will be developed for practically important classes of random graphs (relevant for the visual cortex model and social models) that allow for state-dependent edge connections, and hypergraphs that arise in many-agent interaction models. 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.

NIGMS - National Institute of General Medical Sciences

Abstract Flagella—motile, hair-like appendages extending from the surface of cells—are ubiquitously present across all three domains of life. These organelles carry out diverse functions of cells, including motility, sensory perception, and fluid transport, through their primary ability to move ambient fluids relative to the cells. Thus, understanding the interaction between flagella and their surrounding fluid, particularly their fluid-transport capability, is crucial to addressing a wide range of fundamental biological questions. While advances in electron microscopy and X-ray crystallography have illuminated the ultrastructures of bacterial and eukaryotic flagella, the dynamics of motile flagella in fluid environments remain poorly understood. The challenges in studying flagellar dynamics in fluid media stem from the lack of suitable experimental tools capable of imaging collective flagellar motions in real time at small length scales and mapping the three-dimensional (3D) fluid flow around rapidly beating flagella with high spatial and temporal resolution. Drawing on my unique training and career path, I lead a research group that develops new physical model systems and advanced novel imaging techniques to elucidate fluid-mediated flagellar dynamics in key biological processes. Specifically, we aim to address two critical questions on flagellar dynamics in this R35 MIRA proposal. 1) Resolving the synchronized dynamics of prokaryotic flagella that enable the formation of a bacterial flagellar bundle, a process essential for bacterial motility and chemotaxis. 2) Imaging the 3D fluid flow generated by beating eukaryotic flagella and their various mutants, a long-standing challenge that is central to the understanding of the functional consequences of normal and dysfunctional flagella and the key step towards the development of treatments for ciliopathies. Specifically, in Goal 1 of our proposed research, we will integrate experiments on peritrichous bacteria Escherichia coli and their genetically engineered mutants with a scaled physical model of a bacterial flagellar bundle constructed in my lab. This unique approach will help to reveal the detailed mechanisms, through which different physical factors, such as hydrodynamic interactions, the elastic properties of flagellar hooks, and motor torque fluctuations, control the synchronization and formation of bacterial flagellar bundles. In Goal 2, we will develop a new imaging technique—high-speed tracking holographic microscopy—to measure the temporal variations of the three-dimensional flow around the beating flagella of a green alga, Chlamydomonas reinhardtii, which serves as a premier model for eukaryotic flagella. Our research will deliver the first comprehensive characterization of the 3D flow field generated by isolated motile eukaryotic flagella in their natural, unperturbed state and directly correlate abnormal flagellar structures with their functional deficiencies in fluid transport. Thus, through the innovative model system and the advanced experimental techniques pioneered in our lab, our study will address crucial open questions on the dynamics of motile prokaryotic and eukaryotic flagella in fluid media.

NSF

The ocean beneath Antarctica’s sea ice plays a critical role in Earth’s system and supports unique polar ecosystems, yet it remains one of the least studied parts of the planet. This project focuses on understanding how turbulent mixing in the ocean moves heat, nutrients, and other properties between layers of water. These processes influence the stability of Antarctic ice shelves, the productivity of marine ecosystems, and the ocean’s ability to store heat. By collecting new observations from a rarely visited region in the western Weddell Sea, where thick multi-year sea ice hinders the access of research vessels, this research will improve scientific understanding of how the Antarctic Ocean functions. The research will quantify turbulence and vertical mixing processes in the western Weddell Sea, a region characterized by dense water formation, thick sea ice cover, and strong ocean currents. Microstructure profilers will be deployed from the German research icebreaker RV Polarstern to collect direct measurements of turbulent kinetic energy dissipation. The study will examine the influence of tides, topography, and wind forcing on mixing rates and evaluate their effects on vertical fluxes of heat and nutrients. Observations will be used to estimate diapycnal diffusivities across a range of environmental conditions, vertical heat and nutrient fluxes. Results from this project are anticipated improve model predictions of ocean–ice interactions and contribute to a better understanding of the Antarctic system. 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.

