University Of California At Davis

NIH Research Projects · FY 2025 · 2022-09

Project Summary High-density lipoproteins (HDL) are the single strongest predictors of longevity and protect against a wide array of diseases, from chronic conditions like cardiovascular disease and neurodegeneration, to acute infection and sepsis mortality, and everything in between. If we can get HDL right, we can live long, healthy lives. Yet despite over 50 years of research, HDL have remained an enigma and therapeutic approaches for improving HDL function have proven elusive. HDL are highly heterogeneous and difficult to isolate and characterize because of their colloidal, multi-molecular nature yet very small size (< 20 nm in diameter). A critical barrier to progress is the lack of technologies to simultaneously quantify the size and number of HDL particles, and isolate them such that they remain intact and amenable for a variety of both compositional and functional analyses. The objectives of this project are to gain new technological knowledge on the application of our instrument using size exclusion chromatography coupled with multiple inline static and dynamic optical detectors, and to measure the quantitative advantages of this technology over state-of-the-art approaches for the isolation and physicochemical characterization of HDL particles. In particular, this project will solve the critical problem of quantifying the number of particles using a non-destructive approach that simultaneously measures and fractionates the particles by size, making it possible to evaluate the function and composition of different size-based HDL subclasses on a per particle basis. Currently, researchers are limited by the simple problem of not having a good denominator: the only option is to express the amount of an important constituent or functional capacity in the HDL we have measured based on a rough substitute for “concentration” (e.g. total protein in the isolated fraction). Therefore, if there is more of a certain protein (or higher functional capacity) in sample A vs. B, there is no way to distinguish whether that is simply because sample A has more particles in it or whether there are more molecules of that protein (or higher functional capacity) per particle. Different sizes of HDL carry different absolute and relative amounts of individual proteins, lipids, and other components, from as few as 2 molecules of the main apolipoprotein, apolipoprotein A-I, and 12 molecules of cholesteryl ester in the smallest HDL, to as many as 4-6 molecules of apolipoprotein A-I and hundreds of molecules of cholesteryl ester, with similar variability in the concentrations of other critical components that confer dozens of functions, from antioxidant, to immunomodulatory, to anti-proteolytic to name a few. And because particle size determines binding affinity to receptors, clearance rates, and likely even whether HDL can cross the blood-brain-barrier, knowing the number of particles of different sizes, and also the per particle composition of the cargo they carry is critical to the development of sensitive, actionable diagnostics, and targeted, effective therapeutics. Thus, the technology developed in this project will profoundly enable the biomedical research community to answer critical questions about HDL functional biology across a broad array of clinical and therapeutic applications.

NIH Research Projects · FY 2025 · 2022-09

Project Summary Chemoenzymatic construction of synthetic human milk oligosaccharide (HMO) glycome Human milk oligosaccharides (HMOs) constitute a major component of human milk which provides everything that breast-fed infants need in the first several months of their lives. There is an increasing appreciation of the multifaceted contribution of HMOs to the health of breast-fed infants. Exploring the applications of HMOs as infant formula additives, nutraceuticals, and/or therapeutics has begun but has been slow due to the limited access to structurally defined HMOs in sufficient amounts. The structures of more than 150 HMOs are known. Despite efforts and advances in developing chemical, enzymatic, chemoenzymatic, and fermentation methods for HMO synthesis, the access to a complete HMO glycome has not been achieved synthetically. HMOs can be purified from human milk but the amount is limited. We plan to lower the technical barrier to access HMOs by developing highly efficient user-friendly glycosyltransferase-based chemoenzymatic methods and construct a comprehensive synthetic HMO glycome. Other than the enzymes, the chemoenzymatic synthetic strategies, and the production processes that have been developed, additional innovation will be introduced for substrate and process engineering. New enzymes will be identified, engineered, characterized, and used for the synthesis of HMOs in a systematic target-oriented manner. Maps for chemoenzymatic synthetic routes will be developed. A comprehensive library of HMOs including branched and long-chain linear structures with or without L-fucose and/or sialic acid that have been identified from human milk and potential isomers that have not been identified will be constructed. The synthetic HMO glycome will provide well characterized pure compound standards for identifying and profiling of HMOs in the milk from different nursing mothers, at different lactation stages, and with or without infections or other diseases. The chemoenzymatic synthetic process is programmable, can be adapted for automation, and is readily scalable for large-scale production of HMOs in the future.

NIH Research Projects · FY 2025 · 2022-09

Project summary Our lives unfold over time, weaving rich, dynamic, and multisensory information into a continuous experience. However, we remember this as a series of discrete events. For example, the memory of a two-hour movie consists of a few memorable moments tied to the main story. During encoding, we segment deviant events and associate relevant events. During retrieval, we utilize the temporal association among encoded events to search for specific memory information. The hippocampus (HPC), prefrontal cortex (PFC) and substantia nigra (SN) are thought to support cognitive computations (i.e., conceptual prediction, prediction error detection, temporal association) that are critical for the encoding and retrieval of episodic memory. However, how these three regions work together to facilitate the construction of episodic memory in humans remains unclear. The proposed study aims to address this by identifying neural dynamics in the HPC-PFC-SN network and revealing circuit-level neural mechanisms of event segmentation and its relationship with human episodic memory. The central hypothesis is that event segmentation, which is influential in episodic memory formation and retrieval, emerges from the difference between the HPC perceptual predictions and received sensory inputs, which is tracked by dopaminergic neurons in the SN to update event models stored in the PFC. To test this, I will record both single neuron activity and local field potential signals in the HPC-PFC-SN network while patients, who have depth electrodes implanted for clinical purposes, encode, and retrieve the memory of semi-realistic experience created by well-controlled video clips. I will also build a computational model that can rigorously reproduce the observed behavioral and neural signatures. The trained model will be used as a proxy of the HPC-PFC-SN network to study the causal link between this tripartite network and memory behaviors by simulating computational “lesions”, which will provide insightful guidance for real electrical stimulation. To achieve the proposed goals, I will pursue training mentored by a group of experts in different fields, including the intraoperative recordings (Dr. Ziv Williams and Dr. Adam Mamelak), analyses of inter-regional neural dynamics and electrical stimulation (Dr. Ueli Rutishauser), and computational modeling (Dr. Gabriel Kreiman). The comprehensive analytic approaches spinning from behavior measurements, invasive neural recordings from both microscopic and mesoscopic levels, computational modeling and electrical stimulation will provide valuable opportunities to strengthen our understanding of human episodic memory system. The expected outcomes of this proposal will potentially advance the development of therapeutic interventions for memory-related disorders.

