University Of California, San Diego

NIH Research Projects · FY 2025 · 2024-08

SUMMARY Monitoring of the incidence, morbidity, and mortality of respiratory infections has largely been performed by collecting and analyzing data from hospitals and clinical laboratories. While these data sources provide valuable information on risk factors, incidence, therapeutic response, and outcomes of severe disease, they do not reflect the range of potential clinical presentations and courses of disease, factors that increase or decrease the risk of community transmission, and the impact of disease on education and employment. We therefore propose to create “PREVENT: Preparedness through Respiratory Virus Epidemiology and Community Engagement,” which will serve as one of the CDC Pandemic Preparedness Network Cohorts and the Network’s Data Hub. We will participate in Components A1, A2, B, and C, with a catchment that spans San Diego County in HHS Region 9 adjacent to the U.S./Mexico border. Our relevant experience includes establishment of innovative programs for large-scale COVID-19 clinical testing, environmental surveillance through monitoring of wastewater and surface swabs, viral genome sequencing, and monitoring of immunity using co-created community-based sample collection strategies that are highly accessible and culturally sensitive. Major PREVENT activities will include: Component A1: We will enroll and retain a diverse longitudinal cohort of 2,000 individuals for: weekly symptom screening; surveys on knowledge, attitudes, and behaviors related to preventative measures; extraction of outcome and vaccination data from electronic health records and immunization information systems; and collection of follow-up data from participants on use of preventative/therapeutic measures and healthcare resources, missed school/work, symptom type/duration, and long-term sequelae. Symptomatic swabs will be collected and tested for 20 high-priority respiratory pathogens. Viral genome sequencing will be performed on a subset of samples using targeted and metatranscriptomic methods. Samples will be banked for >5 years. Component A2: Serial blood samples will be collected, analyzed, and banked from 20% of participants in Component A1. Samples will be collected at enrollment, in the months flanking the respiratory infection season, before/after vaccinations, and after infection. Quantitative immunoassays for antigen-specific antibody (Ab) levels and neutralizing antibody (nAb) levels against contemporary circulating virus isolates will be performed. Component B: For >100 index cases from A1 per year, we will collect and test daily nasal swabs from >75% of household members for >2 weeks. A subset of swabs (including at least 1 per index case) will be analyzed by viral genome sequencing, and high-priority pathogens/variants will be cultured. For a subset of households, we will also explore the relationships between viral load (quantified by qPCR) and viral titer (by in vitro cell-based assay), and between viral culture positivity and transmission. Component C: We will serve as the Data Hub and Warehouse, and support protocol development across the network, provide data entry and management tools, analyze data; and develop dashboards/visualizations.

NIH Research Projects · FY 2024 · 2024-08

The dystonias overall are a rare neurologic disorder. Blepharospasm (BSP), is one of the most common forms of dystonia. BSP is characterized by involuntary abnormal facial expressions and eye closures. In addition to these overt motor abnormalities, the disorder is also associated with non-motor symptoms including anxiety and depression. Treatment options for BSP are suboptimal. Many oral medications have been tried but their efficacy is minimal and limited by dose-dependent adverse side effects. Botulinum neurotoxin (BoNT) injections repeated every 3-4 months are the primary treatment of choice. Although BoNT is highly efficacious for many patients, for a variety of reasons about 1/3 of patients discontinue BoNT treatment, and of those who continue treatment about 1/3 are unsatisfied with the response. Because treatment options are suboptimal, there is an active effort to find better strategies for treating BSP, as evidenced by dozens of trials listed on ClinicalTrials.gov. However, the most common clinical outcome assessments used to measure motor abnormalities are intrinsically subjective assessments and therefore suffer from inter-rater variability. This reduces our power to detect treatment effects in clinical trials. Technology-based objective measures have the potential to circumvent this variability. Advances in computer vision technology have enabled the measurement of facial expressions and eye closure from 2-D images of the face in conventional video recordings. One of the long-term objectives of our group is to leverage these advances to develop software that can capture and quantify motor abnormalities across multiple types of focal dystonia. We are calling this system the Computational Motor Objective Rater (CMOR). In this project specifically targeting BSP, our aims are 1) to evaluate CMOR’s convergent validity with patient reports of severity of facial spasms and excessive blinking and 2) to determine CMOR’s sensitivity to changes in severity associated with interventions. To accomplish these aims, we will conduct CMOR analyses of motor symptoms from video recordings of 100 BSP patients enrolled in a separate Dystonia Coalition project to evaluate the variability of efficacy of BoNT. That project will also acquire patient reports in the form of a patient centered outcome with specific questions about the prominent motor features of BSP and the patient’s global impression of change (PGIC) in response to each BoNT treatment. Collectively the results will provide important information about CMOR’s validity and a quantitative basis for sample size estimates for future clinical trials in BSP.

NIH Research Projects · FY 2025 · 2024-08

Project Summary Pelvic floor disorders (PFDs) are common conditions that affect ~25% of U.S. women. PFDs are morbid, with more than 50% of afflicted patients rating them as “worse than death”. As vaginal delivery is the greatest epidemiologic risk factor for PFDs—likely due to the pelvic floor muscle (PFM) dysfunction it often incites— greater understanding of vaginal delivery biomechanics and birth injury is needed. But in order to accurately study the mechanical behavior of the PFMs during childbirth, their structure, function, and integrity just before childbirth must be known. Acquiring this knowledge is not trivial given the degree of pregnancy-induced remodeling that soft tissues undergo during gestation. Thus, this study aims to implement multiscale experimental and computational methods to characterize and simulate pregnancy-induced remodeling of PFMs. Phase 1 (K99) is the experimental arm of this proposal. In Aim 1 cell culture of primary 1) skeletal muscle stem cells and 2) fibro-adipogenic progenitors isolated from female rat PFMs will be used to determine the impact of sex hormones (e.g., estrogen) and mechanical stretch on resulting 1) myotube growth and 2) collagen secretion by fibroblasts, respectively. After the cultured cells have differentiated, myotube size, fusion index, and the amount of collagen secreted (quantified as a percentage of the sampled area) will be quantified via bright field (myotubes) and fluorescence (fibroblasts) microscopy. These will serve as proxies for muscle fiber growth and collagen deposition in vivo, allowing for the determination of the effect of sex hormones and mechanical stretch on the contractile and extracellular matrix (ECM) components of the PFMs. Meanwhile, Aim 2 will define changes in whole PFM active and passive mechanics across the nonpregnant—postpartum continuum. Whole PFMs will be harvested from rats at various stages throughout the pregnancy and postpartum, and then ex vivo active and passive mechanical testing will be performed. This will establish changes in force generating capacity (active properties) and load bearing capacity (passive properties) across the continuum, revealing how the function of both the contractile (active) and ECM (passive) components of PFMs are altered by pregnancy and childbirth. Phase 2 (R00) is the computational arm of this proposal. Aim 3 will generate intracellular signaling network (cell level) and finite element (whole muscle level) models, calibrate and validate those models using literature and Phase 1 data, and then couple those models; resulting in a multiscale computational model of pregnancy- induced PFM remodeling. This coupled model will consider sex hormone levels, the degree of mechanical stretch acting on myofibers and the ECM, myofiber growth, and collagen deposition collectively while simulating their impact on whole PFM active and passive function. Together, these aims will characterize the multiscale (intracellular and whole muscle) mechanisms of pregnancy-induced PFM remodeling and identify the most influential sex hormones and mechanical properties driving these adaptations; thus, promoting translational studies evaluating the PFMs' ability to withstand vaginal birth and avoid injury.

