Pennsylvania State University, The

NIH Research Projects · FY 2025 · 2025-08

Project Summary Abstract Mental disorders, including major depressive disorder, schizophrenia, and others, all share a central feature – cognitive impairment which results in individuals confronted with difficulty in memory, concentration, and decision-making. Emerging evidence points to two key factors contributing to cognitive decline beyond the underlying disease pathology - exposure to 1) environmental chemicals such as endocrine disrupting compounds (EDCs) during development and 2) chronic stress in adulthood. The interaction of chemical exposure and stress are unknown; but together may exacerbate cognitive impairment. First, EDCs exert their toxicity by disrupting nuclear receptor signaling during sensitive brain developmental periods. Numerous EDC studies have detected cognitive impairments in humans and animals. One group of understudied EDCs are organophosphate flame retardants (OPFRs) acting on nuclear and steroid receptors linked with cognition. The association between perinatal OPFR exposure and cognitive processing has not been explored. We previously identified an association between perinatal OPFR exposure on neonatal and juvenile hypothalamic gene expression and adult locomotor activity and approach/avoidance behaviors. Second, mental disorders share a common feature: exposure to stress, which contributes to cognitive dysfunction by exacerbating symptoms. A common paradigm to recapitulate chronic stressors in rodents is to apply mild stress for 6 weeks, known as chronic variable mild stress (CVMS). Using CVMS, the neural circuits underlying maladaptive effects of stress include corticotropin releasing factor (CRF) neurons. CRF is co-released with norepinephrine (NE), acetylcholine (ACh), and dopamine (DA), which control key brain regions (hippocampus, prefrontal cortex), and all are involved in cognition and mood. Based on our prior work and the literature, I hypothesize that perinatal OPFR exposure can disrupt cognition, alone or when combined with adult chronic stress exposure. My central hypothesis is that EDCs such as OPFRs influence the developing cognitive and stress neurocircuitry potentially inducing long-lasting functional deficits in cognitive processing and sensitize adults to exposure to chronic stress in mice. In Aim 1 (K99 phase), I will first determine if perinatal OPFR exposure disrupts adult cognition on the behavioral level and through alterations in ACh synaptic transmission using electrophysiology. In Aim 2 (K99), I will examine the effects of OPFR exposure on regional concentrations of NE and DA and CRF and associated gene expression in adults, and the role of hippocampal CRF neurons using optogenetics. Lastly, in Aim 3 (R00), I will combine my prior expertise in spine density analysis and immunohistochemistry, and new training in electrophysiology, high-performance liquid chromatography, and optogenetics to determine if the combination of perinatal OPFR exposure and adult CVMS alters cognition. The ultimate goal of my research program will be to determine the interactions of perinatal EDC exposure and adult chronic stressors on cognitive processing by influencing CRF and neurotransmitter signaling throughout the brain.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY Individuals with severe disabilities who cannot use speech to communicate and use augmentative and alternative communication (AAC; pointing to pictures, using a speech-generating device) are at high risk for life-long health issues that are exacerbated by illiteracy and limited communication skills. Over 90% of these individuals leave high school illiterate, resulting in reduced communication skills and a higher probability of life-long health issues. The long-term goal for this line of research is to maximize communication and literacy outcomes for individuals who use AAC through equitable access to evidence-based literacy practices. Daily instruction in literacy practices that are phonics focused and evidence-based have the potential to change the current poor outcomes. Literacy intervention with ALLSTAR (Accessible Literacy Learning [application] with Scripted Teaching and Alternative Response methods) has proven to support acquisition of important phonics-based literacy skills for students who use AAC (i.e., intervention group (N=20) had a +44% gain after 100 lessons using ALLSTAR on pre-post literacy assessment). Despite large gains, at the end of the study, 37% of schools who used ALLSTAR with high fidelity across 100 lessons resorted back to literacy practices that included no phonics instruction or no daily literacy instruction for AAC learners. It is evident that district-wide adoption and sustainability of the current intervention is at risk without adaptations and a better understanding of implementation outcomes. The project goal is to determine contextual factors that influence school capacity for daily implementation of ALLSTAR and then refine implementation strategies by core and adaptable components to improve fit. We will employ a concurrent mixed methods study design, collecting and analyzing both qualitative and quantitative data simultaneously. Through partnership with 16 schools and 175 service providers, we will 1) iteratively use PRISM to assess multilevel contextual factors throughout pre-implementation/planning, implementation, and post-implementation/evaluation phases, and 2) Use the Framework for Reporting Adaptations and Modifications- Expanded (FRAME) to map, document, and revise core and adaptable components of ALLSTAR that influence school capacity for daily implementation. Our expected outcome is a co-developed refined ALLSTAR by mapping models of adaptations through FRAME and using PRISM for understanding key implementation outcomes that will improve implementation, sustainment, and the “fit” of the reading intervention. This proposal is timely, in that it is responsive to the NIDCD D&I mission and responsive to AAC users research priorities. The study is innovative in applying implementation science methods to the school context with students with limited or no speech, with the potential for high clinical impact in changing poor literacy outcomes for a population that unjustly denied evidence-based literacy instruction.

NIH Research Projects · FY 2025 · 2025-08

Accurate and sensitive measurement of neuropsychological change is essential for advancing dementia prevention, especially during midlife when changes related to Alzheimer's disease and Alzheimer's disease- related dementias (AD/ADRD) begin but symptoms are not yet evident. In response to RFA-AG-25-005, we propose to develop the NIH Precision Brain Health Network (PBHN) to provide the research community with open, flexible, and usable tools to enhance the measurement of cognitive change and promote applied brain health. Our objectives are as follows: Aim 1: Establish an organizational and governance structure that prioritizes transparency and broad-based scientific collaboration in developing and validating measures. The network will be organized into four scientific Cores: Data, Measures, Applied Validity, and Dissemination, each co-led by experts from different institutions. An Administrative Core will manage operations, financial oversight, and communication, with governance provided by a Steering Committee. Aim 2: Compile, publish, and evaluate a comprehensive inventory of measurement tools for AD/ADRD prevention research. By leveraging existing resources and input from researchers and practitioners, we will create a publicly available inventory that will be updated annually. Tools will be assessed for scalability, openness, scientific utility, and sensitivity to change across a range of study settings and contexts. Aim 3: Develop new tools and collect additional data to address unmet needs. We will establish an innovation pipeline supporting data collection initiatives, pilot studies, and mentored projects, with a focus on measurement approaches adaptable to a variety of real-world settings. This includes repurposing proprietary measures for open-source distribution. Aim 4: Disseminate and implement open measurement tools into research studies through a public-facing website and the PBHN Open Measures Toolkit. This web application will provide plug-and-play assessments, documentation, protocols, resources, and educational content, ensuring usability across different expertise levels. Feedback from key partners will enhance educational materials. The PBHN will establish foundational infrastructure to support future AD/ADRD primary prevention research, foster collaboration, drive measurement innovation, and develop reliable tools for precision monitoring of brain health.

