University Of Texas At Austin

NSF Awards · FY 2024 · 2024-08

Dmitrii E Makarov of the University of Texas at Austin is supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry to develop theoretical descriptions of chemical transformations involving molecules of life, as observed with single-molecule resolution. Molecular machines, powering nearly every process in a living organism, have efficiency that is unmatched by artificial mechanisms. As a result, the energy consumption by, for example, an adult human at rest is comparable to that of a single incandescent lightbulb. Single-molecule studies offer an unprecedented opportunity to explore the fundamental origins of this efficiency and to look under the hood of molecular machines by observing individual molecules and molecular machines in action, but their spatial and temporal resolution is severely limited by the fundamental physical laws such as those governing the light emitted by molecules. The Makarov group will tackle this challenge and develop theoretical models describing how biomolecules move and perform their biological functions through a synthesis of chemical theory and computational data analysis, and in collaboration with experimental groups performing measurements on individual molecules. These efforts will be integrated with education and outreach activities that will introduce middle and high school students to modern science, involve undergraduate students in research, and educate young researchers in the cross-disciplinary field of single-molecule science through organization of international summer schools. To tackle the challenge of deciphering molecular mechanisms from inherently incomplete single-molecule observations, Makarov will employ ideas and techniques from information theory. Two broad objectives will be pursued: The first one will focus on developing computational data analysis tools, such as compression-algorithm-based entropy estimators, enabling one to learn about hidden degrees of freedom from experimental observables, particularly with the focus on the emerging multidimensional single-molecule spectroscopies. The second objective will be to develop information-theoretical tools that will address the long-standing problem in stochastic thermodynamics: inferring directionality, entropy production, and energy dissipation from noisy trajectories and/or from partial single-molecule observations. Being at the intersection of chemistry, nonequilibrium statistical mechanics, mathematics, and computer science, these efforts will promote interactions and collaborators among graduate students, postdoctoral researchers and senior scientists across multiple disciplines. Further broader impacts of this project will include developing ties with Texas universities serving underrepresented groups, mentoring middle and high school students, and extensive involvement of undergraduate students in the Makarov group’s research. 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 2024 · 2024-08

With support from the Chemistry of Life Processes Program in the Chemistry Division, Dr. Yi Lu at the University of Texas at Austin is studying how copper (Cu) enzymes play vital roles in nature, driving important chemical reactions. Their activities are driven by two main factors: the Cu-binding primary coordination sphere (PCS) and the non-binding secondary coordination sphere (SCS) around PCS. The SCS effects are not well understood due to the weak, non-covalent interactions within the complex protein environment. While studying native copper enzymes has provided valuable information, it is difficult to draw general conclusions across different classes of proteins from this approach. This project uses simplified model proteins to study how the SCS affects Cu enzymes in processes such as breaking down plant biomass and transferring nitric oxide (NO), a molecule that performs important signaling functions in humans and other animals. The findings could enhance our fundamental knowledge of metal biochemistry and could lead to practical applications in biocatalysis in sustainable energy and artificial NO storage and transportation systems. Additionally, this research will support the Chemical Biology program in the Department of Chemistry at the University of Texas at Austin. Latest research results will be incorporated into educational programs for high school and undergraduate students from diverse backgrounds. This project employs a novel biosynthetic approach to impart new or improved activity at protein Cu centers, aided by unnatural amino acids and loop-directed mutagenesis to deconvolute factors controlling activity. The research could advance fundamental knowledge of the roles of the SCS in controlling Cu enzymatic activity by obtaining a holistic understanding of how this environment can modulate the reactivity of copper enzymes, including 1) tuning the reduction potentials of the T1Cu center in small laccase to modulate its activity towards the oxygen reduction reaction in fuel cells and lignin degradation, 2) controlling polysaccharide degradation activity by a designed Cu-histidine-brace center in azurin, mimicking lytic polysaccharide monooxygenase, and 3) regulating reversibility of S-nitrosylation and trans-nitrosylation between the enzymes and small molecules in azurin. By imparting new activity on a scaffold lacking SCS as in native enzymes, the knowledge gained from the proposal may be transformative not only within the Cu enzyme chemistry, but more broadly beyond bioinorganic chemistry, because most systems require fine-tuning of the SCS environment to achieve efficient catalysis. 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 2024 · 2024-08

NON-TECHNICAL SUMMARY Cracks in solids have been studied for many years, yet some basic questions about them are barely understood. What is best known are the minimal, necessary, conditions for a crack to run. What is much less well known is how to predict the speed at which they run once they begin to move. Even questions about what speeds are possible for cracks in principle are unsettled. Resolving such questions will be an important part of the work in this project. The most important applications would be to cases where considerable uncertainty surrounds the question of when or whether a crack will actually begin to move. One example is earthquakes, which remain notoriously hard to predict. The work will also involve mechanical instabilities in fluids. They are particularly of concern for oil recovery, when oil is pushed out of the ground by water. In this case the instability comes from the formation of fingers of water that run into the oil and eventually reduce production. The work in this project will investigate the phenomenon taking into account the fact that the underground environment is tremendously lumpy and complicated, requiring an advance beyond theories assuming it is uniform. The Principal Investigator is involved in a number of educational activities. These include overall supervision of UTeach, a STEM teacher preparation program preparing around 800 middle and high school STEM teachers a year at 54 universities, teaching and developing the UTeach Research Methods course, which provides an organized research experience for prospective teachers in the program, serving as faculty lead for OnRamps Physics I, which provides the opportunity to earn college physics credit to over 6000 high school students each year, helping develop workforce plans so young people can have access to good jobs as semiconductor manufacturing returns to the United States, and activities to improve the ethics of the physics community. TECHNICAL SUMMARY This project will involve theoretical and computational investigations into the failure of solids and into two-phase fluid flow. A common theme in these problems is that they involve dynamical instabilities of moving structures in solids and liquids, and they have applications in geophysics. The project will follow up on recent experimental evidence that supersonic cracks exist and show how to deduce their behavior from materials properties. This work will rely on special analytical techniques based on the Wiener-Hopf method developed over many years, and will advance both the understanding of cracks and the reach of the techniques. Improved understanding of the conditions under which supersonic cracks exist will have application in the interpretation of earthquake dynamics. The project will also develop theoretical understanding of two-phase flow in disordered media, and the fingering instabilities that make these flows difficult to predict. This work has application to enhanced oil recovery. The existence of supersonic cracks represents a shift in the understanding of how cracks move. Recent experimental observations of these cracks create an opportunity to settle the matter of their existence and to delve into unsettled questions that include understanding how crack motion is related to microscopic structures, and the conditions under which supersonic cracks are stable and unstable. New approaches to two-fluid flow will provide novel ways to approach this classic problem in pattern-forming physics, and extend it to the context of highly heterogeneous materials. Each of the subjects in this project has practical importance. Fracture mechanics has been essential in areas that range from designing airplanes that will not fail in flight, to trying to predict conditions for initiation of earthquakes. Looking carefully at supersonic earthquakes, which have an enormous amount of available energy when they run, allows one to recast the question of earthquake prediction; instead of asking when they move, ask why so frequently they do not move although they can. Two-phase flow lies behind secondary recovery of petroleum, and improved understanding will impact the ability to make greatest use of existing oil fields during the challenging energy transition from hydrocarbons. The PI will continue activities impacting education that include serving as Executive Director for UTeach, one of the country's largest university-based networks for preparation of STEM teachers, faculty lead for OnRamps Physics I, which provides the opportunity to obtain university physics credit to over 6000 high school students a year, developing a workforce plan to meet challenges created by the Chips and Science Act, and activities that follow from having been the founding chair of the Ethics Committee of the American Physical Society. STATEMENT OF MERIT REVIEW 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 2025 · 2024-07

