Pennsylvania State University, The

NIH Research Projects · FY 2026 · 2026-06

Modified Project Summary/Abstract Section Although health disparities between rural and urban communities have been known for decades2–5, there is evidence individuals from rural areas are less likely to participate in translational research and clinical trials6. Rural communities face higher mortality than urban communities for the six leading causes of death in the US–heart disease, cancer, unintentional injuries, COVID-19, stroke, and chronic lower respiratory disease.20–23 This has been referred to as the ‘rural mortality penalty’ as rural areas show slower declines in mortality compared to urban areas.14,24 Barriers to research participation among rural populations include participation costs (e.g., travel time, monetary), limited Internet connectivity, and socio-cultural barriers (e.g., perceived lack of anonymity)6. NCATS’s More Treatments for All People More Quickly initiative outlines the need to develop effective treatments that can reach underserved populations, which highlights the need for a research tool that can collect data and administer interventions in the privacy of participants homes regardless of Internet connectivity. Given the ubiquity of smartphones (~90% ownership in rural areas), the planned research will test the Wear-IT app,7 a smartphone research platform that can reduce barriers for rural populations by 1) ensuring a fast and responsive experience even when Internet is limited; and 2) delivering automatic, personalized interventions. Wear-IT is unique in the mHealth space due to its on-device processing model which allows for real-time responsiveness when Internet is unavailable7 with data uploaded to the cloud for more computationally intense processing when a participant passively encounters better connectivity (e.g., travel to town, WiFi). Wear-IT can flexibly assess complex clinical targets through multi-modal ecological momentary assessments (EMA) including video, photo, geolocation, and survey responses. On-device processing of multi-modal EMA or sensor data (e.g., step count) also enables delivery of just-in-time adaptative interventions (JITAI)7, which aim to provide personalized information or support at the exact moment it is needed.8 The proposed study will demonstrate the translational and clinical utility of Wear-IT by assessing diet-related health behaviors in 100 rural families with children from the Appalachian region. Using Federal Communications Commission fixed and mobile Broadband coverage data, targeted recruitment will ensure half the families (n = 50) have at-home Broadband and half (n = 50) have poor/no at-home Internet. Parents will use the Wear-IT app for three weeks. During the 3-week period, parents will receive EMA prompts and JITAI messages related to the three diet-related health behaviors: 1) home food environment; 2) home meals; and 3) food shopping (Figure 1). Assessing the acceptability and feasibility of Wear-It in rural communities will help to increase rural representation in health research and clinical trials, which is the first step in addressing persistent health disparities in rural communities.

NIH Research Projects · FY 2026 · 2026-06

Project Summary/Abstract Increasing the number of infants in the neonatal intensive care unit (NICU) who can be fed using mothers’ own milk (MOM) is crucial for reducing expensive co-morbidities experienced by premature and ill infants. Mothers on NICU infants have delayed secretory activation (SA) and challenges to maintain SA, and coming to volume (≥500 mL/d by d 14 postpartum, CTV). However, the biological mechanisms that are involved in inhibiting the initiation and establishment of lactation in this at-risk population are generally poorly understood. SA involves the closing of tight junctions in the mammary gland and the transition to copious milk production. Following this transition, the mammary gland transitions from endocrine to paracrine/autocrine regulation of lactation, leading to an increase in milk volume. Both SA and CTV are critical for initiation and maintenance of lactation, and prior data suggest that both may be impacted by maternal health factors. In our prior work, we found that both transcriptomic gene expression and lipid metabolism are associated with milk production in mothers of term infants later in lactation. However, similar work has not been done during early lactation or in the NICU population. In this project, we will use samples from a highly-controlled parent trial to investigate the molecular and metabolic pathways that are associated with the achievement of SA and CTV in the first 2 weeks postpartum (pp). We will use transcriptomics, as well as biochemical analysis of inflammatory and lipid metabolism pathways to elucidate the biological mechanisms associated with 1) the achievement of SA by week 1 pp and 2) pumped milk volume at 2 weeks in a population of mothers with infants in the NICU. As participants in the parent clinical trial, all mothers will receive consistent, state-of-the art lactation support and care, reducing the possibility of variability in access and quality of care. The results of this study will provide evidence to support the development of future interventions that are targeted to promote sufficient milk production and prevent lactation problems in vulnerable populations.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT Unlike higher eukaryotes, unicellular organisms like the malaria parasite Plasmodium falciparum rely on the precise regulation of molecular events that stabilize the development of one sex lineage and/or repress the alternative fate. The development of P. falciparum is closely tied to its complex life cycle where sexual differentiation within a subpopulation of host red blood cells is critical for transmission to the mosquito vector. This sexual lifecycle stage, known as gametocytogenesis is a lengthy process, taking approximately 12 days to transition from immature sexual stages (stage I) to mature, differentiated male and female stages (stage V) that can be taken up by the female anopheles mosquito. Despite extensive research efforts, the molecular mechanisms governing sexual development and dimorphism in P. falciparum remain poorly understood. Recent studies have begun to shed light on sexual development using single-cell RNA sequencing (scRNA-Seq) and have defined a Malaria Cell Atlas,. These studies suggest that sexual fate in malaria parasites is likely determined downstream of commitment, following a branch point during gametocytogenesis. However, significant knowledge gaps persist, particularly regarding the timing and regulation of sex dimorphism. To address these gaps, we propose a comprehensive study leveraging scRNA-Seq to uncover the molecular mechanisms of cell fate determination using a combination of parasite genotypes from different geographical locations and unique genetic mutants in key regulators of gametocytogenesis. Our approach is structured around two specific aims. The first aim will determine the temporal, single-cell transcriptional landscape of gametocytogenesis using the 10x Genomics chromium platform with short-read (Illumina) sequencing using P. falciparum strains from varying genetic backgrounds of Africa, South America, and Southeast Asia origin. We will also refine the classification of gametocyte clusters associated with distinct stages (I-V) of gametocytogenesis and better delineate the earliest lineage bifurcations along the sexual trajectory. To accomplish this, we will measure and compare temporal, scRNA-Seq data from genetically modified strains with defects in known regulators of sexual-stage development. The second aim will capture the evolutionary dynamics of sex-specific transcript isoform diversity. To assess the downstream impact of isoform regulators on gametocyte development, differentiation efficiency, morphology, and reproductive success, we will couple long-read (PacBio) sequencing to better elucidate masked transcriptional modules and differential exon usage during gametocytogenesis. Additionally, we will validate the role of candidate hub isoform regulator(s) using genetic manipulation techniques such as DiCre-inducible conditional knockout (cKO). The outcomes of this proposal include identifying key regulators of sexual dimorphism and lineage-specific transcript isoforms used by malaria parasites to prepare for mosquito transmission.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY The human genome has two sex chromosomes—the Y, harboring genes critical for male fertility, and the X, carrying genes important for reproduction, cognition, and immunity. Because of their high repetitive element content and haploid nature in males, the X and the Y have been completely sequenced and assembled by the Telomere-to-Telomere (T2T) Consortium only recently. The repetitive organization of the Y is critical for its survival without interchromosomal recombination. Indeed, the Y does not recombine with the other chromosomes over most of its length, except for the short pseudoautosomal regions where it recombines with the X. The repeats on the Y—tandem repeats and palindromes (inverted repeats) in particular—enable intrachromosomal recombination and facilitate gene conversion, restoring sequences of multi-copy gene families. We have recently discovered that the X also has many gene-rich palindromes, which also likely undergo gene conversion. Yet, we currently lack information on variation in the organization and expression of sex chromosome genes located in repetitive structures across multiple humans. Our overarching goal is to decipher the molecular processes governing structural changes of sex chromosomes leading to phenotypic consequences. As an essential step towards fulfilling this goal, here we will focus on the following Specific Aims. In Aim 1, we will study variation in prevalence, structure, and gene content of palindromes and tandem repeats on the human X and Y chromosomes. We will investigate which palindromes and tandem repeats are conserved in terms of presence/absence, structure, and gene content across hundreds of nearly T2T human genome assemblies generated by the Human Pangenome Reference Consortium (HPRC). In Aim 2, we will evaluate potential natural selection acting on expression levels of multi-copy genes on the X and the Y. Most Y genes, and many X genes, are expressed in testis. Thus, we will examine variation in their expression levels across hundreds of testis transcriptome datasets generated by the Genotype-Tissue Expression (GTEx) project. Using these data, we will test for selection acting to maintain optimal expression for sex chromosome genes. Overall, our project will make an essential contribution to uncovering variation in organization, copy number, and expression of sex chromosome genes. Our results evaluating such variation in healthy humans will serve as a baseline for inquiries into disease conditions. Our thorough investigation of variation of multi-copy genes on sex chromosomes will significantly contribute to our understanding of human reproductive disorders, including male infertility. Our project requires access to large-scale data sets and computational resources enabled by the ANVIL platform.