NIEHS - National Institute of Environmental Health Sciences

Project Summary/Abstract Methylation of cytosine bases in DNA to 5-methylcytosine (5-mC) acts as a key regulator in gene expression for vertebrate animals and is associated with DNA packaging into heterochromatin. DNA demethylation is initiated by ten-eleven translocation (TET) methylcytosine dioxygenases like TET2, which oxidizes 5-mC, marking it for removed by thymine DNA glycosylase (TDG), which is then replaced by an unmethylated C by base excision repair. It remains poorly understood how the presence of chromatin impacts the efficiency of active DNA demethylation, although both TET2 and TDG interact with nucleosome core particles. Preliminary studies from our lab have shown that TDG diffuses on DNA to search for modified bases, and encountering nucleosomes can interrupt this search. Further, TDG was also demonstrated to interact directly with TET2. Based on these findings, we hypothesize that TET2 and TDG act together and utilize NCPs as a scaffold to efficiently remove methylated cytosines wrapped within. The experiments to test this hypothesis will be performed in two phases. In the mentored K99 phase, the candidate will be trained in several new techniques, including how to design and create knock-in cell lines with CRISPR/Cas9, perform single-particle tracking within live cells, reconstitute nucleosome core particles, and generate high-resolution structures with cryo-electron microscopy. This training will occur during AIM 1 where the candidate will determine the dynamics of TDG diffusing and binding chromatin in living cells, as well as binding oxidized 5-methylcytosine on a defined DNA tether in a single-molecule approach. Further, the structure of TDG on a nucleosome will be determined using cryo-EM. Each training goal will be performed with respective experts in the field and will be complemented with professional development courses at Pitt. In the independent R00 phase, the candidate will capitalize on these new skillsets gained during AIM 1: in AIM 2, the candidate will use innovative techniques to generate site-specific base modifications at defined genomic positions and chromatin states. Then, repair dynamics of TDG will be tracked via single-particle tracking of live cells. In AIM 3, the skillset gained in AIM1 for TDG will be applied to TET2, where the live-cell single-molecule dynamics of TET2 will be determined on duplex DNA and chromatin, on endogenous levels of 5-mC and induced higher levels of DNA methylation. These results will be complemented with studies of TET2 on long DNA tethers with defined substrates. Finally, in AIM 4, the candidate will utilize the training in generating reconstituted nucleosomes to test how TET2 and TDG cooperate on chromatin or on duplex DNA with enzymological, structural, and single-molecule approaches. These experiments will provide mechanistic insights into how TET2 and TDG work together to achieve oxidative demethylation in the context of chromatin. The training components of this project will supply the candidate with the skillset and background to establish the basis of his independent work in his future academic career.

NSF

With support from the Chemical Structure and Dynamics (CSD) program in the Division of Chemistry, Professor Francesco Paesani of the University of California, San Diego and Professor Mircea Dincă of Princeton University are investigating the molecular mechanisms that govern ion transport in confined environments and using the resulting insights to design metal-organic frameworks (MOFs) as quasi-solidstate electrolytes (QSSEs). MOFs are porous, chemically tunable materials with the potential to enable safer and more efficient energy storage systems. However, the mechanisms controlling ion migration in MOFs remain poorly understood. This project integrates computer simulations, advanced spectroscopic measurements, and artificial intelligence (AI) to study how pore geometry, cation identity, solvent environment, and chemical functionalization affect ion solvation and mobility under confinement. Professors Paesani and Dincă will work with their teams to characterize ion–solvent–framework interactions and free-energy landscapes and to establish predictive structure–function relationships. Their discoveries could guide the design of MOFs optimized for ion conduction and contribute to a broader framework for materials with tunable transport properties. Educational activities will engage undergraduate and graduate students in interdisciplinary training across computational chemistry, experimental materials chemistry, and AI for molecular and materials discovery. This research integrates experimental methods, such as solid-state nuclear magnetic resonance (NMR), vibrational spectroscopy, and electrochemical impedance spectroscopy, with data-driven many-body molecular dynamics (DD-MB MD) simulations that employ highly accurate potential energy functions to model confined ion–solvent systems at the molecular level. Together, these tools will be used to investigate how MOF structure, pore chemistry, solvent composition, and applied electric fields influence solvation structures, transport mechanisms, and free-energy landscapes. The data generated from these studies will be used to train a physics- and chemistry-informed AI platform designed to identify and optimize MOFs for QSSE applications through high-throughput screening of large structural databases. By integrating simulation, experiment, and AI, this project will establish a scalable and transferable framework for understanding and designing materials that control molecular transport in confined environments. The resulting design principles will advance not only the development of next-generation QSSEs, but also porous materials for applications in catalysis, sensing, nanofluidics, and environmental separations. 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