PROJECT SUMMARY Recent findings from the EMBARC study have shown that small lipid molecules called eicosanoids, which act as both activators and suppressors of inflammatory activity as well as modulators of innate and adaptive immunity, are known to have a significant impact on the subacute and chronic sequelae of SARS-CoV-2, in addition to risk for unresolved immune-mediated inflammatory conditions such as CVD. Eicosanoids have also been found to be a contributor of chronic neuroinflammatory conditions such as depression in other studies. Advanced mass spectrometry methods now allow for the rapid and accurate quantification of hundreds of upstream eicosanoid mediators representing multiple enzymatic origins. Hence, this proposal aims to provide a more detailed understanding of how upstream eicosanoid pathways can be variably active, imbalanced, and perturbed in relation to an individual’s propensity for developing depression. We will leverage the expertise of an interprofessional team, including current members of the EMBARC research study team, to test the hypothesis that: 1) SARS-CoV-2 infection and reinfections moderate development of chronic immune-mediated neuroinflammatory condition such as depression as evidenced by changes in eicosanoid profiles; and 2) health impacts of SDOH compounds depression risk following SARS-CoV-2 infection and reinfection by moderating the neuroimmune-inflammatory response. We propose a systematic approach to comprehensively investigating the components of upstream inflammatory activity in relation to outcomes across the spectrum of depression risk through the collection of longitudinal (survey, clinical, biomarker) data from a large population of people already enrolled in the EMBARC research study and will use a variety of methods (e.g., eicosanoid profiling, use of demographic data set) to assess SARS-CoV-2 infection and the SDOH impact on neuroinflammation that is associated with depression. This work will pave the way for follow-up studies investigating the efficacy of anti-inflammatory therapies, including both existing and novel agents, for modulating variation in distinct eicosanoids and, in turn, mental health outcomes such as depression.

NSF Awards · FY 2024 · 2024-07

Data center networks rapidly evolve with higher speeds and increased programmability, accommodating communication between various elements in the data center such as central processing units, graphics processing units, and other accelerators. Emerging applications, particularly in artificial intelligence and high-performance computing, require efficient data transport across networks. Traditional transport stacks struggle to meet these demands, necessitating redesign and adaptability. This project plans to develop an end-to-end framework called Transcraft to streamline the design and implementation of network transport stacks. Transcraft aims to reduce development time and costs by providing an intuitive interface for developers to quickly create and verify transport design and implementation. The project addresses key challenges in computer networking, systems, and formal methods. It introduces techniques for specifying and verifying infrastructure constraints, workload requirements, and objectives, enabling automatic design synthesis based on formal specifications. To assist developers, Transcraft offers an intuitive interface for specifying properties and encoding pseudocode, which is iteratively refined through formal verification techniques. Additionally, the project will develop reusable templates for transport blocks, ensuring efficient integration and performance optimization across various platforms. Transcraft also includes benchmarks for performance tuning and validation tailored to workloads, properties, and configurations. This project has strong potential for broader impacts. The project will benefit practitioners and students by releasing open-source tools, models, implementations, and benchmarks, fostering innovation and learning. Research findings will be integrated into courses spanning networking, computer systems, and formal methods, enhancing educational programs. Collaboration with industry partners will ensure the effectiveness of Transcraft in diverse settings and promote its adoption. Additionally, the project will organize workshops and tutorials to share insights with practitioners and continue to mentor undergraduates and underrepresented communities, supporting educational and diversity initiatives. The open-source software, hardware, data, and results will be available for public use under a permissive open-source license on the project website: https://transcraft.io. 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 2024 · 2024-07

The project focuses on researching atomic memristors, a type of memory device critical for artificial intelligence and emerging communication systems, The research objective is to significantly advance scientific understanding of their physical operation and improving their reliability. These devices, made from ultra-thin atomic materials, promise a significant advancement in computing power and efficiency, overcoming current limitations in memory technology. The primary contemporary challenge is the durability of the memristor devices. The research aims to understand and improve the durability of these memristors by collaborative effort involving US and UK investigators with complementary expertise. The US investigator will lead the research on device engineering and circuit applications while the UK investigators will focus on advanced electrical characterization and reliability engineering. The successful completion of this research can substantially benefit artificial intelligence, computing, and communication systems. In addition, the research project will train several students in advanced electronic devices as part of workforce development, in line with the national goal to advance semiconductor chips. The research activity and outcomes are planned to be broadly disseminated to the public via publications in journals, presentations at conferences, and podcasts on media platforms. The objective of the project is to realize advanced memristors by researching atomically-thin materials with improved device endurance and reliability, which are the contemporary issues preventing practical applications. The research involves collaboration between US and UK researchers with complimentary expertise in electronic devices and device reliability. The proposed research employs a multi-disciplinary approach, combining device science, advanced materials characterization, and reliability engineering, to investigate the mechanisms of atomic memristor performance degradation and identify strategies for their mitigation. The US investigator will lead the research on material-device co-design, characterization, and circuit applications. The UK investigators will focus on research on electrical testing protocol, and reliability engineering. The research aims include understanding of ageing, fatigue and reliability issues, exploring the use of interfacial layers and optimized electrodes, and demonstrating high-performance computing and communication switching devices. The collaborative research intends to produce an engineered device structure and associated programming protocol for high endurance atomic memristors. The successful fulfilment of this research will lead to atomic resistive switching devices with orders of magnitude enhanced durability, suitable for applications in artificial intelligence and sixth-generation communication systems. This endeavor could significantly advance resistive switching devices based on atomic materials and enable practical applications in computing and communication technology, offering a path towards more energy-efficient and reliable electronic systems. 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 · 2024-07

