Washington State University

NSF Awards · FY 2024 · 2024-08

Evolution and persistence of animal populations depend in part on the presence of variation within those populations in how individuals cope with environmental challenges, but that variation is not constant over time. This project will explore when and how changes in the environment - specifically, changes in body temperature - can alter physiological functional diversity among individuals living in proximity to one another. The research team will combine experiments on intertidal invertebrates (mussels) with comprehensive study of their protein expression patterns to document how individuals differ in their molecular response to environmental fluctuations. The work will also identify connections between functional diversity at the molecular level and measures of each individual’s performance. Climate change is expected to negatively impact many populations, but the aggregated outcomes will depend on how individuals respond to their unique conditions. This project will disentangle important complexities in biological responses to the increasing frequency and intensity of environmental extremes, ultimately contributing to more accurate biological forecasting. Through this work, the research team will mentor a diverse set of trainees including a postdoc, Ph.D. students, and undergraduates, each of whom will receive support to present their findings at conferences. The project also will support a collaborative scientific working group that will foster the merging of physiology and genomics to better predict how animals will perform in the future in more variable, and perhaps entirely novel, environmental conditions. Individuals vary in their physiological rates, tolerances, and other aspects of function. The magnitude of this variation itself can change over short periods, in different environmental conditions, or for different representations of physiology, but key uncertainties remain. In particular, both theory and prior results alternately suggest that stress "masks"/reduces functional variation or "unmasks"/increases otherwise hidden variation. This project will explicitly quantify how environmental stress and environmental heterogeneity mask variation in some aspects of function while unmasking variation in others and/or reorganizing connections in the molecular phenotype (the proteome). It will connect environment-driven shifts in the architecture of "subnetworks" of the proteome (i.e., groups of co-expressed proteins) both "up" in scale to organismal performance and "down" to physiological mechanisms that differentiate individual mussels in their stress resistance. The team will combine manipulative experiments with state-of-the-art quantitative proteomics approaches, using the intertidal California mussel (Mytilus californianus) as a tractable model, to evaluate shifts in the architecture of protein expression subnetworks in different thermal treatments. The treatments will vary in the mean intensity and inter-individual heterogeneity of body temperature before and during acute heat stress events. The integrative, omics-to-organisms approach will stimulate conceptual advances and generate novel insights into the role of context-dependency in environmental physiology. The results should also provide vital environmental context to the genomes-to-phenomes framework, in line with goals of Rules of Life. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-08

1 Project Summary 2 The Thiamine HPLC-FLD quantification project is proposed by the WADDL-ASL laboratories to 3 fill the analytical gap in the Vet-LIRN network by developing a standardized HPLC-FLD 4 (fluorescence) method to quantify the concentration of thiamine, thiamine 5 pyrophosphate(diphosphate), and thiamine monophosphate in animal feeds, tissues, and blood 6 that can be implemented by all in-network laboratories with HPLC-FLD capabilities. Thiamine is 7 an essential vitamin that must be supplied in the diet of many animal species and severe 8 disease can quickly develop in deficient diets. The current gold standard for diagnosis relies on 9 recognition of clinical signs and response to treatment as thiamine testing in tissue and blood 10 samples is not readily available in veterinary diagnostic laboratories despite being routine in 11 human clinical laboratories. A method utilizing HPLC-FLD instrumentation will be extrapolated 12 from an HPLC method validated in fish tissues and roe into an HPLC-FLD method for increased 13 sensitivity and the matrices expanded to include animal and pet feed and animal (non-fish) 14 tissues (liver, brain, and muscle) and blood. A Level 2 FDA validation will be done in the lead 15 laboratory using prepared and verified homogeneous test materials including animal and pet 16 feed, animal tissues (liver, brain, and muscle), blood, and three species of fish roe. A Level 3 17 FDA validation will then be done by collaborators at the Cornell University Animal Health 18 Diagnostic Center and supply additional recommendations for optimization of the method. After 19 completion of the validation, the SOP for the Thiamine HPLC-FLD quantification method will be 20 made available to Vet-LIRN network laboratories and added to the literature in a peer-reviewed 21 journal. Oral and/or poster presentations at appropriate conferences will be made to increase 22 visibility and awareness of the new standardized SOP available for use and implementation. 23 Additionally, method development will be completed to expand the method to an HPLC-UV/VIS 24 to increase accessibility in Vet-LIRN laboratories without HPLC-FLD testing capabilities in case 25 of an event requiring significant surge analysis capacity.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY / ABSTRACT As the population of individuals 65+ grows, so too will the number of individuals who struggle to manage chronic health conditions. Exacerbations, or sudden symptom worsening, of chronic conditions place a burden on the health care system and cause decreased quality of life and accelerated decline. Forecasting health exacerbations can prevent life-threatening events or limit their impact. The long-term goal of this work is to create a clinician-in-the-loop (CIL) smart environment that empowers individuals in managing their chronic health conditions. Our proposed CIL framework partners clinical expertise with pervasive computing and machine learning. In this system, sensor data are collected continuously by ambient and wearable sensors. Our ML algorithms extract behavior markers to show to a clinician. Behavior changes are detected due to internal (i.e., condition exacerbation) or external (i.e., wildfire smoke, shutdown due to COVID-19 pandemic) events. Trained by clinicians, prediction of future condition exacerbations and health states are generated with corresponding reliability scores. Correspondingly, clinicians will provide summaries of observed behavior, reasons to confirm likely exacerbations, and recommendations to prevent health events. These summaries are used to train a language model that will provide interactive explanations of future data and ML predictions. Data are collected continuously by ambient sensors in the smart home and wearable sensors in Apple watches to validate the findings and provide more complete monitoring. From smartwatch sensors, we will analyze the predictive relationship between external events, social determinants of health, socialization, environment quality, behavior, and health state. The result of these steps is an automated technology that can assist with self-management of chronic conditions and monitor the impact of interventions. The proposed aims will be validated using data collected in our prior study for n=44 older adults and in a new data collection with n=20 older adults. Participants in the restrospective study with historic data and prospective study with new data will be older adults age 50+ living in independent homes who are managing one or more chronic health conditions. Expanding the smart environment to encompass ambient sensors and wearable sensors increases the accessibility of the technology for underserved communities and, when used in combination, improves model robustness through joint prediction. Although clinical oversight of patient health will always be valuable, the technology can provide an “informatics triage” that allows a clinician to remotely monitor a greater number of individuals at a time and provide valuable information to the individual to assist in self-management. Outcomes of this proposed study include open-source software for forecasting condition exacerbations, software to train language models from clinician input, and the corresponding trained models; results of analyses linking external influences, socialization, behavior, and health; apps for collecting ambient and wearable data; and data that will be prepped for integration into the NIH RWDP platform.