NIH Research Projects · FY 2025 · 2025-08

PROJECT SUMMARY/ABSTRACT Chronic pain is one of the most common reasons for seeking medical care, affecting 50 million Americans. While often treated with opioid pharmaceutical or surgical interventions, complementary traditional health approaches to pain management may offer safer, more effective, and cost-efficient options. Ghost pipe (Monotropa uniflora, Ericaceae) is a North American medicinal plant that has been used historically for its analgesic effects and is still popular today. Yet, there are zero modern publications on either the phytochemistry or efficacy of the plant. Based upon our extensive survey of ghost pipe consumers, and preliminary data suggesting pain response modulation in a murine model, I hypothesize that ghost pipe is a botanical analgesic capable of exerting effects on neurological and analgesic responses via novel bioactive compounds. This proposal provides novel research training in pharmacognosy and analgesic screening methods to identify compounds from ghost pipe that modulate pain. Ghost pipe extracts and fractions will be chemically profiled to provide a metabolomic baseline and insight into the chemical diversity of this plant. They will be evaluated for their binding affinity for a panel of human neuro-receptors in a radioligand binding assay, after which a biochemometric model will be constructed to deduce which compounds are primarily responsible for the receptor binding. In addition, the ghost pipe extracts and fractions will be examined in in vitro systems to establish anti-inflammatory activity, as well as a murine in vivo models to determine potential analgesic effects. The bioassay data will be concatenated with the metabolomic profiling to identify the compounds responsible for observed activity. Active compounds will be isolated and characterized using high-resolution mass spectrometry (HRMS) and nuclear magnetic resonance (NMR). This research sets the stage for future in-depth mechanistic studies and assaying the addictive potential of ghost pipe metabolites. This will advance the understanding and characterization of herbal analgesics, while the experimental design experience, collection of data, development of phytochemical interventions, and professional development activities described herein will result in the development of a well-rounded, independent researcher.

NIH Research Projects · FY 2026 · 2025-08

Adolescence is a period of high risk for the onset of risk behaviors including substance use and escalation of use. Children exposed to parental substance use beginning prenatally are more likely to engage in risk behaviors, and at earlier ages. Maternal prenatal tobacco and cannabis use are also markers of continued postnatal use, and both prenatal and postnatal use co-occur with higher maternal psychological distress (pre- postnatal risks). Parent-child processes play a critical role in the etiology of adolescent risk behaviors. However, the impact of pre-postnatal risks on parent-child warmth, conflict, and dyadic synchrony, parent support of adolescent autonomy, developmental trajectories of externalizing behaviors and child regulation, and how these increase adolescent risk behaviors are not well understood. The goal of this application is to examine developmental cascades linking pre-postnatal risks to adolescent risk behaviors (measured at macro and micro time scales) via parent-child interpersonal processes and child behavioral and autonomic regulation. We will leverage a longitudinal sample of 247 families who were recruited in the 1st trimester of pregnancy and oversampled for prenatal tobacco and co-exposure to tobacco and cannabis. Prospective biological and self- report data were collected once in each trimester of pregnancy and at 2, 9, 16, 24, and 36 months of child age, school age, and in middle childhood with 82% retention. Assessments for the current study will include five biannual waves of data collection between 14-16 years (Early Adolescence; EA) and 16-18 years (Later Adolescence; LA) and ecological momentary assessment (EMA) collected at LA for 21 days from both parent and adolescent in order to identify proximal predictors of adolescent risk behaviors (substance use, delinquency, risky sex) in LA. Interpersonal processes will be assessed across macro (longitudinal time-points from prenatal to LA) and micro (lab based interactions, real world processes via EMA) levels. Onset of substance use and other risk behaviors will be measured at all time points and expanded from prior assessments to include EMA and biomarkers of substance use at LA. The specific aims include: 1) To examine the prospective association between pre-postnatal risks and changes in adolescent risk behaviors from EA to LA; 2) Following a developmental psychopathology framework and developmental cascade models, we propose to test three theory driven pathways to late adolescent risk behaviors: a behavioral regulation cascade, an autonomic regulation cascade, and an interpersonal cascade; 3) To examine within-person effects of interpersonal processes and regulation on proximal adolescent risk behaviors in real world settings.

NIH Research Projects · FY 2025 · 2025-08

Abstract: A physical-plasma catheter for treatment of cardiovascular disease will be optimized, manufactured, and tested and its effects on S. aureus biofilms associated with infective endocarditis will be evaluated. Infective endocarditis (IE) is a bacterial infection of the endocardium of the heart or prosthetic implants that has a high rate of mortality (25 – 30 %) and a high necessity for surgical intervention (50%). Multiple species are potential causative agents of endocarditis including S. aureus, S. epidermidis, enterococci, and streptococci, but the leading pathogen is S. aureus. Physical-plasma, an ionized fluid consisting of electrons, ions, and chemically- reactive neutral and excited species has been demonstrated to have many applications in biomedicine, particularly related to infection control. Physical-plasma has shown efficacy against a wide range of pathogens including bacteria, virus, fungi, and spores. In addition, it has also been demonstrated to disrupt protective biofilms on bacteria. We have previously developed and demonstrated a physical-plasma device that can produce plasma in biological liquids, killing biofilm-protected S. aureus bacteria without producing bubbles that would lead to gas embolism in clinical application. Complementary addition of vancomycin further increased the efficacy. It has also been demonstrated benign on cultured murine endothelial cells and human endothelial cells (HAEC) under the same treatment conditions. However, this previous work has shown that the spatial effect of physical-plasma needs to be increased to be an effective intervention. Our hypothesis is that physical-plasma delivered directly to the site of endocarditis by means of a cardiovascular catheter will reduce mortality and decrease reoccurrence of the infection. Moreover, it is expected that physical-plasma can be used as a complementary therapy with antibiotics by disrupting biofilm protection of bacteria and allowing antibiotic molecules to reach the underlying bacteria. Three specific aims will be pursued to prove this hypothesis: (1) Integrate an micro-electrode physical-plasma array (MEPPA) and extruded catheter body while optimizing design and materials for animal trials and future clinical applications; (2) Evaluate physical-plasma efficacy against biofilms in a dynamic, flowing environment including potential for circulating vegetative bacteria, biofilm fragmentation, and interaction with complementary antibiotics.; (3) Evaluate the physical plasma catheter for safety and efficacy in a New Zealand white rabbit model of infective endocarditis. Overall success of these specific aims will result in the development of a fully-integrated physical-plasma catheter that demonstrates effective destruction of S. aureus biofilms associated with infective endocarditis, including in an appropriate animal model. Next steps will include larger animal studies and clinical trials of this ground-breaking technology.