NSF Awards · FY 2024 · 2024-08

Plant leaves have a very large number of tiny pores, named stomata, that regulate water loss while providing the pathway for carbon dioxide (CO2) to enter leaves. CO2 is a vital plant nutrient, and is required for plant growth and crop production. However, a typical plant loses between 150 and 500 water molecules through these stomatal pores for every carbon atom that is absorbed from CO2 for nutrition and growth. The opening and closing of these stomatal “breathing” pores in leaves is regulated by the concentration of CO2 inside leaves. Since the concentration of CO2 in the air is now 50% higher than it was 150 years ago, plants could more easily take up CO2 from the air while losing less water. Yet important mechanisms and genes that enable this agriculturally important CO2 response of stomatal pore regulation are unknown. This research will identify proteins and genes of a recently discovered CO2 sensor in order to determine cellular signaling mechanisms through which carbon dioxide controls plant water loss and CO2 intake. The ability to improve the response of stomatal pores to carbon dioxide is important for unfavorable weather conditions, agricultural ground water availability, and droughts that are becoming more frequent in several of the major agricultural regions in the US. Project personnel will prepare graduate students for professional careers and further conduct an outreach program with scientific training internships and professional preparation of students and mentoring with the public Preuss School for disadvantaged high school students in San Diego County, as well as training and professional preparation of visiting underrepresented summer research interns with UC San Diego’s STARS and ENLACE program. The researchers will be active with community outreach work that brings science and innovation close to the public. The PI will also conduct outreach through presentations and discussions with students and K-12 teachers in San Diego. Atmospheric CO2 is predicted to double during this century and the ensuing concentration rise in CO2 rise will reduce stomatal conductance of plants globally, which will have severe effects on gas exchange, leaf heat stress, plant water use efficiency, and plant robustness, but can also benefit plant growth. A network of signal transduction mechanisms senses and transduces CO2 changes to regulate stomatal movements for optimization of CO2 influx, water loss and plant growth under diverse conditions. In recent research these researchers have identified a major CO2/bicarbonate sensor consisting of a complex of a Raf-like kinase (HT1) and a MAP kinase (MPK12 & MPK4). Major questions and new hypotheses have arisen from this advance as to the unknown cellular locations and protein properties of the recently discovered reversible MPK12/4 – HT1 CO2/bicarbonate sensor, the molecular nature of unknown protein phosphatases that are predicted to be required to “shut off” this CO2 sensing core, and a gap in molecular and cellular mechanisms linking this proposed CO2 sensing core to downstream guard cell signaling mechanisms. Moreover, no forward genetics stomatal CO¬2-specific response screen in grasses has been reported, despite the agronomic important of grasses. New hypotheses will be directly investigated based on the team’s recent discoveries. This project will leverage interdisciplinary cell biological, molecular genetic, biophysical, biochemical and genomic approaches to identify new critical molecular components of the CO2 signaling network and characterize how this network operates to regulate stomatal pore apertures, plant transpiration and CO2 influx. This award is funded by the Cellular Dynamics and Function Cluster of the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences. 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

ABSTRACT One of the most astonishing feats in all of biology is the process by which chromatin, the complex of DNA, histone proteins and associated factors, becomes compacted from a length of 2 m into nuclei that measure just microns across. Unsurprisingly, our understanding of the principles that govern this process is in its infancy. My lab became interested in this process after we identified the Ferguson-Bonni ANAPC7 neurodevelopmental syndrome caused by mutation of the degradative ubiquitin ligase Anaphase-Promoting Complex (APC). We discovered that Ki-67 was the major APC7-dependent target in post-mitotic neurons, where it accumulated in constitutive heterochromatin. Subsequent experiments in complementary mouse mutants demonstrated a much broader role for the APC in regulating the composition of neuronal heterochromatin, where we also observed dramatic accumulation of the chromosome passenger complex (CPC) and its product phosphorylated histone 3 (H3S10ph). Like Ki-67, the contributions of the CPC and H3S10ph to neurologic disease had been previously unknown. Although these observations established an APC-dependent ubiquitination-phosphoprotein axis in neurodevelopmental chromatin regulation, how Ki-67 and H3S10ph control heterochromatin remained poorly defined. We hypothesize that Ki-67 and H3S10ph control liquid-liquid phase separation (LLPS), a physicochemical process driven by multivalent interactions of disordered proteins like Ki-67 and phosphoproteins like H3S10ph. Studies from other labs showed that LLPS of constitutive heterochromatin requires the small protein HP1α, which interacts with Ki-67. Data from my lab showed that neuronal Ki-67 undergoes rapid relocalization away from heterochromatin upon disruption of LLPS, indicating Ki-67’s association with constitutive heterochromatin requires LLPS. This compelling series of observations leads us to the central hypothesis of this proposal: LLPS of heterochromatin-associated APC targets is required for neurodevelopment and when perturbed contributes to the pathogenesis of APC-related neurodevelopmental disorders. In Aim 1, we will explore the role of Ki-67 in the formation of heterochromatin in neurons using imaging and molecular analyses of a novel mouse model of Ki-67 mutation. In Aim 2, we will employ elegant in vitro assays to determine how Ki- 67 enhances LLPS of HP1α and nucleosome arrays. In Aim 3, we will explore the liquid-like behavior of APC substrates Ki-67 and the CPC by imaging heterochromatin dynamics in live neurons. Armed with novel in vivo genetic systems, powerful in vitro assays, and world-class expertise in the wet lab and computational methods, we are poised to generate fundamental insight into chromatin regulation by ubiquitin and LLPS in neurons.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY/ABSTRACT Identification of neural and behavioral processes that drive eating disorder (ED) symptomatology is critical for the development of more effective interventions for these serious and sometimes deadly disorders. One candidate transdiagnostic mechanism underlying divergent but often overlapping symptoms in anorexia nervosa (AN) and bulimia nervosa (BN) is avoidance learning. The ability to learn how to avoid harm is critical for health and survival, yet excessive avoidance learning leads to chronic maladaptive avoidance or compulsive behaviors. Both AN and BN are characterized by elevated trait harm avoidance and maladaptive behaviors to avoid aversive outcomes such as weight gain, ranging from extreme dietary restriction to repetitive cycles of binge eating and purging (e.g., self-induced vomiting, excessive exercise). This raises the question of whether symptom heterogeneity corresponds to differences in an individual’s strategy to avoid aversive outcomes that fall on a continuum of anxious-avoidant vs compulsive behavior. Distinguishing between excessive active avoidance learning (learning from successful actions that reduce harm) and passive avoidance learning (learning what to avoid doing to prevent harm), which are thought to differentiate compulsive and anxious-avoidant behavior, might critically inform etiological models of ED. This proposal tests the novel hypothesis that instrumental avoidance learning is altered in ED, with corresponding differences in corticostriatal and limbic-prefrontal prediction error BOLD response and functional connectivity, and that associations between active vs passive avoidance learning and ED symptoms might differentiate bulimic-type from restricting behaviors, informing compulsive vs anxious-avoidant mechanisms underlying symptom heterogeneity in ED. Participants (26 AN, 26 BN and 26 healthy controls (HC) ages 18-35) will complete a probabilistic card gambling task during fMRI that assesses instrumental learning strategies to avoid heat pain. Computational modeling approaches will be used to distinguish active from passive learning bias. Aim 1 will compare avoidance learning bias in AN, BN and HC and will evaluate the association of active and passive avoidance learning with ED symptoms. Aim 2 will examine whether corticostriatal and limbic-prefrontal function associated with avoidance learning differs in AN, BN and ED, and in particular whether dorsal caudate response associated with active and passive avoidance learning differs in AN and BN and relates to symptoms. Aim 3 will examine group differences in corticostriatal and limbic- prefrontal PE-related functional connectivity associated with active and passive avoidance learning to better characterize avoidance learning functional neural architecture in ED. Elucidating the relationship between avoidance learning, ED symptoms and brain function to inform mechanistic understanding of the neurobiological underpinnings of ED is both innovative and significant. Outcomes will be of clinical importance by providing foundational knowledge to identify new behavioral and neural therapeutic targets. Data will provide methodological groundwork for an R01 application examining avoidance learning across a broader ED spectrum.