NIH Research Projects · FY 2026 · 2024-08

Project Summary/Abstract Pediatric chronic pain is a critical public health problem, affecting up to a third of adolescents and contributing to significant emotional distress, poor sleep, and difficulties in social functioning. These difficulties include social isolation, friendship instability, and high rates of peer victimization both on and offline. Whether peer relationship problems are a cause, correlate, or consequence of chronic pain is largely unknown. Although research has long demonstrated links between social pain (e.g., social exclusion, loneliness) and physical pain—little research has examined the prospective, daily, or chronic impact of peer relationship problems on pain persistence and pain-related disability in childhood. Further, no research has examined how positive peer relationship factors (e.g., social connectedness, social support) may promote recovery or protect against the development of disabling pediatric chronic pain. The objective of the proposed research is to identify specific peer relationship processes that influence pain persistence, exacerbation, and recovery in a cohort of 450 early adolescents (ages 11-14) at risk for developing chronic pain (i.e., youth seeking treatment for an acute pain problem). Longitudinal studies that model the trajectories of peer relationship processes are needed to establish temporal relationships and disentangle social risk and protective factors from outcomes. If peer relationship factors contribute to pain persistence and pain-related disability, improving these relationships should become an immediate goal of both prevention and intervention efforts. Here we combine 1) a large- scale longitudinal cohort design, 2) comprehensive assessment of peer relationship processes and pain, and 3) a model-based approach to determine whether and how specific peer relationship processes (e.g., social exclusion, cyber-victimization, social connectedness) contribute to pain outcomes in at-risk youth during the critical transition from early to middle adolescence (Aims 1 and 2). Electronic daily diary monitoring of peer victimization experiences and pain, incorporating objective assessment of social media use and sleep, will be combined with qualitative interview data to characterize the temporal dynamics between peer victimization, social media use, shared comorbidities, (i.e., poor sleep, low mood) and pain outcomes (Aim 3). Our broad hypothesis is that peer relationship problems will contribute to pain persistence and disability, directly and indirectly (through mood and sleep mechanisms)—and that these effects will be mitigated by the presence of strong social support and social connectedness. The proposed methodologically rigorous mixed-methods investigation of peer relationship trajectories from early to middle adolescence will advance our understanding of the specific peer relationship processes that contribute to pain risk and resilience in childhood. Mechanistic insights regarding the role of modifiable social contextual factors will influence clinical practice guidelines and the development of preventative interventions designed to reduce risk of high impact chronic pain in childhood and beyond.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY A growing body of research shows that ableist attitudes and beliefs are widespread among healthcare providers and that many healthcare settings still lack necessary accommodations for patients with physical, psychiatric, sensory, neurological, and learning disabilities. This medical ableism likely contributes to the substantial health disparities experienced by people with disabilities. However, public health research to date has not evaluated the frequency and variety of medical ableism experiences among patients with disabilities, nor has it measured how these experiences adversely affect the care and health of disabled patients. The long-term goal of our research is to develop a nuanced and comprehensive understanding of medical ableism that will ultimately allow us to develop targeted interventions to mitigate its effects on the care and health of people with disabilities. The objective of this observational study is to conduct quantitative analyses of the medical ableism phenomenon and its impact on the healthcare and health outcomes of people with disabilities. This research will move the field beyond abstract assessments of internal ableism among providers by providing detailed evidence about how people with disabilities experience medical ableism. The specific aims of the project are: 1) to create and field survey modules measuring medical ableism and its adverse care and health impacts, 2) to characterize experiences of medical ableism, and 3) to identify the adverse care and health impacts of medical ableism. These aims will be met using a large, diverse, and well-established survey developed by the research team: the National Survey on Disability and Health (NSHD). The 5th wave of the NSHD is currently open, and the previous wave had a sample size of 2,725 adults with a variety of disabilities, providing sufficient statistical power for subpopulation analyses. The project research team and its expert advisory panel, comprised solely of researchers with disabilities, will model best practices in disability inclusion and representation in disparities research. It will offer researchers and advocates a new, publicly accessible, and user-friendly data source on critical dimensions of medical ableism. The large and diverse survey sample will allow users to explore intersections between disability and race, ethnicity, gender, sexual orientation, and socioeconomic status. The survey questions can be adopted or modified by advocates to assess discriminatory practices and environments among local healthcare providers. The findings will also allow educators to develop and refine disability curricula and target anti-ableist practices in medical education. The project further the National Center on Medical Rehabilitation Research’s mission to foster the development of scientific knowledge needed to enhance the health, productivity, independence, and quality of life of people with disabilities.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY The legalization of recreational and medicinal cannabis in several states across the US has increased the need to better understand its effects on the body, brain, and behaviors in diverse populations. Notably, people 50 and over are the fastest growing group of cannabis users in the US. Among this group are women who have undergone the transition to reproductive senescence, known as menopause, which occurs at the average age of 51. Menopause and the attending decrease in circulating estrogens is associated with a variety of symptoms including mood, anxiety, and cognitive impairments as well as metabolic changes that are linked to poor health outcomes. As an increasing number of post-menopausal women use cannabis, either recreationally or medicinally to treat menopause symptoms, it will be important to evaluate the health risks and benefits of cannabis use in this unique population. Here, preclinical mouse models are particularly valuable, as they provide precise control over cannabis treatment (composition, frequency etc.) and enable researchers to dissociate the contribution of age and endocrine status to various neural, behavioral, and metabolic outcomes. To produce readily translatable findings from mice to humans, preclinical models should closely resemble human patterns of cannabis consumption. To this end, along with co-I Dr. Ryan McLaughlin, the Delevich lab has recently validated a novel vapor inhalation model of whole plant cannabis extract for use in mice. Thus, the objective of this R21 proposal is to utilize this model of cannabis use to model the consequences of chronic cannabis use in the post-menopausal state. To this end, in Aim 1A we will first establish the pharmacokinetics of vaporized cannabis in young adult (postnatal day 90) and aged (18 month) female mice who differ by endocrine status (ovarian intact vs. ovariectomized). Next, in Aim 1B we will assess the effect of chronic cannabis vapor exposure on energy balance, including weight gain, body composition, food intake, and home cage locomotor activity, in these same groups. In Aim 2A we will examine how chronic cannabis vapor exposure influences mood-related endpoints and cognitive flexibility in young vs. aged OVX and ovarian intact female mice. Finally, given the co- expression of estrogen receptors and endocannabinoid system components within the medial prefrontal cortex (mPFC), and this region’s function in mood regulation and cognitive flexibility, in Aim 2B we will assess the effect of chronic cannabis vapor exposure on glutamatergic and GABAergic synaptic transmission onto layer II/III and V pyramidal neurons within the prelimbic subregion of the mPFC in young vs. aged OVX and ovarian intact mice. Together, these aims employ a conceptually and technically innovative approach to study the brain, body, and behavioral effects of chronic cannabis use in a vastly understudied population. Funding this R21 proposal will establish the vaporized cannabis exposure model within a mouse model of menopause and generate necessary pilot data to support future collaborative proposals to investigate the impact of cannabis use on women’s health during aging.