NIH Research Projects · FY 2025 · 2025-07

The Pennsylvania State University (PSU) ‘Biotechnological & Integrative Opportunities in Microbiome Sciences” (BIOMS) Predoctoral Training Program will be the first NIH T32 training program dedicated exclusively to training graduate students in the microbiome sciences and its biotechnological underpinnings. BIOMS will be anchored by the PSU One Health Microbiome Center (OHMC) to enhance curricula and educational training via the world’s first Dual Title PhD program in Microbiome Sciences, which will bridge eight established graduate programs: Biomedical Sciences, Food Sciences, Biology, Anthropology, Plant Biology, Plant Pathology, Entomology, and Ecology. The convergence of these programs under the BIOMS program will foster unique perspectives and collaborations to advance the biomedical sciences, particularly in basic host-microbiome and microbe-microbe interactions research. The OHMC serves a community of over 520 individuals including >160 graduate students. Nearly all the BIOMS training components will be available to this broader community, increasing the impact of program investments. The BIOMS program is designed to equip Fellows with the skills and knowledge needed to advance microbiome biotechnology, including technologies shaping the discovery and characterization of microbial taxa, probiotics, antimicrobials, and prebiotics, as well as microbiome-based diagnostics and transplant therapies. The microbial biotechnology market is expected to reach a $300 billion USD value by 2030, underlining the knowledge and workforce development necessary in this area. The BIOMS cohort will undergo training aimed at advancing research and education in human health through a One Health lens by recognizing, as the World Health Organization and National Academy of Sciences has, that microbes are the base of the biosphere, and human health depends upon how microbes (beneficial to pathogenic) flow across environmental, agricultural, and human-associated systems. The program will cultivate an integrative understanding of fundamental concepts in microbiome sciences and biotechnology with rigorous coursework from a set of 36 course options, monthly workshops, and weekly seminars. Fellows will emerge proficient in the application of reproducible and responsible experimental, theoretical, and computational methods. Additionally, they will benefit from professional development experiences, including a biotech internship, mentorship from multiple industry scientists, and “Beyond the Lab” workshops focused on science communication, patents, and more. BIOMS applicants will be recruited through a network of OHMC partners. Importantly, the BIOMS program promotes skill development and student achievement through a foundational skills Summer Jumpstart Bootcamp, an expanded curricula for PhD trainees, and cohort events. With combined NIH and PSU support, the BIOMS program proposes to train a minimum of 28 Fellows over five-years. Trainees will generally be supported in Years 2 and 3 of their PhD program. Overall, BIOMS Fellows will be prepared to be leaders in the microbiome biotechnology field.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Many causes can trigger excessive production of inflammatory cytokines (i.e., cytokine storm). Elevated circulating cytokines induce extensive cell death (i.e., inflammatory cell death) that causes severe organ injuries, eventually leading to acute respiratory distress syndrome (ARDS) and multi-organ dysfunction (MODS). Patients with ARDS and MODS have extremely high mortality (~46%). There is an unmet clinical need for novel therapeutics capable of inhibiting inflammatory cell death to mitigate ARDS and MODS. Recent studies find that the excessive expression of inducible Nitric Oxide Synthase (iNOS) and over-production of nitric oxide (NO) play a critical role in inflammatory cell death. Therefore, inhibiting iNOS/NO represents a promising therapeutic approach. Hydrogen sulfide (H2S), a gaseous signaling molecule in our body, is known for its capability to inhibit iNOS and quench NO. However, due to its gaseous nature, its therapeutic application is limited by the challenge of administering a precise dose into the target cells sustainably. Preliminary studies developed five polymeric micelles containing H2S donating-anethole dithiolethione (ADT) groups to overcome the problem. The micelles enter cells via endocytosis and release H2S upon oxidation by reactive oxygens species (ROS) inside cells. The release rate can be controlled by changing the polymer design. The micelles have no significant cytotoxicity. In a proof-of-concept study, the micelles effectively inhibited cytokine-induced cell death. In short, the data show that the micelles are promising drug candidates. This project proposes systematically evaluating their therapeutic potential using vitro and mouse models, with the goal of gathering robust evidence to support their advancement into full drug development. The hypothesis is that the micelles can effectively mitigate iNOS/NO, inflammatory cell death, ARDS, and MODS. Aim 1 will test the hypothesis that micelles can mitigate iNOS/NO activity and inflammatory cell death in vitro. Aim 2 will test the hypothesis that micelles can mitigate cytokine storm, inflammatory cell death, organ injury, and mortality in mouse models. This project will collect essential efficacy/potency data, identify the most promising candidates, and provide valuable insights into polymer structure-property relationships to optimize these candidates further. The work is significant, as it has the potential to lead to novel therapeutics for managing ARDS and MODS, conditions responsible for ~11 million deaths annually. In terms of innovation, this is the first to investigate H₂S as an iNOS/NO inhibitor to reduce inflammatory cell death, cytokine storms, ARDS, and MODS. The micelle design is also highly innovative, enabling sustained, targeted, and ROS-responsive intracellular delivery of H₂S - a combination of features currently unmatched by any existing technology.

NIH Research Projects · FY 2026 · 2025-07

PROJECT SUMMARY Protein post-translational modifications are ubiquitous events that regulate the core functions of the cell. This project focuses on lysine acetylation, which was first characterized in the context of chromatin structure and transcription. Recent proteomic data demonstrate that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, the mechanisms whereby lysine acetylation regulates function are still poorly understood. To overcome this knowledge gap, the PI’s laboratory has recently established protocols for transfer of 13C-acetyl groups to recombinant proteins and developed nuclear magnetic resonance (NMR) experiments that provide one resonance per acetyllysine sidechain without introducing sterically bulky chemical modifications that would impair investigation of downstream interactions. The current proposal seeks to generalize this 13C- enhanced NMR strategy to broaden the enzyme/substrate scope, enable structure determination for complexes, and demonstrate the utility of the method for non-histone proteins. This plan aligns with the PI’s track record of technology development in 13C direct-detect biomolecular NMR, which is used to probe the biophysics of disordered proteins and the complexes they form. In this context, the current project’s first specific aim is to develop a broad platform for production and chemical shift characterization of acetyllysine. To demonstrate breadth while using well-described systems for proof-of-concept, the approach will target Ada2/Gcn5, p300, and MOF to represent the three well annotated families of nuclear lysine acetyltransferases, using histone H3 and H4 as substrates. To enable chemical shift assignment, NMR pulse sequences will be developed that correlate acetyllysine resonances with backbone chemical shifts that define position in the primary structure of proteins. The second specific aim is to design NMR experiments that will enable structure determination of complexes with bound acetyllysine. The approach will be to develop a set of 3D 1H- and 13C- detect nuclear Overhauser and exchange (NOESY) spectroscopy techniques based on established isotope filtering platforms. Utility will be demonstrated by solving structures of histone tails in complex with Gcn5 and Brd4 bromodomains, for which high resolution crystal structures are available as gold-standards for assessment. The third specific aim is to demonstrate the applicability of the new technology beyond histone peptides using reconstituted nucleosomes and the transactivation domain of FoxO1 as biomedical examples. FoxO1 acetylation, which is catalyzed by p300, read by Brd4, and reversed by Sirt6 serves as the capstone. The new technology proposed here will enable applications including authentication of in vitro derived acetylation patterns against those known from proteomics, investigation of novel binding modes as new reader proteins are discovered, and determination of solution NMR structures based on isotope filtered NOE measurement. The generality of the developed technology will provide sustained benefits for the transcription and signaling communities, potentially driving translation of biological toward the clinic.