Abstract Understanding how DNA is damaged and how the damage is repaired is critical. This is because DNA damage contributes to genome instability, aging, and diseases, and DNA-damaging agents are used in chemotherapy. Covalent DNA-protein cross-links (DPCs) are ubiquitous and bulky DNA lesions. Despite that it has been well accepted that DPCs are highly toxic, compared to other types of DNA damage, DPCs are much less well studied mainly due to the lack of approaches to detect, quantify, and synthesize DPCs. My research program studies DPCs at 3′-DNA termini (3′-DPCs) within single-strand breaks (SSBs). They are derived from the apurinic/apyrimidinic (AP) site that is one of the most frequently formed DNA lesions and induced by many endogenous and exogenous genotoxins including some anti-cancer drugs. If left unrepaired, 3′-DPCs will block DNA replication and transcription, prevent the SSB repair, cause genome instability, and may lead to cell death. We hypothesize that 3′-DPC formation is a previously uncharacterized cytotoxic mechanism of the AP site and its inducing agents, 3′-DPCs are new biomarkers of oxidative stress-related diseases, and inhibiting 3′-DPC repair will synergize DNA methylating agents. Our goal is to elucidate the formation and repair mechanisms of 3′-DPCs. In past work, we have detected 3′-DPCs in human cells using a novel mass spectrometry pipeline, but their cellular abundance and to what extent they are induced by genotoxins are unknown. We have chemically synthesized 3′-DPCs and demonstrated that they can be repaired by three human nucleases, but only when the cross-linked proteins are initially digested by trypsin. How 3′-DPCs are proteolyzed in cells remains elusive. We will fill these knowledge gaps. Notably, during studying 3′-DPC repair, we discovered in vitro that proteolyzed 3′- DPCs and an AP site repair intermediate (i.e., 3′-PUA) are excised by human three-prime repair exonuclease 1 (TREX1). This unexpected finding is the first to report a direct role of TREX1 in DNA repair and challenges the previous notion. It opened a new and exciting research direction that we will also pursue in this MIRA application. Our hypothesis is that TREX1 is a 3′-DNA lesion processing enzyme and a promising therapeutic target. Our goal is to delineate the functions and regulatory mechanisms of TREX1 in DNA repair. We will focus on several important questions. For instance, does TREX1 play a role in cells in response to DNA damage? If so, is that dependent on its exonuclease activity? And how is TREX1 recruited and regulated? We will address these questions and study 3′-DPC formation and repair mechanisms using interdisciplinary techniques including organic synthesis, quantitative mass spectrometry, proteomics, biochemistry, molecular and cell biology-based approaches. This research will advance fundamental understanding of DNA damage and repair. Such new knowledge will inform the development of novel therapeutic interventions.

NSF Awards · FY 2024 · 2024-07

Over the past decades, NSF has played a central role in enabling the transformation of Science and Engineering (S&E) research using computation-based methods, not only as a leading funder of pioneering research for all of S&E but also as a funder of the nation’s advanced research computing ecosystem. The Leadership-Class Computing Facility (LCCF) project is part of NSF’s broad, holistic advanced computing strategy intended to provide unique resources and services to enable discoveries in the largest and most computationally intensive S&E frontiers that could not advance otherwise. NSF’s stewardship of the LCCF draws on decades of leadership and experience in serving the full S&E research community with transformative cyberinfrastructure(CI). This award supports the construction of LCCF. The LCCF project, led by the Texas Advanced Computing Center (TACC), is envisioned as an advanced distributed leadership computing facility that will serve as a nexus for world-class computational capabilities. Integral to the facility will be the delivery of software and services that will support the continued transformation of the scientific discovery enterprise. At its core, the project will deploy a system called Horizon to support S&E simulation-based inquiry, data analytics, and Artificial Intelligence research at unprecedented scales. The Horizon system will be hosted at a commercial hyperscale datacenter by establishing a partnership to enhance academic-industry exchange. The project will partner with four Distributed Science Centers (DSCs) to expand its geographical footprint and leverage the deep expertise in our nation’s CI ecosystem. Moreover, the project will include a broad range of education and public outreach (EPO) activities designed to grow the future S&E workforce and ensure the entire nation benefits from access to the facility. The EPO plans include programs and exhibits based at a Visitor Center that will be constructed at TACC. These programs and exhibits will be piloted, assessed, and evolved during construction and are designed to reach a nationwide audience. 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 2024 · 2024-07

Algae are essential photosynthetic organisms that profoundly affect the global environment, ecology, and economy. The Culture Collection of Algae at the University of Texas at Austin (UTEX) is one of only a handful of large, publicly available algal biodiversity collections in the world, one of just two such collections in the U.S., and the sole collection in the U.S. focusing on freshwater and soil algae. The UTEX Collection is among the most diverse assemblages of living organisms available to the public and many of the algae maintained by UTEX are unique and irreplaceable. UTEX distributes thousands of living algal cultures to scientists, educators, and students throughout the U.S. and the world. Great interest in algae as sources of transportation fuels, human food, animal feed, pharmaceuticals, and many other uses makes the cultures and services provided by UTEX essential resources for researchers. Every year, approximately 1,000 published research articles, many of which recognize NSF support, reference the use of UTEX algae. UTEX provides extensive student training, hands-on workshops on managing algal cultures, an informative interactive web site, species identification services, chemical composition analysis, and extensive correspondence with students engaged in algal research. UTEX personnel give presentations at public schools, conduct tours of UTEX facilities, assist teachers and students in conducting high school science projects, and provide presentations on the scientific importance of algae to hundreds of school children at local open house events. UTEX is a curated public collection that serves as a permanent, living repository of algal biodiversity. It provides uniformity and stability of stocks and related materials that are necessary for the continuity and reproducibility of algal research and education. UTEX currently maintains 3,077 accessioned strains of living algae, including representatives of the cyanobacteria and all major eukaryotic clades, with 1,587 named species spanning 580 genera. The UTEX mission is to promote, support, and enable the use of algae for research, education, and practical applications. The primary goals of UTEX that fulfill this mission are (1) maintaining a well-curated permanent repository for algal biodiversity that insures the continuity and consistency of algal research; (2) providing living algal cultures and related materials to the user community at a modest cost; (3) acting as a source of information regarding algae to researchers, educators, and the interested public; and (4) participating in outreach to the user community through training, support services, and materials. The UTEX website facilitates a secure means for ordering goods and services, provides links to other resources pertaining to algae, and includes diverse algae-related information. Rigorous quality-control procedures are in place and a handbook of standard operating procedures is maintained and updated in order to ensure a high level of security for UTEX strains and safety for those who work with them. 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 2024 · 2024-07

Land surface characteristics of urban cities have long been known to affect rainfall amount, intensity, and timing. There is also growing appreciation of the role of a warming Earth as a driver of extreme precipitation amplification. This project will study the combined role of urban expansion and large-scale climate change on precipitation enhancement near urban areas through advanced numerical modeling. The results of the work will be disseminated to local stakeholders in Texas and Arizona to help inform decisions about infrastructure development, land planning, and resilience. The project will include training and educational opportunities for up to 8 early career scientists and students. The project will test the following hypothesis: ‘Large scale climate change will be the dominant factor responsible for increased extreme summertime rainfall; urban expansion will amplify impacts that will intensify existing events’. The project seeks to advance fundamental knowledge characterizing the processes impacting the spatio-temporal evolution of extreme summer rainfall over two rapidly expanding metropolitan areas across the US Sun Belt: Austin (TX) and Phoenix (AZ). The project work will: (1) conduct a set of Weather Research and Forecasting (WRF) simulations comprising of a suite of historically representative extreme wet summer seasons; (2) conduct a set of WRF simulations with identical configuration as the historical experiments, comprising of a suite of projected extreme wet summer seasons that account for urban expansion and greenhouse gas emissions, separately, and in tandem, using two contrasting dynamical downscaling methods (dynamical, and the pseudo-global warming approach); (3) conduct a process-based examination of the key physical drivers responsible for projected extreme summer season rainfall changes relative to the historical baseline. The high-resolution output in time (hourly) and space (2km grid spacing for the innermost domain) will permit improved process-based understanding of the mechanisms driving simulated extreme rainfall changes. 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 2024 · 2024-06