NIH Research Projects · FY 2026 · 2022-09

Infectious diseases such as scrub typhus, melioidosis, and typhoid fever remain difficult to measure through routine surveillance because many infections are undiagnosed or lack laboratory confirmation. These bacterial pathogens produce dynamic antibody responses that rise and decay following infection, creating opportunities to estimate infection incidence from serologic data. All three infections are directly relevant to American health. Scrub typhus, caused by Orientia tsutsugamushi, has emerging molecular and serologic evidence of possible domestic transmission in North Carolina. Typhoid fever, caused by Salmonella enterica serovar Typhi, causes hundreds of travel-associated infections in the United States annually and remains a concern for travelers and deployed military personnel. Melioidosis, caused by Burkholderia pseudomallei, has caused localized outbreaks in the Gulf Coast region of the United States and is recognized as a pathogen of biodefense concern. The overall objective of this K01 is to develop and validate scalable seroepidemiologic methods to estimate population-level incidence from cross-sectional antibody data. This project leverages a collaboration with Mahidol University in Thailand, where the substantially higher incidence of acute febrile illnesses provides epidemiologic conditions, clinical cohorts, and longitudinal immune response data that are not available in the United States. The Specific Aims are Aim 1A) To model longitudinal antibody responses for scrub typhus and melioidosis and estimate peak antibody response, decay rate, and decay shape, and Aim 1B) To determine if antibody responses vary according to age; Aim 2) To develop an analytic approach for estimating the seroincidence of scrub typhus, melioidosis and typhoid fever from cross-sectional survey data; and Aim 3) To quantify the magnitude of selection bias induced by a school-based sample relative to a random population-based sample when estimating the incidence of scrub typhus, melioidosis, and typhoid fever. Data sources include existing longitudinal data from confirmed melioidosis, scrub typhus, and typhoid fever cases; high-dimensional simulated data; and prospective population-level serosurveys in Northeast Thailand. This mentored International Research Scientist Development Award will support Dr. Kristen Aiemjoy, Assistant Professor of Epidemiology at the University of California, Davis, in developing an independent research program focused on quantitative seroepidemiology and infectious disease surveillance. The training program will provide expertise in immunology, advanced analytic methods, and serologic data science through mentorship from investigators at Mahidol University and Stanford University with extensive expertise in tropical infectious diseases, diagnostics, and mathematical modeling. The sustained collaboration between UC Davis and Mahidol University will strengthen international research partnerships while developing surveillance methods applicable to infectious disease threats in both Thailand and the United States.

NIH Research Projects · FY 2025 · 2022-09

Project Summary There is growing consensus that environmental factors influence risk for Alzheimer’s disease and Alzheimer’s disease-related dementias (AD/ADRD). Consistent with this hypothesis, cognitive trajectories of participants in the UC Davis Alzheimer’s Disease Research Center (UCD ADRC) Longitudinal Diversity Cohort (LDC) differ geographically. These geographical differences may arise from differential exposures to environmental contaminants. In this translational study, we will test our central hypothesis that ultrafine particulate matter (UFPM) enters the brain of exposed individuals and increases risk of cognitive decline and incident AD/ADRD. Human and animal studies have largely focused on PM2.5 (fine particulate matter with an aerodynamic diameter < 2.5 µm) in AD/ADRD risk. UFPM is a subset of PM2.5. Because of its smaller size (< 0.1 µm), inhaled UFPM can cross biological barriers to gain access to multiple organs, including the brain. Our prior work found UFPM in the brain of rats exposed to traffic-related air pollution (TRAP), but not filtered air controls, indicating UFPM may be a mechanism of brain injury. To date, no human studies and few animal studies have focused specifically on UFPM in AD/ADRD. Unlike most air pollutants that are relatively spatially homogeneous, UFPM are more concentrated near pollutant sources, so they are geographically discrete. To test our hypothesis, we will leverage resources unique to UCD: (1) the LDC, which has already geocoded 500 individuals in Northern California at the census tract level with associated longitudinal cognitive measures; (2) neuropathological samples on some of these individuals, (3) an UFPM exposure model that quantifies levels and sources of specific air pollutants over the LDC capture area from 2000 to 2019; (4) brains containing UFPM from rats exposed to unchanged ambient TRAP in real time; and (5) hyperspectral and Raman spectroscopy for characterizing the chemical composition of UFPM in rat and human brains to assess brain distribution and further inform source. Using these resources, we will address the following Aims: 1. Identify the source of UFPM in brains of TgF344-AD rats exposed to TRAP and assess the spatial relationship of UFPM to AD-relevant neuropathology in rat brains. 2. Determine whether human exposure to UFPM is associated with (a) incident cognitive impairment and AD/ADRD and (b) accelerated rate of cognitive decline. 3. Initiate exploratory studies in human AD/ADRD brain samples to determine whether UFPM in select brain regions of LDC individuals are related to AD pathology. Data from this project will identify AD/ADRD-relevant neuropathology associated with UFPM, a first step in developing mechanistic hypotheses that can be tested in future studies. Additionally, this project addresses (1) biological plausibility and clinical relevance of UFPM in air pollution as an environmental factor that modifies AD/ADRD initiation and progression and contributes to AD/ADRD racial/ethnic disparities; (2) relevance of the AD/ADRD rat model to humans exposed to UFPM in polluted air; and (3) generation of data needed to support public health and regulatory strategies for controlling key sources of UFPM associated with AD/ADRD.