NIH Research Projects · FY 2025 · 2025-07

Project Summary Oral diseases, such as dental decay, periodontal disease, and tooth loss, are the most common chronic disease in the United States today, and some American adults experience these diseases at up to 3x higher rates, such as Black or Mexican Americans compared to non-Hispanic White Americans. The root cause of these diseases may be linked to the oral microbiota – the diverse communities of bacteria, archaea, viruses, and fungi – that live within the human mouth. We also know that oral microbiota are distinct in people of different backgrounds in the US and that microbiota variation can be mediated by social, behavioral, and economic (SBE) factors. However, there has been little research into how one’s background and SBE factor intersect in driving microbiota variation, or if that variation is linked to oral health differences. This study utilizes 16S ribosomal RNA data from individuals who participated in the National Health and Nutrition Examination Survey (NHANES) during the 2009-10 and 2011-12 survey waves (n=6,224 adults across four ethnicities) to transform the way we understand the roles that oral microbes play in oral health differences in the United States. Our central hypothesis is that the oral microbiome plays a critical role in oral health differences and mediates the relationship between one’s background and traditional SBE factors that have been used to explain these differences. The core scientific objective of this R21 is to disentangle how one’s background and SBE factors shape oral microbial diversity and determine the extent that microbes linked to these factors underpin oral health differences in the US. In Aim 1, we will test how the oral microbiota diversity, composition, and abundance of individual species differs across US backgrounds. In Aim 2, we will test if SBE factors are also linked to oral microbiota variation in the context of one’s background. In Aim 3, we will perform a mediation analysis to understand how specific oral microbes identified in Aim 2 and 2 mediate the relationship with oral health. Understanding if oral microbes contribute to health differences and the factors that guide their presence and abundance is critical for the development of targeted interventions and policies to promote effective oral health therapies in all people. This project is innovative because it will be the first examination of the role of the oral microbiota in population-level oral health differences in the US. Expected outcomes from this project will inform evidence-based public health intervention policies and the foundation to develop mechanistic understandings of the roles microbes play in differential disease outcomes. This information will also be used in the development of microbial therapeutics that target the oral microbiota’s role in oral health differences, thereby promoting effective oral health therapies for all people. This work can also be integrated into studies examining health differences elsewhere in the body, ensuring that US health-based research works to reduce different rates of disease in other areas. This represents an unprecedented opportunity to understand how SBE factors shape oral microbial diversity in people of different backgrounds and contribute to oral health differences.

NIH Research Projects · FY 2026 · 2025-06

PROJECT SUMMARY/ABSTRACT Reconstructive surgery is the main treatment strategy to repair craniomaxillofacial (CMF) injuries. However, surgical options are often antiquated, leading to suboptimal outcomes, both functionally and cosmetically. Tissue engineered ‘replacement grafts’ represent the next era of reconstructive surgery. However, clinical translation is still profoundly limited by the lack of prompt vascularization following implantation. This leads to necrosis and reconstructive failure. Thus, there exists significant clinical need for an effective method that circumvents current limitations of graft vascularization. Our premise, based upon extensive clinical and tissue engineering expertise along with rigorous preliminary data is that new surgical and engineering approaches can be used to not only augment graft vascularization but also purposely orient microvascular ingrowth. We have recently developed a novel microsurgical tactic termed “vascular micropuncture” (MP) that significantly augments the angiogenic potential of the surgical site. With MP, we use an ultrafine needle (e.g., 60 µm) to create perforations in the targeted recipient macrovasculature to enable cell extravasation and angiogenesis, expediting the time to adjacent scaffold vascularization. With these compelling results, we propose to advance our microsurgical method using emerging three-dimensional (3D) printing technologies. Based on our unique approach, our overarching hypothesis is that MP will improve vascularization and survival of 3D printed or bioprinted bone grafts. To test this hypothesis, we will work on two complementary, but independent, aims. In Aim 1, using a rat model we will test the effectiveness of MP in vascularizing calvarial defects directly from the sagittal sinus vein. Following a defined implantation period, vascularization will be quantified via laser doppler, angiography, immunohistochemistry, and protein analysis. Next, a novel 3D air printing technique will be used to generate vascularized channels within 3D scaffolds, which will be used to guide the orientation of microvascular ingrowth. We will also perform a sheep study to demonstrate MP scalability and translatability. In Aim 2, we will assess the potential of sagittal sinus MP to directly induce the vascularization of bioprinted bone grafts. Sagittal sinus MP will be coordinated with implantation of an engineered bone graft fabricated via a novel high-throughput bioprinting method using high-cell density osteogenically committed spheroids. Vascularized bone volume/density will be evaluated using micro-computed tomography and histology. Accomplishment of these independent aims together will allow us to establish a groundbreaking surgical approach for tissue engineered graft vascularization and ultimately improve patient care.

NIH Research Projects · FY 2025 · 2025-06

Abstract The complex interplay between the gut microbiome and the host is mediated by the constant exchange of macromolecules of both host and microbial origin, among which bile acids (BAs) hold profound importance. Microbes convert host-derived primary bile acids into secondary bile acids, such as 7α-dehydroxylated deoxycholic acid (DCA) and lithocholic acid (LCA), which constitute a significant part of the gut metabolome and influence the chemical environment of the gastrointestinal lumen. In this proposed project, I will test the hypothesis that cross-species metabolism is necessary to shape the bile acid pool that modulates the structure and function of microbial communities in the gut. To test this hypothesis, I will focus on pathways of 7α-dehydroxylation of bile acids, which create the most abundant secondary bile acids in humans and mice: DCA and LCA. While the 7α-dehydroxylation of bile acids is attributed to bacteria encoding the bile acid-inducible (bai) operon, our preliminary findings suggest an alternative mechanism in a microbial community devoid of the bai. I hypothesize that a subset of this community orchestrates the 7α-dehydroxylation reaction through an uncharacterized pathway involving polymicrobial cross-feeding of intermediates. Through combinatorial testing, quantitative LC/MS methods, and comparative genomics approaches, we aim to elucidate the chemical substrates and the microbial and genetic determinants necessary to complete this alternative polymicrobial pathway. Furthermore, bacterial cross-feeding facilitates the chemical modifications of BAs that shift the overall chemical property of the luminal space, which impacts the diversity and the ecology of the microbial community in the gut. I will investigate this reciprocal relationship between bile acids and the microbiome by focusing on a model opportunistic pathogen, Clostridiodes difficile. The effects of BA on C. difficile are multifaceted and complex, and the role of the microbiome in modulating the chemical environment to inhibit C. difficile proliferation is not fully understood. I will determine how shifts in the microbial composition in the gut and the subsequent alteration in the bile acid metabolism impacts the growth of a single organism, C. difficile. Ultimately, a deeper mechanistic understanding of microbial bile acid will significantly contribute to our knowledge of the origin of the abundant bioactive and physiologically relevant metabolites in the gut. Moreover, it contributes to unraveling the complex interplay between the chemical landscape and bacterial ecology in the gut to harness the microbiome to combat pathogens and improve gut health.