NSF Awards · FY 2024 · 2024-08

Communication flows in cyber-physical systems (e.g., aircraft, automobiles, industrial systems) have stringent timing and performance constraints. Late delivery of important messages can result in safety violations or system failure. For instance, critical components of a car, such as the anti-lock braking module, may fail to function properly if they do not receive timely signals from the brake pedal through the communication bus—this puts the passengers’ safety at risk. These networks are carefully engineered to ensure resource requirements are met at runtime. This is a highly complex process since it is up to the designers of such systems to ensure correct and reliable network-wide (global) behavior, even in the face of failures. This project aims to ease this process and devise techniques for more efficient utilization of network resources, providing better end-to-end quality-of-service and resiliency guarantees. The results from this project will make many critical cyber-physical systems of modern society more resilient and, hence, much safer. Modern complex safety-critical networks, such as those used in avionics, automobiles, and power grids, need more sophisticated solutions to ensure that their end-to-end service guarantees (i.e., timing and data rate requirements) are met. The techniques developed for more general-purpose and data-center networks are not readily adaptable to safety-critical cyber-physical networks with stringent “real-time” requirements. The key innovations of this proposal involve creating holistic models, algorithms, and software designs to achieve the scalability, adaptability, and resiliency required for real-time applications. The proposed work will explore design methodologies for critical networks by combining real-time scheduling theory with new and emerging networking paradigms (viz., software-defined networks and programmable switches). Specifically, this foundational research devises novel routing, flow scheduling, and fault tolerance techniques for real-time networks, resulting in better admissibility and resilience, thus enhancing overall resource utilization. The project has two related research thrusts. The first thrust ensures end-to-end quality-of-service guarantees. Due to their safety-critical nature, real-time networks must be resilient to failures by design. Communication flows must reach their destinations even when there is a network failure. The second thrust addresses this aspect and devises resilient routing schemes. The mathematical frameworks constructed in this research for analyzing such systems will provide strong guarantees, potentially facilitating faster testing, integration, and verification efforts. The proposed solutions will be evaluated and tested on various platforms, from simulation engines to real hardware testbeds. All data, insights, results, and implemented frameworks will be publicly available online. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

Hurricanes can have devastating impacts on coastal areas. This research will evaluate the ecological and evolutionary effects of hurricanes on island ecosystems. Climate change caused by humans has increased the strength and frequency of hurricanes in the North Atlantic over the past 20 years. Using decades of data on the lizards, spiders, insects, and plants living on islands in a hurricane-prone region, this project will determine how storm intensity is related to natural selection, extinction risk, and species interactions. This research seeks to establish a better understanding of the ecological and evolutionary consequences of climate-change driven increases in the frequency and magnitude of hurricanes. A better understanding of the biological impacts of extreme weather events on ecosystems will increase the accuracy of predictions needed to protect and manage biodiversity. The publications and synthesized data sets from this project will be useful to a broad range of stakeholders, including basic and applied scientists, resource managers, and policy makers. This research will capitalize on decades of annual measurements of trait variation in a lizard, spider community composition, and food-web interactions across three trophic levels from dozens of small islands in the Bahamas. During this time, 17 hurricanes and tropical storms passed close to the study site, generating variation in hurricane impacts across time and space. This retrospective analysis will integrate long-term biological data with meteorological models that generate island-specific estimates of wind speed, storm surge, and wave energy during storms. Tests of synthetic hypotheses aim to 1) reveal thresholds for natural selection and extinction risk for lizards related to variation in hurricane intensity, 2) determine recovery trajectories for spider communities related to the interactive effects of hurricane intensity, dispersal, and species interactions, and 3) elucidate the roles of top-down and bottom-up pathways in hurricane-driven increases in herbivory. The simultaneous consideration of many storms and the integration of detailed estimates of hurricane-specific damage adds substantial value to long-term data on lizards, spiders, herbivores, and plants in these island ecosystems. The analytical approach will serve as an example for integrating biological and meteorological data sets to address the effects of other increasingly common and strong extreme weather events. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

The merger of two neutron stars, or a neutron star with a black hole, involves extremes of all the fundamental forces: strong gravity, nuclear matter denser than atomic nuclei, incredibly strong magnetic fields, and huge energies released in the form of radiation of neutrinos and gravitational waves. Such systems give off gravitational waves as the neutron star and its companion spiral together and electromagnetic waves (visible light, infrared, gamma rays, etc) after the merger. Probing the extreme physics involved requires comparing observations with predictions from models. Modeling these events requires computer simulations including general relativity, turbulent magnetized fluid, and radiation. However, the post-merger evolution (which produces important electromagnetic signals and outflows of gas) lasts seconds, while most numerical simulations last less than a tenth of this time and so miss most of it. This project will probe these later times with numerical relativity, following the story of the merger through to completion, when nothing but a stable, quiescent black hole or neutron star remains. The key to evolving to late times is to treat the fluid properties as a combination of average, large-scale components and complicated mulit-scale turbulence. One can take advantage of a rough symmetry in the former about a rotation axis to do less computationally demanding (2D) simulations, so long as the effect of the turbulence on the average flows and magnetic fields are properly incorporated. Part of this project will be to improve models of these effects of turbulence. Another part will be to determine how the properties of matter and spacetime immediately after merger affect the subsequent output of radiation and gas. The PI will train students in STEM areas. The PI proposes to undertake long-time (multi-second) studies of these strong-gravity, dense-matter systems using the Spectral Einstein Code (SpEC), which includes magnetohydrodynamics, nuclear microphysics, neutrino transport, and a turbulence/dynamo model to capture previously omitted qualitative effects. Long-time 2D simulations will extend existing compact binary merger simulations for multiple seconds, yielding accurate predictions about outflows from disk and remnant, delayed remnant collapse, magnetic field evolution, and GRB energetics. The 2D axisymmetric evolution techniques will be imported into the numerical relativity code SpECTRE. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-07

PROJECT SUMMARY Mental health disorders are the leading cause of disability in the U.S., affecting approximately 1 in 5 people. While the causes are likely multifactorial, hippocampal glutamatergic synapse formation and number are strongly correlated with mental health outcomes. In utero environmental cues critically alter development of hippocampal synapses. Over 30% of people in the US are obese and maternal obesity now affects more than 1 million developing babies in the US annually. Children of obese mothers have a higher risk of anxiety, autism spectrum disorder (ASD) and reduced cognition. In contrast, maternal exercise (ME) is associated with increased cognition, emotional resilience, and reduced risk of ASD. The mechanisms underlying both the positive and negative effects of maternal metabolic state on development are largely unknown. Insulin is a key metabolic hormone that is upregulated with maternal obesity (MO); however, MO is associated with insulin resistance. Interestingly, insulin sensitivity is restored by exercise in both MO mothers and offspring. However, critically we do not know how MO, ME, and insulin affect hippocampal synapse formation. Our preliminary data show that insulin increases glutamatergic synapse formation through induction of a novel factor called apelin. Moreover, both insulin and apelin require FNDC5/irisin to promote the effects of BDNF on glutamate synapse formation. BDNF is a classic neurotrophic factor whose levels rise during development at a critical time for glutamatergic synaptogenesis. Disruptions in BDNF or its receptor, TrkB, in humans lead to impairments in both cognition and emotionality. Here, our preliminary data shows that maternal obesity leads to a decrease in hippocampal synapse formation in vivo. However, a critical gap in our knowledge is how maternal obesity causes this effect. In contrast, we have found that maternal exercise increases hippocampal synapse formation. Our collaborators showed that apelin is required for the beneficial effects of maternal exercise on metabolic function in their offspring. However, while we have found apelin increases synapse formation in vivo, it is not known if it is required to mediate the effects of exercise, or how this links to the effects of insulin. Our central hypothesis is that insulin increases synapse formation in the developing hippocampus through the actions of apelin and irisin to increase BDNF, and that this pathway is blunted by maternal obesity and increased by maternal exercise. We will test this with the following Specific Aims: 1. Determine if insulin’s neurotrophic actions are mediated by apelin, irisin and BDNF. 2. Determine if maternal obesity alters synaptic development by miss-regulating insulin, apelin, irisin and BDNF signaling. 3. Determine if maternal exercise stimulates synaptic development and plasticity via insulin and apelin regulating the expression of hippocampal BDNF. The rationale for the proposed research is that understanding how insulin, MO and ME impact BDNF and glutamatergic synapse development, will allow us to better predict the long-term consequences of different maternal environments and help direct behavioral and therapeutic strategies to alleviate cognitive and emotional disorders.