Project Summary New approaches to antibiotic development are needed to combat multidrug-resistant bacteria, and especially Gram-negative pathogens. The Gram-negative outer membrane prevents most molecules from entering the cell and is one of the greatest hurdles to new antibiotic development. A remarkable strategy to overcome this permeability barrier is shown by the new clinical antibiotic cefiderocol, which binds outer membrane siderophore receptors and uses active transport systems to pull itself into the periplasm. Using energy-coupled import allows otherwise exclude molecules, like the antibacterial component of cefiderocol, to enter bacteria. Unfortunately, few molecules capable of this translocation have been identified, and we have been largely limited to using siderophore conjugates to develop these innovative Trojan horse antibiotics. Our work on the understudied class of bacteriocins called microcins provides a rare opportunity to study a broader class of antibacterials with this membrane translocation ability. Microcins are small antibacterial proteins (<10kDa) that selectively bind Gram-negative outer membrane proteins and hijack active transport processes to enter the periplasm. Microcins have are effective at controlling pathogen growth in vivo and have many characteristics that could make them attractive antibiotic scaffolds. Despite their potential value, advances in microcin biology have been impeded by the challenges of their identification and the limited characterization of the only 15 known examples. To overcome the discovery bottleneck, we developed an approach for systematic identification and validation of new microcins. We have focused our research on class II microcins due to their prevalence among Gram-negative bacteria. Coupling an in silico pipeline with a new method for microcin activity screening, we are identifying microcins across phylogenetically diverse bacteria, including phylogroups that have never been examined for microcin activity. We have already validated over 50 novel class II microcins, which is 5X what has been discovered in the past 40 years. Our new appreciation for class II microcin diversity has made plain the critical need to develop detailed knowledge of their sequence-activity relationships to empower their future use in antibiotic development. Foremost among our gaps in knowledge is our lack of understanding of microcin cell entry and the diversity of receptors that microcins can target. These factors dictate the initial step required for microcins to cross the outer membrane and are central to controlling microcin spectrum of activity. To pursue these critical gaps in knowledge, we will take advantage of the large exclusive repertoire of unrecognized class II microcins we have discovered and will (Aim 1) provide the first in-depth microcin sequence- activity study to uncover postions import for receptor binding, cell entry, and antibacterial activity, (Aim 2) reveal how sequence variations among microcins influence their spectrum of activity, and (Aim 3) uncover the range of outer membrane receptors that can be targeted by microcins for cell entry.

NIH Research Projects · FY 2025 · 2024-06

Highly aggressive cancers are frequently characterized by tumor cell emboli within the lymphatic and blood vasculature. Termed lymphovascular space invasion (LVSI), this phenomenon has been of high interest to cancer researchers as it may represent one of the necessary events during progression from a localized to metastatic cancer. Despite these biological implications, relatively little is known about the mechanisms that directly enable and promote LVSI formation. Existing in vitro systems lack the multi-tissue and vascular complexity to model these events. In vivo models, while available, are not amenable to mechanistic studies or pharmacological screening because of the sheer number of animals required for such experiments. Therefore, a critical need in the field is to develop models that can faithfully recreate specific phenomena related to metastatic spread, such as LVSI. Using our novel, multi-cellular, vascularized 3D in vitro platform, we were able to model intravasation of epithelial emboli and LVSI formation of inflammatory breast cancer (IBC) ex vivo for the first time. IBC is an aggressive breast cancer variant characterized by extensive LVSI. Gene expression data from IBC patients identified stromal infiltration and activation as a critical component of LVSI. Using our new in vitro platform and animal models, we were able to confirm this finding when we discovered that macrophages in the microenvironment directly promote LVSI formation. Leveraging our new in vitro platform, we propose to answer three major questions relating to LVSI: What mechanisms promote 1) formation, 2) migration, and 3) intra-vessel survival of tumor emboli? We hypothesize that LVSI formation is a two-step process where matrix properties and epithelial marker, E-cadherin which is strongly expressed in IBC, regulate tumor emboli formation and survival, while the cytokine axis, CCR7/CCL21, homes epithelial emboli to lymphatics. To test this hypothesis, we propose to use our new in vitro platform in three aims: 1) Determine the role of matrix mechanics and lymphatic pumping in the temporal kinetics of LVSI, 2) Determine the role of E-cadherin in emboli formation and survival, and 3) Identify the mechanisms that promote emboli homing to vasculature. Despite the strong clinical evidence that LVSI is a critical, pre-metastatic phenomenon, our inability to fully recreate LVSI in vitro has severely limited our mechanistic understanding of responsible pathways. For the first time, our team was able to recreate LVSI ex vivo using a novel microfluidic platform. Here, we propose to use our in vitro platform to define the signaling steps that promote LVSI formation and survival in vasculature to better define critical targets related to cancer progression. To execute the proposal, we have assembled a team composed of experts in tissue bioengineering, clinical research, and preclinical models of breast cancer. If successful, our work will offer novel and customizable platforms for studying LVSI and new biological discoveries that hold therapeutic potential for patients with advanced breast cancer.

NIH Research Projects · FY 2026 · 2024-06

PROJECT SUMMARY/ABSTRACT Emerging evidence suggests that age and depression, even the modest levels common in aging, may interact to produce a “double jeopardy” for episodic memory impairment and may predict cognitive decline and Alzheimer’s disease (AD). The underlying cause/s of this double jeopardy is unknown. Even less is known about depression- related memory impairments in Black/African American and Mexican Americans, despite evidence of more disabling depression, and AD prevalence than in non-Hispanic Whites (NHWs). Multiple race-related proxy factors (e.g., discrimination, vascular burden, religiosity) that may exacerbate or reduce depression-related memory impairments but they have seldom been explored. Executive dysfunction may be an important contributor to depression-related episodic memory impairments but studies of depression-related memory and executive functioning impairments have been conducted in parallel. We propose a new conceptual framework in which depression-related executive and associated PFC dysfunction underlie depression-related memory impairments, double jeopardy effects, and ethnoracial disparities in these impairments. We will enroll 330 adults from Black, Mexican, and NHW groups across the adult lifespan. Consistent with an RDoC framework, we will assess depression along a continuum and examine depressive symptom dimensions (i.e., somatic, depressed mood, etc.), and consider age of onset and chronicity that may differ by age and race/ethnicity. We will use a combination of cognitive neuroscience and clinical neuropsychology approaches, innovative memory tasks manipulating executive functions, univariate, multivariate, and multimodal neuroimaging, and longitudinal clinical and cognitive assessments to identify the neural mechanisms underlying depression-related memory impairments. With 2 fMRI experiments that use different approaches to manipulate demands on executive functioning (Aim 1: inhibition of mnemonic interference and Aim 2: spontaneous and instructed emotion regulation), we bridge across diverse literatures with our unifying executive dysfunction framework. In Aim 3, we test racial/ethnic group differences in depression-related memory alterations, neural mechanisms underlying them, and psychosocial factors that may influence group differences. In exploratory Aim 4, we use cutting-edge analyses to explore multi-modal neuroimaging markers of depression-related memory impairment and decline in older adults. Should the neural mechanisms by which depression negatively impacts memory depend upon age, race/ethnicity and related psychosocial factors, it would suggest a need to update and advance current theories of depression-related cognitive impairment to incorporate the influence of these factors. These results may reveal who may be most sensitive to the negative cognitive effects of depression and identifying reasons why, informing future, personalized brain stimulation or lifestyle interventions, tailored to one’s age, race/ethnicity and related factors to reduce depression-related cognitive impairment.