NIH Research Projects · FY 2025 · 2022-09

Project Summary Myofascial pain syndrome (MPS) is a prevalent and debilitating condition representing a significant burden to society. This syndrome may occur as an isolated condition, often localized in the lower back area, or be part of more complex clinical scenarios, such as hemoglobinopathy, inflammation, cancer and trauma, that affect the myofascial unit. There is a paucity of validated biomarkers for qualitative or quantitative assessment of MPS. The objective of this proposal is to establish novel measures derived from Total-body-Positron Emission Tomography/Computed Tomography (TB-PET/CT) as quantitative biomarkers to monitor response and predict outcomes for interventions that have potential to relieve myofascial pain. The TB-PET/CT measures we will assess include those reflective of myofascial tissue metabolism, perfusion, and fatty infiltration. These processes are intimately associated with myofascial tissue dysfunction and monitoring them may provide means to assess sources of pain. Therefore, this proposal is responsive to the RFA-AT-22-003 and addresses the interest area: “Quantitative evaluation of tissue metabolism, perfusion, oxygenation, and fatty infiltration”. The condition assessed in this proposal is chronic low back pain. We hypothesize that TB-PET/CT measures will (1) offer a unique insight into myofascial tissue pathology in this condition; and (2) provide biomarkers that will associate with myofascial tissue dysfunction and response to interventions. The proposed project will have two phases. The first is the R61 phase where we will conduct an observational, cross-sectional study. In this phase we will establish the association of quantitative TB-PET/CT measures with HEAL outcome measures and will determine TB-PET/CT measures that differentiate diseased versus healthy myofascial tissue. The second phase will be the R33 phase where we will carry out a randomized, controlled longitudinal interventional study. Participants will be randomly assigned to the intervention arm or the control arm. In this phase we will determine the capability of TB-PET/CT measures to track with changes in HEAL outcome measures in response to the intervention. We have defined quantitative transition criteria that will be applied to the imaging measures in the R61 phase before introducing them into the R33 phase. Therefore, through this work we hope to establish TB-PET/CT measures as potential biomarkers for providing the much-needed objectivity, sensitivity, and precision for characterizing myofascial tissue, and as surrogate measures for dysfunction, pain and for predicting and monitoring response to interventions.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY Blood flow and cellular metabolism are two basic but vital physiological processes that are often dysregulated in major diseases. Imaging of flow-metabolism mismatch or coupling is of broad clinical and research significance in many diseases, for instance, in ischemic cardiomyopathy for assessing myocardial viability, in cancer for grading tumor aggressiveness, and in neurodegenerative diseases for studying brain function. A major challenge in PET imaging of flow-metabolism is that scanning for these two processes requires two different radiotracers–18F-fluorodeoxyglucose (FDG) for metabolism and a second flow radiotracer for perfusion imaging. While FDG is widely available in the clinic for metabolic imaging, perfusion imaging by PET is clinically limited, resulting in underutilization of flow-metabolism imaging in both research and clinics. The goal of this project is to develop a single-tracer multiparametric PET imaging solution for simultaneous flow- metabolism imaging using only 18F-FDG without the need for a second flow-specific radiotracer. Early attempts from others and our group have used FDG blood-to-tissue delivery rate (K1) as a proxy of blood flow. However, the accuracy of FDG K1 approximating blood flow largely depends on the FDG extraction fraction in tissues and is also compromised by the correlation between FDG K1 and blood glucose levels. Our preliminary work has tackled these problems specifically in the myocardium and demonstrated the feasibility of using FDG for measuring myocardial blood flow. The focus of this proposal is to extend the effort to a large study and to the whole body, and further develop the enabling techniques to improve FDG blood flow quantification. We will (1) develop glucose-normalized extraction fraction correction for FDG blood flow quantification in various organs using total-body dynamic PET; (2) develop high-temporal resolution kinetic modeling for improved FDG blood flow quantification; (3) improve FDG blood flow imaging on short PET scanners using advanced image reconstruction. Successful completion of this project will develop a new technical capability of 18F-FDG for simultaneous multiparametric imaging of blood flow and glucose metabolism with reduced radiation dose, imaging time and cost. This would also open up many new opportunities for clinical applications that require multiparametric imaging biomarkers but have been historically restricted by the accessibility of perfusion imaging, thus making a broad impact in multiple PET applications for patient clinical care and research.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY The overall goal of this K08 Mentored Career Development proposal is to provide me with the essential mentorship and career development opportunities, necessary to become an independent investigator with expertise in translational research. Kidney cancer is among the top ten most common cancers, with an estimated 76,000 new cases every year in the Uniter States. Management of patients with localized or locally advanced clear cell renal cell carcinoma (ccRCC) involves surgical resection, following which, half of the patients will have a recurrence within five years. Adoption of adjuvant therapies to lower this risk has been poor due to inconsistent results across trials. There is a lack of biomarkers to predict the recurrence risk accurately, a critical barrier in directing adjuvant therapies to this group of patients. This proposal will investigate novel translational approaches to identify patients at high risk of relapse after surgical removal of the primary kidney tumor. In Specific Aim 1, I hypothesize that a prognostic transcriptomic signature comprised of genes corresponding to electron transport chain (ETC), mitochondrial ribosomal proteins (MRP) and major histocompatibility complex-II (MHC-II) will result in stratification of localized ccRCC tumors into the two subtypes- those at risk of early relapse vs. not. In Specific Aim 2, I hypothesize that Cu-bound to mitochondrial cytochrome c oxidase (Cu-COX), measured by size exclusion chromatography inductively coupled plasma mass spectrometry will be indicative of mitochondrial respiration and will be predictive of early relapse, thus making for a simple and inexpensive biomarker. In addition, we will be evaluating the clinical relevance of different pools of copper in serum as predictors of high copper content in corresponding ccRCC tumors, thus enabling a serum-based biomarker to detect aggressive ccRCC. Data generated from this proposal will allow me to perform additional research, including validation of these biomarkers in larger studies, development of novel clinical-trials to direct adjuvant therapies in a biomarker specified population at high risk of relapse, and ultimately improve outcomes for patients with kidney cancer. University of Cincinnati, provides me collaborative opportunities with several laboratory and clinical researchers, thus making this an ideal environment to conduct my research while providing clinical and administrative support. My background in clinical and translational cancer research, including experience in collaborating with laboratory scientists and focus on biomarker development, will help me to successfully attain my short-term goals including training in the fields of cancer biology, functional genomics and bioinformatics. To this end, I have assembled a team of mentors and advisors, all of whom are expert investigators in these disciplines. To supplement my training aims, I plan on completing relevant workshops. Through the K08 Career Development Award Program, I will generate data, and enhance knowledge and skills in translational research to submit an R01 application, and ultimately transition to an independent investigator.