NIH Research Projects · FY 2025 · 2024-07

Summary The ability of Borrelia burgdorferi to cause Lyme disease is highly dependent on its capacity to establish a successful infection upon entering the mammalian host. Moreover, survival of the pathogen in nature is completely dependent on its enzootic life cycle involving both a tick and reservoir host. The transition between these two very different host types requires the ability to rapidly adapt through changes in gene expression. Recent studies in our lab have provided evidence of the importance of lp17-resident genes for plasmid copy number control and resultant gene dosage effects that may have significant roles in host adaptation by B. burgdorferi. Despite this advance, there remains a fundamental gap in our understanding of the functional and mechanistic aspects of currently identified lp17-encoded factors. The overall objective of this application is to establish the functional outcome of lp17 copy number on gene dosage effects that correlate to the ability of the pathogen to adapt to the host environment. Additionally, we aim to determine that mechanism of action by the regulatory sRNA of lp17, SR0726, during host infection. Based on published and preliminary data, the central hypothesis is that bbd21-22 are important for proper copy number control of multiple B. burgdorferi plasmids that result in dosage effects of lp17-resident genetic factors important for host adaptation and tissue colonization. The rationale for the proposed research is that the expected outcomes will significantly advance our knowledge of the role that lp17 genes play in host adaptation by B. burgdorferi, and could ultimately lead to the identification of potential targets for the development of a vaccine and/or therapeutics against human infection. Thus, the proposed research is relevant to that part of NIH’s mission that pertains to developing fundamental knowledge that will potentially help to reduce the burdens of human illness and disability. Guided by our preliminary data, our hypothesis will be tested by pursuing two specific aims: 1) Establish the importance of bbd21 and bbd22 for copy number control of B. burgdorferi plasmids and gene dosage effects, and 2) Determine the regulatory mechanism of SR0726 during host infection. Under the first aim, the effects of bbd21 and/or bbd22 deletion on copy number control of plasmids other than lp17 will be examined, the ability of BBD21 and BBD22 to interact assessed, and the capacity of BBD21 and/or BBD22 to specifically bind DNA regions of multiple plasmids established. In the second aim, the approaches used will include RIL-seq analysis of SR0726 binding to target mRNA, mutational analysis of predicted complementarity binding regions of SR0726, and delineation of the upstream region necessary for regulated expression of SR0726. The proposed work is innovative because it involves the first mutational analysis of these lp17- resident genes in an infectious background strain to assess their mechanistic importance for both plasmid maintenance and gene regulation. When applied, the knowledge gained from the proposed studies have the potential to elucidate new drug targets to treat and prevent Lyme disease.

NIH Research Projects · FY 2025 · 2024-07

Herpes simplex virus (HSV) causes lifelong latent infections in humans. It is responsible for significant disease, ranging from cold sores and genital infections to blindness and fatal encephalitis. There is no effective vaccine and no cure. The long-term objective of this project is a detailed understanding of the intracellular pathway taken by HSV entering during infection. The endocytosis pathway utilized by HSV during entry into human epithelial cells was identified 20 years ago. However, the specific vesicular compartments traversed by HSV during its journey to the nucleus are not known. We demonstrated that HSV does not travel the conventional lysosome-terminal endocytosis pathway during viral entry. Based on our previous results and new preliminary studies, we hypothesize that incoming HSV utilizes a retrograde transport pathway to the Golgi apparatus for successful entry into physiologically relevant cells. Completion of this pilot study will demonstrate that HSV transits the Golgi complex prior to arrival at the nucleus during successful entry. Our experimental design employs techniques of cell biology, biochemistry, microscopy, and molecular virology. Completing this study will establish critical features of the entry pathway taken by HSV in epithelial cells, the in vivo target of primary and recurrent infection. These studies will support the innovative concept that the Golgi complex and Golgi-related functions mediate HSV entry and will lay the foundation for identification of the intracellular site of HSV membrane fusion. Furthermore, the results will aid in the development of new preventions and therapeutics for HSV.

NSF Awards · FY 2024 · 2024-07

This IUSE Computer Science Level 2 Engaged Student Learning project aims to serve the national interest by preparing software engineering students to make high-quality contributions to team software projects. The goal of this project is to develop and evaluate a pedagogical approach for undergraduate software engineering courses that include team software development projects. In these courses a significant problem is assessing the contributions that a student makes to their team. This problem will be addressed by deriving the desirable qualities of four key software engineering artifacts that team members contribute to a software project. Based on these qualities, students will learn how to contribute high-quality artifacts by assessing and reflecting on their and their peers’ artifact contributions. This project will strengthen software engineering education by developing rigorous methods for assessing the quality of software project contributions. This project will iteratively refine and empirically evaluate a valid, reliable, practical, and just approach to assessing the software engineering artifacts that individual software engineers contribute to team software development projects. By taking a rigorous empirical approach to deriving the desirable properties of individuals’ contributions, developing a valid and reliable method for assessing individuals’ contributions against those properties, and making assessments practical through a software tool that enables assessments to be easily performed on samples of individuals’ contributions, this project will (a) contribute a novel pedagogy for fostering software engineering competence through peer review and reflection; (b) improve instructors’ ability to assess their students’ learning, and (c) enhance researchers’ ability to study and evaluate pedagogies for team projects in software engineering education. The NSF IUSE:EDU Program supports research and development projects to improve the effectiveness of STEM education for all students. Through the Engaged Student Learning track, the program supports the creation, exploration, and implementation of promising practices and tools. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