NIH Research Projects · FY 2026 · 2026-05

Engineering artificial endosymbiosis in mosquitoes using synthetic biology first principles Symbiosis (the intimate association of dissimilar organisms) is a defining feature of biological life forms. The fact that living organisms do not exist on their own, but rather exist in association with microbes that significantly affect their biology, was recognized for almost 150 years. Endosymbionts (microorganisms that live within the cells of eukaryotic organisms) are ubiquitous in nature. Bacterial endosymbiosis is often obligate, where both the host and the symbiont are reliant upon one another. Obligate endosymbionts often provide resources to their hosts including nutritional supplementation of necessary metabolites (such as vitamins or amino acids) in many species. Some obligate endosymbionts (such as Wolbachia) have been co-opted by humans for applied purposes, where they have been deployed as an agent to control arbovirus transmission in mosquito populations. While understanding the presence, distribution, function, and evolution of symbionts in animals has been revolutionized by advances in parallel sequencing technology, basic, even simple questions such as “what makes a symbiont a symbiont?” are still not well understood. This is coupled with the problem that obligate endosymbionts, by their very nature, are difficult to culture and manipulate. Together, this means that for applied purposes we are reliant on identifying natural endosymbionts that have the characteristics we require for specific translational purposes, leading to suboptimal strains for control. What is desperately needed is a system to study the functional biology of obligate endosymbionts, even those that cannot be cultured or manipulated. This is essentially a catch-22; if a good model or set of techniques was available to address this question, the problem would already be solved. In this project, we propose to use the tenets of modern synthetic biology to engineer E. coli into an obligate, vertically inherited nutritional endosymbiont in mosquitoes from the ground up. These principles can be logically extended to any system, perhaps even systems of clinical importance to humans and animals. Once this platform is established, we can investigate engineering and testing specific applied bacterial phenotypes, such as secreted anti-viral effectors that will limit the replication of arboviruses in mosquitoes or engineering E. coli to express the Wolbachia cif genes that cause CI, as well as basic questions about the evolution, maintenance, and ecology of symbiosis.

NIH Research Projects · FY 2026 · 2026-05

Project Summary Malaria is still one of the greatest disease burdens of the world today. In this proposed work, we will apply cutting-edge reverse genetic, transcriptomic, proteomic, and microscopy-based approaches to study how malaria parasites can control their gene expression in the moments before and after transmission from a mammalian host to a mosquito vector. In this proposed work, we will test the hypothesis that the release of translational repression in female parasites occurs due to multiple, distinct, triggering events that lead up to fertilization. We will use both reverse genetics and protein-based blocking approaches to determine the required contribution of the male gametocyte or male gamete toward the release of translational repression. Together, we will determine and validate mechanisms that control the release of translational repression and address hypotheses focused on understanding how malaria parasites use and deploy translational controls to overcome its mosquito vector to establish a productive infection.