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY/ABSTRACT Inflammatory bowel disease (IBD) is an umbrella term for gastrointestinal (GI) diseases where chronic inflammation and its sequelae significantly impact a patient’s physical health, quality of life, and healthcare utilization. Early diagnosis of GI inflammation could prompt earlier medical intervention with a direct impact on patient’s prognosis and quality of life. There is a need for novel methods capable of detecting early and low- grade GI inflammation. The goal of this proposal is to demonstrate the feasibility of fluorescence lifetime imaging (FLIm) for detecting early colorectal inflammation in vivo. Without requiring exogenous labeling agents, FLIm is sensitive to changes in cellular metabolism, which is altered at the onset of inflammatory processes. Our specific aims focus on establishing FLIm as a research tool to quantify and monitor inflammation at the tissue level using the in vivo murine colon as a model. In Aim 1 we will (sub-aim 1.1) fabricate a side-viewing endoscopic probe for nondestructive, in situ, and in vivo intraluminal imaging of the full length of the colon and (sub-aim 1.2) show that FLIm is sensitive to epithelial metabolism using wild-type and PPAR-g knockout mice treated with antibiotic (streptomycin) to generate transient dysbiosis and with 5-ASA to protect against antibiotic effects. In Aim 2 we will test the relevance of FLIm for detecting early inflammatory changes with a model that recapitulates aspects of pre-IBD (high-fat diet and antibiotics). Using image processing and statistical analysis, we will validate the FLIm parameters with histopathology and biochemical assays (H&E, tissue hypoxia, intracellular lactate, NAD+/NADH, ADP/ATP, PDH activity) performed after necropsy (n = 6 animals/group for both male and female mice). The broad range of inflammatory responses generated with this study will demonstrate the sensitivity of FLIm as a research tool for label-free, nondestructive, in vivo intraluminal detecting and monitoring the host response to GI inflammation. Results from this research are expected to provide convincing preliminary data for subsequent R01-type research grant applications that build on the proposed concept. The long-term goal of the PI is to establish FLIm as a nondestructive and label-free, in situ and in vivo, mesoscopic imaging modality to study 1) pathogenesis and treatment of GI inflammation over time, 2) the host-microbiota relationship with pharmacological and dietary changes, and 3) to translate this approach into a clinical tool for in vivo endoscopic imaging of the human GI tract. We anticipate that the applications of the proposed implementation of FLIm range from early detection of inflammatory and infectious diseases and cancer to the close monitoring of pharmacological and nutritional treatments on the GI tract.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY/ABSTRACT Hemorrhage from intra-abdominal injuries (IAI) is a leading cause of traumatic deaths in children. Several consensus panels have placed management of injured children as a high research priority. Many children with IAIs have subtle symptoms, making the diagnosis difficult, and missed or delayed diagnoses result in increased morbidity. The combination of limited scientific evidence and concern over missing IAIs has resulted in excessive use of abdominal computed tomography (CT). CT is highly accurate in diagnosing IAIs, decreases the level of clinical monitoring required, and is an important factor in determining the need for surgical treatment. CT scanning also presents risks to children, however, most notably radiation-induced malignancies. Thus, compelling reasons exist to both aggressively evaluate injured children for IAIs and to limit abdominal CT evaluation to just those at non-negligible risk. Abdominal ultrasonography can help focus patient evaluation in just this manner by potentially decreasing abdominal CT use in low risk children. The focused assessment with sonography for trauma (FAST) examination uses abdominal ultrasonography to detect the presence of intraperitoneal fluid in injured patients. Use of the FAST examination has primarily evolved in injured adult patients and two randomized controlled trials (RCT) in injured adults demonstrate that an evaluation strategy including the FAST improves multiple aspects of patient care including safely decreasing abdominal CT use. Limited and conflicting data, however, exist in the pediatric population on the utility of the FAST examination. A large multicenter, observational study suggests FAST safely decreases abdominal CT use in children considered low risk for IAI. The only RCT in children was a single center study that demonstrated FAST use significantly decreased clinician suspicion of IAI following a negative FAST. This decrease in clinician suspicion, however, did not translate to a decrease in CT use. The conflicting results from these studies strongly suggest the need for a multicenter RCT powered to definitively answer this critical question. The long- term objective of the research is to determine appropriate evaluation strategies to optimize the care of injured children, leading to improved quality of care and a reduction in morbidity and mortality. The specific aims of this proposal are to: 1) perform a RCT of the FAST examination in injured children and compare the frequency of abdominal CT scanning between children in the FAST and non-FAST arms; 2) identify if an evaluation strategy including the FAST examination results in similar numbers of missed or delayed diagnosis of IAIs than a strategy without the FAST examination; and 3) identify patient, physician, and system factors associated with obtaining abdominal CT scans in patients considered very low risk for IAI by the clinician after a negative FAST examination. This study will enroll a large sample size (3,180 children) at six diverse sites, and the results will provide definitive evidence for the role of the FAST examination in children with blunt torso trauma.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY / ABSTRACT The goal of this proposal is to improve our fundamental understanding of speech production, and to translate this knowledge into medical devices called intracortical brain-computer interfaces (iBCIs) that will enable people who have lost the ability to speak to fluently communicate via a computer just by trying to speak. The study will enroll participants who have lost or are actively losing their ability to as part of the ongoing BrainGate2 clinical trial (a multi- site trial investigating the feasibility and safety of iBCIs in people with paralysis.) We will place four chronic 64- channel silicon microelectrode arrays in speech areas of cortex and use simultaneously recorded speech (or attempted speech) data and action potential-resolution neural data to characterize and decode in real time the link between neural activity and speech production. A key advance of this approach is our ability to record simultaneously from hundreds of individual neurons. This will provide a much more detailed view of the underlying neural computations at their fundamental resolution – spikes – and much higher signal-to-noise ratio signals for decoding attempted speech. The project is divided into two research areas. First, we seek to understand how networks of neurons in two closely interacting cortical areas – ventral (speech motor) precentral gyrus (PCG) and superior temporal gyrus (STG) – generate speech. These areas have not previously been recorded from at scale with single neuron resolution and characterizing their dynamics will be critical for designing an effective speech iBCI. We will examine “what” parameters of speech neurons in these two areas encode, and “when” during the preparation and production of speech different neural computations occur. We will apply cutting-edge dynamical systems and “neural population doctrine” analysis approaches to disentangle various components of neural activity (e.g., motoric, sensory feedback, error-processing) that are distributed across neurons. Second, we will apply state-of-the art artificial intelligence (AI) and control theory- inspired iBCI methods to translate the neural activity that accompanies the person’s attempt to speak into words that appear on a computer (“Brain-to-Words”) and directly into sound (“Brain-to-Voice”). Brain-to-Words, in which speech units such as phonemes are decoded from a slightly delayed window of neural activity, is more constrained because the final output is whole words (which could then be spoken by the computer), without the full richness of the person’s voice. However, it allows for powerful AI techniques to be applied to automatically correct for errors based on the known statistics and rules of language. Brain-to-Voice can potentially restore the full expressive range of speech but requires higher accuracy for intelligible real-time voice synthesis. However, we hypothesize that control theory-based iBCI design and the brain’s immense ability to learn motor tasks will lead to high performance. The two project goals work in concert: achieving the most detailed understanding to date of how neural ensembles produce speech will equip us with the insights needed to develop a medical device that allows people to speak again with speed and accuracy approaching that of able-bodied performance.