The meandering variability of upper-tropospheric jet streams have a strong influence on the surface weather of the middle latitudes, and very large meanders of the jet streams lead to extreme surface weather including heat waves, cold air outbreaks, and heavy precipitation. Classical linear wave theory can account for jet meanders but the theory assumes that the meanders have small amplitude, an unfortunate limitation since the meanders that matter for extreme weather are quite large. In earlier NSF-funded work the Principal Investigator (PI) pioneered a theory of wave dynamics which overcomes the small-amplitude constraint of linear theory and is thus better suited to real-world weather. The theory is based on a conserved quantity called Local Wave Activity (LWA), a measure of the waviness of the atmospheric circulation that can be used to identify the dynamical mechanisms responsible for important forms of wave behavior in the jet streams. Work performed here uses the LWA framework to address three longstanding problems in middle-latitude atmospheric circulation dynamics, the first of which is the suppression of cyclonic weather activity in the storm zones of the North Pacific and North Atlantic, which is typically weaker in midwinter than in October and March despite seemingly more favorable conditions for cyclogenesis. The work is guided by the hypothesis that the key issue is the exchange of LWA between weather systems and lower-frequency flow variations. The second problem is the unexplained dynamics that leads to Sudden Stratospheric Warmings (SSWs), in which the stratosphere over the North Pole warms dramatically as the stratospheric circulation flowing around it breaks down. The work focuses on the role of wave resonance, with different resonant modes responsible for different forms of SSWs (splitting versus displacement). The third problem is explaining the duration of blocking events, in which a high-pressure center forms in the upper troposphere and persists for many days as the air flow moves around it. The LWA framework is used to understand the lifecycle of the block and the various factors, including condensational heating in clouds, that could contribute to its persistence. The work is of practical as well as scientific interest given the potential for all of the above phenomena to create extreme weather. In addition, the work contributes to the efforts of the Model Diagnostics Task force of the National Oceanic and Atmospheric Administration's Geophysical Fluid Dynamics Laboratory. The project also has educational value through its support of graduate students and a postdoctoral research fellow. 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

This grant will support research that looks to contribute to new knowledge related to the nonlinear dynamics of acoustic cavitation enhanced by vortex ultrasound. Acoustic cavitation is the process of bubble formation, oscillation, and collapse in a liquid exposed to intense ultrasound. Acoustic cavitation has been widely used in the biomedical field for tissue ablation, thrombolysis, drug delivery, etc., and in industry for metal cleaning in manufacturing processes. Vortex ultrasound is a type of acoustic wave with a helical wavefront rotating as the wave propagates. Previous studies of vortex ultrasound-induced acoustic cavitation in deionized water show that vortex ultrasound can induce acoustic cavitation at a much lower intensity threshold and with stronger cavitation activity than focused ultrasound. However, the fundamental mechanism(s) behind the lower intensity threshold and stronger cavitation activity driven by vortex ultrasound are still unknown. Without this important knowledge, it is challenging to use vortex ultrasound reliably and safely in the suggested biomedical and industrial applications. This research project seeks to understand the fundamental bubble dynamics driven by acoustic cavitation induced by vortex ultrasound and the mechanism behind the reduced cavitation threshold, as well as enhanced cavitation activities. A novel theoretical model of bubble dynamics driven by vortex ultrasound looks to be developed and verified by experimental measurements underwater with and without microbubbles or nanodroplets as ultrasound contrast agents. The results from this research seek to advance knowledge in acoustics, dynamics, fluid mechanics, as well as biomedical engineering, and can potentially lead to novel medical therapy with better efficacy and safety and industrial cleaning with less power consumption. Students at all levels, including graduate and undergraduate students as well as K-12 students, will participate in the interdisciplinary research, which will help train the next generation of leaders in science and engineering. The objective of this research is to create a new theoretical model that will provide a precise characterization of acoustic cavitation dynamics driven by vortex ultrasound and validate the model through experimental studies via high-speed camera tracking, infrared temperature mapping, and underwater acoustic measurements. This research project looks to understand the fundamental mechanism(s) that lead to the reduced cavitation threshold and enhanced cavitation activities driven by vortex ultrasound compared with conventional focused ultrasound. The central hypothesis of this research is that the strong shear effect induced by the large in-plane pressure gradient perpendicular to the propagation direction of vortex ultrasound enhances bubble formation and collapse in acoustic cavitation. This hypothesis will be tested by a newly developed theoretical model as well as experimental characterization in degassed, deionized water. The cavitation bubble dynamics driven by vortex ultrasound will be investigated using lipid-encapsulated microbubbles. The bubble formation and phase transition driven by vortex ultrasound will be studied using phase-transitioning nanodroplets. 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