NIH Research Projects · FY 2026 · 2026-05

Project Summary This project aims to harmonize and share data about immigrants who are without permanent residence (IWPR). Few national surveys include questionnaire items on immigrants’ permanent residence, and when available, these surveys are often met with skepticism due to their questionable validity. And while some organizations use indirect demographic methods to produce estimates of IWPR sub-populations, it is difficult for researchers to obtain information about detailed groups of interest. This is an important shortcoming given that the IWPR population makes up one-third of all adults and children born abroad. In addition, nearly 80 percent of children of the IWPR population are U.S.-born citizens. In this project we harmonize data across existing data sets (American Community Survey, Department of Homeland Security admission data, and demographic estimates of mortality, emigration, and ACS survey coverage rates) that together provide a detailed demographic estimates and projections of the IWPR population and its children. We will deposit the harmonized data and documentation in Data Sharing for Demographic Research archive (DSDR). Specifically, the project has three aims. First, it will harmonize data in order to produce detailed estimates of the size of the IWPR population and its children ages 0-17. These estimates will be produced by harmonizing and layering pre-existing public data and using long-standing residual methods based on an innovative, transparent, peer-reviewed methodology. The estimates will be available by year, age, sex, year of arrival, age at arrival, duration of U.S. residence, and visa classification. The project will also produce estimates of the population’s dynamics, such as annual in-flows, out-flows, and net growth. Second, the project will project the IWPR population and its children 10 years into the future under various scenarios. These scenarios will vary both demographic conditions (e.g., high versus low levels of inflows) and potential program changes (e.g., eligibility rules for SNAP). Third, the project will deposit the data from Aims 1 and 2 into DSDR for dissemination to researchers, along with accessible and comprehensive documentation. The confidentiality of human subjects will be protected by collapsing these data and providing all data at the national level. Understanding the changing size and characteristics of the IWPR population is important to assess this group’s public health and services delivery needs, especially given they comprise nearly one-third of the adult and child population born abroad generally. Compared with other individuals born abroad, IWPR individuals and their children have high rates of poverty and food insecurity, and they also have low access to health care and health insurance. By providing accessible data on the IWPR population and its children, this project can help planners, service providers, and researchers better evaluate child health and well-being.

NIH Research Projects · FY 2026 · 2026-04

Alzheimer’s disease and Alzheimer’s disease related dementias (AD/ADRD) are urgent public health challenges, imposing a $345 billion annual economic burden in the U.S. and causing profound personal suffering. Early detection of cognitive changes during the preclinical stages, years or decades before diagnosis, is critical for advancing prevention and intervention strategies. However, traditional cognitive assessments lack the precision and sensitivity required to detect subtle changes and adapt to evolving research needs. This U19 proposal aims to establish the Mobile Monitoring of Cognitive Change (M2C2) Platform, an open-source, scalable, mobile-first system designed to administer ultra-brief cognitive tasks, collect high-frequency data, and apply advanced analytics to detect subtle cognitive changes linked to AD/ADRD risk. Aim 1 provides centralized coordination and shared resources through four specialized cores. The Administrative Core ensures alignment across components, the Technology and Data Management Core develops software for data collection and sharing, the Analytics Core delivers statistical tools for validation and interpretation, and the Community Engagement and Accessibility Core prioritizes accessibility, community engagement, and advancing availability of cognitive health resources. Together, these cores provide critical infrastructure to support the ambitious goals of the U19. Aim 2 evaluates how different high-frequency assessment (HFA) protocols using M2C2 tasks capture cognitive changes across multiple timescales and their relationships with AD/ADRD risk factors. Project 1 will assess the sensitivity of M2C2 tasks to biomarkers and contextual factors, such as social engagement, physical activity, and stress, generating actionable recommendations for task selection and protocol design to optimize measurement sensitivity while minimizing participant burden. Aim 3 focuses on developing, refining, and disseminating the M2C2 Platform to deliver robust tools for measuring cognitive change. Project 2 will prioritize flexible, user-friendly solutions that can integrate into different research workflows while ensuring long-term sustainability through open-source development and a multi-provider dissemination network. The M2C2 Platform will deliver validated tools and protocols for precise cognitive assessment and a scalable infrastructure to support prevention trials and accelerate research progress. These innovations will enhance our ability to identify and address AD/ADRD risks, ultimately reducing the burden of these diseases and improving quality of life for individuals and families.

NIH Research Projects · FY 2026 · 2026-04

ABSTRACT Per- and polyfluoroalkyl substances (PFAS) are persistent environmental pollutants known for their widespread use and adverse effects on human health (e.g., metabolic disease, cancer). Early-life exposure to PFAS is of particular concern as developmental periods are a critical window of vulnerability during which disruptions to the gut microbiota and host metabolism can have long-lasting consequences. Infants and young children are exposed to PFAS through breast milk, formula, and contaminated food or water. Despite the recognition that many environmental pollutants influence the gut microbiota, there is a lack of research assessing PFAS-induced microbiome toxicity using quantifiable and biologically meaningful endpoints. Further, given the essential connection between the host and microbiome, there is a critical need to study the impact of PFAS on the physiology and function of gut microbes and the resulting effects on host health. The proposed studies will address these gaps by elucidating the mechanisms by which PFAS influences host-microbiome interactions. The central hypothesis of this grant is that gut microbes modify PFAS toxicokinetics and mediate PFAS- associated health outcomes via the disruption of host-microbe homeostasis. Herein we present a paradigm- shifting view of bacterial-mediated mechanisms of PFAS toxicity. Two specific aims will test this hypothesis: Specific Aim 1 will evaluate the effects of PFAS on diverse gut microbes to understand microbial toxicity, bioaccumulation, and adaptation in microbial species key to health. For Specific Aim 2, mouse models will be used to determine how early-life PFAS exposure disrupts the host-gut microbiome axis leading to metabolic disorders in adulthood. Our interdisciplinary team combines expertise in perfluorinated chemical toxicology, microbiology, metabolomics, and biostatistics. To comprehensively study how PFAS exposure is linked to detrimental health outcomes, our studies use state-of-the-art technologies (e.g., metagenomics, metabolomics) to explore microbial toxicity and the broader effects of environmental chemicals on gut microbiome and its community structure and function. Results from the proposed studies will provide new and impactful data that will provide for more personalized risk assessment frameworks and support the development of microbiome- centered therapeutic strategies to mitigate the health impacts of PFAS.