NIH Research Projects · FY 2025 · 2024-06

PROJECT ABSTRACT 40% of patients who are diagnosed with cocaine use disorder are considered to have a severe cocaine use disorder meeting six or more criteria from the DSM-5. The lack of effective medication for cocaine use disorder demonstrates an urgent need to better understand the effect of cocaine on neurobiology and behaviors. Cocaine- induced increase in striatal dopamine release is essential for cocaine reinforcement, however, the mechanisms of striatal circuit adaptations inducing cocaine seeking is not well established. The overall objective of this proposal is to determine the mechanism by which cocaine affects striatopallidal circuit activity to facilitate cocaine seeking and taking. My central hypothesis is that 1) cocaine-induced increases of the opioid peptide, enkephalin in the striatum suppresses GABA transmission from striatal neurons via δ/µ opioid receptors and, as a result, disinhibits VP GABA neurons, and 2) striatal enkephalin plays a key role in cocaine seeking. Aim 1: Determine the necessity of striatal enkephalin in cocaine-induced adaptations in the striatopallidal circuit: Based on our preliminary data and previous findings, I hypothesize that increase in enkephalin in the striatum during withdrawal from a history of cocaine exposure leads to suppression of GABA transmission from enkephalin-expressing striatal neurons, which increases excitability of the postsynaptic VP GABA neurons. We will test this by performing whole-cell electrophysiology recordings in D2-MSN-selective enkephalin knockouts with a history of cocaine exposure, and measure GABA transmission from striatal neurons onto VP GABA neurons and VP neuron excitability. The use of exogenous enkephalin and opioid receptor selective antagonists will confirm striatal enkephalin and determine the type of opioid receptor as a mechanism for depression of GABA transmission and increased excitability. Immunohistochemistry will confirm the type of recorded VP neurons. Aim 2: Determine the role of striatal enkephalin in cocaine self-administration: Based on our preliminary data, I hypothesize that striatal enkephalin facilitates self-administration and cocaine seeking. We will test this by performing operant self-administration using striatal neuron-selective enkephalin knockouts and examine the effect of striatal enkephalin deletion on cocaine seeking and taking and the motivation for cocaine. Through completion of this proposal, and under the guidance of my sponsors, Drs. Lauren Dobbs and Robert Messing, who are experts in substance use disorder research, I will receive extensive training to develop professional skills, expand my laboratory skillset, and improve my communication skills for post-doctorate research career in neuroscience. Combined with the training resources and expansive research expertise available at University of Texas at Austin, I will be well-supported throughout this fellowship and make a successful transition to a post-doctoral research position.

NIH Research Projects · FY 2026 · 2024-06

ABSTRACT Natural products offer a rich and plentiful source of novel compounds with biological activities from which fresh inspiration can be drawn for the discovery and design of new pharmaceuticals. Moreover, the rapid pace at which bioinformatic and genomic technologies are developing has led to a wealth of untested leads and intriguing questions regarding the biosynthetic pathways for these compounds. Enzymes utilizing radical intermediates are featured prominently here catalyzing chemical transformations that would otherwise not be possible under physiological conditions. Consequently, secondary metabolism is characterized by a multitude of unusual chemical structures rarely observed in primary metabolism. However, the instability of free radicals can easily lead such enzymatic reactions to go awry due to even minor perturbations. Not only does this suggest a mechanism for the evolution and diversification of radical-mediated transformations as proposed for radical SAM (S-adenosyl-L-methionine) enzymes but also implies that these enzymes may be engineered to catalyze similarly challenging transformations with applications in synthetic biology. In the spirit of helping to realize this potential, we have identified two primary areas of investigation with additional exploratory worked planned as well. The first direction involves study of the homologous pair of dehydratase and dehydrogenase twitch radical SAM enzymes BlsE and HikC, which respectively participate in the biosynthesis of the fungicide blasticidin S and antihelminthic agent hikizimycin. Given their evolutionary relationship, we hope to tease apart their catalytic properties in a comparative manner in order to understand how the fates of their radical intermediates are channeled to effect two distinctly different catalytic outcomes. The second direction focuses on biosynthesis of the antiviral nucleosides oxetanocin A and albucidin. Where one would normally expect a ribose, these natural products instead possess a four-membered oxetane ring that is constructed via radical-mediated transformations catalyzed by B12-dependent radical SAM enzymes. This chemistry is thus unique among the cobalamin- dependent radical SAM enzymes, which are primarily known to function as methyltransferases. These two projects are not only designed to offer new insights into the mechanisms of secondary metabolic enzymes that utilize radical intermediates but also to open new avenues of study. Nevertheless, a third component of the proposal is specifically designed to probe high risk systems including biosynthesis of the cis-fused cyclobutane ring system of ladderanes; a non-heme iron enzyme with a unique quadruple-histidyl/carboxylysyl coordination sphere newly discovered in the biosynthesis of oxazinomycin; as well as a radical SAM enzyme that catalyzes an unusual sulfur-for-oxygen bridge swapping reaction during biosynthesis of the Trojan horse antibiotic albomycin. Collectively our efforts are intended to provide a solid and principled foundation on which chemical biologists and biotechnologists can ground their own research and discovery efforts for the betterment of human health and wellbeing.

NIH Research Projects · FY 2026 · 2024-06

Project Summary Cholera is a deadly diarrheal disease caused by the bacterial pathogen Vibrio cholerae. It remains poorly controlled in many parts of the world and outbreaks have been surging despite global efforts to reduce infection. New antibacterials for Gram-negative bacteria like V. cholerae are greatly needed but are also the most challenging to make because the outer membrane of these bacteria excludes nearly all molecules from entering the cell. An innovative strategy to overcome this permeability barrier is shown by the new clinical antibiotic cefiderocol, which binds outer membrane siderophore receptors and uses active transport systems to enter the periplasm. Unfortunately, few molecules are known that are capable of this feat, and we have been largely limited to using siderophore conjugates to develop these innovative Trojan horse antibiotics. Our work on the understudied class of bacteriocins called microcins provides a rare opportunity to investigate a broader class of antibacterials with this membrane translocation ability. Microcins are small antibacterial proteins (<10kDa) that selectively bind Gram-negative outer membrane proteins and hijack active transport processes to enter the periplasm. Microcins have are effective at controlling bacterial pathogen growth in vivo and have many characteristics that could make them attractive antibiotic scaffolds. Despite their potential value, advances in microcin biology have been impeded by the challenges of their identification and the limited characterization of the only 15 known examples. To overcome the discovery bottleneck, we developed an approach for systematic identification and validation of new microcins. Coupling an in silico pipeline with a new method for microcin activity screening, we are identifying microcins across phylogenetically diverse bacteria, including phylogroups that have never been examined for microcin activity, such as the Vibrionaceae. We have identified potent Vibrio microcins active against all clinical strains of V. cholerae tested and which we show can be delivered by bacteria vectors to reduce V. cholerae colonization in mice. Our new appreciation for class II microcin diversity and their potential to treat V. cholerae infections has made plain the critical need to develop detailed knowledge of their sequence-activity relationships and ability to prevent and treat gut infections using cell-based delivery vectors to empower their use in antibiotic development. To pursue these critical gaps in knowledge, we will take advantage of our exclusive repertoire of unrecognized V. cholerae class II microcins and will (Aim 1) provide the first in- depth microcin sequence-activity study to uncover domains import for receptor binding, cell entry, and antibacterial activity, (Aim 2) investigate the use of different delivery bacteria, dosing regime, and microcin expression systems on microcin efficacy in mouse models, and (Aim 3) expand our understanding of the range of outer membrane receptors that can be targeted by Vibrio microcins for cell entry.