NIH Research Projects · FY 2025 · 2025-06

PROJECT SUMMARY Childhood obesity, conceptualized as a “ticking time bomb”, is a prevalent condition with major adverse health consequences. A potent risk factor for childhood obesity is early-life adversity, such as child maltreatment (e.g. physical/sexual abuse and neglect). Our preliminary data from a cohort of high-risk children with confirmed maltreatment replicates prior studies that have linked early-life adversity with accelerated accumulation of body mass and a dysregulated metabolic profile. Extant research, however, has yet to characterize mechanistic multi-omic pathways of obesity in vulnerable pediatric populations. Prior research in adult populations has shown that when considered separately, child maltreatment and obesity are associated with dysregulated immune and metabolic pathways, and accelerated biological aging, suggesting plausible mechanistic pathways to target for obesity prevention and intervention. The proposed project aims to elucidate biological mechanisms of obesity in a vulnerable population with confirmed child maltreatment using multiple levels of analysis. We will leverage the Child Health Study (P50 HD089922), a prospective longitudinal cohort of 700 maltreated and comparison children aged 8–13 (50% females, 29.5% minority). The study includes a baseline assessment and two follow-up assessments with multiple system-biology and phenotypic measures, including BMI, biological aging measured via telomere length and epigenetic clocks, as well as genomics information. We propose secondary data analysis and collection of new data. Specifically, an important next step is to expand upon the current knowledge by evaluating the impact of maltreatment on obesity through transcriptomics (the comprehensive profiling of gene expression), and metabolomics (the comprehensive profiling of metabolites). We will further seek to replicate findings in independent cohorts. Aim 1 will examine cross-sectional and longitudinal associations between BMI and biological aging (telomere length and epigenetic clocks) at baseline (T1), 2-year post (T2), and 4-year post (T3) baseline, and will evaluate the potential moderation of child maltreatment (including type, onset, severity) and sex. Aim 2 will examine cross-sectional and longitudinal associations between BMI and transcriptomic pathways at T1, T2 and T3, and will evaluate the potential moderation of child maltreatment and sex. Aim 3 will examine cross-sectional and longitudinal associations between BMI and metabolomic enrichment in immune and metabolic pathways at T1, T2 and T3, and will evaluate the potential moderation of child maltreatment and sex. The novel insights gained from this proposal will facilitate future hypothesis generation and downstream mechanistic research by narrowing the focus onto pathways driving holistic dysregulation in maltreated children of biological aging, metabolic and immune systems activity associated with obesity risk and resilience. The effectiveness of future obesity intervention and clinical treatments hinges on developing this mechanistic understanding of how potent childhood stressors akin to child maltreatment ‘stick’ with an individual as they age to increase obesity-associated diseases.

NIH Research Projects · FY 2026 · 2025-06

Project Summary Viruses are serious human pathogens and viral infectious diseases represent a continuing challenge for global human health. The long-term focus of my research program is to uncover host-induced changes in pathogenic human viral dynamics by targeting the first critical steps of virus entry into human host cells. Our specific focus is icosahedral human viruses, that are made up of small individual constituent protein monomers compiled into repeat triangle units to generate a spherical virus assembly. The defining feature of these icosahedral virus particles is metastability or the ability to be reversibly assembled or disassembled, in response to the shifting environmental conditions encountered as part of its lifecycle. This ability to transition between assembled and disassembled states arises from viruses in solution being ‘spring-loaded’ high energy states that are continuously undergoing reversible fluctuations, referred to as ‘breathing’. These intrinsic dynamics of all viral particles allow environmental sensing, facilitate receptor recognition while evading detection by the immune system. Consequently, when a virus encounters an unsuspecting host cell, it binds the receptor, undergoes endocytosis and undergoes a program of viral disassembly to release its genome inside the host cell. These intrinsic dynamics of the viral particle further allow the virus particle to traverse multiple host-specific environments, evade host immune systems, to propagate viral replication and complete the viral lifecycle. An understanding of dynamics is critical for a deeper understanding of the precise mechanisms of how viruses enter human host cells. The study of dynamics of virus-host cellular entry has lagged structure determination. Structures of numerous-antibody complexes by cryo-EM offer powerful insights into how these viral particles appear in ‘snapshots’. However, they do not directly provide information into the inherent ‘breathing’ of viral particles in solution, nor do they delineate the dynamic mechanisms by which these viruses undergo conformational changes upon encounter of, and entry within, human host cells. Our research program will unravel dynamics of host entry in several classes of pathogenic icosahedral viruses- enveloped RNA viruses- flaviviruses (dengue, zika), non-enveloped RNA viruses (Coxsackie viruses) and non-enveloped DNA virus (Human Papilloma virus). This will be achieved through integration of cryo-EM with dynamics mediated by structural mass spectrometry and biophysical and RNA chemistry probes. The goals of our research program on viral particle dynamics, host entry and genome egress will advance therapeutic antibody and small molecule discovery for improving human health outcomes against viral diseases.

NIH Research Projects · FY 2025 · 2025-06

PROJECT SUMMARY/ABSTRACT Cystic fibrosis (CF) is the fifth leading cause of death in the US. As a life-shortening genetic disease, CF is characterized by abnormalities in the pulmonary and digestive systems due to systemic inflammation, fibrosis, and tissue degradation. About half of adult CF patients experience cystic fibrosis related diabetes (CFRD). Unlike the common type I or type II diabetes, CFRD develops at the very early stages of life of people with CF and leads to greatly worsened lung disease. Although new therapeutics – such as the triple combination CFTR modulator therapy TRIKAFTA – are impacting lung function for many patients, these therapies do not appear to be solving the endocrine problems experienced by people with CF. More precise and effective methods of early detection of this disease are urgently needed for progression prevention and to drastically lower the death rate. This project, if successful, will transform the management of patients with CFRD into more effective treatment strategies. Our first goal is to understand the role of MT1E on β-cell functions and survival during the development of CFRD. Our second goal is to elucidate the impact of exocrine cells expressing mutant CFTR on endocrine islets. Our third goal is to resolve a single-cell (scRNA-seq) map of islets from healthy, CFRD, and TRIKAFTA-treated CF ferrets. Our central hypothesis is that redox imbalance and tissue remodeling contribute to CFRD progression by altering endocrine function through the metallothionein 1 E pathway. First, this project is expected to shed light on the molecular mechanism of Metallothionein 1E (MT1E) in regulating pancreatic damage in patients with CFRD, using pluripotent stem cell-derived human pancreatic exocrine and endocrine organoids. Second, by using cutting-edge collagen-based magnetic resonance imaging, this project will map the location and severity of fibrosis in the pancreas during the development of CFRD. Finally, performing high throughput single-cell RNA sequencing analysis of the pre-clinical model of CFRD, the CFTRG551D/-KI ferret, this project will identify essential biomarkers during the progression of CFRD. Ultimately, these studies broaden our understanding of the pathogenesis of CFRD and provide the basis for using Magnetic resonance imaging (MRI) as a potential diagnostic approach for disease early detection. The project also serves as an opportunity for the PI to shift directions in his research program, learning new techniques that will greatly enable his future career.

NIH Research Projects · FY 2026 · 2025-06

PROJECT SUMMARY / ABSTRACT Along with the structural development of the prefrontal cortex (PFC) during adolescence, innervation of the PFC by several local neurotransmitter systems also develops, including the gamma-aminobutyric acid (GABA) system. Somatostatin (SST)-expressing GABA cells undergo significant developmental changes throughout adolescence, including in structure and function (Du et al., 2018) – importantly, SST neurons are a cell population known to be vulnerable to alcohol in adulthood (Dao et al., 2020, Dao et al. 2021). However, little is known about how developmental alcohol exposure may influence this key GABAergic and peptidergic population in the PFC – which could, in turn, lead to catastrophic, irreversible changes in PFC signaling and functional connectivity. Additionally, sex differences in the development of the PFC SST system may render it uniquely vulnerable to adolescent alcohol consumption. The objectives of this application are to characterize changes in behavior, overall cortical adaptations in SST neuron function and peptide signaling, and functional connectivity following developmentally relevant periods of adolescent binge alcohol consumption. Using the drinking-in-the-dark (DID) model of voluntary binge alcohol consumption, we will assess how adolescent-specific exposure to alcohol alters sex-specific long-term behavioral phenotypes, somatostatin peptidergic circuits, and overall brain systems, thereby linking a localized cell- type specific change with behavior and brain dynamics on a network scale. Using complementary approaches, we will systematically and comprehensively test the hypothesis that adolescent alcohol changes behavioral profiles, SST neuron and peptide function, and functional connectivity of the PFC. We will use a multidisciplinary approach spanning slice electrophysiology, in vivo signaling, quantification of cycling sex hormones, and resting-state functional connectivity to systematically characterize this system. Additionally, we will identify risk factors for later alcohol-induced behavioral changes using non-invasive imaging throughout drinking. These high-impact experiments have significant public health implications. By understanding the role of an understudied population of cortical peptidergic neurons, new treatment targets may be informed. Additionally, the rapid timescale of animal developmental models allows for a faster and more in-depth characterization of the effects of adolescent binge drinking compared to human studies, which span decades. This work is likely to significantly inform prevention and intervention efforts related to adolescent binge drinking.