NIH Research Projects · FY 2026 · 2026-04

Abstract The global HIV response in 2025 is at a pivotal moment. While progress has been made, 1.3 million new infections occurred in 2023, far exceeding the 2020 target of 500,000. The 2021 Political Declaration on HIV emphasized the unmet prevention and treatment needs among different populations and regions as the key barrier to the 2030 target of fewer than 200,000 new infections. A critical bottleneck hindering an efficient and comprehensive response to HIV control is the lack of precise, actionable information derived from existing data. This proposal aims to address these information gaps to accelerate the fight against the entire HIV epidemic. We will leverage newly available HIV-related data and state-of-the-art methodologies to identify where and for whom the HIV response is lagging, in order to support the design of more effective and efficient policies and programs. Our proposal consists of the following specific aims: 1. Provide longitudinal and spatial estimates of key populations in countries with generalized HIV epidemics in sub-Saharan Africa (SSA). 2. Infer HIV incidence for sub-national areas and populations at high risk. 3. Produce freely available, open-source software to implement the proposed methods, and collaborate with global and local organizations to disseminate the methods and findings.

NIH Research Projects · FY 2026 · 2026-04

Project Summary/Abstract Phenotype control, an active area of research in network control, is applicable to interacting biomolecular systems and can identify targeted interventions that lead to desired cell phenotypes. Phenotype control distinguishes itself from classical control theory in that (i) its objectives are related to dynamical attractors (e.g., stable states), and (ii) its interventions don’t need to be continuously adjusted based on the state of the system. This type of control is well-suited for guided cell differentiation, inducing cell fate changes, or inducing apoptosis of a target cell population. This research program will further develop two phenotype control methods. Feedback vertex set (FVS) control is based on the interaction network that underlies a biological system, and stable motif (SM) control is based on a dynamic model of the system. The PI has participated in the establishment of both of these methods, and has a track record of collaborative construction of experimentally validated dynamic models of biological systems. This research program will overcome the remaining challenge to the wide implementation of each phenotype control method. The barrier to wide application of FVS control is that in many systems the characterization of the target cell phenotype (e.g., the known state of a few biomarkers) is not sufficient to specify the desired state of all FVS nodes. This barrier will be eliminated by identifying the most parsimonious and sufficiently discerning characterization of each phenotype and extrapolating the existing biological knowledge to achieve this characterization. The bottleneck to the wide application of SM control is the long time needed for the development and verification of dynamic models. Automating the key steps of model construction and refinement, building on the recently developed BOOLean MOdel REfiner (boolmore) tool, will substantially decrease this time. The FVS and SM control methods will be implemented on networks constructed from curated pathway databases, on ensembles of dynamic models generated for each network, as well as on select dynamic models constructed in collaboration with domain experts. Integration of the two methods will identify multiple high-confidence interventions for each system. The predicted interventions will be validated via experiments done by the PI’s collaborators (see letters of Prof. Nobile and Prof. O’Rourke). The outcomes of the next five years will include a publicly shared suite of computational methods for efficient control of cell phenotypes as well as novel control protocols for multiple specific systems.

NIH Research Projects · FY 2026 · 2026-04

Project Summary/Abstract Enzymes that activate dioxygen or (su)peroxide at transition metal cofactors to cleave strong X– H bonds (X = C/N/O) are prevalent in central and specialized metabolic pathways in organisms from all three domains of life. Their abilities to generate highly reactive carbon and heteroatom radicals and direct them down specific reaction pathways bestow a chemical versatility that inspires admiration and mimicry among synthetic chemists. Within several highly represented (privileged) protein architectures, Nature has evolved diverse reactivities from nearly identical cofactors and common reactivities from structurally distinct cofactors, including cofactors made up of different metal ions. The three classes of metalloenzymes under study in the proposed program exemplify these phenomena. Iron(II) and 2-oxoglutarate-dependent (Fe/2OG) oxygenases (Project 1) use a common iron(II) cofactor and oxoiron(IV) intermediate to promote hydroxylation, halogenation, desaturation, chain/ring-expansion, and cyclization reactions. Heme- oxygenase like diiron enzymes (HDOs) (Project 2) use unstable diiron(II) clusters that are (dis)assembled in concert with profound protein conformational changes to form µ- (hydro)peroxodiiron(III) intermediates that cleave strong X–H bonds to initiate N-oxygenation and complex fragmentation reactions. Class I ribonucleotide reductases (RNRs) (Project 3) use diverse diiron, manganese/iron, dimanganese, or flavin cofactors to form protein radicals that initiate – again, by cleaving a C–H bond – the common reduction reaction that provides all organisms with DNA precursors. The proposed program aims to use biochemical, biophysical and computational methods to understand (1) how largely conserved protein scaffolds can initiate different reactivities from similar cofactors or a common outcome from diverse cofactors and (2) how these diverse outcomes and cofactor usage have evolved. The emerging understanding will be tested in experiments aiming either to rationally redirect reactions to different outcomes (Projects 1 and 2) or to alter cofactor usage (Project 3) and will ultimately be useful in formulating directed evolution of new-to-nature reactivities.