NIH Research Projects · FY 2025 · 2024-06

PROJECT SUMMARY/ABSTRACT Down Syndrome (DS) impacts approximately 1 in about 700 babies born in the United States. Language and motor development in DS are significantly delayed in early childhood; however, little research has investigated how language and motor skills interact and support each other. In response to the NIH INCLUDE Down Syndrome Research Plan, the proposed study will address several gaps in our understanding of DS. First, we will implement multiple methods, including technology, to measure language and motor development across direct assessments, naturalistic measurements, parent reports, and free play observations. Second, we intend to actively recruit and enroll over 60% of participants from racially/ethnically minoritized backgrounds. Finally, we will collect longitudinal data to track measures that may be sensitive to developmental change. Using multiple methods, we will track developmental trajectories of language and motor skills in infants with Down Syndrome (DS) and typically developing infants over a 12-month period. The goal is to measure language, communication, motor skills, and physical activity to better understand how these skills develop and interact with each other over time. If funded, we will recruit 36 infants with DS (age 6 months – 18 months) and 36 typically developing (TD) infants (age 6 months – 18 months) and follow them for 12 months. We intend to recruit at least 60% of our sample from racial/ethnic minority backgrounds (i.e., Hispanic/Latino, Black/African American, Asian, Native American). Infants and their caregivers will complete standardized questionnaires and assessments at study entry, then two more times, 6 months apart, for a total of three assessments in a 12- month period of time. This research will provide critical data on the early development of racially/ethnically diverse infants with DS to inform intervention strategies and supports.

NIH Research Projects · FY 2026 · 2024-05

Summary There is a dire need for research addressing caregivers of persons with Lewy Body Dementias (LBD), the second most common cause of dementia. LBD encompasses Dementia with Lewy Bodies and Parkinson’s Disease with Dementia and accounts for 4 to 15% of dementia cases. Core symptoms of LBD present a distinct profile of caregiving demands driving high stress: fluctuations in cognition, hallucinations, delusions, and behavioral sleep disturbances (including acting out dreams). These are compounded by cognitive symptoms of AD and motor symptoms of Parkinson’s Disease, shared by LBD. Caregivers living with a spouse or romantic partner who has LBD (N = 150 caregivers) will complete a baseline interview and Ecological Momentary Assessment surveys (EMA; 5 minute surveys) every 3 hours for 4 days. The surveys involve reports of care recipient symptoms, caregiving tasks and stress, self-efficacy, support and well-being. Caregivers will wear a Fitbit to measure cardiovascular functions (heart rate) and sleep as indicators of stress reactivity. The care recipient will wear a FitBit to assess agitation via physiological indicators (e.g., heart rate). Aim 1: Identify associations between care recipient symptoms, caregiver tasks and stress throughout the day. The Caregiver Stress and Coping Model addresses caregivers’ stress reactivity (associations between appraisal of stress and well-being). To intervene effectively for LBD caregivers, we must ascertain which combinations of symptoms and caregiving tasks have the greatest immediate and cumulative impact on caregiver stress throughout the day. Example hypothesis: Caregivers will report greater stress when dealing with LBD symptoms than other caregiving demands. Aim 2: Examine how caregiver stress is associated with mood and cardiovascular stress responses throughout the day. The Stress Pile Up Model suggests that demands and stress may accumulate throughout the day generating worse outcomes at the end of the day. Caregivers will sleep more poorly when they report more cumulative caregiving demands, particularly symptoms unique to LBD. Aim 3: Investigate two possible resilience factors (efficacy and social support) to buffer LBD care-related stressors on well-being. Based on Self Efficacy Theory, during periods of the day when caregivers experience greater efficacy, they will appraise caregiving as less stressful and experience better mood and cardiovascular functioning. LBD caregivers report greater difficulty obtaining social support than caregivers for other dementias. Social support theories suggest that when caregivers have respite or social support during the day, they will be less reactive to caregiving stress. LBD is a highly challenging form of dementia with shared symptoms of other dementias, and unique core symptoms (e.g., hallucinations, cognitive fluctuations) that may exacerbate caregiver stress. Studies of caregiver stress, interventions, and services have largely used samples with AD and other dementias. To enhance the well-being of caregivers for older adults with LBD, we must gather the information necessary to design LBD-tailored interventions with an understanding of the daily contexts in which symptoms, caregiving, and stress occur.

NIH Research Projects · FY 2026 · 2024-05

Project Abstract Current treatments of Alcohol Use Disorder (AUD) have shown moderate success in reducing heavy alcohol drinking but are marred with the problem of treatment adherence. In the clinic, opiate receptor pharmaceutics are often combined with cognitive behavioral therapies to improve long-term abstinence. These findings suggest an important relation between endogenous opioid signaling and cognitive factors in the treatment of AUD; however, lapses in treatment can quickly reinstate alcohol drinking, highlighting a knowledge gap in our understanding of how these mechanisms may influence long-term misuse. In this regard, alcohol consumption stimulates the release of endogenous opioids, including enkephalins that bind to mu-type opioid receptors (MOR) commonly found in limbic areas of the brain. The manipulation of MOR signaling alters the rewarding properties of alcohol, with agonists facilitating reward and consumption, and antagonists blocking these responses. The shared relation between opioidergic responses that underlie motivation and cognition are not well understood but present a focal point for addressing complex pathologies that may underlie alcohol-related sensitivities. In this regard, MORs are found in frontal cortical regions that modulate cognitive function, such as the medial prefrontal cortex (mPFC). Preclinical studies in our laboratory demonstrate that alcohol dependence in rats decreases the phosphorylation of MOR in the mPFC, and increases expression of the neuropeptide precursor, proenkephalin (PENK). This pattern of changes overlaps with clinical observations of MOR desensitization in AUD patients. The findings suggest that dependence may dysregulate opioidergic signaling in the mPFC, although the extent to which such conditions surmise changes in the endogenous ligands is unclear. A better understanding is warranted given that adherence to opiate antagonists diminishes over protracted abstinence and may be undermined by molecular intermediates in the processing of small-opioid peptides. Here, we will explore the central hypothesis that non-canonical PENK signaling in the mPFC plays a pivotal role in dysregulating cognitive function during abstinence. Towards this goal, discovery-based and quantitative mass spectrometry approaches will be combined with in vivo microdialysis to broadly capture PENK-mediated signaling in alcohol-dependent rats undergoing abstinence (Aim 1). We will then explore the functional relevance of non-canonical PENK signaling in relation to hyperexcitable states of withdrawal (Aim 2) and induced-deficits in cognitive flexibility (Aim 3). The results are expected to provide insight into druggable targets that extend beyond conventional opioidergic signaling processes and will establish a framework for mechanisms of cortical excitability that may be influential in AUD pathology and cognitive behavior.