NIH Research Projects · FY 2025 · 2022-09

Project Summary Microbial production of fucosylated human milk oligosaccharides This proposed project aims to establish efficient and specific microbial production processes for human milk oligosaccharides (HMOs). HMOs are potent bioactive compounds that modulate neonatal health and are of interest for development as potential drug treatments for adult diseases. HMOs are a class of over 200 compounds present at 20-23 g/L in colostrum and 12-14 g/L in mature milk. Unlike their common precursor lactose, HMOs are indigestible by human infants and instead improve neonatal health by serving as effective antimicrobials and antivirals, prebiotics, and regulators of inflammatory immune cell-response cascades. These and other potential benefits of HMOs make them attractive targets of study for preventing or treating diseases in both children and adults. β1−3-Linked galactosides Galβ3GlcNAcβOR, which are called Type 1 glycans, are major HMO components found in more than 100 HMOs. Among the 20 HMO core structures that have been identified, 11 contain at least one Type 1 glycan-terminated branch. Lacto-N-tetraose (LNT, Galβ3GlcNAcβ3Lac) is the simplest Type 1 glycan HMO. LNT and its fucosylated derivatives are among the most abundant HMOs. While Type 1 glycan structures are predominant in human milk, they are less abundant (and sometimes completely absent) in the milk of other mammals. Investigating the biological functions of individual Type 1 glycan-containing HMOs and their potential applications as prebiotics and antimicrobials requires access to sufficient quantities of these structurally defined compounds. The potential of these molecules, their limited access from natural sources, and difficulty in large-scale isolation of individual HMOs for studies and applications have motivated the development of novel production methods. Chemical and in vitro enzymatic syntheses of HMOs based on current methods are expected to be costly for industrial-scale synthesis. Whole cell biocatalysts are emerging as alternative self-regulating production platforms that have significant potential to reduce the production cost of HMOs. Short-chain, linear and small monofucosylated HMOs have been produced in whole cell biocatalysts, but structures with higher complexity have not been explored. In this proposed project, we will establish a strategy for producing fucosylated HMOs including lacto-N-fucopentaose II (LNFP II), lacto-N- fucopentaose I (LNFP I) and lacto-N-difucosylhexaose I (LNDFH I) from lactose and L-fucose in live engineered Escherichia coli cells. Notably, we will develop an innovative method to control the order and the site of glycosylation in whole cell systems to lay the groundwork for future microbial production of other complex HMOs.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY Improvements in health care access and infection control have led to life expectancy increases in Low- and Middle-Income Countries (LMICs) in Latin America. As the population ages, the Latin American cancer burden has dramatically increased. By 2030, Latin America is expected to have annual averages of 1.6M new cancer cases and 1M cancer deaths. A Latin America Lancet Oncology Commission report highlighted the small amount of preclinical and clinical oncology research originating in the region as a limitation to control cancer burden. Colombia and Peru, the Latin American LMICs with the first and second largest populations, have state-funded national cancer institutes (NCIs) that are cancer treatment reference centers, and which lead national efforts in cancer control and care. However, cancer risk assessment and patient treatment at these institutions is primarily based on tools developed in North American and European patients. Despite having exceptional researchers and physicians, most cancer centers in Latin America lack training programs that would allow them to develop or adapt precision prevention or treatment tools that are appropriate to the ancestry or mutation profiles of individuals from the region. The current funding opportunity is the ideal program to formalize and enhance ongoing collaborations between US-based healthcare researchers and providers in Colombia and Peru. It will provide a solid foundation for precision oncology research knowledge transfer and to build local human capital necessary to develop precision cancer medicine in Latin America. Building on our extensive expertise on Latin American population demography, cancer epidemiology and genetics, NIH funded cancer studies in Latino populations, and a strong track record of research collaboration and training with Colombian and Peruvian researchers, the overall goals of the UC Davis Multidisciplinary Cancer Research Training Program to Advance Precision Cancer Prevention and Care in Latin America are to: 1) Enhance local capacity for precision cancer medicine research in Colombia and Peru by implementing a curriculum that complements and addresses gaps in local training programs and provides hands on experience and support for research project development relevant to the region, 2) Provide hands on training on research resource development including ethics training, biobanking best practices, and cloud-based bioinformatics; and 3) allocate pilot funding for mentored research for basic science and clinically-oriented term trainees. We propose to establish a curriculum to train graduate students and postdoctoral/clinical fellows in precision oncology research. We will prepare trainees to implement and share their new skills in their home countries and to collaborate with U.S-based investigators. We will leverage ongoing collaborations among the program Principal Investigators, universities, and NCIs of Colombia and Peru to identify relevant areas of research that could be enhanced by the training program.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract A major advantage of coincidence detection of annihilation photons from positron-emitting radiotracers is the availability of time-of-flight (TOF) information, and the ability to measure TOF differences to better localize the positron emitter. Normally for positron emission tomography (PET), TOF information is used as a weighting kernel during image reconstruction and results in an effective sensitivity gain that can be used to reduce radiation dose, improve signal-to-noise ratio, or reduce scan duration. The magnitude of these benefits depend on the TOF resolution, which is governed by the timing performance of the detectors. Current state of the art for PET scanners is ~220 ps which corresponds to a localization of ~3.3 cm. A transformational change would occur, however, if a TOF resolution of <30 ps could be achieved. This would localize events within 4.5 mm, allowing images to be directly generated without a reconstruction algorithm at a spatial resolution that matches what is achieved in clinical PET scanners today. We refer to this as direct positron emission imaging (PEI). With this superb TOF resolution and reconstruction-free imaging, we enter a new regime where we expect major increases in image signal-to-noise, both due to the additional TOF information, and the removal of noise amplification inherent in reconstructing noisy data with noisy corrections from projection data. We propose to develop a first proof-of-concept imaging system that uses ultra-fast detectors to directly produces cross-sectional images without reconstruction and to quantify the performance of PEI both through simulations and experimentally. Since direct PEI does not have the same sampling constraints for data collection as PET, it creates opportunities for portable, and flexible imaging devices, with implications for patient-tailored or task-specific imaging applications (i.e. cardiac or breast imaging), as well as open designs for general purpose applications. To achieve the unprecedented TOF capabilities needed for direct PEI, we will exploit promptly emitted Cerenkov radiation that is generated with <10 ps in certain materials, including scintillators, in response to a 511 keV photon interaction. Our proposed novel detector design integrates a Cerenkov radiator directly into the entrance window of an ultra-fast microchannel plate photomultiplier tube, which is the fastest photon detector currently available with a response time of 25 ps. This approach eliminates all optical reflections between the point of light generation and the photocathode, preserving the prompt timing nature of Cerenkov photons. We then combine the integrated Cerenkov radiator detector with auxiliary photodetector read-out for robust coincidence detection, and complement this with advanced signal processing algorithms we have pioneered using convolutional neural networks to extract all possible timing information from the digitized detector waveforms and ultimately to perform reconstruction-free imaging using only the digitized waveforms as input. In summary, we aim to prove that direct PEI is possible, to characterize its properties and to provide the technological and algorithmic foundations for eventual translation for human imaging.