NIH Research Projects · FY 2026 · 2026-04

Project Summary/Abstract Fear is important for survival, but excess fear can be problematic when it interferes with daily functioning. One disorder marked by such exaggerated fear responses is post-traumatic stress disorder (PTSD) in which exposure to a traumatic event predisposes an individual to show excessive subsequent fear responding. Notably, women are nearly twice as likely as men to develop PTSD, suggesting there may be sex-specific mechanisms that gate sensitivity to acute stress. Recent work from our lab has identified the repressive histone deacetylase 3 (HDAC3) as a key mechanism that modulates the persistent effects of stress. Specifically, we found that acute stress reduces HDAC3 in the amygdala and locally blocking HDAC3 during weak stress transforms this event into one that drives persistent fear sensitization in male mice. Surprisingly, in female mice, the same mild stress drove persistent and robust fear sensitization that was not further enhanced by HDAC3 inhibition, suggesting that the threshold for inactivating HDAC3 is much lower in females. This proposal aims to systematically investigate the role of HDAC3 and histone acetylation more broadly in regulating stress-enhanced fear learning in male and female mice. Specifically, we hypothesize that acute stress establishes an epigenetic molecular memory in the amygdala primarily via histone acetylation, opening the local chromatin at key fear memory genes to enable their excessive transcription in response to subsequent mild fear conditioning. We further hypothesize that females require less intense stress to establish these changes. To fully test this hypothesis, we propose three aims. In Aim 1, we will determine the role of HDAC3 in establishing stress-enhanced fear learning in males and females. We will bidirectionally manipulate HDAC3 in the amygdala during varying amounts of acute stress and test whether that alters subsequent fear learning in male and female mice. In Aim 2, we will determine the mechanisms through which acute stress persistently enhances subsequent fear memory in both sexes. Using RNA- and ChIP-seq, we will test whether intense acute stress establishes an epigenetic molecular memory that enables excessive or aberrant expression of key fear memory genes in response to subsequent fear conditioning. Then we will use HSV-CRISPRi to causally test whether top candidate genes are required for this sensitization. Finally, in Aim 3, we will determine how HDAC3 modulates susceptibility in a sex-specific manner. Using 2-shock stress that establishes persistent sensitization only in female mice, we will determine which genes might support sex-specific sensitization. We will also determine which of these genes might promote sensitization in male mice when HDAC3 is blocked. Finally, we will bidirectionally manipulate these genes with our established HSV-CRISPRi and HSV-CRISPRa systems and directly test whether HDAC3 functions through these genes to promote stress-enhanced fear learning. Together, our findings will identify sex-specific mechanisms through which acute stress persistently changes the brain’s response to subsequent fear.

NIH Research Projects · FY 2026 · 2026-03

Project Summary The Burghardt lab at Penn State University studies the evolution of host-microbe mutualisms. Unlike obligate pathogens, mechanisms and rules governing facultative, mutualistic symbiosis remain largely unexplored. These relationships are characterized by the ability of each partner to survive independently, live in close physical proximity, and provide benefits to the other. Increasingly, mutualisms are recognized as crucial in protecting and maintaining host health. However, we still have limited knowledge of host genes that influence microbial adaptation, the impact of microbial generations outside hosts, and how mutualisms persist in nature. My lab creates new insights into the genomics of microbe-host interactions by utilizing whole- genome sequencing methods, innovative bioinformatics tools, and field and lab experiments. To achieve this goal, we harness the mutually beneficial symbiotic relationship between leguminous plants and rhizobial bacteria. This symbiosis is established when soil-dwelling bacteria invade root hairs and trigger the development of specialized structures called nodules, which can contain hundreds of millions of bacteria. Inside nodules, the bacteria convert atmospheric nitrogen into a form that plants can utilize, while the plants supply the bacteria with abundant sugars produced during photosynthesis. Most of the bacterial population at any given time lives in the soil and the symbiosis is established anew for each plant generation. Thus, these bacteria are exposed to soil selection and multiple hosts, allowing us to study the effects of host and soil variation on mutualism evolution. Our model system is Medicago truncatula and Sinorhizobium meliloti, which have a long history of functional genetic advancements. My lab is uniquely suited to pursue the work as it houses significant collections of sequenced isolates and host accessions. This rich toolkit allows the examination of plant and bacterial genes simultaneously, providing a clear path for the validation of bacterial genes underlying host fitness and vice versa. Another key feature is that the hosts specifically enrich a single species of bacteria enabling cost-effective whole-genome sequencing to monitor strain competitive fitness in laboratory experiments and changes in allele frequency in the field. Over the next five years, I will lead projects on three themes: 1) characterizing the function of and inferring selection on genes underlying bacterial fitness within hosts; 2) examining the interplay between adaptation to host and non-host environments; and 3) identifying the mechanisms behind the evolution of mutualism. Results from this research program will provide insights into the genetic mechanisms of beneficial host-microbe interactions, offering clues for understanding gene function in less tractable systems. In addition, results will establish a framework for predicting if evolution outside of a host will undermine or facilitate host adaptation and uncover the selectivity and reward mechanisms underlying mutualism persistence. Ultimately, this research advances our ability to deploy beneficial microbes to enhance overall host health across systems.

NIH Research Projects · FY 2026 · 2026-03

Project Summary / Abstract Animal behavior manifests from a coalition of physiological states to enable effective navigation of a world which perpetually challenges homeostatic regulation. Whereas homeostatic feedback regimes maintain physiological thresholds, allostasis describes the flexible adjustment of thresholds during the experience of novel stressors. To achieve whole-body allostasis, multi-organ physiology must be coordinated through bidirectional communication between the brain and body, but the mechanisms driving this synchronization are still poorly understood. Astrocytes are a type of glia (non-neuronal) cell in the brain that have been classically described as the brain’s chief homeostatic regulators, but little is known regarding their role in facilitating brain state shifts. Interestingly, astrocyte networks display large, synchronized intracellular calcium events that occur across the entire brain and correlate with pupil dynamics. This suggests that astrocytes may be key players in coordinating the brain with whole-body allostasis, but little research has explored this possibility. Furthermore, the enteric glia surrounding the gut show similarities to astrocytes and could be a conserved mechanism by which whole-body allostasis is achieved. My laboratory aims to bridge astrocyte-linked brain states with allostatic shifts across other organ systems. To do this, we leverage simultaneous in vivo recording of a range of physiological readouts including sympathetic outflow, hormone circulation, cardiovascular dynamics, gut signaling, widefield brain imaging, and behavior in a head-fixed mouse model. We will also model ‘autonomy’ using a quantifiable sensory- motor feedback system to titrate brain states related to environmental control. Over the next five years, I will lead research projects under three main themes: 1) Characterizing brain-body physiology in a stress acclimation model of allostasis; 2) Investigating the role of augmenting environmental control in whole-body allostasis; and 3) Developing new soft-tissue fiber photometry to link enteric glial physiology with whole-body allostasis. Unfortunately, there is no shortage of psychological stress in the world today, especially in medical settings. It is time to bridge our understanding of the brain states underlying psychological stress with whole-body physiology. The allostasis model championed here promises to unify theories and evidence currently isolated to specific organ systems, and will improve individualized medicine, post-operative care, and therapeutic discovery.