NIH Research Projects · FY 2025 · 2024-08

CPMV-Polymer Devices to Enhance the Outcomes of Intratumoral Immunotherapy Steinmetz (PI) and her colleagues have developed a plant virus nanoparticle immunotherapy that activates innate immune cells in the tumor microenvironment (TME) to launch adaptive, systemic, and durable antitumor immunity. Specifically, we found that nanoparticles based on cowpea mosaic virus (CPMV) stimulate a potent antitumor response in solid tumor mouse models and in canine cancer patients. Intratumoral immunotherapy CPMV overcomes immunosuppression within the TME launching adaptive antitumor immunity and immunological memory to prevent cancer recurrence. CPMV interacts with the immune system in a multivalent manner, resulting in a cascade of events boosted by avidity to achieve unprecedented potency. The intratumoral immunotherapy development pipeline is advancing quickly, but its effectiveness faces challenges, necessitating better delivery methods. Key issues include: (1) Large tumors often need more drugs or multiple injections, complicating procedures and possibly affecting therapy results due to variability. (2) High fluid pressure in tumors, caused by factors like vascular issues and confined cell growth, can impede drug delivery and even push drugs out of the tumor. (3) Frequent dosing can discomfort patients (and/or owner’s when patients are dogs), affecting their willingness to continue treatment. Therefore, we propose slow-release CPMV-polymer blend formulations for delivery as injectable devices. CPMV will be incorporated into polymer blends by applying scalable hot melt extrusion (HME) processing technology. Pokorski (MPI) is an expert in HME processing of biologics and our preliminary data confirm the structural and biological stability of CPMV released from the device technology. Finally, protein/polymer melts will be converted into injectable implants and microparticles using routinely available milling and molding equipment. We will fulfill the following aims: First, we will formulate CPMV-laden slow- release devices, establish and tune the release rates, confirm the structural integrity and biological activity released CPMV from the delivery technology. Second, we will perform clinical testing to establish efficacy, mechanism of action, and safety as a function of dose and delivery device. While the approach and CPMV intratumoral immunotherapy is tumor-agnostic, we will focus on metastatic breast cancer. To mimic a patient population with different subtypes of breast cancer, we will use immune-competent mouse models of metastatic disease including models of triple negative breast cancer, HER2+ and ER+/HER2- tumors. Third, as a prelude toward translation, we will perform a phase 0 canine trial enrolling canine patients with non- metastatic and metastatic mammary tumors; in collaboration with Co-I Peña. Companion dogs with spontaneous tumors provide a uniquely powerful resource that can be used for translational research as well as treatment of someone’s well-loved pet.

NIH Research Projects · FY 2026 · 2024-08

Project Summary Recent decades have revealed the profound impacts that gut microbiota have on human health. Far beyond being simply pathogenic vs benign, gut microbes impact a variety of health and disease states, including metabolic, digestive, and mental health, as well as propensity to cancer. Adding to the complexity, gut microbes can influence the metabolism, and thereby action, of drugs developed to promote health and treat disease. This suggests that many conditions would benefit from a more personalized treatment plan that takes individual gut microbiota into account. Stratifying by microbial profile may also benefit drug development, by removing a confounding variable in clinical trials. The current standard method of measuring the gut microbiota is via fecal samples. However, while convenient, inexpensive, and non-invasive, these samples do not accurately reflect the details of gut communities. Up to a third of intestinal microbes can be effectively absent from fecal samples, which also fail to preserve information about spatial structure. Therefore, new measurement techniques are needed to more accurately profile gut microbiota. Here, we will develop an innovative approach that uses living biosensors to record extracellular DNA as they traverse the gut, preserving a record of the internal microbial composition and spatial structure. This strategy relies on naturally competent bacteria, which we recently used to detect DNA released from colorectal tumors in vivo. The first two aims will develop complementary strategies to store extracellular DNA, and the third will demonstrate them in mice. In Aim 1, we will store snippets of environmental DNA in CRISPR arrays for later readout. This aim includes the endogenous CRISPR-Cas system, as well as alternative systems that may be better suited for the target DNA. In Aim 2, we will test the hypothesis that environmental DNA can instead be stored by casposases, which could allow storage of longer snippets. These two aims serve as alternative approaches for each other, and both approaches will also encode bio-spatial information in the order of recorded DNA sequences. In Aim 3, we will validate the gut DNA recorder in vivo using mouse models of dysbiosis. This work will develop highly innovative approaches, with risk appropriate for this mechanism and ameliorated by multiple alternatives. The result of this work will be a novel diagnostic technique that can record and measure the microbiota across the entire intestinal tract, with no invasive prodedures required.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT Social Determinants of Health (SDoH), or the environment and conditions in which one lives, can greatly impact one’s health and quality of life. In the White House conference on Hunger, Nutrition and Health, the president stressed the importance of good nutrition and healthy eating on child academic and health outcomes.1 The Council outlined a national strategy that included the need to improve food access and affordability, integrate nutrition programs and education in healthcare, provide support for these activities through Medicaid and Medicare, and increase nutrition and food security research.2 Thus, there is an urgent need to develop and test effective and acceptable workflows that connect families experiencing food insecurity with healthy nutrition support programs. In this proposal, we will conduct a pilot type 2 hybrid effectiveness- implementation trial of the I-FRESH (Implementing Food Referrals for Equity and Sustained Health) program using a Roll-Out Implementation Optimization (ROIO) design among families with children with nutrition-related illnesses who receive Medicaid or Supplemental Nutrition Assistance Program (SNAP) benefits. I-FRESH, our food security nutrition support program that was developed with several community stakeholders, involves 4 main components: screening and identification of families experiencing food insecurity (FI); social worker/care navigator-led discussions with families to determine need and readiness to receive support; referrals and assistance to engage with these programs; and follow-up assessments to determine fit, track utilization, and determine need for additional referrals. This program will be tested at Rady Children’s Hospital San Diego in the Type 1 and Type 2 Diabetes, Metabolic Dysfunction-Associated Steatotic Liver Disease, and general gastroenterology clinics as these conditions are heavily affected by nutritional intake. These settings are conducive to testing the initial implementation and effectiveness of the program because they already have dietitian and social work support and built the FI screener in the electronic health record. To aid in this work, we have obtained funding from USDA/NIFA to provide nutrition incentives or a fruit and vegetable prescription (FVRx) program to families receiving SNAP benefits. We will apply the PRISM4, 5 implementation determinant framework and RE-AIM6, 7 implementation outcome framework to guide implementation processes and evaluation, and engage stakeholders. The specific aims of this proposal are: 1) To engage our Community, Clinical, Administrative, and Research Advisory Board (CARAB) to refine and optimize the program before and after each roll-out in 4 clinics; 2) To assess implementation outcomes; and 3) To examine preliminary impact and effectiveness outcomes on family-level food insecurity and pediatric nutrition-related health outcomes. This information will be important as health system leaders, insurance providers, community programs, public health agencies, and policy makers strive to integrate these programs into our healthcare system.