NIH Research Projects · FY 2026 · 2022-09

PROJECT SUMMARY The applicant seeks this Administrative Supplement in relation to her R00 award, which examines the association between regional tau deposition and domain-specific cognitive decline given that pathological and clinical evidence of Alzheimer’s disease converges to suggest that both episodic and semantic memory are vulnerable years before the onset of dementia. During the K99 phase, she examined how regional tau deposition relates to episodic and semantic memory decline in two large cohorts consisting of Aβ- clinically normal (CN), Aβ+ CN, and Aβ+ mild cognitive impairment (MCI) individuals. Episodic and semantic memory were measured by traditional neuropsychological test scores as well as innovative spoken language features of cognition extracted from recordings of in-person neuropsychological assessments. The applicant received training in three areas critical to her independence: (1) longitudinal study design and analysis in Alzheimer’s disease, (2) amyloid and tau PET imaging, and (3) spoken language features of cognition. She also received guidance from her expert mentorship team who has an established record of mentoring junior scholars to full independence, and obtained comprehensive training through a detailed training plan. Her research aim, in combination with the training and mentorship she received, prepared her for independence by the R00 phase as evidenced by her transition to an tenure-track Assistant Professor position in the Departments of Radiology and Neurology at UC Davis. During the R00 phase, she will examine the relation between regional tau deposition and domain-specific cognitive decline assessed frequently through smartphones, an increasingly ubiquitous platform. Specifically, she will administer verbally based mobile cognitive tests and assessments of mood every 3 months for 1 year to Aβ- CN, Aβ+ CN, and Aβ+ MCI individuals with tau PET data. Episodic and semantic memory will be measured by neuropsychology scores and spoken language features extracted from structured responses captured in the real world. Thus, the K99/R00 award tests the overarching hypothesis that where tau deposition occurs in the brain relates to domain-specific cognitive decline. This knowledge will improve the accuracy of Alzheimer’s disease diagnosis as well as enhance the screening and monitoring of those at risk for dementia. Completion of the R00 phase will generate data to support a future R01 application integrating multimodal imaging and spoken language features extracted from passively collected unstructured voice recordings that maximize ecological validity and minimize participant burden. This approach can also be applied to Alzheimer’s disease and related dementias more broadly. The K99/R00 award has provided the applicant with a platform to launch an independent career and this Administrative Supplement will ensure research continuity and retention after the applicant’s critical life events.

NIH Research Projects · FY 2025 · 2022-09

Acute organophosphate (OP) intoxication, resulting from chemical warfare, industrial accidents, and intentional exposures, remains a significant global health crisis, leading to substantial morbidity and mortality. Survivors can quickly develop status epilepticus (SE), which may progress to spontaneous recurrent seizures (SRS), cognitive impairments, and chronic neurological dysfunction. Current standard of care (SOC) treatments, including atropine, pralidoxime (2-PAM), and midazolam (MDZ), improve acute survival but often fail to prevent SE progression, the onset of SRS, and long-term impairments. This is especially concerning during adolescence, a critical period of neurodevelopment and evolving seizure susceptibility, yet little is known about how OP intoxication and SOC treatments, including MDZ, affect disease progression. Additionally, while prolonged acetylcholinesterase (AChE) inhibition has been linked to elevated seizure burden in adult models, its recovery trajectory during adolescence remains poorly understood, along with its relationship to seizure development, benzodiazepine efficacy, and cognitive deficits. To address these gaps, we propose a first-of-its-kind longitudinal study investigating acute OP intoxication in adolescent rats (postnatal day 35) using clinically relevant outcome measures. This study will systematically assess the natural history of seizure development, changes to neural oscillatory activity, and cognitive function over an eight-week period following acute diisopropylfluorophosphate (DFP) intoxication, while also evaluating the effects of SOC with and without MDZ. In parallel, we will track AChE suppression and its recovery profile to determine its relationship with SRS development and learning and memory impairments. We hypothesize that DFP intoxication during this developmental period will result in SE, the emergence of SRS, persistent disruptions to network oscillations, and cognitive deficits. Furthermore, we expect that while MDZ treatment will mitigate SE-related mortality, it will have minimal impact on the long-term trajectory of disease progression. Finally, we anticipate that AChE recovery will be prolonged during adolescence, with delayed restoration correlating with greater seizure susceptibility and cognitive deficits, revealing a critical mechanistic link between cholinergic dysfunction and behavioral alterations. This study will establish the first comprehensive model of acute OP intoxication during adolescence, providing key insights into age-dependent vulnerability, treatment efficacy, and long-term sequelae. By aligning this model with previously established adult paradigms, these findings will directly inform more effective treatment strategies, guiding the identification of targeted countermeasures that consider both age and sex as key variables.