NIH Research Projects · FY 2026 · 2026-03

Project Summary Chromatin structure and function are dynamically regulated by ATP-dependent chromatin remodelers and Sirtuin histone deacetylases, two critical enzyme families that play pivotal roles in DNA transcription, replication, repair, and genome stability. Chromatin remodelers use ATP hydrolysis to reposition and modify nucleosomes, while Sirtuins, NAD⁺-dependent histone deacetylases, modulate chromatin states through site-specific histone deacetylation. These enzymes often work in concert to fine-tune chromatin accessibility and gene expression. Although their roles have been studied to some extent, their precise mechanisms and the nature of their interplay remain poorly defined, underscoring the need for further investigation into their complex interactions with chromatin. Building on my laboratory’s strong track record in chromatin biology, structural studies, and functional assays, as well as compelling preliminary data, my research program aims to uncover the individual molecular mechanisms of chromatin remodelers and Sirtuins, as well as focus on their coordination in regulating nucleosome dynamics and chromatin structure. Supported by a highly collaborative network and innovative methodologies, this work aims to tackle fundamental unanswered questions in chromatin biology, with the potential to drive significant advancements in the field Two major themes drive this research. The first explores ATP-dependent chromatin remodelers, specifically CHD and ISWI ATPases, examining their catalytic mechanisms, substrate specificity, and the influence that histone post-translational modifications (PTMs) have on their remodeling activity. State-of-the-art approaches, including high-resolution cryo-electron microscopy (cryo-EM), molecular dynamics simulations, and advanced biochemical assays, will reveal the dynamics of remodeling cycles and interactions with chromatin. The second theme focuses on the Sirtuin family of deacetylases and their interplay with chromatin remodelers. Structural and functional studies, coupled with tools like synthetic nucleosomes with defined PTMs, real-time FRET-based translocation assays, and cross-linking mass spectrometry, will provide unprecedented insights into their coordination and regulatory roles. By leveraging our expertise, robust preliminary data, and a world-class support network, this research will not only advance our understanding of chromatin modulation but will also drive the entire field forward, offering critical insights into gene regulation, genome integrity, and the development of therapeutic strategies targeting chromatin dysfunction in diseases such as cancer and neurodegeneration.

NIH Research Projects · FY 2026 · 2026-02

Project Summary Tyrosine kinases cause Mendelian disorders, cancer, contribute to polygenic risk scores in common diseases, and have led to 62 approved drugs for cancer, inflammatory disorders, and lung fibrosis. However, the function of every kinase domain residue across the large number of existing germ-line and somatic variants in the kinome remains largely unknown. While current techniques allow us to comprehensively measure the effects of every possible mutation in a single gene, we still do not know how to scale residue-by-residue functional discovery across a gene family. We hypothesize that the shared evolutionary and functional characteristics across a protein family can be leveraged to make comprehensive functional predictions of mutations, both in the context of the reference genome and in the context of other segregating and somatic variants. Here we propose a hybrid experimental/computational approach to comprehensively predict and test the effects of point mutations across all tyrosine kinases in the presence and absence of xenobiotics. This joint approach could dramatically decrease the experimental scale of residue annotation by exploiting the phylogenetic understanding that mutational effects across gene families are highly--but not completely--conserved. In Aim 1 we will generate mutational scanning data across at least 15 diverse tyrosine kinases alongside 3 ancestral reconstructions and investigate family- wide models of mutational effects using Gaussian process regression and transformer-based protein language models. In Aim 2 we will complete a benchmarking effort for CRISPR Cas9 base editors as a tool for variant annotation and in parallel we will use our existing approach to study all editable segregating variants in kinases and their interactions with xenobiotics. In Aim 3 we investigate higher-order epistatic interactions inferred from kinase super-family multiple sequence alignments and test our epistasis predictions with medium throughput experiments. The completion of these independent but synergistic aims will provide a comprehensive understanding of the genotype-phenotype relationship across human tyrosine kinases with respect to natural kinase function, xenobiotic drug phenotypes and protein coding variants relevant to hereditary disease. Moreover, it will provide a proof-of-concept and a generalizable workflow for extending residue discovery genome-wide one protein family at a time.

NIH Research Projects · FY 2025 · 2026-01

PROJECT SUMMARY/ABSTRACT Binge drinking among women presents a significant public health crisis, with both binge and heavy alcohol use among women surging over the past decade. Alcohol Use Disorder (AUD) is characterized by the presence of two or more clinical criteria indicating a sense of losing control over drinking habits. Estrogen (E2) levels are correlated with binge alcohol consumption levels across species, and repeated findings of menstrual cycle follicular/ovulatory phase and peak E2 promoting alcohol consumption are a strong argument for a mechanistic role in E2 for potentiating alcohol consumption in humans. Despite this, the mechanistic role of E2 in the sex differences in binge drinking behaviors driven by microcircuits of the prefrontal cortex (PFC) remains understudied. This fellowship proposes a comprehensive investigation into how E2 signaling influences binge drinking microcircuits of PFC somatostatin (SST) neurons in mice, through the following aims: Aim 1: Leveraging single molecule fluorescence in situ hybridization (RNAscope) and serum E2 measurements, transcriptional profiles of estrogen receptor α (ERα; Esr1) and β (ERβ; Esr2), Sst, and CaMKIIa in PFC neurons across the estrous cycle and following binge alcohol exposure will be assessed for their correlation with alcohol consumption with the voluntary Drinking in the Dark (DID) binge alcohol model. Aim 2: Whole-cell patch-clamp recordings of ex vivo SST-Ai9 brain slices will be assessed for changes in intrinsic excitability across estrous stages, and membrane potential with exogenous E2 after binge alcohol consumption. Furthermore, isotype specific estrogen receptor antagonists will be used to separate the contribution of ERα versus ERβ on changes in membrane potential with E2 bath application. Aim 3: Viral-mediated shRNA knockdown of ERα and ER expression specifically in PFC SST neurons will reveal the impact of ERα/ levels on binge alcohol consumption in female mice. This approach will allow direct assessment of the role of ERα/ in modulating alcohol consumption behavior. By integrating these approaches across transcriptional, electrophysiological, and behavioral levels of analysis, the proposed aims will provide a comprehensive understanding of how E2 signaling influences binge drinking microcircuits within the PFC. This research has significant implications for developing targeted interventions for alcohol use disorder, particularly in women, and underscores the importance of considering sex-specific hormonal influences in addiction research and treatment.