NIH Research Projects · FY 2026 · 2024-04

Project Summary Childhood obesity remains a significant public health problem and obesity risk begins early in life. There is a need for accessible and comprehensive interventions focused on modifiable behaviors in infancy. This proposal is an efficacy trial for the virtual Mothers and CareGivers Investing in Children (MAGIC) FEED+ program designed to foster responsive bottle and infant feeding and healthy eating habits starting in infancy, compared to an attention control arm. Our pilot work has successfully implemented the MAGIC-FEED program with responsive feeding coaching and focusing on complementary feeding to under and un-insured families in the Austin area. The proposed research builds upon our partnerships and expands the intervention period to earlier in infancy to include responsive bottle- and breast-ffeeding and includes longer-term follow up of infants to disentangle the role of the intervention on child self-regulatory behaviors and longer-term adiposity. Our trial will enroll 266 predominately low-income and Hispanic caregivers in early infancy and will deliver the intervention starting at child age 3 weeks with intervention visits at 3 weeks, and 3, 6, 8, and 10 months. In- person assessments of growth and body composition and child self-regulation will occur at child age 3 weeks, and 13 and 24 months. Aim 1 focuses on main intervention effects on child growth and body composition. Aim 2 focuses on intervention effects on caregiver nutrition knowledge, and quality, caregiver responsive feeding and child self-regulation, and examines the effect of MAGIC-FEED+ and the role of potential drivers of growth (caregiver feeding practices and child self-regulatory skills) in infancy on children’s propensity to eat in the absence of hunger and adiposity/body fat at 24 months. Aim 3 determines whether MAGIC-FEED+ demonstrates the factors necessary to be a successful intervention for broader dissemination. This proposal is the first dynamic and interactive virtual trial designed to support heathy breast-, bottle and complementary feeding with robust measurements of responsive feeding, self-regulation and adiposity. These results will inform a pragmatic trial, and if effective, the MAGIC-FEED+ program is poised for wide dissemination and public health impact.

NIH Research Projects · FY 2026 · 2024-04

PROJECT SUMMARY Chronic obstructive pulmonary disease (COPD) is the third leading cause of death in the United States, imposing a significant economic burden due to its high morbidity and mortality. The Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria is a universally accepted disease severity staging score. However, GOLD score is not a strong predictor for mortality or progression risk at early or pre-disease stages. Early intervention is crucial for slowing COPD progression and improving quality of life. Therefore, there is a need to develop robust, quantitative metrics for characterizing disease state and progression risk. Existing quantitative computer tomography (CT) methods are based on analyzing variations in CT Hounsfield Units (HU) and have shown moderate to strong correlation with disease state. However, HU values are known to be breathing-effort dependent. As a result, quantitative CT methods require heuristic normalization schemes to adjust for varying lung inflation levels and are known to lack reproducibility. We previously developed a robust class of CT-derived ventilation (CTV) methods that calculate breathing-induced volume changes apparent on inhale/exhale CT (IE- CT) image pairs, as a surrogate for ventilation. In addition to numerical stability, our CTV demonstrated a higher correlation with nuclear medicine-based ventilation imaging than any other method in the literature. We recently extended the CTV framework to calculate changes in blood mass apparent on IE-CT, as a surrogate for pulmonary perfusion. Our novel CT-Perfusion (CTP), taken together with CTV, comprise our CT-derived functional imaging (CTFI) methodology. CTFIis the first to mathematically describe changes in inhale/exhale HU values in terms of ventilation and perfusion. This allows us to compute VQ (ventilation/perfusion) ratio imaging that is inherently normalized to patient breathing effort. Thus, any early microvascular changes or VQ mismatch associated with COPD disease severity can potentially be detected and quantified on IE-CT images. We hypothesize that a CTFI-informed machine learning model has higher discriminative power in assessing survival and disease progression than traditional methods such as FEV1, BODE index and other quantitative imaging markers. To test this hypothesis, we will utilize data from the Genetic Epidemiology of COPD (COPDgene) study, a multicenter observational study designed to identify genetic factors associated with COPD. We will adapt state- of-the art unsupervised deep learning methods and fully leverage the rich COPDgene data set to train a lung lobe segmentation model and automate the CTFI calculation pipeline. Next, we will develop and validate both physics-based and deep learning-based CTFI VQ scoring methods. Finally, we will develop a machine learning model which takes clinical information and patient CTFI lobar scores (ventilation, perfusion, & VQ) as input, and quantifies disease severity, predicts 5-year survival, and predicts future exacerbation and progression risk. All developed software and training data will be made publicly available to encourage further research in this field.

NIH Research Projects · FY 2025 · 2024-04

PROJECT SUMMARY/ABSTRACT Precise control of voluntary movement is crucial for almost all behaviors and the quality of life. While many brain regions are involved in the process, the interaction between the cerebral cortex and the cerebellum is particularly essential. When the cerebellum communicates with the cerebral cortex, it sends signals to the thalamus, which relays the information to the cerebral cortex. This cerebello-thalamo-cortical circuit has been studied extensively because of its functional significance. However, the current understanding of the circuit is based mainly on anatomical connection and the assumption that neurons within each brain region behave similarly. Molecular and physiological heterogeneity within the neuronal population is barely considered, posing a challenge in understanding how the circuit allows coordinated movements of the entire body. First, although the cerebellum projects axons to various thalamic subregions, the strength of synaptic transmission substantially varies. Therefore, the anatomical connection does not accurately represent the functional organization of the circuit. Second, many recent studies showed that a neuronal population, traditionally considered a single group, can be divided into several subtypes based on their distinct gene expression profiles. These molecularly defined neuronal subtypes often show different physiological properties and anatomical connectivity, engaged in distinct functional circuits. Recently, we studied the functional properties of the ventrolateral thalamus (VL), one of the thalamic subregions and the primary target of the cerebellum. While the VL is traditionally considered a homogenous neuronal population, our preliminary data showed substantial variation in their excitability and synaptic properties, which might reflect previously unrecognized connectivity between the cerebellum and the VL. Furthermore, a recent study showed that VL neurons consist of several subtypes exhibiting distinct patterns of gene expression. These data suggest that the functional organization of the cerebello-thalamo-cortical circuit is finer and more sophisticated than previously thought. In the proposed research, we will perform whole-cell patch-clamp recordings and circuit tracing with the transgenic mice that label the molecularly defined VL neuron subtypes. We will study their projection patterns to the cerebral cortex and their contribution to the functional heterogeneity in the VL (Aim 1). We will also examine their presynaptic origin in the cerebellar nuclei and the extent to which the cerebellar nuclei contribute to the functional heterogeneity in the VL (Aim 2). Successful completion of this project is expected to provide novel insight into the organization of the motor circuit.