NIH Research Projects · FY 2024 · 2022-09

Project Summary/Abstract Spoken language rapidly conveys information over time. Current theories hold that listeners make continuous predictions about the importance and the timing of information as it arrives. Prior psycholinguistic studies have investigated whether listeners pre-allocate attention to points in time when important information is predicted to occur, but the results have not been consistent, and the underlying neurocognitive mechanisms remain unclear. Non-linguistic studies of auditory and visual perception have shown that people use temporal predictions to guide attention in time to behaviorally relevant events. This is achieved through two primary mechanisms: rhythm-based and memory-based predictions. This proposal will take an interdisciplinary approach, by investigating the role of these perceptual temporal attention mechanisms in language comprehension through a psycholinguistic theoretical framework. Candidate sources of temporal prediction in language are the rhythmic regularity of speech (the alternation of stressed and unstressed syllables) and discourse cues (introduced by the linguistic context). This project will contribute to the lively contemporary debate in speech neuroscience concerning the importance of neural entrainment, a mechanism of temporal prediction. There are three specific aims: (1) Examine if rhythm-based temporal predictions arise from greater rhythmic regularity in speech. (2) Determine whether memory-based temporal predictions are elicited by discourse cues. (3) Elucidate the respective effects of speech rhythmic regularity and discourse cues on semantic processing, a core component of language comprehension. Two experiments will employ electrophysiological (EEG) measures of neural activity to characterize these mechanisms. The fellowship applicant’s primary training goal is the acquisition of electrophysiological skills for cognitive neuroscience research, including experimental design, data collection, analysis and interpretation. She will be supervised by sponsors Drs. Mangun and Swaab, world leaders in the use of EEG methods to study attention and language, respectively. Dr. Mangun is the Director of the UC Davis Center for Mind and Brain (CMB), an acclaimed hub for research, methods development, and training using EEG to study cognition. The applicant will benefit from the rich research and training environment at the CMB, including the NIMH-supported summer training programs in electrophysiology (led by consultant Dr. Luck) and cognitive neuroscience (led by Dr. Mangun). She will also be trained in computational modelling by the consultants Drs. Oganian and Breska during a 3- month visit to Tübingen, Germany. This project will provide a better understanding of the role of temporal prediction and attention in language comprehension, contributing to theoretical models and methodological advancements in the cognitive neuroscience of language by reconciling diverging lines of research. Elucidating the role of temporal prediction in language comprehension in healthy individuals is vital for understanding the cognitive-neural bases of language disorders, which will inform the development of effective forms of therapy.

NIH Research Projects · FY 2025 · 2022-08

Although highly effective, biologics targeting IL-23/Th17 axis should be continuously injected to suppress recurrence of psoriasis. My long-term goal is to cure psoriasis without recurrence guided by personal immune tolerance. The overall objectives in this application are to (i) identify regulatory immune cell interactions induced by anti-IL-23p19 antibody administration in the skin of patients whose psoriasis is cleared without recurrence and (ii) develop pre-treatment predictive models for psoriasis patients that anticipate disease recurrence after short-term anti-IL-23p19 antibody injection. The central hypothesis is that IL-23p19 inhibition promotes regulatory immune cells in psoriasis patients whose disease is cleared without recurrence, and their pre-treatment single-cell immune signatures are different from those of patients whose disease recurs. The rationale for this project is that molecular evidence of immune tolerance induction by IL-23p19 inhibition in human skin is likely to offer a strong clinical framework whereby new strategies to prevent recurrence of chronic inflammatory diseases can be developed. The central hypothesis will be tested by pursuing two specific aims: 1) Testing the hypothesis that regulatory immune cell interactions are promoted by short-term anti-IL-23p19 antibody administration in the skin of psoriasis patients whose disease becomes clear without recurrence; and 2) Developing predictive models with pretreatment skin biopsy single-cell genomic data that anticipate long-term disease clearance off drug after short-term anti-IL-23p19 antibody administration. To achieve the specific aims, we have recently developed two innovative complementary single-cell approaches to obtain gene expression profiles of heterogeneous immune cells from psoriasis and control skin without enzyme digestion. The first single-cell experimental approach is microfluidic partitioning of emigrating cells from human skin after 48-hour incubation in culture medium without enzyme digestion, which empowers single-cell transcriptomic profiling of heterogeneous immune cells and keratinocytes in different layers of epidermis under ex vivo condition. The second single-cell experimental approach is Combinatorial indexing RNA sequencing, developed by the co-mentor of the proposal, which enables co-profiling transcriptome and single-cell chromatin accessibility. At the completion of the proposed research, our expected outcomes are to have novel single-cell genomic techniques to study immune cell interactions in human skin, defined single-cell gene signatures of regulatory immune cells that are promoted by anti-IL-23p19 antibody administration in psoriasis skin, and the ability to elucidate how pathologic immunity is suppressed at the single-cell level by highly effective biologics. We also expect to have pre-treatment biomarkers that can predict long-term disease clearance off drugs after short-term anti-IL-23p19 antibody administration.

NIH Research Projects · FY 2025 · 2022-08

Aging is a hugely variable process. Some people age well, with sustained memory, generally positive emotional experiences, healthy social relationships, and good physical health into old age, while others experience significant age-related detriments to both psychological and physical health. Predicting who is vulnerable to poor aging outcomes and specifically to Alzheimer’s disease and Alzheimer’s disease-related dementias (AD/ADRD) is critical for developing early interventions and deploying treatments in a timeframe in which they are most efficacious. Nonhuman primate models have long been used to understand the causal biological mechanisms underlying aging trajectories and vulnerability to AD/ADRD pathology, with the goal of developing treatments and interventions to promote human health. Such research is particularly challenging because the experimental testing in these domains requires extensive training (typically 6-18 months), precluding the use of large samples that would allow for genetic studies or studies of naturally occurring variation. The proposed project is inspired by human literature which has a number of quick, resource-light screening tools for psychological health across the lifespan, of which the Mini Mental State Examination (MMSE) is one of the most popular to predict cognitive aging outcomes and are predictive to the presence/occurrence of AD/ADRD. The proposed work develops a monkey version of MMSE (the mMMSE) – a high throughput screening tool to measure cognitive functions across a variety of domains as well as social and affective processing which are broadly implicated as behavioral and psychological symptoms of dementia. Validity will be established via “gold standard” time-intensive tasks across psychological domains. This tool will allow for rapid cognitive assessment for large sample studies correlating biomarkers of neurodegenerative disease risk with functional status, identification of subgroups of vulnerable monkeys, and enhanced maintenance of aging nonhuman primate colonies by identifying monkeys at risk of poor health. Understanding nonhuman primate aging trajectories and developing interventions to promote their well-being is critical to maintain colonies of aging monkeys as a national resource and also to have those monkeys be appropriate animal models for the study of human health and age-related diseases like AD/ADRD.