This project aims to serve the national interest by generating significant new insights and developing an improved understanding of contexts in which web-based experiments may be more beneficial than physical experiments. Experiential learning, a pedagogical approach that engages students in hands-on experiences, improves students’ conceptual understanding of abstract concepts and enables them to connect theoretical knowledge learned in the classroom to real-world situations. In this IUSE Level 2 Engaged Student Learning project, experiential learning acquired through in-class physical experiments using low-cost desktop learning modules (LCDLMs) is compared with that acquired through web-based interactive digital experiments (WIDEs). Although both LCDLMs and WIDEs offer educational institutions a cost-effective, accessible way to provide high-quality laboratory experiences in engineering, this potentially transformative project seeks to directly compare the efficacy of LCDLMs and WIDEs. The main advantages of WIDEs are that they are inexpensive, highly scalable, easy to maintain, and deployable across digital devices. The collaborating institutions – University of Colorado Boulder and Washington State University - intend to make the WIDEs experiments freely available to engineering and engineering technology students online, through the widely used LearnChemE website and on YouTube. Comparative assessments will be made at five institutions, including a minority-serving institution. The project is expected to generate transformative new insights on teaching through virtual and physical experiments by identifying contexts in which physical (LCDLMs) may be more beneficial, as well as identifying how to improve virtual experiments (WIDEs) to best achieve specific learning objectives. Fifteen WIDEs for each of three engineering courses and two new LCDLMs will be created. The WIDEs will be prepared using JavaScript and/or Python so they play directly in most browsers thus permitting use on Windows-based or Apple computers, as well as iPads and other tablets. For WIDEs, the accompanying screencasts will be recorded and processed using special software (Camtasia), then embedded on pages within the WIDE. Additionally, the same screencasts will also be located on a YouTube channel so that they reach the widest possible audience. The hypothesis that WIDEs will achieve comparable learning outcomes to LCDLMs will be tested through a quasi-experimental design study in which students from a given class will be randomly assigned to use either the simulation (WIDE) or the physical experiment (LCDLM). All students will be given the same pretest before the activity and post-test after the activity to measure cognitive gains. These tests will use the Qualtrics® survey instrument in which students can complete surveys on their mobile devices. The NSF IUSE: EDU Program supports research and development projects to improve the effectiveness of STEM education for all students. Through the Engaged Student Learning track, the program supports the creation, exploration, and implementation of promising practices and tools. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-07

Project Summary/Abstract: Neuroendocrine prostate cancer (NEPC) is a fatal prostate cancer (PC) subtype with aggressive clinical features and a poor prognosis. Although it rarely occurs de novo, treatment-induced NEPC shows a significantly increasing incidence after widespread use of more potent antiandrogens for treatment of castration-resistant prostate cancer (CRPC) in recent years, constituting up to 25% of advanced therapy- resistant CRPC. Currently, NEPC remains incurable with a median overall patient survival of less than a year from time of diagnosis. These dismal facts underscore a pressing clinical need to identify new molecular determinants of NEPC pathogenesis and progression and develop an effective targeted therapy to prolong survival. In preliminary studies, we found that tryptophan hydroxylase 1 (TPH1), the rate-limiting enzyme responsible for biosynthesis of peripheral serotonin known as a neurotransmitter enriched in neuroendocrine tumors and a classical neuroendocrine biomarker, is critically required for maintaining NEPC differentiation, development and growth. Genetic or pharmacological inhibition of TPH1 in NEPC cells profoundly represses neuroendocrine markers, cell proliferation and invasion, and xenograft tumor growth in mice. Importantly, our data showed that TPH1 is upregulated in human NEPC and CRPC carrying neuroendocrine features relative to prostatic adenocarcinoma in multiple independent patient cohorts. Mechanistically, our transcriptomic, bioinformatic and biochemical analyses demonstrated that TPH1 activates mTOR signaling and subsequently E2F1 and a NEPC-promoting oncogenic transcriptional program mediated synergistically by FOXM1 and TAZ. These new findings support our hypothesis that TPH1 plays an active role driving NEPC and represents a therapeutic target of NEPC. To test this hypothesis, Aim 1 will delineate the molecular mechanism of TPH1 signaling in NEPC, specifically dissecting how TPH1 activates the mTOR-FOXM1/TAZ/E2F1 signaling axis and how this axis confers NEPC growth advantages and neuroendocrine traits in the context of TPH1. We will also establish the clinical relevance of our mechanistic findings and assess their prognostic value in a large collection of human advanced PC samples. Aim 2 will define the functional and biological impact of TPH1 on NEPC differentiation, growth and progression using a series of in vitro and in vivo phenotypic and pharmacological assays coupled with complementary human and mouse NEPC cells and organoids, cell line- and patient-derived xenograft mouse models, and TRAMP transgenic mice. Successful completion of this project will greatly deepen our mechanistic understanding of NEPC development and progression and provide a compelling rationale for repurposing clinically available TPH1 inhibitors for NEPC therapy with quick translational potential to benefit late-stage PC patients in the near future.

NIH Research Projects · FY 2025 · 2024-07

Enter the text here that is the new abstract information for your application. This section must be no longer than 30 lines of text. The mission of the Protein Biotechnology Training Program (BTP) at Washington State University (WSU) is to create research opportunities and access to research-related careers by helping PhD trainees attain essential experiences, skills, and knowledge in protein research and biotechnology creation, and by promoting research-informed graduate education that fosters doctoral completion. Our objectives are shaped by recommendations from the National Academy’s 2018 report on Graduate STEM Education for the 21st Century, from NIGMS’s T32 objectives, and from 34 years of BTP program experience. Our program connects participants from five world-class graduate programs in four WSU colleges that share interests in protein-focused chemistry, biochemistry, engineering, and molecular biology. This multi-department model creates an environment where a 40–45 trainee cohort gains experience with transdisciplinary collaboration to generate technologies and solve problems. Our emphasis on biotechnology creation and industry engagement is conducive to trainee-centered, project-based learning that builds skills that are applicable to a wide range of biomedical careers in private, public, and academic settings. Our twelve core program components include didactic instruction in biotech commercialization and rigorous research practice, a self-directed 2–3 month mentored internship with a biotech company, a monthly professional development forum for trainees, a research-informed mentorship training forum for faculty, connections with a biotech industry group, and a trainee-centered annual symposium. Our activities help trainees attain career awareness and develop operational and professional skills that complement technical achievements through increasingly self-directed mentored research. Commitment to mentorship, mentorship training, and building safe, ethical, and rigorous research environments are criteria for selection of our 41 faculty trainers. In this application we show that our program has continuously evolved activities, mentoring, and evaluation to better serve trainees, including our 120+ doctoral graduates. We shape graduate and mentored research training at WSU with innovative implementation of mentorship training, multidimensional evaluation, and project-centered course designs. Every NIH-funded position is matched with a unit-funded position (including associated tuition and fees, travel funds, annual symposium support, and commitments for bridging funds and assistance with childcare expenses). With no other predoctoral T32 program at WSU and being in a region that lacks other biotechnology training opportunities, we are well positioned to deliver value to trainees, our institution, the region, and country.