NSF Awards · FY 2024 · 2024-08

The research project focuses on making advanced AI technologies, like the neural networks used in language models and for image generation or analysis, more efficient and environmentally friendly. Today, these technologies require significant computational power, which makes them both costly and energy-intensive. This project aims at developing algorithms for replacing such networks with functionally equivalent ones that require fewer computational resources, without losing their effectiveness. The resulting reduction in computational complexity will also help enable the use of AI in real-time applications and on devices with limited resources, further expanding this critical technology's reach. Thus, the expected scientific outcome is the development of robust, efficient, practical algorithms that are also backed by rigorous theoretical guarantees. Moreover, we anticipate that the theoretical tools we develop in order to analyze these algorithms will find broader use in other application areas. The project also emphasizes the importance of education and academic community involvement. By integrating research findings into university courses and involving students from potentially diverse backgrounds, the project will help prepare the next generation of mathematicians and engineers. Additionally, it aims to share breakthroughs with broader communities through journal publications, workshops, and conferences, while also connecting students with real-world industry applications. As previously stated, the project aims to address the challenge of compressing large neural networks, which are pivotal in modern AI applications but are resource-intensive. Thus, the research will focus on developing algorithms that reduce the computational demands of these networks by minimizing the memory and power needed without compromising their performance. Our approach involves three main strategies, quantization, pruning, and low-rank approximation. Among these, quantization transforms neural network parameters into formats that require fewer bits, thus reducing memory usage and computational intensity. Meanwhile, pruning selectively removes less important parameters from the network to streamline computations. Finally, low-rank approximation replaces large matrices representing the weights in the network with products of smaller matrices, in a way that retains essential information while requiring less memory and computation. We will develop algorithmic approaches for quantization, pruning, and low-rank approximation that are underpinned by rigorous mathematical theories to ensure the reliability and effectiveness of the compressed models. In our analysis, we will utilize stochastic process theory, geometric functional analysis, discrete geometry, discrepancy theory, optimization theory, compressed sensing, and dimensionality reduction, to name a few. These diverse areas will help us establish a solid theoretical foundation for our algorithms consisting of lower bounds on best-possible theoretical error guarantees as well as upper bounds on the errors resulting from our algorithms. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY/ABSTRACT Defining the forms of neural representation and temporal dynamics of neuron ensembles in the hippocampus and related neocortical regions such as retrosplenial and entorhinal cortex has led to a deep understanding of the brain’s ‘cognitive map’ of the environment. Such work has direct relevance to understanding the pathologies and cognitive impairments attending neurological disorders such as Alzheimer’s disease as well as intact learning and memory processes associated with navigation, episodic memory, and orienting. The dorsal subiculum is highly interconnected with these brain structures and important for normal spatial cognition, yet the unique contributions it makes to the cognitive map and flexible navigation behavior have yet to be defined. Prior work has suggested that subicular neurons are far less spatially-specific in their firing activity than those of hippocampal area CA1, a brain region forming a prominent input to subiculum. A role for subiculum in encoding and learning orientational relationships between an organism and its environment has been suggested and is consistent with its receiving input from the anterior thalamus. A major output target for subiculum is the retrosplenial cortex, a region that contains neurons with left/right turn-related activity and which has been hypothesized to form a transition of spatial cognition into action through projections to secondary motor cortex. Our project is designed to systematically investigate orientation tuning in the subiculum within environments where navigation is constrained to a network of interconnected pathways. More specifically, we will examine the question of whether individual subiculum neurons can encode multiple directions of travel as observed in preliminary data. The experiments also address context-dependence and learning in orientation tuning. The work will have implications for theories on function of the brain’s cognitive map. It is poised to identify a system by which environmental locations affording transitions between two or more directions of travel can be encoded with directional signals, which could drive left/right turning actions via outputs to retrosplenial cortex. More broadly, the project is poised to form a new direction for study of subicular function and the role of multi-directional tuning in spatial cognition.

NIH Research Projects · FY 2025 · 2024-08

Project Summary/Abstract: Regulatory DNA encodes signals that are recognized by transcriptional regulators to drive development- and stimulus-specific patterns of gene expression. While individual DNA binding sites recognized by transcription factors are often short and promiscuous in the genome, functional regulatory elements usually contain several closely spaced binding sites that specify the cooperative assembly of regulatory factors on DNA. Multiple lines of evidence suggest the configuration of these binding sites, including their relative binding affinity, spacing and orientation, play important roles in the context-dependent recruitment of RNA polymerase II to drive transcription. Furthermore, regulatory elements do not function independently in the genome. Proper gene regulation often depends on multiple regulatory elements scattered across gene loci that work in concert to enhance or silence target promoters. Yet despite extensive research efforts, our understanding of how regulatory DNA is organized is still rudimentary, limiting our ability to accurately model transcriptional networks and interpret the function of genetic variants. My laboratory seeks answers to these fundamental biological questions using a combination of experimental and computational approaches to decode regulatory DNA. Previous efforts to investigate the function of regulatory regions have typically relied on indirect measurements of transcriptional activity, such as the profiling of epigenetic markers, transcription factor binding, chromatin accessibility, or the expression of nearby genes or reporters. We have found that precise measurements of transcription initiation, which record the frequency and base positions where RNAPII initiates transcription, yield novel insights into the roles of transcription factor motifs and other regulatory DNA features in regulating transcription. Transcription initiation profiling also provides sensitive and precise measurements of activation at promoter-distal regulatory elements, enabling us to track the functional interactions between promoter and enhancer elements in the genome in the context of chromatin modifications and changes in 3D genome structure. Using these approaches we will explore how transcription factors exert activating or inhibitory effects on individual transcription start sites (TSS), depending on their spatial location within regulatory elements, and investigate how multiple regulatory elements work together to drive the transcription of target genes. These studies will greatly expand the ruleset to interpret how regulatory DNA and genetic variation affect gene regulation.