NIH Research Projects · FY 2025 · 2025-05

Project Summary/Abstract This proposal seeks funding for a Lumicks C-Trap instrument for biomedical researchers at The Pennsylvania State University. The C-Trap, a unique commercially available optical trap instrument, integrates scanning confocal microscopy and microfluidics with a user-friendly interface. Correlated force and fluorescence spectroscopies have transformed single molecule studies in life sciences research, bridging high-resolution structures with their dynamical changes. Currently limited to specialized labs, the C-Trap is designed as a turn- key system, allowing non-expert laboratories to conduct cutting-edge single molecule studies with unparalleled spatial and temporal resolution. Key features include dual optical tweezers for piconewton force manipulation, three-color laser confocal fluorescence detection, precise temperature control, nano-stage positioning, laminar flow microfluidics for high sample throughput, a user-friendly Bluelake data collection and Pylake data analysis software. This proposal represents shared equipment use for ten major users and five minor users spanning five departments (Chemistry, Biochemistry and Molecular Biology, Bioengineering, Cellular and Molecular Physiology, Medicine, Microbiology, and Immunology), three colleges (Eberly College of Science, College of Engineering, and College of Medicine), and two campuses (University Park and Hershey). The C-Trap will advance fifteen ongoing interdisciplinary NIH-funded projects studying gene regulation, RNA and protein structure-function, mechanobiology, phase condensates, transcription, replication, translation, and DNA repair. The breadth of single molecules studies will encompass a diverse range, from molecular motors, cardiovascular proteins, cytoskeletal filaments, viral protein-RNA complexes, metalloproteins, LLPS in situ and nucleic acid processing enzymes, to multi-compartmentalized membraneless organelles and in vivo-like conditions. Scientific directors of the C-Trap core facility, Drs. Lee and Yennawar, will provide equipment oversight, expertise, and training to new users, while the Huck Institutes at Penn State will commit substantial institutional resources and support for effective utilization. The recent leasing of the C-Trap equipment has enhanced various research programs and centers at Penn State and synergized with other NIH S10 funded capabilities at the core, contributing to the discovery of impactful healthcare-related knowledge. Currently, there is no homemade optical tweezers setup in operation in any of the cores or any individual labs. The absence of commercially available instruments that match the unique capabilities of the Lumicks C-Trap across the twenty- four campuses of The Pennsylvania State University underscores the urgent need to acquire this advanced equipment. The C-Trap's high-resolution dual optical tweezers, ultra-stable force detection, five-channel flow cell microfluidics, and three-color imaging confocal microscopy system would significantly enhance the university's research capabilities, enabling cutting-edge studies that are currently unattainable with existing resources.

NIH Research Projects · FY 2025 · 2025-05

Project Summary / Abstract AD-related dementia (ADRD) are devastating brain diseases with unmet medical needs. Abnormal aggregations of amyloid-like proteins such as Aβ and tau proteins are pathologic hallmarks. The FDA granted accelerated approval to the anti-amyloid drugs aducanumab and lecanemab, signifying the potential of amyloid- lowering strategies in AD drug development. While the detrimental effects of amyloid aggregations are well- documented, the current challenge lies in identifying risk factors that directly or indirectly influence the accumulation of these proteins in the nervous system. Notably, recent studies have identified a group of RNA binding proteins (RBPs) with significant protective effects against neurodegeneration. However, the molecular functions of these newly identified neuroprotective genes in AD pathophysiology remain unexplored. Therefore, it is imperative to elucidate the molecular mechanisms by which these RBPs mitigate AD-related cellular dysfunction. Our long-term goal is to design innovative interventions to prevent and treat brain abnormality in neurodegenerative disorders including AD. Our group has previously revealed critical molecular regulators implicated in AD. We have identified an RBP, RBM8A that is significantly downregulated in human postmortem AD brains and consistently reduced in 5XFAD mouse brains. Intriguingly, our preliminary data have shown that increased dosages of RBM8A at different ages alleviate Aβ amyloid formation in 5XFAD mice. Our objectives are to examine how different gene dosages of RBM8A affect pathological and behavioral changes in 5XFAD mouse and to identify targets most relevant for RBM8A-dependent neuronal protective effects. Our rationale for this project is that its successful completion would provide a robust, evidence-based framework for developing therapeutic strategies for AD or other neurodegenerative diseases. To achieve our objectives, we will rigorously test two Specific Aims: 1) Determine the role of Rbm8a in AD pathological and behavioral changes in 5XFAD mouse model; and 2) Determine molecular targets of RBM8A during neurodegeneration in 5XFAD mouse brains. It is anticipated that the proposed studies will provide the underlying mechanism(s) by which RBM8A modulates neurodegeneration in AD. What is learned here will be utilized to identify cell type-specific, phenotype-relevant mRNA targets that can serve as novel drug targets for AD patients. The successful completion of the proposed studies would have an important positive impact on developing therapies to prevent and/or treat patients at risk for AD or other neurodegenerative diseases.

NIH Research Projects · FY 2026 · 2025-04

Project Summary/ Abstract Inborn Errors of Purine Metabolism are linked with specific and often severe neural and muscle dysfunctions. However, the precise mechanisms through which mutations in enzymes involved in the synthesis of key biological molecules lead to these distinct outcomes remain unclear. This proposal focuses on the investigation of adenylosuccinate synthase (ADSS), specifically the deficiency of the muscle-specific isoform, ADSSL1, linked to progressive myopathy in humans. Because of the importance of the purine nucleotide cycle in maintaining energy stores (ATP levels) in tissues like muscle with intense energy requirements, the perturbation of the purine nucleotide cycle upon loss of ADSS activity is proposed to underlie phenotypes. However this hypothesis has not been investigated because there are no established animal models for study of this disorder. The primary objective of this research is to develop a C. elegans model for ADSS deficiency. C. elegans, with its powerful genetic system, provides an ideal platform for uncovering the etiology of myopathy and mobility phenotypes associated with ADSS deficiency, a crucial step in envisioning novel therapeutic strategies. ADSS deficiency in C. elegans manifests in mobility dysfunction and metabolic perturbations. The specific aims are structured as follows: Aim 1 focuses on developing genetic tools for the analysis of adss-1 function. The plan focuses on developing a degron-based system for temporal and spatial control of ADSS-1 function and engineering human disease allele knock-ins. These tools will be used to determine tissue-specific, developmental, or acute functions of ADSS-1, as well as to characterize structural defects in muscle cells and broader metabolic changes in metabolism that are associated with adss-1 knockdown. Aim 2 involves investigating alternative hypotheses about the etiology of various adss-1 phenotypes and testing candidate therapeutics. Comparisons with other genes in the de novo purine biosynthesis pathway and purine nucleotide cycle pathway will elucidate the role of these pathways in phenotypic outcomes. Supplementation and genetic experiments will assess the role of ADSS-1 product (S-AMP) and purine homeostasis in phenotypic outcomes. Finally, candidate therapeutics, including the ADSS product S-AMP, will be tested using the C. elegans model. The anticipated outcomes include significant progress toward therapeutic strategies for a disorder lacking treatment options. Insights gained will contribute to understanding how purine metabolism influences cellular processes and biochemical pathways, potentially revealing novel therapeutic targets for other muscle disorders associated with aberrant purine metabolism.