NIH Research Projects · FY 2025 · 2024-03

Project Summary There is an urgent need to address the current public health crisis of opioid abuse and overdose deaths through development of effective treatments for opioid use disorder (OUD) and non-addictive therapeutics to manage pain. Ultimately, achievement of these goals would be greatly facilitated by the existence of novel ex-vivo models that recapitulate key features of neurobiology underlying the addictive process using human cells and advanced imaging systems that can monitor the interactions between multiple neurotransmitter actions driving opioid responses and reward pathways. This proposal aims to develop new technologies to create such ex-vivo models and imaging systems, aiming at probing dynamic behaviors within the models at high spatial and temporal resolution. Aim 1 will focus on recapitulating neuronal pathways in the ventral tegmental area (VTA) and nucleus acccumbens core (NAc), which have long been recognized to form the basis of substance abuse disorders. Specifically, we propose an additive manufacturing approach based on 3D bioprinting of human induced pluripotent stem cells (hiPSCs) to establish 3D cultures within brain-mimetic scaffolds. Moreover, use of an innovative, self-healing biomaterial as a printing medium and 3D culture scaffold enables “stitching” of unique neuronal tissues constructs into integrated, yet regionally defined, complex networks. For example, we propose to integrate tissue modules representing the GABAergic/dopaminergic circuitry of the VTA with tissue modules representing the GABAergic medium spiny neurons on the NAc. In addition, these tissue-engineered networks are optically transparent and easy to image, making them great models to study neural networks driving opioid responses and reward pathways. In Aim 2, we will separately develop a TIRF (Total Internal Reflection Fluorescence) microscopy technique to probe agonist-dependent dimerization of MOR (human µ-opioid receptor) at the single-molecule level and a hyperspectral and lifetime imaging system to monitor the dynamics of dopamine, GABA, glutamate and Ca2+ simultaneously. Together, these new imaging methods will enable dynamic monitoring of the effects of opioids, and other small-molecule therapeutics, on the neuronal circuitry underlying addictive processes. Overall, we expect these technological innovations to provide crucial tools for development of new therapeutics which can effectively combat the opioid crisis.

NIH Research Projects · FY 2025 · 2024-03

SUMMARY Human cytomegalovirus (CMV) is an enveloped, double-stranded DNA beta-herpes virus that has co-evolved with humans for ~200 million years. Over 90% of octagenarians are seropositive for CMV antigens, often with no knowledge that they harbor the virus. While its prevalence goes relatively unnoticed by the general public, CMV is the primary infectious cause of congenital birth defects and causes significant morbidity and mortality in immunocompromised individuals. Despite considerable effort, the many therapeutic antibodies and vaccines evaluated in clinical trials have not progressed, while commonly used antivirals have significant toxicities and induce resistance. The largest vaccine trial to date observed ~50% efficacy, which correlated with non- neutralizing antibody responses, suggesting key roles for antibody-dependent effector functions in protection. A challenge in developing CMV antibody therapeutics and vaccines is the arsenal of immune evasion strategies deployed by this virus. Antibody MSL109 failed phase II trials apparently due to an escape mechanism that resulted in new viral particles being coated with MSL109. The mechanism appeared to involve viral proteins that bind human IgG Fc domains (viral Fcg receptors or vFcgRs) and impeded antibody effector functions by blocking interactions with host Fcg receptors on immune cells. We hypothesize that blocking antibody capture by viral Fcg receptors will enhance protection by anti-CMV antibodies. We will evaluate this hypothesis using two complementary aims with translational relevance. Aim 1 will engineer the human IgG1 antibody Fc to identify variants that resist vFcgR capture and could be incorporated into future anti-CMV therapeutics, while Aim 2 will evaluate the ability of antibodies whose Fab domains bind the vFcgRs to block Fc capture and thereby enhance antibody protection. The antibodies produced in this project will be rigorously characterized in vitro for antigen and host Fc receptor affinities, the ability to mediate antibody-dependent cellular cytotoxicity and prevent viral spread using CMV-infected cells in vitro since there is no simple animal model of CMV disease. The long-term goal of this research is to support development of potent antibody therapeutics and vaccines that prevent cytomegalovirus disease in high-risk populations, including newborns and organ transplant recipients. The specific objective of this proposal is to determine the impact of antibody Fc capture on anti- CMV antibody activities and the potential for strategies blocking these interactions to eliminate CMV-infected cells and prevent viral spread. The expected outcomes include (i) engineered human IgG1 Fc variants that resist capture by the two best characterized vFcgRs and (ii) determining the increased protection that can be gained by blocking Fc capture. This project will provide insights into a key CMV immune evasion strategy and the contributions of Fc-dependent functions to CMV protection with relevance for future CMV therapeutics.

NSF Awards · FY 2024 · 2024-03

Genetically engineered crops remain controversial because of the unknown impacts these crops and their engineered genes have on human and ecological health. While genetically engineered crop genes can give helpful traits like pesticide resistance to crops, some can also be harmful if they are released in the environment. Antibiotic resistance genes (‘ARGs’) and silencing RNA genes are two examples of genes that are potentially harmful. ARGs can increase the number of antibiotic resistant bacteria in the environment, which is a threat to public health. Silencing RNA genes can affect the genetic material of other organisms and the behavior of these genes in the environment is not well understood. Persistent pollutants like microplastics have been shown to make these genes more stable in the environment, making it more likely that they can be transported widely and negatively affect beneficial organisms. The goal of this research is to assess the transport, persistence, and uptake of ARGs and silencing RNA genes that are attached to microplastics in the environment. Understanding how genetically engineered crop genes behave in the environment is important for many fields including agriculture, medicine, and water treatment. The results have strong potential to advance knowledge and benefit society through the development of risk-based management policies to protect health by minimizing the spread of harmful genes. The use of genetically engineered (GE) crops has remained controversial due to uncertainty regarding the ultimate fate and potential impacts the engineered genes can have on the surrounding environment. Common transgenes contained in modern GE crops include ARGs and silencing RNAs that have recently been detected in wastewater treatment plants and other environments. These findings are concerning because transgene contributions to global antibiotic resistance and their potential impacts to gene expression in environmental microbes are highly uncertain. Transgenes have also recently been shown to adsorb to the surfaces of micro- and nano-scale plastics (‘MNPs’) that are frequently found in wastewater treatment plants and soils, suggesting their transport potential and resistance to degradation in the environment may be greater than currently estimated. The goal of this research is to understand how MNPs impact the transport of GEs in the environment. This goal will be achieved using a combined modeling and experimental approach to: i) Quantify transgene adsorption kinetics to MNPs, soils, and wastewater biosolids; ii) Assess the effects of key environmental factors on the persistence and uptake of GE transgenes; and iii) Evaluate transgene transport and transformation of model soil bacteria in agricultural soils. Successful completion of this research directly addresses important research gaps concerning transgene adsorption to MNPs, their behavior in the environment, and translation of experimental data to modeling frameworks that can be utilized by diverse stakeholder groups. Benefits to society result from interdisciplinary research training for graduate and undergraduate students to improve the Nation’s STEM workforce. Additional benefits result from enhanced scientific literacy through learning modules for undergraduate classes and development of outreach materials focused on microplastics in the environment for K-12 schools in the Palouse region of Washington State. 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.