Two-dimensional geometry has been a cornerstone of mathematics since antiquity. In addition to geometry on the xy-plane, mathematicians today study geometry on surfaces such as the crust of the Earth or the glaze of a donut. Most of these surfaces exhibit hyperbolic geometry, a type of non-Euclidean geometry in which parallel lines spread apart. Because of its ubiquity, two-dimensional hyperbolic geometry is a common meeting point for many branches of mathematics. Recently, the PI strengthened a connection linking hyperbolic geometry with certain transformations of two-dimensional Euclidean geometries, which were motivated by the kinetic motion of particles and the flow of electrons. The goal of this project is to further investigate this connection between non-Euclidean and Euclidean geometries in order to better understand both worlds. The project will also support professionalization, mentorship, and enrichment activities for a broad range of students. The research component of this project has three main prongs of attack. The first is to further develop (and complicate) the link between the earthquake and horocycle flows, dynamical systems on moduli spaces of hyperbolic surfaces and quadratic differentials, respectively. This will allow the PI both to leverage decades of progress on quadratic differentials to study hyperbolic surfaces, and to leverage new geometric features afforded by hyperbolic space to study quadratic differentials. The second prong is to study the structure of optimal Lipschitz maps between hyperbolic surfaces and their related renormalization dynamics. The final prong is to use all of these tools to investigate related counting problems on both flat and hyperbolic surfaces. 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.

U.S. National Science Foundation

Dynamics, Control and Systems Diagnostics

NCCDPHP - National Center for Chronic Disease Prev and Health Promo

Project summary Type 1 and type 2 diabetes mellitus (T1D, T2D) continue to rise in youth and young adults (YYA) worldwide, with disproportionately high rates of T2D among historically underserved populations. Young people with early-onset diabetes face decades of managing a complex chronic disease and are at heightened risk of complications. Despite advancements, key knowledge gaps persist regarding trends in early onset T1D and T2D incidence, disease management, and outcomes in real-world settings, particularly for young adults, rural communities, and those receiving care outside specialty centers. The transition to adulthood, which often involves changes in residence, employment, and insurance, complicates surveillance through traditional methods. To address these challenges, we have brought together a highly collaborative, multi-institutional team of endocrinologists, biostatisticians, epidemiologists, nephrologists and informaticists with experience in diabetes surveillance and electronic health record-based research. We have established a unique regional network of five major health systems across the Pacific Northwest (PNW) to conduct comprehensive diabetes surveillance in YYA. This network includes Seattle Children’s Hospital, University of Washington Medicine, Providence Health System, Virginia Mason Franciscan Health, and the Veterans Affairs VISN 20 region, collectively serving diverse urban and rural populations across Washington, Oregon, Idaho, Montana, and Alaska. By integrating EHR, claims data, and established research infrastructure, we will conduct systematic surveillance of diabetes incidence, prevalence, clinical management, and complications in YYA. Our central hypothesis is that tracking diverse demographics, including rural and Native populations, will uncover critical disparities in the diabetes burden, healthcare delivery, and outcomes amenable to targeted interventions. Data will be harmonized across the health systems in our network. We will contribute to and implement the shared protocol developed with other funded sites in this cooperative grant mechanism. This project will deliver the first large-scale, real-world surveillance system for YYA with diabetes in the PNW, capturing underrepresented populations and addressing a pressing need for timely data on evolving trends in care and outcomes. By systematically identifying disparities in disease burden and clinical management, results will inform interventions to prevent disease progression, reduce complications, and improve long-term quality of life. The focus on rural and Native populations ensures that our approach is inclusive, contextually relevant, and poised to directly influence public health efforts in regions often overlooked by surveillance studies.