NIH Research Projects · FY 2025 · 2025-09

Overall Project Summary/Abstract Whole genome sequencing (WGS) is an established method for identifying and tracking foodborne pathogens in the United States and in other countries. Maintaining its impact requires active sequencing of circulating pathogens, and development of bioinformatic tools that are accessible and leverage the rapid growth of WGS databases. Penn State and the Pennsylvania Department of Health have an active nine-year collaboration using WGS to address public health problems primarily through the US Food and Drug Administration’s GenomeTrakr program. We have met all yearly goals and continuously supported a postdoctoral fellow or graduate student to collect and sequence the isolates. Over the next five years of our partnership, we propose to continue generating sequences of foodborne pathogens within Analytical Track A5. Simultaneously, we aim to enhance our existing wastewater-based surveillance programs by developing pipelines capable of assessing the relatedness of Salmonella enterica sequences within wastewater metagenomes to genomes deposited on NCBI through Analytical Track A8. The team includes established investigators with complementary expertise in microbial genomics, epidemiology, and metagenomic analysis pipelines, leveraging the excellent facilities and collaborative environment of our two organizations.

NIH Research Projects · FY 2025 · 2025-09

ABSTRACT The first 24 months of life set the foundation for healthy eating, sleep, and activity patterns that decrease the risk of obesity during childhood. More than one in ten infants in the U.S. are at risk of overweight, and one in five preschool-aged children are living with obesity. Young children living in rural contexts are more likely to experience poverty and limited access to nutritious and affordable foods, contributing to a higher prevalence of obesity and cardiometabolic diseases. To reduce health disparities among young children living in rural low-income contexts, there is a critical need for effective and scalable evidence-based interventions to support parents of young children starting early in life. Leveraging existing settings such as health care (standard well-child visits) and social care (Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) visits) for evidence-based intervention delivery is an effective way to reach the parents of young children living in low-income contexts, who have multiple visits with providers in these settings across the first 24 months of life. A series of reports from professional organizations including the American Academy of Pediatrics have called for solution-oriented approaches, moving away from siloed health care (primary care providers (PCPs)) and social care (WIC nutritionists) towards integrated care between these settings using health information technologies to enhance obesity prevention efforts and reduce health disparities. The goal of this research is to leverage existing care settings and use health information technologies to digitally integrate care and deliver an evidence-based responsive parenting intervention to mother-infant dyads living in rural low-income contexts who experience health disparities. This research will include a two-arm cluster randomized controlled trial to test the effectiveness of an integrated, patient-centered responsive parenting intervention on rapid infant weight gain and child BMI z-score at age 24 months (Aim 1), the effectiveness of the intervention on responsive parenting practices and child diet quality (Aim 2), an evaluation of whether the intervention is more or less effective in certain groups (Aim 3), and an evaluation of factors influencing effective implementation across health care, social care, and home settings (Aim 4). We hypothesize that compared to standard care (siloed PCP and WIC nutritionists care), children in integrated PCP-WIC nutritionist care will gain weight less rapidly from birth to 6 months and have a lower BMI z-score at age 24 months. Integrating care between trusted providers creates an opportunity to increase the time spent discussing child health in these often time-constrained settings and deliver consistent, integrated care on responsive parenting to inform scalable efforts to promote healthy child growth from the start and reduce health disparities among children living in rural low-income contexts.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY As average global temperatures continue to rise, the frequency, duration, and severity of extreme heat events are also increasing. Further, the population of aged adults is increasing globally, resulting in a larger population of those who are most vulnerable to heat-related morbidity and mortality. Recent heat waves report older women (65+ yrs) as the most vulnerable group during extreme environmental heat events due to an inability to maintain heat balance at lower temperature and humidity combinations than age matched men. Female reproductive hormones alter thermoregulatory responses to heat stress through central and peripheral mechanisms. Reductions in reproductive hormones throughout and after menopause could mediate this age specific sex difference, however, the extent to which the increase in heat vulnerability in older women can be attributed to menopause-induced estrogen reductions separate from age-related physiological declines is unclear. The purpose of the current study is to determine the independent role of estrogen on reflex control of cutaneous vasodilation and sweating in pre and postmenopausal women of equal age. Through an estrogen knock down and add back model, we will mechanistically examine the impact of estrogen on thermoregulatory mechanisms during passive whole-body heating. Our global hypothesis is that estrogen mitigates age-related impairments in convective and evaporative heat loss and reductions in estrogen throughout the menopause transition accelerates the aging process, impairing thermoregulation and increasing heat vulnerability. This project and associated training plan will serve as a vehicle for exceptional predoctoral training for the candidate.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY We intend to demonstrate that casein proteins from bovine milk can be used to create amorphous solid dispersions (ASD) of insoluble active pharmaceutical ingredient (API). These casein-based API-ASD can be readily dispersed in water and used as ethanol-free oral liquid formulations for infants and children. In this proposal, first we will elucidate the key environmental stimuli conducive to the formation of casein-based ASD with high loading capacity, and excellent instant properties. The core of the experiments will be conducted using ritonavir, furosemide, and tristearin as hydrophobic probes. Second, we will determine the stability and release kinetics of ASD in response to pH and to model digestion systems. We will investigate the environmental stimuli leading to the delivery of the API form the ASD to the aqueous phase. Third, we will determine the in vivo bioavailability of one casein-based ritonavir ASD and one casein-based furosemide ASD. We will formulate the two ethanol-free API ASD, disperse in water, and administrate to mice models to determine bioavailability vs. commercial formulations containing ethanol. The latter experiments will demonstrate that API-ASDs are dispersible in an aqueous phase and exhibit appropriate absorption through the intestinal lumen.