NSF Awards · FY 2024 · 2024-07

Nonequilibrium phenomena, where the state of a physical system changes (as, for instance, when water freezes or boils), are found everywhere in Nature. As such, their study is important not only in physics but also in many other disciplines. With the development of quantum technologies, it has become possible to precisely engineer and measure these processes in quantum systems. Ultracold quantum gases, which consist of millions of particles cooled down to almost zero temperature, are one of the most powerful systems to study dynamical quantum effects due to their high controllability. This project aims to explore a variety of nonequilibrium processes in ultracold quantum gases. It is expected that the outcomes of the project will not only increase our understanding of these systems, but also contribute to other areas of quantum research, including quantum optics, nonlinear optics, and quantum information science. Moreover, the project involves the training of undergraduate and graduate students, contributing to the development of the next-generation workforce in quantum science and economy. The project will be tailored and expanded for potential REU students and local high school students. The PI will actively collaborate with students from under-represented groups, such as women and minority students. The project aims to investigate a range of beyond-mean-field physics including scattering, dynamical instabilities, critical behavior near quantum phase transitions, and quantum fluctuations near resonances in dynamical Bose-Einstein condensates (BECs). Focusing on the dynamics of BECs, three scenarios will be studied: (a) the dynamics of BECs with multiple momentum components; (b) the quench dynamics of synthetic spin-orbit coupled BECs across quantum phase transitions; and (c) the dynamics near spin-spatial resonances in spinor BECs. The PI and graduate students will develop theoretical frameworks and numerical tools to characterize the quantum and thermal fluctuation effects on the collision and thermalization of cold atoms, quantum phase transitions like the Kibble-Zurek mechanism, and the performance of the spinor quantum simulator and sensor. The project will provide a comprehensive description of recent pertinent experimental results in the literature. The outcomes of the research project will directly stimulate potential collaboration with the in-house cold atom experimental group. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY More than 40% of adults in the United States are obese, and that number is expected to rise to over 50% by 2030. Obesity is a critical health concern as it is associated with several leading causes of death including diabetes, heart disease, stroke, and cancer. Ingestion of a meal can elicit both positive and negative feelings. However, the pathways underling these different valences are not well understood, but maladaptive changes could have broad implications for both overeating and emotional disorders. Drugs that inhibit food intake (FI) also often lead to aversive side-effects like nausea. Understanding what mediates the positive or negative feelings associated with satiety is therefore critical to help drive the development of treatments for obesity without aversive side-effects. Recent work has identified a population of cholecystokinin (CCK) expressing neurons in the nucleus of the solitary tract (NTS). Stimulation of these neurons leads to a decrease in FI, but stimulation of terminals in the paraventricular hypothalamus (PVH) is rewarding, while stimulation of terminals in the parabrachial nucleus (PBN) is aversive. However, it remains unclear what drives these divergent projections physiologically and how terminals activate neurons in the PVH and PBN. To investigate this, I first characterized what types of vagal afferents innervate NTS-CCK neurons and what currents they express. My results suggest that there are two subpopulations of neurons: one that is downstream of both CCK and serotonin (5-HT) sensitive afferents and another that is downstream of only CCK sensitive afferents. Information carried by 5-HT sensitive afferents is thought to be aversive, while information carried by CCK sensitive afferents is thought to be rewarding. Thus, I hypothesize that NTS-CCK neurons projecting to the PVH are driven primarily by CCK sensitive afferents, while PBN projecting neurons receive inputs from both CCK and 5-HT sensitive afferents. Further, I posit that release of fast transmitters and peptides will have different effects on downstream cells in the PVH and PBN. These studies will provide valuable information regarding the cellular mechanisms underlying previously reported behavioral findings. They will also help guide future studies aiming to develop more selective and less aversive therapies for the treatment and prevention of obesity. To accomplish the proposed experiments in the F99 phase, I will need to learn stereotaxic injections as well as in-slice photostimulation techniques. My sponsor, Dr. Suzy Appleyard, and co-sponsor, Dr. Shane Hentges, have expertise in all proposed techniques as well as established mentoring records. During the K00 phase, I plan to build on the skills learned during the F99 phase by identifying a supportive and knowledgeable postdoctoral mentor. Specifically, I will receive training on in-vivo opto and chemogenetic stimulation, in-vivo neuronal recording techniques, and computational models for behavioral analysis. The cellular techniques learned in the F99 phase, combined with the behavioral techniques learned in the K00 phase will optimally position me to interrogate feeding circuitry from behavior to cellular mechanisms as an independent investigator.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY/ABSTRACT Targeting the hallmark biomarker prostate specific membrane antigen (PSMA) has been a successful small molecule drug-delivery strategy for various payloads to prostate tumor cells, which is evident in the FDA's recent approval of 177Lu-PSMA-617 and the clinical advancement of our 18F-CTT1057 (an irreversible-binding phosphoramidate-based) PSMA-targeted PET-imaging agent (NCT04838626, NCT04838613). However, efforts to develop PSMA-targeted chemotherapeutic nanomedicine have had limited clinical therapeutic efficacy. Our long-term goal is to develop a versatile and intelligently designed platform for the selective delivery of synergistic therapeutic payloads to offer novel treatment options for lengthening and improving the quality of life for metastatic castration-resistant prostate cancer (mCRPC) patients. The overall objective of this project is to develop a PSMA-targeted small-molecule dual drug conjugate (SMDDC) to serve as a companion therapeutic to our PSMA-targeted PET-imaging agent (NCT02916537, NCT03427476). Our central hypothesis is that tumor-site activation and release of two distinct chemotherapeutic payloads for prostate cancer can be achieved and will be more effective than small molecule drug conjugates (SMDCs) releasing only a single chemotherapeutic payload. The rationale for developing SMDDCs is to set the groundwork for a new, dual- drug therapeutic strategy for patients with mCRPC and advanced malignancies with PSMA(+) neovasculature. Two specific aims will be pursued to test the central hypothesis: 1) Assess the spatio-temporal cargo-release in prostate tumor cells with a PSMA-targeted small-molecule dual probe conjugate (SMDPC); and 2) Determine the potency enhancement of a SMDDC bearing dual payloads in prostate cancer cell lines. For Aim 1, PSMA(+) and PSMA(-) prostate cancer cell lines will be used to assess the spatio-temporal cargo-release of a PSMA-targeted SMDPC bearing two distinct turn-on probes, 7-Amino-4-methylcoumarin and hydroxymethyl rhodamine green. Established PSMA activity assays will be used to determine the IC50 and mode of binding for the PSMA-targeted SMDPC. In Aim 2, in vitro effectiveness of an SMDDC bearing both MMAE and Exatecan vs. an SMDC bearing either MMAE or Exatecan alone will be evaluated in PSMA(+) and PSMA(-) prostate cancer cell lines. The proposed work is innovative because it aims to utilize a unique combination of drug- delivery strategies; PSMA-ligand promoted internalization, a novel acid-labile linker for pH-triggered drug release, and two distinct chemotherapeutic drugs with differing mechanisms of action. This will be a significant achievement because it will provide proof-of-concept for developing clinically relevant chemotherapy for mCRPC and other malignancies with PSMA(+) neovasculature. Future plans include expanding the selection of drug payloads for PSMA-targeted SMDDCs and initiate preclinical IND-enabling studies. The expected positive impact of these studies is that they will, in all likelihood, set the foundation for a general, dual-drug strategy for targeted chemotherapy for other biomarker-characterized diseases.