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

Summary Type 1 diabetes (T1D) affects ~2 million people in the US, including children. T1D is a major burden to society in terms of health costs, loss of productivity; it reduces quality of life and expectancy and causes loss of life due to acute and chronic complications. Its incidence is rising worldwide. T1D is mediated by an autoimmune process that destroys insulin-secreting pancreatic beta cells, leading to lifelong insulin-deficiency and hyperglycemia. No cure or fully effective prevention is available, but the key requirements for diabetes reversal are apparent: (1) preservation of residual beta cell mass; (2) promotion of beta cell regeneration; and (3) induction of immune tolerance. The discovery that inhibitors of the dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) enhance human β-cell regeneration empowers exploring regimens that simultaneously address autoimmunity, β-cell dysfunction and, for the first time, β-cell loss. We will advance this concept in nonobese diabetic (NOD) mice and immunodeficient mouse models, supported by preliminary data showing that: 1) DYRK1A inhibitors together with the GLP-1 receptor agonist (GLP1RA) exenatide synergistically increase human β-cell proliferation and expand β-cell mass in vivo in human islet grafts transplanted into immunodeficient mice; 2) this combination affords protection from cytokine-induced human β-cell death and decreases immunogenicity in vitro; and 3), it rapidly reverses diabetes in newly diagnosed NOD mice pre-treated with anti- CD3 antibody. However, efficacy of short course immune therapies wanes over time and there is a need for safe, chronic treatments that promote immune regulation without inducing immunosuppression. A promising agent is IL-2: at low dose, it selectively promotes regulatory T cells (Tregs) and was safe and effective in treating autoimmunity in experimental models and in clinical trials for several immune-mediated disorders. Our central hypothesis is that DYRK1A inhibition with GLP1R activation in combination with effective, long-term immunomodulation induces stable T1D remission in NOD mice. We propose that this therapy improves β- cell health and number, decreases immunogenicity, and is synergistic with immunomodulation that includes low dose IL-2 therapy to stimulate Treg cells. Specific Aim 1 will advance an expanded combination therapy with immunomodulators (anti-CD3 and IL-2/CD25 fusion protein), a novel and safer DYRK1A inhibitor, and clinically used GLP1Ras, for T1D reversal. Specific Aim 2 will establish the immunological basis by which Treg-targeting by low dose IL-2/CD25 together with immune modulation by anti-CD3 and β-cell enhancement by DYRK1A inhibition/GLP1R activation leads to T1D reversal. Specific Aim 3 will determine the mechanisms impacted by this combination therapy on the human β-cell and human immune cells. This highly translational work will characterize the therapeutic potential of the combination of DYRK1A inhibitors, GLP1RAs and immunomodulators to induce T1D remission, and the cellular/molecular mechanisms involved in the beneficial effects of this treatment, with relevance to both recent onset and established T1D.

NIA - National Institute on Aging

Abstract: Dysfunctional mechanisms of the mitochondrial redox-sensitive signaling response to exercise in aged skeletal muscle. Individual: This career development award application details training and scientific research for Matthew D. Campbell, Ph.D. a skeletal muscle and mitochondrial biologist in the Radiology department at the University of Washington, Seattle. His short-term goals are to take his background in mitochondria, redox biology, and contraction dynamics in aged muscle and expand them with tools evaluating tissue metabolism and mitochondrial protein interactions using novel 3D engineered tissue and in vivo mouse models. His long-term goals are to form an independent research laboratory focused on the mechanisms of muscle contraction/relaxation dynamics that interact with metabolic function in muscle. Research: Aging in skeletal muscle is a complex pathology involving redox signaling, metabolic deficits, oxidative damage, neuromuscular junction defects, and protein expression and interaction changes. Previous work by Dr. Campbell has shown that restoring basal redox state improves mitochondrial and skeletal muscle function. This proposal builds on his previous work to establish that dysfunctional redox-sensitive signaling alters substrate utilization following exercise (Aim 1), impacts beta oxidation and TCA cycle flux (Aim 2), and mitochondrial protein interactions (Aim 3). Career Development Plan: The proposed work in this application would support Dr. Campbell’s short-term and long-term goals by enhancing his current expertise in muscle and mitochondrial function with work focused on developing novel human induced pluripotent stem cell lines, assays of in vivo whole tissue metabolism, dissecting mechanisms of redox signaling, and generating/analyzing large datasets of metabolomics and peptide/protein interactions. His professional development activities will include technical training, formal coursework, guest lecturing on mitochondrial metabolism, presentation of his research at local and national conferences, grant writing and review, routinely scheduled lab meetings and individual meetings with his mentors. Research Environment: The University of Washington offers an outstanding environment for the training in muscle research and aging and includes the Northwest Metabolomics Research Center, Center for Translational Muscle Research, and a Nathan Shock Centers of Excellence in the Basic Biology of Aging. Dr. Campbell’s mentorship team includes senior faculty members that are well-known and respected for their work in 3D engineered tissue, metabolism, and mitochondrial protein interactions.