NIH Research Projects · FY 2024 · 2024-08

Alzheimer’s disease (AD) is known to cause subtle changes in language production years before diagnosis, yet current behavioral tests take limited advantage of linguistic tools to diagnose AD at early stages. Most language tasks focus on single word production (e.g., picture naming), missing many critical aspects of language. Some tasks focus on connected speech (e.g., picture description), but they heavily rely on complex computational modeling methods, thus are hard to implement in clinical settings. Addressing these issues, autocorrection is a type of error produced in connected speech that is easy to elicit, easy to analyze, and is sensitive to AD biomarkers. Thus, the long-term goal of this proposal is to maximize this sensitivity, facilitating the development of the autocorrect task as a non-invasive, simple, and low-cost diagnostic tool for early detection of AD. Our proposed study will lay foundation to achieve this goal through investigating the underlying cognitive mechanisms that drive the sensitivity of autocorrection to AD. In the autocorrect task, participants read aloud short paragraphs in which some words are replaced by unexpected words that are similar in form (e.g., Think about they concept replaced the concept). Participants are told to read exactly what they see, but occasionally, they automatically correct the unexpected words and produce the expected words instead, i.e., they produce an autocorrect error (e.g., say the concept instead of they concept). Participants with AD or preclinical AD (i.e., those at risk for AD based on CSF biomarkers) produce more autocorrections than healthy controls, especially with function word targets with rich syntactic properties (e.g., the, and). This is probably because 1) AD decreases attention thus eliciting more misperception, 2) AD increases monitoring difficulty thus making it more difficult to detect planned errors, and/or 3) AD makes it more difficult to overcome competition from syntactically well-formed expected targets. We will combine behavioral and eye-tracking measures to test each account. In Aim 1, we will investigate the attention and monitoring accounts by manipulating the font color of autocorrect targets: they will be either in black or red font. We hypothesize that the red font will reduce sensitivity to AD, and skipping rate and regression rate in eye movements will reveal whether the effect is driven by facilitating attention or monitoring or both. In Aim 2, we will investigate the monitoring vs. syntactic constraints accounts. The autocorrect targets and their corresponding expected words will either match (e.g., much/more are both adverbs) or mis-match (e.g., then/that is an adverb/pronoun pair) in syntactic category. Mismatching pairs elicit greater syntactic anomaly than matching pairs, and thus should be harder to produce but be easier to monitor. This contrast, combining with regression rates in eye movements, will differentiate the syntactic constraints vs. monitoring account. The proposed project will be the first that combines the analysis of autocorrect errors with eye-tracking in preclinical AD, shedding light on how complex aspects of language production are affected by AD in its earliest stages in a simple way.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Latina adolescents report especially low activity,2,3 being less than half as likely to meet physical activity guidelines as Latino boys. Compared to non-Latino White girls, Latina adolescents have 50% higher rates of overweight/obesity and 60% higher rates of metabolic syndrome4,5 and these disparities continue into adulthood.6,7 Effective physical activity counseling delivered through Federally Qualified Health Centers could have broad impacts on Latina teens, yet it is estimated that only 50% of pediatric visits include any discussion of physical activity. Due to constraints on provider time and expertise, referrals to exterior programs may be necessary. Through iterative research, including pilot trials (R03NR014329), interviews, design workshops, and beta testing with a youth advisory board, we have developed a theory-based multi-technology MVPA intervention for Latina teens, Chicas Fuertes, which is currently being tested in a fully powered trial with a healthy community sample (R01NR017876). Intervention content is delivered via web, Fitbits, individually tailored text messages, and Instagram; preliminary data show high engagement and excellent retention (>90%). Given the use of scalable mobile technologies to deliver the intervention, an adapted version of the intervention that focuses on guideline adherence has good potential for a referral system; effectiveness or implementation of such interventions in clinical settings has never been tested. Therefore, we will conduct a hybrid type 1 effectiveness-implementation trial of FQHC referrals to an augmented, EMR-integrated, remotely delivered version of the intervention (Chicas Fuertes 2). In the proposed study, providers at Family Health Centers of San Diego, the largest FQHC in San Diego County, will refer N=200 adolescent Latinas (age 13-17) to receive a wearable tracker integrated into EMR; they will be randomized 1:1 to receive no other intervention (comparison arm) or to receive the Chicas Fuertes 2 intervention. We will build a bidirectional data sharing system in EMR which allows for referral to the program and documentation of MVPA back to EMR as a vital sign. Adherence to guidelines will be measured at six and 12 months via accelerometers. We will also evaluate change over time in physical and mental health measures (e.g., BMI, blood pressure, depression), and examine daily guideline adherence throughout the course of the intervention using data from wearables (Fitbits). Finally, we will conduct a thorough mixed methods analysis of facilitators, barriers, and outcomes of implementation guided by the PRISM framework to inform future scale-up across FQHC’s and future sustainability, including staff time needed to run the intervention and potential to integrate tasks into existing staff roles. The proposed study will build a foundation for broad implementation, using existing clinical systems and widespread technologies to shift health behaviors across the life course and promote health equity.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY: Transient cerebral ischemia occurs in various clinical scenarios, including transient ischemic attack (TIA), cardiac arrest, hypovolemic shock, cardiac surgery, and medical conditions related to brain edema or brain vasospasm. The majority of cerebral ischemia survivors experience long-term neurological sequelae due to brain ischemia-reperfusion injury (IRI). The objective of the proposed research is to investigate a novel mechanism of the dysfunctional mitophagy and the subsequent excessive accumulation of damaged mitochondria (mito hereafter) after cerebral ischemia. These damaged mito release apoptotic factors and reactive oxygen sciences (ROS) contributing to brain IRI. Mitophagy, a subtype of (macro)autophagy, selectively delivers damaged mito to lysosomes for degradation. N-ethylmaleimide sensitive factor (NSF) is the sole ATPase for regulating cellular membrane fusion events. We have found that NSF is deposited into inactive protein aggregates in neurons destined to die after cerebral ischemia. These NSF-deficient neurons progressively accumulate with substantial amounts of damaged mito and autophagic/mitophagic structures, suggesting that NSF is a crucial limiting factor for regulating mitophagic degradation activity, i.e., mitophagic flux. Furthermore, we recently generated a novel neuron-specific NSF-deficient mouse line. In the absence of brain ischemia, neurons of the NSF-deficient mice exhibit a substantial accumulation of mitophagic structures and damaged mito, which subsequently leads to autonomous neuronal death. This phenotype replicates major neuropathologic features observed in wildtype (wt) mice after cerebral ischemia. Moreover, our recent studies have demonstrated that NSF-overexpression (overexp) protected, while NSF-deficiency exacerbated brain IRI in the mouse model. Based on these discoveries, we propose to test a novel hypothesis strongly supported by our data: NSF inactivation results in dysfunctional mitophagy, leading to an excessive buildup of damaged mito after cerebral ischemia. These damaged mito release apoptotic factors and ROS, contributing to brain IRI. We will test this hypothesis by investigating: (i) whether, where, and why NSF inactivation disrupts the mitophagy pathway after cerebral ischemia using NSF- deficient, NSF-overexp, and wt mice (Aim 1); and (ii) the mechanism responsible for the post-ischemic NSF inactivation as well as the corresponding treatment strategies using pharmacological agents in the mouse cerebral ischemia model. The proposed studies will help to: (i) determine if NSF inactivation induces brain IRI via disrupting mitophagic degradation activity; (ii) distinguish the mitophagy-related and -unrelated impairments that are explicitly caused by NSF inactivation from those affected by NSF-independent events; and (iii) discover the mechanism and treatment strategies for alleviating NSF inactivation after cerebral ischemia. These studies will provide the necessary foundation for developing therapeutics to restore the mitophagic degradation activity after cerebral ischemia.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY Cardiometabolic disease refers to a set of clinically overlapping diseases, including coronary artery disease, stroke, type 2 diabetes, hypertension, kidney disease and liver disease. These `cardiometabolic' diseases are distinct but share common risk factors, including low density lipoprotein, triglycerides, systolic blood pressure, central adiposity and glycemic measures. We label this set of inter-related and heritable metabolic and hemodynamic traits the `cardiometabolic' (CM) heath profile. The CM health profile builds and extends the metabolic syndrome paradigm to interrogate the disease risk heterogeneity, variables underlying pathophysiology and predisposition to specific adverse consequences. Our focus is on examination of the shared biology of the components and their role in the pathophysiology of CM disease endpoints, rather than consideration of disease syndromes. Differences in end-organ consequences suggests that there may be subtypes of the CM health profile with potentially different underlying pathophysiology and propensity for adverse outcomes. We hypothesize that genetic analyses can enhance biological insights into CM health profile component and disease endpoints by exploiting our mega-scale size sample of 1,365,750 subjects, across five racial-ethnic groups, and consideration of pleiotropy, genetic subtyping, environmental modulation, and causal inference analyses. We propose the following specific aims: 1) Pleiotropy, genetic classification and association analysis of CM health profile components; 2) Gene x environment (GxE) interaction analyses of CM disease endpoints; and 3) Causal inference analysis of CM health profile components, risk factors and disease endpoints. There is a pressing need to better understand the genetic architecture of CM health profile, relationship of components and their role in disease endpoints. If successful, this proposal will increase genomic discovery, identify novel loci, and pathways, and enhance biological insights of CM health profile and disease morbidity. We anticipate that our comprehensive approach to understand CM health profile biology will bring us several steps closer towards identifying novel molecular targets and modifiable risks to achieve this goal.