NIH Research Projects · FY 2025 · 2024-06

ABSTRACT Transcription coupled-nucleotide excision repair (TC-NER) plays a critical role in the maintenance of genome stability by removing DNA lesions that would otherwise block RNA polymerase II (Pol II) transcription. The importance of TC-NER to human health is highlighted in Cockayne syndrome (CS), in which an inherited genetic defect in a TC-NER factor (CSA or CSB) results in a severe neurodegeneration, rapid aging, and UV sensitivity syndrome. Recently, a new TC-NER factor known as ELOF1 in humans and Elf1 in yeast has been identified. ELOF1/Elf1 are required for efficient TC-NER in both yeast and human cells. In human cells, ELOF1 functions to recruit the key TC-NER factor UVSSA, which is required for TFIIH recruitment, by promoting RNA polymerase II ubiquitination. However, yeast and many other species lack UVSSA, so the function of Elf1 in promoting TC-NER in these species is unclear. Our preliminary data indicate that a unique C-terminal domain (CTD) present in Elf1 plays a critical role in TC-NER by recruiting TFIIH. Our preliminary data also suggest the hypothesis that the Pol II elongation factors Spt4/Spt5 (Spt4/5), which normally function to repress TC-NER, do so by inhibiting the Elf1 CTD. We hypothesize that eviction of Spt4/5 from the Pol II elongation complex (EC) by the CSB homolog Rad26 initiates repair by releasing the Elf1 CTD so it can recruit TFIIH. In Aim I, we will use a combination of yeast genetics, genome-wide mapping of DNA damage and repair, and in vitro biochemistry to test this hypothesis. Cyclobutane pyrimidine dimer-sequencing (CPD-seq) method will be used to investigate the interplay of the Elf1 CTD and Spt4/5 in genome-wide repair of UV damage in yeast and characterize key functional residues in the CTD. We will also use in vitro protein interaction studies to determine the key CTD residues in Elf1 that are required to bind and recruit TFIIH, and test whether this interaction is inhibited by Spt4/5. Finally, we will test the hypothesis that Drosophila homologs of Elf1 are responsible for TC-NER activity in this species, despite the absence of Drosophila homologs of CSA, CSB, or UVSSA. In Aim II, we will investigate the role of phosphorylation of the Elf1 CTD in regulating its activity in TFIIH recruitment and TC-NER. Previous studies and our preliminary data indicate that the Elf1 CTD is phosphorylated at multiple residues, in many cases by casein kinase II (CKII). In this aim, we will systematically mutate Elf1 phosphorylation sites and determine their impact on TC-NER. In parallel, we will screen for new UV-induced phosphorylation sites in the Elf1 CTD. We will also determine whether CKII phosphorylation of the Elf1 CTD in vitro regulates its binding to TFIIH and/or Spt4/5 and determine the potential role of CKII in TC-NER. These studies should elucidate a new molecular mechanism by which CSB/Rad26-dependent modulation of the Pol II EC regulates TFIIH recruitment and TC-NER.

NIH Research Projects · FY 2026 · 2024-04

Obesity is a major health problem in the United States and a leading contributor to cardiovascular disease, diabetes mellitus and stroke. One region essential for the control of meal size is the nucleus of the solitary tract (NTS) in the brainstem. Vagal afferent fibers carrying different types of satiety information from the GI terminate in the NTS, and NTS neurons process this information before relaying it on to other brain regions to terminate a meal. Activation of NTS neurons therefore critically impacts meal length. However, NTS neurons are extremely heterogeneous in their expression of peptides and receptors. Activation of most NTS neuronal populations inhibits FI, including general activation of NTS neurons expressing catecholamines (NTS-CA). However, recently a subpopulation of NTS-CA neurons that express NPY and project to the arcuate nucleus were found to stimulate FI. Interestingly, intra NTS injections of NPY stimulates FI. Furthermore, our preliminary data suggest that both NPY and NE inhibit vagal activation of NTS neurons and that stimulating NTS NPY neurons inhibits neighboring NTS neurons. Taken together, these are intriguing results, but there are critical gaps in our knowledge about how these neurons impact the activity of other NTS neurons, how NTS NPY neurons are activated and if their function changes with metabolic state. Our central hypothesis for this proposal is that NTS NPY neurons release NPY and NE locally to inhibit anorexigenic NTS neurons and the level of release is determined by a balance of excitatory vagal drive and GABA inhibition, which is impacted by fasting and diet. We will test this hypothesis rigorously and comprehensively by pursuing the following specific aims: Aim 1. Determine the effects of locally released NPY and NE on NTS neuronal function. Aim 2. Elucidate what determines the activity of NTS NPY expressing neurons. Aim 3. Determine whether the activity of NTS NPY neurons and the effects of NPY and NE are altered during a fast and following a high fat high sugar (HFHS) diet. These studies are conceptually innovative because they focus on an under-investigated area: how orexigenic neurons integrate with other NTS neurons and the effect of metabolic state. They are rigorously and comprehensive as they use multiple complementary approaches. These results are expected to positively impact the field as they will elucidate underappreciated circuitry in a brain region well established for being critical for the control of food intake. This is anticipated to help direct and improve therapeutic strategies for the prevention and treatment of obesity.

NIH Research Projects · FY 2025 · 2024-04

Project Summary/Abstract Atopic dermatitis (AD) is a common chronic skin condition that affects over 10% of children in the US. AD can significantly impact the quality of life by causing unbearable itching, leading to sleep loss and infections. Unfortunately, there is currently no cure. The microbiome in both the skin and gut is significantly altered in patients with AD. However, very few studies have investigated the role of microbiome in the onset of AD in infants when AD symptoms usually appear. Moreover, little is known about how the skin and gut microbiome interact with each other during the onset of AD, known as the gut-skin axis. To fill this critical gap in our knowledge, Dr. Shen will utilize genomic, bioinformatic, and experimental approaches to an unprecedentedly large pool of skin swabs, nasal swabs, and stool samples from 608 infants, including 258 paired skin and stool samples, to facilitate the investigation of the gut-skin axis. Dr. Shen will use ultra-deep shotgun metagenomic sequencing to capture bacteria, fungi, and viruses in infants with AD at the species and strain level resolution. The preliminary data have achieved high classification rates of metagenomic reads, and have indicated a multi-kingdom decrease in skin microbial diversity and numerous differential gut microbial species associated with AD. These data lead to a central hypothesis that the microbiome of both the skin and gut plays an important role in the onset of AD in infants. This study aims to reveal full microbiome signatures and the gut-skin microbiome relationships associated with the onset of AD. In Aim 1, Dr. Shen will perform large-scale bioinformatic analyses to identify skin microbial taxa and genes associated with the early onset of AD in infants, in the context of host genetics. Additionally, Dr. Shen will experimentally test the effects of AD-associated microbes with neonatal wild-type mice. In Aim 2, Dr. Shen will extend the computational approaches from Aim 1 to the gut metagenomic data and integrate the skin and gut microbiome to reveal the gut-skin microbiome relationships in AD. Furthermore, Dr. Shen will apply deep learning techniques to build the first microbiome-based predictive model for AD outcomes, facilitating early prevention and intervention of the disease. The proposed research and training plan will build on Dr. Shen’s strengths in the fields of bioinformatics and microbiome, help him to develop necessary skills in experiments, and build his own professional networks through conferences. Dr. Shen’s long-term goal is to extend the computational and experimental techniques of this proposal to study the host-microbe interactions of the gut-skin axis in AD. The unique environment of the NIH/NHGRI and the strong mentoring team of Dr. Shen will enhance his research and career development, facilitating his transition to independence.