NIA - National Institute on Aging

PROJECT SUMMARY/ABSTRACT The increasing prevalence and severity of metabolic dysfunction associated steatohepatitis (MASH) and its sequelae resulted in a rise in mortality in the aging population. MASH-related hepatocellular carcinoma (HCC) has a poor prognosis in older patients, and the effects of aging-mediated pathways on MASH-driven HCC are not well understood. The Src homology 2 domain containing collagen-related (SHC) adaptor proteins increase during aging in the liver, and inhibiting Shc in MASLD/MASH either genetically or pharmacologically increased beta oxidation and improved inflammation and fibrosis. Based on this, we now propose that age-related maladaptive responses via Shc create a niche that predispose to HCC by mitochondrial dysfunction, decrease in FAO, lipid peroxidation, modulating matrix mechanics to promote cell invasion. To address this hypothesis in Aim 1 we will study dietary as well as Shc isoform-specific knockdowns and inducible transgenic models for MASH/HCC in young vs. old mice. We will evaluate mitochondrial OXPHOS, β-oxidation, as well as the effects of beta hydroxybutyrate production, including HDAC1/2, and p53 acetylation. In Aim 2, we will study matrix mechanics and architecture that are modulated via Shc mediated advanced lipoxygenation products. Force maps will be multiplexed with CODEX to evaluate cell interactome and mechanical characteristics, in situ in MASH/HCC. Detailed analyses of the matrix by LC-MS, SHG microscopy, and modeling using 3D hydrogel systems will be performed. In Aim 3, will investigate how p46Shc and p52Shc inhibition with small-molecule Shc blockers improves MASH and MASH-to-HCC transition, evaluating biochemical, physiological, metabolic as well as matrix endpoints in aged mice, and by in vitro experiments. These studies will elucidate age-specific metabolic-matrix pathways that favor hepatocarcinogenesis and set the stage to develop effective treatment options for the elderly.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

PROJECT ABSTRACT Psoriasis affects 3% of the US population and a third of patients develop Psoriatic Arthritis (PsA), usually with a delay of 5-7 years. Delayed therapy leads to poorer PsA control, yet diagnosing PsA early remains challenging. Among the most effective therapies for Psoriasis and PsA are those that target IL23, IL17, and TNF; yet, these therapeutics incompletely control arthritis, indicating the existence of other arthritogenic immune pathways. We hypothesize that cutaneous inflammatory processes play a key role in triggering psoriatic joint inflammation, which evolves following cutaneous priming to include additional immune drivers. Addressing these hypotheses may reveal early biomarkers and novel therapeutic targets for PsA. To investigate how skin inflammation drives PsA, we developed a novel mouse model of immune dysregulation initiated within the epidermis. This model, termed A20eKO, uses temporal and keratinocyte- specific loss of the gene A20 (Tnfaip3), polymorphisms of which reduce its expression and are strongly linked to both Psoriasis and PsA in humans. A20 is a key negative regulator of innate immune signaling, and its loss unmasks spontaneous pathogenic tissue immune processes. Remarkably, A20eKO mice not only develop psoriasiform skin disease but also synchronous and fully penetrant PsA-like joint disease. We show that skin and joint pathology in A20eKO mice requires IL23, IL17A, and T cells, demonstrating that epidermal signals alone can drive arthritogenic T cells. This offers a clear model to study how psoriatic skin disease drives PsA. In Aim 1 we focus on the pathogenic T cells triggered by keratinocyte A20 deficiency. We will use single cell transcriptomics and paired TCR sequencing to determine the phenotype and clonal diversity of memory T cells that expand in A20eKO skin prior to clinical onset of dactylitis. Using bioinformatic methods, we aim to identify phenotypically similar cells in human psoriatic plaques, potentially representing skin-educated arthritogenic T cells. In Aim 2 we dissect the pathogenic contributions of two distinct signaling pathways, IL1/TLR and cGAS/Sting, that we discover as potently restricted by A20 in keratinocytes. Using A20eKO mice interbred with loxP-bearing alleles of MyD88 and Sting, we will determine how unrestrained keratinocyte signaling from these two pathways distinctly impacts psoriatic inflammation and PsA-like pathology in A20eKO mice. In Aim 3, we dissect how the immune mechanisms driving PsA-like inflammation evolve after triggering by cutaneous immune dysregulation. We find that delayed anti-IL23 treatment no longer prevents PsA-like inflammation in A20eKO mice. Using Spatial Transcriptomics we will determine the immune mechanisms that drive IL23-independent arthritis following cutaneous priming. Combining the A20eKO model with a novel method to reversibly trigger keratinocyte innate immune signaling, we will dissect how PsA-like inflammation responds once cutaneous immune triggers are reversed.