NSF Awards · FY 2024 · 2024-08

Gateways 2024 is the major event for the science gateway community in the US to discuss challenges and solutions in the area, to identify new issues, to shape future directions for research, foster the exchange of ideas, standards and common requirements and push towards the wider adoption of science gateways. The topics covered by the Gateways conference series range from technical topics to use cases to related content such as usability or sustainability of science gateways. The knowledge transfer can be transformative between different research domains and technical content. The building blocks of science gateway frameworks are re-usable in diverse research areas evident in widely used frameworks such as Hubzero and Tapis. The Gateways conference series sets the stage for learning, engaging and empowering the different stakeholders in the community who are science gateway users, developers and providers as well as funders and decision makers. Providing travel grants for students and early-career researchers allows to include a diverse audience and support underrepresented minorities. Science gateways are a key part of NSF funded Cyberinfrastructure, and they are used by hundreds of thousands of researchers and students, supporting both publication-quality science and at-scale education. Science gateways involve a comprehensive set of research domains that has a broad impact on society, addressing considerable challenges such as pandemics, climate change, global sustainability of food, water, and land use driven by growing populations and rising per capita incomes. In recognition of their importance, NSF has funded the Science Gateways Community Institute (SGCI) and more recently the SGX3 Science Gateways Center of Excellence to provide leadership for the science gateways community. The Gateways conference series is one of the of flagships of SGCI and SGX3 and the major event in the US to bring the science gateways community together. The conference series has existed since 2016 and has attracted each year between 100-170 participants. In 2023 it has moved from an SGX3-organized conference to a community-driven conference with the first time the general chair being selected by a newly established advisory board for the conference and who is not part of the SGCI/SGX3 team. The goal is to attract additional research domains and tap into the chair's networks that are not already in contact with SGCI/SGX3. SGX3 continues to guide the conference while inviting each year since 2023 a different general chair. Gateways 2024 features various program formats such as keynotes, presentations, tutorials, demos, panels, posters and Bring Your Own Portal. Accepted submissions are published in open-access proceedings and accepted papers are invited to a special issue in a journal. SGCI/SGX3 has an impressive record of underrepresented minority involvement within the science gateway community. The travel grant allows to involve more students and early-career researchers at Gateways 2024 and they are selected under consideration of diversity, equity and inclusion. 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