NIH Research Projects · FY 2026 · 2024-02

PROJECT SUMMARY/ABSTRACT One third of US children have overweight or obesity; children are developing obesity at higher rates than at any other time in human history. Social determinants of health (SDoH) are strong and especially intractable risk factors for childhood obesity, creating a structural context of stress in early life. Compared to children in high socioeconomic status (SES) households, children in low SES households have 3-4 times higher odds of obesity and elevated biomarkers for chronic stress (cortisol) after adjusting for individual level behaviors. Thus, studies aimed at enhancing resilience to structural SDoH risk factors are critically important for reversing the childhood obesity epidemic. Situated at the intersection of structural SDoH and individual behavior, outdoor preschools present an ideal research opportunity for research to build resilience to low family SES for both the prevention and management of childhood obesity. Rigorous research on this topic is nearly nonexistent, but its plausibility is supported by mounting evidence that outdoor time may influence biological causes of childhood obesity. Specifically, imbalance in microorganisms found in the digestive tract, referred to as the gut microbiome, is associated with childhood obesity. Environmental factors strongly affect gut microbiome diversity, and urban environments reduce gut microbiome diversity by limiting contact with green spaces and microbe-rich soil. Contact with nature improves resilience and reduces stress in children; neighborhoods with lower household income often lack access to parks and green spaces, exacerbating existing inequities. Thus, the gut microbiome, may be an especially informative marker of the effectiveness of outdoor preschools for enhancing biological resilience to obesogenic SDoH. No study in any population has longitudinally characterized gut microbiome diversity with obesity in early childhood, nor has the interaction of stress and gut microbial diversity been evaluated. In this application, “Childhood Obesity: the role of the gut Microbiome, outdoor Time, and Stress” we will conduct a longitudinal natural experiment evaluating the impact of a novel outdoor preschool model on gut microbial diversity and stress biomarkers, and the association with obesity. We will partner with Tiny Trees, an entirely outdoor preschool in Seattle, WA, and the largest outdoor preschool in the US. Tiny Trees reserves 50% of enrollment spots for families eligible for free/reduced tuition. We will recruit 300 children 3-5 years of age; 150 attending Tiny Trees and 150 from the Tiny Trees waitlist attending an indoor preschool that provides tuition assistance to income eligible families. To maximize sample size and statistical power, we will analyze ~400 stool samples collected using an identical protocol and population as part of Dr. Fyfe-Johnson’s K01. Our Specific Aims are to: 1) estimate the effect of an outdoor preschool model on gut microbiome diversity, stress biomarkers, and body mass index, 2) evaluate gut microbiome diversity as a mediator on BMI and SDoH as a potential modifier of effects on primary outcomes, and 3) conduct cost-benefit and cost-effectiveness analyses of the outdoor preschool model to assess the return on investment for childhood obesity prevention.

NIH Research Projects · FY 2026 · 2024-01

PROJECT SUMMARY Rickettsiales are a diverse order of obligate, intracellular bacteria often transmitted by arthropods and pose a substantial threat to public health. Rickettsial organisms manipulate a wide array of host cell processes to gain entry and establish a replicative niche, while simultaneously avoiding host cell defenses. How rickettsial pathogens mediate this complex network of interactions is not well understood. A central feature of all rickettsial pathogens is the Type 4 Secretion System (T4SS), which secretes effector proteins into the cytosol and manipulates biological processes in the host cell. However, few T4SS translocated effectors have been identified or characterized from rickettsial organisms owing, in part, to the lack of genetic tools available among these bacteria. Their obligate intracellular nature has historically hindered genetic manipulation of Rickettsiales. Recently, we achieved targeted gene deletion in the rickettsial pathogen A. phagocytophilum using allelic exchange by homologous recombination. In the R61 portion of this proposal we will leverage this technique to add to the A. phagocytophilum genetic toolbox by developing 1) a T4SS effector translocation assay for use in the organism of study, 2) conditional expression systems, and 3) luminescent reporters. Using these tools in the R33 phase we will: 4) characterize the A. phagocytophilum T4SS effector repertoire, 5) evaluate the contributions of essential A. phagocytophilum effectors to infection, and 6) monitor the expression kinetics of effectors in vivo. The objectives of this proposal will expand the tractability of A. phagocytophilum and our understanding of the host-pathogen interactions it navigates during infection through elucidation to the T4 effector repertoire, and an understanding of how, when and where these genes are regulated. The impact of this proposal will extend to other rickettsial organisms, as these approaches can be adapted for use in related intracellular pathogens.

NIH Research Projects · FY 2026 · 2024-01

Environmental factors can affect American Indian/Alaska Native (AI/AN) health via effects on traditional food systems, but there is substantial underappreciation for the environments from which foods consumed during pregnancy are sourced. Furthermore, maternal diet and nutrition are highly influential in pregnancy and can affect the short- and long-term health of both mothers and their offspring. Certain adverse pregnancy outcomes (APOs) have also been linked to maternal diet and nutrition, and AI/AN groups have overall higher rates of APOs. Despite the importance of maternal diet and nutrition in improving APO rates within overburdened populations, there is a paucity of literature concerning nutrition during pregnancy in AI/AN mothers. The research proposed will carry out two Specific Aims that will help fill this critical knowledge gap by identifying how environmental factors may be linked to the nutritional quality of a traditional food, and how this may influence AI/AN maternal health outcomes. In Specific Aim 1, we will determine if relationships exist between land use, traditional foods, and AI/AN maternal health by analytically integrating several publicly available government and foundation databases. In Specific Aim 2, we will determine if the nutritional content of a specific traditional food contributes to pregnancy outcomes by surveying Pacific salmon consumption in pregnant AI/AN mothers, and using super learners (machine learning technology) to: 1) develop a model describing the relationship between Pacific salmon-specific nutritional contributions to maternal diet and pregnancy outcome; and 2) apply the model developed to manipulated data to test if changes in Pacific salmon-specific nutritional contributions to maternal diet can influence maternal health outcome. We use Pacific salmon here because many AI/AN Tribes in our region have been consuming Pacific salmon as a vital traditional food from time immemorial. The research will be carried out with Washington State University community health centers such as the Institute for Research and Education to Advance Community Health, and in close collaboration and partnership with non-profits serving regional AI/AN Tribes. I will be guided by experts in the skills and techniques that I will gain training in. To enrich my research training, I will attend various workshops, seminar series, and scientific meetings to expand my professional network and prepare me as I transition to an independent scientist. Together, the research and training program developed will enhance the innovative potential of my future research and support my long-term goal of promoting pregnancy health.