NIAID - National Institute of Allergy and Infectious Diseases

ABSTRACT Immune-mediated protection against malaria, termed clinical immunity, develops over many years of repeated exposure to Plasmodium, requires continuous exposure to Plasmodium, and correlates with circulating titers of Plasmodium-specific antibodies. Why Plasmodium infections fail to induce long-lasting protection following one or few infections, thereby contributing to the chronic pathogenesis of malaria, remains unknown. The objective of this proposal is to determine the effect of Plasmodium infections on germinal center (GC) B cells and bone marrow (BM) homeostasis towards inefficient generation of long-lived plasma cells (LLPCs). Many infections and vaccines elicit long-lasting antibody titers after one or just a few exposures. The half-lives of circulating antibody titers for viral antigens following infection or vaccination have been shown to range from 10 years to >300 years. In contrast, half-lives of circulating Plasmodium-specific antibody titers are reported to be in the range of several days. Long-term maintenance of circulating antibody titers comes from GC-derived plasma cells (PCs) that migrate to the BM where they receive survival signals and become LLPCs. To investigate why Plasmodium infection induces short antibody half-lives, we compared spleen GC responses and development of BM LLPCs in mice following infection with Plasmodium yoelii 17XNL (Py) to mice immunized systemically with NP-CGG plus the adjuvant AddaVax. Our preliminary data demonstrate that despite the induction of robust spleen GC responses during Py infection, Py-induced GC B cells are inefficient at generating LLPCs in the spleen and BM and that Py-specific IgG-secreting cells in the spleen and BM exhibit decreased IgG production and affinity. These data suggest Py infections exhibit dysregulated humoral immunity by impacting the functional programming of spleen GC B cells or PCs. Py-induced splenic PCs were able to migrate towards the BM homing cytokine CXCL12, suggesting inefficient generation of LLPCs following Py infection could be attributed to functional deficiencies in the BM microenvironment that support engraftment and survival of LLPCs. Consistent with this possibility, there were decreases in the number of BM cells that provide recruitment signals for PCs and survival signals for LLPCs during Py infection that was associated with an increase in multiple cytokines in the BM, including IFN-γ. Blocking IFN-γR signaling during Py infection partially prevented the loss of BM cells and increased BM PC numbers. These observations collectively lead to the hypothesis that failure to engender LLPCs following Plasmodium infection is attributed to intrinsic differences in spleen GC B cell programming that affect PC functionality and changes in the BM microenvironment that fail to support LLPCs. The hypothesis will be tested through the following aims. Aim 1. Identify the functional deficits in spleen GC B cells and PCs following Py infection responsible for inefficient generation and function of LLPCs. Aim 2. Define the cellular and molecular mechanisms by which Py alters the BM microenvironment to impede the development of LLPCs.