Project Summary/Abstract Thyroid eye disease (TED) is a debilitating orbital and ocular condition that affects up to 50% of patients with Grave’s hyperthyroidism. Tissue fibrosis and hyaluronan overproduction in active TED leads to proptosis, eye movement restriction, eyelid retraction, dry eye, and optic nerve compression. After 2-3 years, patients enter a chronic phase of TED where symptoms persist but do not acutely worsen. The molecular basis of acute and chronic TED is a mystery. Prior studies have found insulin like growth factor 1 receptor (IGF-1R) to be an important cell surface protein in effecting the fibrosis and hyaluronan production of active TED. IGF-1R is important in a variety of body processes from metabolism to cancer to TED and was found to be overexpressed in TED orbital tissue. Exactly how IGF-1R effects the phenotypic changes in TED, and how the IGF-1R gene is regulated is unknown. The utility of IGF-1R or other related targets in chronic TED is also not known. This study examines the cell type landscape of acute and chronic TED and how IGF-1R is expressed and regulated in the two phases of TED. Aim 1 will determine the cell type trophism of IGF-1R in acute and chronic TED compared to un-diseased orbit tissue using single nuclei multiome sequencing of orbit tissue isolated from patients undergoing surgery. Spatial transcriptomics will be used to distinguish microenvironments of isolated cell types and interacting cell surface receptors. Aim 2 will investigate the regulation of IGF-1R expression by cis-regulatory elements from single-nuclear Assay for Transposase-Accessible Chromatin (ATAC)-sequencing. Promising targets will be tested through an in-vitro CRISPR-screen on human orbital fibroblasts from acute and chronic TED patients to determine the effect on fibroblast proliferation of knocking down key regulatory regions. These studies will generate a greater understanding of the cell type landscape of TED and how IGF-1R and other key cell surface proteins are regulated in acute and chronic TED. The results could yield new therapeutic targets or better understanding of how to use existing treatments most effectively. The proposed research training plan features mentorship from the basic sciences and clinical sciences and access to state-of-the-art techniques and facilities. This plan also incorporates professional development and unites collaborative resources between the department of cellular and molecular medicine and the department of ophthalmology to maximize my training potential.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY RNA modification is an emerging concept because a diverse set of modified nucleotides are found in mRNA sequences. The m6A modification is catalyzed by RNA methyltransferase complex containing METTL3 that catalyzes the addition of a methyl group at N6 position of adenosine which affects gene expression via regulation of RNA metabolism, function, and localization. N6,2’-O-dimethyladenosine (m6Am) is an abundant RNA modification located adjacent to the 5’-end of mRNA 7-methylguanosine (m7G) cap structure. Since m6Am is found at the first transcribed nucleotide in ~30% of the cellular mRNAs, m6Am can have a major influence on gene expression of the transcriptome. Human Phosphorylated CTD Interacting Factor 1 (PCIF1) as cap-specific adenosine-N6-MTase (CAPAM), that catalyzes cap-specific m6A methylation on 2’-O- methylated A at the 5’-ends of mRNAs. So far, the role of m6Am RNA modification and the catalytic function of PCIF1 in biological and disease processes, especially in regulating viral infections and host-pathogens interactions have not be determined. Despite remarkable success in treating HIV/AIDS, we do not have a functional or complete cure for the disease. The molecular networks of host cell regulating HIV-1 transcription, replication, and latency are not completely understood. The overall objective of this proposal is to delineate the molecular and cellular mechanisms by which HIV-1 (HIV) infection alters host transcriptional and translational programs. Our project has three specific aims: Aim 1: Define the dynamics and mapping of human m6Am RNA methylome by HIV infection and methamphetamine (MA) exposure. Aim 2: Determine how HIV alters m6Am methylome of host cell. Aim 3: Determine how RNA modifications influences HIV pathogenesis. Successful completion of these aims will reveal function of PCIF1, and a new regulatory mechanism involved in HIV gene expression and latency.

NIH Research Projects · FY 2024 · 2024-07

PROJECT SUMMARY This proposal requests sponsorship for the 48th U.S. Ten-Day Seminar. Given the burden of cardiovascular diseases (CVD) and stroke, it is highly appropriate to conduct professional training on epidemiology and prevention. The goals of this proposal align with the NHLBI’s Strategic Vision which seeks to “further develop, diversify, and sustain a scientific workforce capable of accomplishing the NHLBI’s mission.” Training of such a workforce is a key element of the country’s readiness to address the health challenges posed by CVD and the readiness to advance multi-component strategies that promote cardiovascular health (CVH). A prepared workforce will need research competencies in epidemiology and biostatistics, quality of care, and policy and environmental approaches to health promotion and disease prevention. Further, authoritative health agencies and prominent scientists have noted an increasing need for professionals who understand methods related to e-cohorts, large practical clinical trials, dissemination and implementation research, and big data analytics. Scientists will also need expertise in cost-effectiveness research, epigenetics, and biomedical informatics. This Seminar can uniquely contribute to training scientists who can integrate evidence across these fields and translate research findings into effective and impactful policy and practice. We seek primary sponsorship from the National Heart, Lung, and Blood Institute (NHLBI) and if we receive a meritorious score we will request co- funding from NIDDK, NINDS, the NIH Office of Disease Prevention, and the NIH Office of Behavioral and Social Sciences Research. Other funders/partners for the Seminar are the Centers for Disease Control and Prevention (grant), and the American Heart Association (council budgets and in-kind). To assure the successful conduct of the Seminar, we will continue to: 1. Attract a faculty with both the knowledge of relevant content and the personal teaching skills required for the effective conduct of this program, with a continuing emphasis on the recruitment of faculty from underrepresented racial/ethnic groups (currently 31% of the faculty) and female faculty members (currently 56% of the faculty); 2. Adapt program content to maintain its relevance to the training needs of the nation for health professionals with appropriate career interests, while maintaining a consistent central focus on the foundational methods in cardiovascular disease epidemiology; 3. Disseminate information about this program to appropriate groups, using the most effective current strategies for reaching underrepresented racial/ethnic groups, female candidates and historically marginalized groups; and 4. Recruit participants from populations that have been historically marginalized by connecting with diverse professional societies and organizations, and sustained relationships with seminar alumni.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY: Salmonella Typhimurium (STm) and other non-typhoidal Salmonella serovars cause 100 million infections per year worldwide, and treatment options are limited due to the general contraindication of broad-spectrum antimicrobials which can exacerbate the inflammation in which Salmonella thrives. Therefore, there is a need for alternative, targeted therapeutic strategies to mitigate Salmonella infection and subsequent disease. Natural resistance to STm infection is mediated in part by the commensal gut microbiota, the consortium of trillions of microbes encompassing hundreds of individual species that exist in symbiosis with the host. The gut microbiota contributes to colonization resistance against enteric pathogens like STm by forcing the pathogen to compete for resources in order to establish infection; and, to overcome this barrier, STm exploits aspects of host immunity in order to antagonize gut commensals and establish a niche within the inflamed gut. While it is known that the outcome of this competition between STm and the gut microbiota is a critical determinant of whether or not infection is established, the specific mechanisms employed by STm and the gut microbiota respectively during this competition are only partially understood. To address this knowledge gap, herein I employ a combined approach that integrates quantitative metagenomics (metaG), metatranscriptomics (metaT), and a novel sequencing modality, metatranslatomics, (metaRS) to gain unprecedented mechanistic insights into microbial and host metabolism in the STm-perturbed gut. In my preliminary work, application of functional community-level ribosome profiling (metaRS) to STm infection in a resistant mouse model of salmonellosis (Nramp1+) revealed that STm shares a metabolic profile with discrete members of the gut microbiota (e.g. Faecalibaculum rodentium) in vivo. Combined with the observed loss of F. rodentium and other microbes sharing metabolic overlap with STm post-infection, these data suggest their potential role as STm competitors. Furthermore, depletion of F. rodentium also occurred concurrently with increased expression of the host antimicrobial lectin Reg3γ. Based on these findings, my central hypothesis is that elucidating microbial metabolism in the gut, in conjunction with analysis of host responses will unveil new competitors and mechanisms of competition between STm and the microbiota. In the first aim of this proposal, I will analyze bacterial metabolism to identify potential STm competitors, and apply metaRS to predict competition and identify prebiotic substrates to guide this competition in favor of the commensal microbiota. The proposal’s second aim will investigate the role of host Reg3γ in facilitating clearance of STm competitors. Collectively, the expected outcomes of these studies will provide insights concerning mechanisms governing microbial competition in the context of host responses and inform the ultimate implementation of microbiota-directed therapies aimed at reducing STm colonization and maintaining homeostasis.