NIH Research Projects · FY 2026 · 2025-02

Abstract Syphilis cases in the US are increasing at an alarming rate and the need for a rapid diagnostic test that can quickly inform treatment and management decisions is desperately needed. An accurate diagnosis of syphilis relies on recognizing a constellation of symptoms, reviewing medical and sexual history, and performing multiple laboratory tests. The mainstay of routine laboratory diagnosis of active syphilis infection remains serological detection of treponemal and nontreponemal antibodies. Detection of treponemal-specific antibodies is evidence of infection, however, it may indicate past, successfully treated infections since these antibodies persist for decades. Non-treponemal serological response to cardiolipins is suggestive of potential syphilis infection but is not sufficiently specific to support treatment decisions. Further, responses to non-treponemal antigens are generally titered in the laboratory to allow clinicians to assess increases or decreases in titer that support clinical decision making regarding the stage of the disease. There are only two FDA-cleared syphilis rapid tests that would support immediate decision making. However, both are of limited clinical utility because they detect only treponemal-specific antibodies. Currently, there is no point-of-care device available in the US that can test for active syphilis infection, which requires the addition of non-treponemal antibody testing, preferably with a semi- quantitative result. This is necessary to determine appropriate treatment with high sensitivity and low false positive rate. Innovations in this area have yet to be translated into clinical practice. Combining treponemal and nontreponemal assays within the same platform will provide a more definitive, stand-alone diagnosis of syphilis. The proposed rapid assay will fill this gap by utilizing ultra-sensitive electrochemical detection of resistance potential changes that results from the direct interaction of nontreponemal and treponemal antibodies against lipoidal material and T. pallidum antigens respectively. By using 2D nanomaterials (e.g., graphene), which have been successfully used in the development of assays for other pathogens, this electrochemical test can detect subtle interactions between the sensing platform and the targeted analytes. We proposed to use modified cardiolipin for the detection of nontreponemal antibodies and antigens from T. pallidum for the detection of treponemal antibodies. If the target antigen-antibody complex is present, graphene's carrier mobility will change, resulting in a change in electrochemical signal. The proposed electrochemical platform demonstrated ultra- sensitivity of 1 fg/mL for treponemal antibodies, and opened avenues for fast, accurate detection of nontreponemal sera. This project aims to develop a sensing platform that allows simultaneous detection and semi-quantification of treponemal and nontreponemal antibodies that can identify and differentiate active from past cases of syphilis within 10 minutes.

NIH Research Projects · FY 2026 · 2025-02

Project Summary Sexual reproduction is a battleground for inherited bacteria and their hosts, yet how maternally-inherited bacteria modify the reproductive biology of their host species to favor the fitness of infected females is largely unresolved. Wolbachia are the archetypes of this adaptive strategy and exist globally in nearly half of all arthropod species and many filarial nematodes, making them one of the most widespread microorganisms in the animal world. In a variety of arthropod orders, Wolbachia selectively kill sons of infected females in a process termed male killing. This form of sex-specific lethality enhances the spread of the bacteria by increasing the fitness of transmitting females through reduced competition with their dead brothers for limited resources. It can also spur host adaptive responses including male mate choice to avoid the costs of reproductive parasitism or Wolbachia density suppression as males become rare in populations experiencing high levels of male killing. Notably, population genetic models specify that male killing bacteria can speed up the eradication of target pest populations when used in conjunction with the sterile insect technique. However, despite six decades of research on male killing and its relevance to ecology, evolution, cell biology, and vector control, the mechanistic bases remain enigmatic and one of the field’s most central challenges to resolve. We recently identified a gene, hereafter termed WO Male Killing (wmk) from the prophage WO region of Wolbachia, that can cause male killing. When wmk is transgenically expressed in uninfected D. melanogaster embryos, it kills nearly half of male embryos in association with an increase in Dosage Compensation Complex activity and DNA damage. Additionally, the canonical cytological defects caused by male killing Wolbachia are also enriched in wmk-expressing embryos. This project will test the central hypothesis that the Wmk protein kills males by disrupting host transcription in early embryogenesis via host DNA binding and transcriptional misregulation. In Aim 1, we will assess if Wmk acts as a transcription factor to induce male killing by binding host DNA and altering gene expression. In Aim 2, we will interrogate the regions and conserved sites of the Wmk protein necessary to induce male death and the dependency of male killing on early versus late embryonic expression. In Aim 3, we will test if Wmk transport from the cell is mediated by the type IV secretion system, phage particles, or vesicles. Despite decades of intensive research and applications to pest control studies, the details surrounding the mechanistic basis of male killing remain a central question.

NIH Research Projects · FY 2026 · 2025-02

Abstract There is need for an artificial oxygen (O2) carrier to substitute for banked blood in settings where stored blood is unavailable or undesirable. Our goal is to design and optimize a blood substitute prototype (Nano-RBC/nRBC), that is based on a deformable nanoparticle, is morphologically similar to red blood cells (RBCs) and incorporates high per particle payloads of hemoglobin (Hb). This project will use machine learning tools (ML), computational studies, synthetic and biological experiments to design a 'smart' optimized O2-delivery biomaterial with physiological binding and dissociation properties, biodegradability, and no complement activation problems. Prior hemoglobin-based oxygen carriers (HBOCs) have failed because they do not preserve physiologic interactions of hemoglobin (Hb) with O2 and nitric oxide (NO). Nano-RBC design avoids these weaknesses by: 1) encapsulating Hb, 2) controlling O2 binding/release with a novel RSR-13/2,3-DPG shuttle, 3) attenuating NO uptake, and 4) retarding metHb formation. Moreover, Nano-RBC is designed for sterile lyophilization. This design constitutes a new class of Hb-encapsulated, toroidal-shaped nanoparticle formulated by self-assembly of amphiphilic lipopeptides. Toroidal shape affords increased stability, enhanced surface area for gas exchange, and improved rheology and vascular interactions. The toroidal particles are developed from amine rich β-turn peptide amphiphiles. The inherent cationic nature of the peptides enables RSR13 retention via electrostatic interaction. Moreover, these functionalities exhibit significant buffering centered upon physiologic pH; as pH falls below 7.4 (e.g., as in tissue), protonation of the amines increases, displacing RSR13 from the inner shell, thereby linking free [RSR] in the Nano-RBC cavity to ambient pH. Therefore, (as Hb O2 affinity falls in proportion to RSR availability) pH shifts encountered during circulatory transit facilitate O2 release at physiologically appropriate gas tensions. This physiologically responsive RSR reservoir-shuttle differentiates Nano-RBC from all prior HBOC designs. This project will focus upon refining the O2 affinity control system designed to enhance O2 transport under conditions of physiologic stress. Thus, our Aims are: Sp Aim 1: Design and syntheses of β-turn peptide amphiphiles and characterize self-assembly. Sp Aim 2: Develop computational tools to optimize self-assembly and functional properties of Nano-RBC. Sp Aim 3: Analyze and optimize Nano-RBC composition for efficient O2 delivery in vitro. Sp. Aim 4: Exploratory pharmacokinetic (PK) profiling and bio-distribution (Bio-D) studies. Upon project completion, we expect to have successfully optimized and evaluated key Nano-RBC functions: 1) O2 binding/release; 2) NO sequestration; and 3) optimized shell character. As such, we will have prepared Nano- RBC for the next stage of funding, preclinical evaluation, and development, readying the particle for: 1) formulation scale-up and 2) formal evaluation in large animal models of hemorrhage and hypoxemia (completion of both will be necessary prior to Phase I Trials in humans).