NHLBI - National Heart Lung and Blood Institute

Project Summary Abstract Lymphangioleiomyomatosis (LAM) is a devastating rare lung disease almost exclusively affecting young women. LAM is characterized by smooth muscle cell growth and emphysema-like lung destruction. LAM is associated with mutations in the TSC2 resulting in activation of the mechanistic target of rapamycin complex 1 (mTORC1). Although the mTORC1 inhibitor, Sirolimus, stabilizes lung function and improves symptoms in some LAM patients, lung function declines after drug discontinuation and the long-term safety and efficacy of the drug are unknown. There is therefore an urgent unmet need to understand disease-promoting mechanisms for development of optimal interventions. Despite many advances in understanding the role of mTORC1-dependent pathways in LAM progression, the fundamental mechanisms underlying the female predominance of LAM primarily are not understood. In the Multicenter International LAM Efficacy of Sirolimus (MILES) trial, lung function declined five times more rapidly in premenopausal than postmenopausal patients, suggesting that estrogen plays a major role in LAM progression. Considering the actions of estrogen may be mediated by changes in sphingolipid metabolism, our hypothesis is that estrogen promotes sphingolipid metabolism in TSC2-deficient cells, leading to abnormal LAM lung cell growth and emphysema-like destruction of lung parenchyma and lung function decline. In Aim 1, we will use biochemical and single-cell multiome approaches to determine the molecular mechanisms through which TSC2 inactivation and estrogen promote sphingolipid- mediated cell survival. In Aim 2, we will determine the impact of pharmacologic suppression of ASAH1, S1PR1/3, ERα/β, or PR, on E2-induced lung remodeling in vivo. We postulate that that the combined suppression of sphingolipid signaling with Fingolimod, an S1PR1/3 modulator, or estrogen receptor inhibition with Faslodex or a SERM Raloxifene, or PR suppression with Mifepristone, and Sirolimus will, unlike cytostatic treatments involving Sirolimus alone, induce regression of E2-promoted lung remodeling and attenuate lung function decline. In Aim 3, we will test the hypothesis that the combinatorial treatment with 17a, Fingolimod, Faslodex, Raloxifene, or Mifepristone, plus Sirolimus will be well-tolerated and more effective than single agent in a uterine-specific Tsc2 knockout mouse model that closely resembles the human LAM. We will utilize innovative, state-of-the-art technology including single-cell multiome to identify estrogen/progesterone-regulated transcription factor activation, epigenomic alterations, and non-invasive optical and MRI imaging. The significance of this project is that it will reveal for the first time the combined roles of sphingolipid metabolism and E2 in LAM progression. This study will have high impact because current therapies for LAM are cytostatic and limited to stabilizing lung function. As Fingolimod and anti-hormonal compounds are already FDA approved for the treatment of multiple sclerosis and breast cancer, these cell-based and preclinical studies could be rapidly translated into human clinical trials for patients with LAM and other mTORC1 hyperactive diseases.

NHLBI - National Heart Lung and Blood Institute

PROJECT SUMMARY/ABSTRACT Human hematopoiesis requires a complex interplay of genes, transcription factors, and epigenetic modifiers that regulate lineage commitment and maturation. Trisomy 21 (T21), the chromosomal abnormality underlying Down syndrome, is associated with genome-wide gene dysregulation and baseline hematopoietic abnormalities such as polycythemia and thrombocytopenia. Transient abnormal myelopoiesis (TAM) and myeloid leukemia of Down syndrome (ML-DS) are related disorders unique to Down syndrome that arise from a megakaryocyte-erythroid progenitor with blocked differentiation. TAM and ML-DS are characterized by a megakaryocyte (MK) surface marker signature and mutations in the hematopoietic transcription factor GATA1, resulting in exclusive expression of the truncated GATA1s isoform. ML-DS is additionally characterized by “third-hit” mutations in regulators of epigenetics or chromatin structure, such as in the cohesin complex member STAG2. Individuals with germline GATA1s mutations without T21 develop cytopenia(s) without leukemic predisposition, emphasizing the role of chromosome 21-encoded genes, such as the transcription factor RUNX1, in the progression from T21 to TAM to ML-DS. However, the underlying mechanisms remain incompletely understood. This proposal employs a novel isogenic human induced pluripotent stem cell (iPSC) system to isolate the individual and synergistic roles of T21, GATA1s, RUNX1 isoforms, and STAG2 loss in hematopoiesis. My data suggest that T21 and GATA1s synergistically lead to enhanced megakaryopoiesis and cytokine-independent proliferation, a hallmark of myeloproliferative disorders, and that dysregulation of RUNX1 may contribute to this phenotype. STAG2 loss combined with T21 and GATA1s further enhances megakaryopoiesis and results in dysplasia. This proposal builds upon these data through two specific aims: 1) Determine how GATA1s and RUNX1 co-regulate megakaryopoiesis and 2) Determine how STAG2 loss further perturbs hematopoiesis in T21/GATA1s cells. The aims seek to produce medically relevant knowledge on normal and Down syndrome hematopoiesis by combining established and cutting-edge techniques in assessing chromatin architecture, MK biology, and transcriptional regulation. This proposal describes a 5-year training plan for the applicant, Dr. Kaoru Takasaki, to transition to an independent research career in pediatric hematology as a physician-scientist with expertise in the dysregulation of transcription factors and chromatin structure at the intersection between normal and abnormal hematopoiesis. She will be supported by two mentors, Dr. Stella Chou, an international expert on hematopoiesis, and Dr. Mortimer Poncz, a global expert in platelets and MKs, as well as an advisory committee with complementary expertise in epigenetics, chromatin structure, and iPSC disease modeling. Dr. Takasaki’s research and training will take place in the resource-rich environments of the Children’s Hospital of Philadelphia and the University of Pennsylvania that will provide an outstanding foundation to embark on an independent physician-scientist career.

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