NIH Research Projects · FY 2025 · 2024-07

Abstract Background: HIV infection in the brain occurs early after transmission and leads to chronic neuroinflammation. Although modern antiretroviral therapy (ART) controls viral replication, there is no cure for HIV, and successful control of viral replication has not completely ameliorated inflammation and HIV-associated neurocognitive disorders (HAND). Microglia play a central role in other neurodegenerative disorders and are the likely primary reservoir for HIV in the brain, but little else is known about the inflammatory character associated with HAND. Additionally, the inflammatory incitement associated with HIV is potentially determined by its expression of viral proteins, dictated by the epigenetic microenvironment of the provirus, which is poorly characterized. Recently, the Nurr1 receptor was described as an important mediator of HIV-1 silencing in the context of microglia in vitro, making it a prospective focal point for further studies in brain tissue. Study Cohort: We will leverage the unique Last Gift rapid autopsy cohort, which allows us to preserve cellular integrity and nucleic acids in precious tissue samples collected from PWH. We will select frontal cortex and basal ganglia from 15 Last Gift participants to analyze for this proposal. Our goal: Using powerful single cell sequencing techniques, we will characterize the epigenetic regulators of the HIV provirus in brain myeloid cells from 15 PWH using novel epigenetic enrichment techniques and assimilated data on integration sites and the full-length proviral sequence generated as part of the Last Gift project (Aim 1). Next, using brain myeloid cells isolated from a subset of the participants (N=6), we will further explore the mechanistic framework of the HIV provirus in microglia through manipulation of the proviral epigenetic profile using in vitro Nurr1 agonists and epigenetic modulators (Aim 2). Finally, we will use single cell techniques to examine the epigenetic and transcriptomic profile of the inflammatory milieu in the brains of PWH on suppressive ART and correlate them with proviral load and cell-associated viral RNA (Aim 3). How will we advance the field? The epigenetic characteristics of the HIV provirus have not been examined in the brains of people with HIV (PWH). Most evaluation of proviral epigenetics has been focused upon CD4+ T cells, but thus far few have examined epigenetic mechanisms of proviral reactivation in microglia from PWH, and none have been able to define these mechanisms thoroughly in tissue samples or cells isolated from brains of PWH. Therefore, this proposal will advance our understanding of HIV persistence in the brain on multiple fronts. Additionally, the inflammatory pathogenesis of NCI in HIV infection is poorly characterized, but our proposal would not only allow definition of the immune cell character in the brains of PWH, but also the epigenetic and transcriptomic mechanisms at play in all cell types, including neurons and astrocytes.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY / ABSTRACT Traumatic spinal cord injury is a devastating condition that affect about 302,000 people in the United States, with 18,000 new cases each year. The limited ability of axons to regenerate after injury in the adult central nervous system (CNS) underlies the permanent functional deficits and paralysis experienced by people with spinal cord injury. Much research remains to be done to fully understand how regeneration is controlled by molecular and cellular machinery in the neurons. This proposal builds on our recent success of applying Patch-based single cell RNA sequencing technology to interrogate the molecular mechanism of corticospinal axon regeneration after spinal cord injury. By sequencing only hundreds of neurons but at unusually high depths, we developed a regeneration classifier that can be broadly applied to predict the regenerative potential of diverse neuronal types based on their single cell profiles, the first of its kind in regenerative biology. Furthermore, this study implicates key components in mitochondrial biogenesis and antioxidant response in regulating regeneration. Here we propose to expand Patch-seq based single cell RNA sequencing approach in several ways. First, we will refine and extend the regeneration classifier by sequencing additional corticospinal neurons and other neuronal types with different regenerative capabilities. This will allow us to develop a more accurate regeneration classifier and understand its full range of capabilities and limitations. Second, we will investigate the role of antioxidant response and mitochondrial biogenesis with a comprehensive array of genetic gain and loss of function analyses on NFE2L2 and PPARGC1A, master regulators of the two biological processes and two top candidates from our Patch-seq study. Third, we will conduct deep sequencing on young versus old neurons to understand the age impact on axon regeneration, which would be required to develop therapies that are robust across age groups. Together, the proposed experiments using this unique deep single cell RNA sequencing approach will bring a greater understanding of the neuron intrinsic control of axon regeneration, providing the foundation for therapeutic development to promote repair and recovery after spinal cord injury.

NSF Awards · FY 2024 · 2024-07

This project supports a two-day meeting for leaders and researchers from the National Science Foundation's (NSF) CyberTraining and SCIPE programs. The event will be held alongside the meeting for the NSF's Cyberinfrastructure for Sustained Scientific Innovation program. It will serve as a platform for participants to share information about their projects, goals, and outcomes with others, including NSF program directors. The meeting will also feature joint sessions for discussing common interests and exploring opportunities for collaboration between the two NSF programs. The CyberTraining/SCIPE PI meeting aims to advance the community-building efforts of previous workshops by providing a platform for principal investigators (PIs) to share technical information about their projects with peers, NSF program directors, and other stakeholders. This forum facilitates the exploration of innovative topics within NSF workforce development communities, promotes discussions on best practices, and generates new ideas for training and educating CI researchers and professionals. The organizing committee will select speakers and panelists based on their research and expertise in CyberTraining for CI and SCIPE professionals. PIs will also provide valuable feedback on emerging opportunities and challenges, and participants will include projects identified by NSF as complementary to CyberTraining/SCIPE initiatives, fostering potential collaborations. This year's program will explore the impact of AI on the NSF research and training community. The workshop will convene leading experts from the CyberTraining/SCIPE and broader communities to discuss and share innovations and best practices in training CI and SCIPE professionals, aiming to lay the groundwork for the next generation of professionals who will support the development, deployment, and utilization of NSF resources and services. These collaborations will enhance productivity, accelerate research in science and engineering, and significantly increase the impact of NSF's output, particularly within OAC’s programs. The selection of speakers and panelists will ensure diversity and alignment with best practices for broadening STEM participation. Additionally, the organizing committee will extend invitations to relevant NSF program managers. 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

Large random networks naturally arise as models for real-life networks, as various characteristics can be effectively captured and analyzed in such models. In the study of random graphs, stationarity can be viewed as a stochastic homogeneity assumption; while in geometry, homogeneity is associated with a transitive symmetry group. In this project we aim to investigate stationary random networks through the lens of random walks on groups, entropy and boundary theory, and graph limits, while utilizing the growing theory of probability measures on the Chabauty space of subgroups. This project offers collaboration opportunities, mentorship and training for postdoctoral scholars and graduate students. The proposed project primarily focuses on three research directions, with entropy theory of random walks being the underlying fundamental tool used to approach all these threads. The first part focuses on the Furstenberg entropy realization problem for classical matrix groups, with an aim to understand the interplay between rigidity and flexibility in the structure of stationary random systems. The second part focuses on the longstanding amenability problem of a class of groups (called iterated monodromy groups) which originate from conformal dynamics. The conformal geometry of the limit space, which can be viewed as limits of finite level Schreier graphs, plays a crucial role in the recent solution in the strongly recurrent regime. In this part the goal is to shed light on an important critical case where the limit space is the full two-dimensional sphere. In the third part we propose a new procedure called random walk cocycle sampling limit and explore its potential applications. The procedure is inspired by the local-convergence graph limits initiated by Benjamini-Schramm and it naturally produces stationary random systems that carry rich information about random walk transition probabilities. 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.