NIH Research Projects · FY 2026 · 2025-02

PROJECT SUMMARY / ABSTRACT Bacteria utilize numerous sensing and signaling pathways to alter behaviors that allow host colonization of both bacterial infections and microbiomes. Bacteria translate changes in the extracellular environmental into intracellular signals, such as nucleotide-based signaling molecules, to rapidly respond and optimize physiology for survival. Understanding these signaling pathways is necessary to be able to predict bacterial behavior under different conditions and to rationally develop new methods to alter medically relevant bacterial phenotypes. Recently, we have identified roles for atypical nucleotide signals, 2’,3’-cyclic nucleotide monophosphates (2’,3’- cNMPs), in controlling transcription, translation, biofilm formation, and stress resistance in E. coli and Salmonella enterica. This research program will elucidate the molecular mechanisms that control 2’,3’-cNMP-dependent effects, the intersection with paradigmatic nucleotide-based signaling pathways, and the broad physiological effects of 2’,3’-cNMP signaling. To do so, we will synthesize chemical tools and use a variety of in vitro and in cellulo techniques to interrogate the effects of 2’,3’-cNMPs in bacterial transcription, translation, signaling pathways, and phenotypes in E. coli. In addition, we will use biochemical and genetic assays to identify metabolic enzymes and binding partners. Results from E. coli will be extended into other bacterial species to understand the conservation and diversity of 2’,3’-cNMP signaling, as well as determine the potential for targeting 2’,3’-cNMP pathways for development of new antibiotics. Ultimately, this program will provide novel insights into the cellular roles of 2’,3’-cNMP signaling in bacteria, as well as develop (bio)chemical tools and fundamental knowledge that can be applied to investigate 2’,3’-cNMP signaling in other organisms.

NIH Research Projects · FY 2026 · 2025-02

Project Summary DNA transcription by cellular and multi-subunit RNA polymerase plays a central role in gene expression. Our investigations have led to significant advancements in understanding the structural basis of DNA transcription that have been achieved through the use of advanced structural biology techniques such as X-ray crystallography and cryo-electron microscopy single particle reconstruction (cryo-EM). Supported by the MIRA grant since 2019, our investigations have expanded and resulted in groundbreaking discoveries concerning the fundamental processes governing gene expression and regulation in bacteria, archaea, and eukaryotes. Notably, our recent cryo-EM studies have shed light on the structural basis of ribosomal RNA transcription by bacterial RNA polymerase, its regulation by DksA/ppGpp, and NusG-dependent transcription pausing. These studies have underscored the importance of analyzing the heterogeneity of transcription complexes, the dynamics of RNA polymerase, and deciphering the multiple states of the transcription complex to understand the long-range impact of transcription factors on RNA polymerase activity regulation. Over the next five years, our research will focus on investigating heterogeneity and dynamics of RNA polymerase transcription using cryo-EM, single-molecule and biochemical approaches, addressing questions that were previously challenging to explore solely through static views of the transcription complex. Specifically, our objectives are to examine the allosteric influence of upstream DNA and bacterial RNA polymerase interactions on DNA opening and transcription initiation, elucidate the mechanisms underlying allosteric and pleiotropic bacterial transcriptional regulation by DksA/ppGpp, analyze bacterial RNA polymerase transcription pausing in an environment closely resembling the intercellular conditions, comprehensively understand the structural basis of the archaeal RNA polymerase transcription cycle, and investigation of eukaryotic RNA polymerase II transcription complexes directly isolated from Drosophila nuclear extract. We anticipate that our proposed project will significantly advance transcription research and enhance our understanding of gene expression across all three domains of life. Moreover, it will contribute to the continued growth of our research program and establish an even greater scientific impact. Gene expression by cellular polymerase is fundamental to all life forms and investigating the transcription process is critical for understanding cell development, maintenance, and disease. The proposed studies regarding the structure and function of cellular RNA polymerase may lead to new avenues for drug discovery and preventing disease.

NIH Research Projects · FY 2026 · 2025-01

Abstract The Biomedical Data Translator has already established itself as a powerful platform for integrating diverse biomedical data and enabling complex reasoning across a federated architecture. In the Performance Phase, we aim to elevate Translator to a new level of utility and impact by addressing key limitations and expanding its capabilities. Our overarching goal is to transform Translator into a highly versatile and user-centric tool, capable of delivering precise, actionable insights to support both basic and translational research. To achieve this, we will expand Translator's ability to handle a broader range of queries by incorporating new data types such as clinical trials, pharmacogenomics, multiomic, and metagenomic datasets. These enhancements will enable researchers to pose more sophisticated questions utilizing their own data in the context of Translator, uncovering connections and pathways that were previously inaccessible. In parallel, we will improve the transparency and provenance of Translator's outputs by developing new methodologies for evidence tracking and confidence assessment, ensuring that users can fully trust and understand the information they receive. We aim to closely collaborate with the Translator User Interface team to expose these new query and data types, as well as enhance the clarity and interpretability of evidence, provenance, and confidence associated with query results. High performance and scalability are also central to our vision. We will optimize our tools’ architecture to handle larger, more complex datasets, with improved speed and efficiency. This will involve refining knowledge graph integration, decreasing API response time and call frequency, enhancing data caching, and streamlining update processes, all of which will contribute to a more responsive and reliable system. Crucially, we will also expand user engagement, making Translator more accessible and valuable to a broader audience of researchers and clinicians. By implementing advanced user feedback mechanisms and developing new tools for user-supplied data integration, we aim to foster a dynamic, collaborative ecosystem where users can actively shape the future development of Translator. This project brings together an interdisciplinary team from Penn State University, the Institute for Systems Biology, Oregon State University, The Broad Institute, and Grenoble University. Each institution’s team contributes unique expertise, ranging from reasoning agent development and knowledge graph construction to user engagement and molecular data integration. This multi-institutional collaboration is crucial for addressing the complex challenges of expanding and optimizing the Translator system, ensuring that it continues to provide cutting-edge tools and insights for the biomedical research community.