NIH Research Projects · FY 2025 · 2025-09

Project Summary Increased availability of high-energy dense foods has contributed to a pediatric obesity epidemic, with 23% of United States children currently presenting with the disease.11 Recently, laboratory studies identified an ‘obesogenic’ style of eating marked by larger bites, and faster eating and bite rates.12,13 This highlights that how children eat contributes to both overconsumption12,14 and greater adiposity.13,14 These components of ‘eating microstructure’ have been proposed as modifiable behavioral targets for obesity prevention.15,16 However, it is unclear if laboratory measures of children’s eating style generalize to the home environment, where children consume two thirds of their total energy.17–19 NICHD’s Pediatric Growth and Nutrition Branch emphasizes the importance of identifying early risk factors for childhood obesity, therefore, the proposed study will use a smart-phone based research platform to 1) test if child eating styles observed in the lab generalize to more ecologically valid home environments and 2) identify aspects of home food environment that amplify obesogenic eating behaviors. We will assess laboratory and home eating styles (e.g., bite rate) in 100 prepubertal 6-9-year-old children to constrain variability in energy requirements.20 Children will be video-recorded while consuming identical study-provided meals at home and in the laboratory (counter-balanced order) in addition to a ‘typical’ meal at home. Parents will use smart-phone devices and the Wear-IT app10 to video-record children at home. To study how adiposity relates to “obesogenic” styles of eating, gold standard dual x-ray absorptiometry49 will be used. We hypothesize children will have a consistent eating style in the laboratory and at home and that regardless of meal environment or composition, children with higher adiposity will have more obesogenic styles of eating (e.g., faster bite rate, larger bites) compared to children with lower adiposity. Parents will also report social (e.g., feeding practices21) and physical (e.g., foods available22) characteristics of the home food environment, as these can influence child eating behaviors. We hypothesize that home food environments characterized by greater availability of energy dense foods, greater access to technology during meals, and less frequent family meals will be associated with a more obesogenic eating style in the home than the laboratory. The ability to target eating behaviors that drive overconsumption is critical for the prevention of pediatric obesity, a primary goal of NICHD’s Pediatric Growth and Nutrition Branch. Assessing eating behaviors in ecologically valid home settings is a critical step in the prevention overconsumption and obesity. The proposed virtual platform will also lay the foundation for other areas of child health that rely on manual coding of behaviors (e.g., communication, human development, and clinical psychology), setting the stage for longer-term impacts. The use of smart-phone devices also reduces barriers to research and clinical participation for rural and underserved populations (e.g., proximity to research/care centers, transportation) by providing a virtual platform to engage families in their home.

NIH Research Projects · FY 2025 · 2025-09

Project Summary Recent efforts have established the first roles of lanthanide ions in biology. These ions, previously not understood to have a biological role, have been shown to serve essential catalytic and functional purposes. Particularly owing to increased use of lanthanide ions in health applications for imaging and therapeutics, the discovery of biological function comes with a need to understand criteria governing the selection, transport, and utilization of these ions. Unlike main-group and transition metal ions, whose selection and use in biology has been much more thoroughly explored, lanthanide ions have comparatively similar properties to one another. Therefore, understanding the mechanisms by which bacteria sort and transport lanthanides contributes to the growing field of lanthanobiology, but can also add a new perspective to the general study of cellular metal ion trafficking, an essential biological process. I plan to address gaps in understanding of lanthanide recognition and uptake in bacteria through studies aimed at the role of protein-lanthanide and protein-protein interactions in the trafficking of lanthanide ions. These studies will contribute to a strengthened foundational understanding of protein-lanthanide interactions and the contributions of these interactions to the selectivity of lanthanide ion transport in biological systems. The proposed research will take place in the laboratory of Prof. Joseph A. Cotruvo, Jr. at Pennsylvania State University (Penn State). The high level of collaborative research in bioinorganic chemistry at Penn State will afford access to both broad technical knowledge in the study of biological metals and career mentorship in the field. Additionally, I have found many opportunities for continued training in teaching and research mentorship in line with my goal of doing research at a primarily undergraduate institution. Along with Prof. Cotruvo’s expertise in the discovery and characterization of lanthanide-binding proteins, these resources and the proposed research will expand my knowledge of and prepare me for a career in bioinorganic chemistry in addition to advancing understanding of lanthanide ions’ role in biology.

NIH Research Projects · FY 2025 · 2025-09

PROJECT SUMMARY Transport of blood-borne signals into the brain must be tightly controlled to maintain neuronal health. Selective transport across endothelial cells is achieved by receptor-mediated transcytosis, yet little is known about what physiological signals stimulate this transport. Transcytosis is affected by alterations in membrane tension, such as those caused by changes in blood vessel diameter. Hemodynamics are coupled to neural activity via neurovascular coupling (NVC). While disruption of NVC is associated with neurodegeneration, the normal physiological purpose of NVC is unknown. This proposal will test the hypothesis that NVC stimulates receptor- mediated transport of proteins into the brain. To visualize movement of blood-borne proteins out of endothelial cells, plasma proteins will be fluorescently labelled, and injected into mice with fluorescently-labelled endothelial cells and visualized using two-photon microscopy. To understand how vascular dynamics can drive transport, vasoconstriction and vasodilation will be pharmacologically induced. The contributions of neural activity to protein uptake will be tested by sensory stimulation and by chemogenetically modulating the activity of genetically defined neuronal populations. If neurovascular coupling gates protein uptake into the brain, this would provide a novel form of temporally and spatially controllable body-brain communication. These experiments will contribute to our fundamental knowledge of the signaling mechanisms controlling movement of blood-borne protein signals from the body into the brain, which could inform the targeting of therapeutics for neurodegenerative diseases.