NIH Research Projects · FY 2025 · 2022-08

Violent aggressive behavior in children has life-long consequences for perpetrators, victims, their families, and society. Yet the biological bases of juvenile aggression remain largely unknown. This gap in knowledge persists due to a lack of tractable models in which juvenile aggression can be readily observed and manipulated. The proposed project takes an innovative, integrative approach to address this pressing knowledge gap using a novel animal model. Alongside the experimental tractability of classic fish and amphibian models, poison frog juveniles are highly aggressive, providing a powerful opportunity to understand the genomic bases of juvenile aggression. We test the central hypothesis that distinct mechanisms mediate the acute performance of, propensity for, and consequences of aggressive experiences. We pursue two complementary research directions to (1) uncover the mechanistic bases of individual variation and developmental shifts in aggression, and (2) probe the genomic and behavioral consequences of aggressive experiences for both perpetrators and victims. To optimize risk and reward, we tackle these questions from multiple angles, combining unbiased, exploratory approaches with characterization and manipulation of canonical candidates important for social behavior across vertebrates, including humans. Experiences of aggression have long-lasting individual and societal consequences and mechanistic research will have a significant positive impact by illuminating causes, consequences, and potential treatments for violent aggression among the youngest members of our society.

NIH Research Projects · FY 2025 · 2022-08

Adolescence is a complex time of heightened self-consciousness, risk taking and peer orientation which may be especially challenging for teens diagnosed with autism spectrum disorder (ASD). Longitudinal magnetic resonance imaging (MRI) studies of children with ASD that begin at diagnosis and extend into adolescence are extremely rare. This is a critical gap since adolescence is also a period of profound brain changes. The MIND Institute Autism Phenome Project (APP) was initiated in 2006 to discover multilevel phenotypic information enabling definition of clinically meaningful subtypes of ASD. Nearly 300 families have completed an initial assessment with successful MRI. The APP includes autistic children with all severity levels and co-occurring conditions such as anxiety and intellectual disability. Children with ASD and age-matched typically developing controls had their first MRI at 2-3.5 years of age and up to 3 additional scans between ~4 and ~12; 773 MRI scans have been acquired. We propose to extend this study to a 5th time point in middle adolescence (14-17 years). A guiding theme of this research is that different trajectories of brain development will differentiate subsets of children with ASD and some of these differences will become most apparent as the child enters adolescence, which coincides with pubertal development. Because we have carried out pediatrician-based Tanner staging at multiple time points, we will be able to evaluate how puberty influences the emergence of these developmental brain differences across all aims. Capitalizing on the large amount of longitudinal structural MRI data acquired to date, we will use structural covariance analysis and other network level strategies to evaluate developmental differences in gray matter structure across several domain specific networks. Focusing on intrinsic connectivity networks implicated in the triple network model of autism, we predict reduced magnitude and extent of salience and central executive networks in ASD and greater extent with anterior-posterior decoupling in the default mode network. The amygdala is a brain region consistently reported to be altered in ASD. Our previous MRI and postmortem research indicate that there is an abnormal trajectory of amygdala growth in autism with enlargement early on and atrophy in adolescence. We will investigate longitudinal growth of the amygdala to test the hypothesis that it undergoes atrophy in adolescence in ASD. We hypothesize that this preferentially involves those with a form of co-occurring anxiety disorder and is different from teens with anxiety but not ASD. We will also address the critical under-studied question of what neural alterations differentiate children with ASD with, and without, intellectual disability. We will investigate the maturation of brain regions and networks associated with intellectual and language function to explore differences between children with ASD and low verbal/cognitive performance from those with normal verbal/cognitive performance. Finally, we will evaluate trajectories of autism severity change into mid adolescence and explore the neurobiological underpinnings of these changes. We predict that persistent alterations in the salience network will be associated with increased severity over time.

NIH Research Projects · FY 2025 · 2022-08

Project Summary    This proposal investigates the underlying causes of human ocular diseases using mouse  models. Proposed experiments will use complex in vivo conditional (cre-­lox) mouse genetics,  mouse transgenics, histology, immunohistochemistry, confocal microscopy, in situ hybridization,  mouse embryology, single-­cell NEXTgen sequencing, bioinformatics, BAC recombineering,  qPCR, and PCR technologies to address basic, mechanistic questions about optic stalk-­disc  development and astrocyte differentiation.  The Pax2 transcription factor initiates expression in  all optic vesicle cells, but becomes progressively restricted to only the forming optic disc and  stalk.  Consistent with its role in other embryonic tissues, we will test a hypothesis that Pax2  shuts off neural/retinal progenitor gene programs, via global interactions with cell epigenetic  machinery.  This activity initially restricts ocular cells to an astrocytic progenitor cell (APC) fate,  regulates their rate of cell division, and initiates glial gene expression profiles.  In Aim 1, we will  test evolutionarily-­conserved Pax2 noncoding sequences as long-­sought optic disc-­nerve  enhancer(s) by creating a new Pax2-­Cre driver. This tool will be used to conditionally remove  Hes1 and assess the consequences to optic stalk development, APC differentiation and mature  astrocyte functionality.  For Aim 2, we will take advantage of previously characterized Rax-­Cre  BAC transgenic mouse line, Pax2GFP knock-­in and new Pax2 floxed allele to follow the ocular  GFP lineages in control and Pax2 conditionally mutant cells.  We will also generate and  compare the gene expression profiles of Pax2 E11 and E12 heterozygous and homozygous  mutant eyes.  Here we will use single-­cell RNA sequencing and the growing wealth of publicly  available information regarding chromatin configurations, and mRNA expression levels during  the normal development of mouse ocular cells.

NIH Research Projects · FY 2025 · 2022-08

A distinguishing feature of the mammalian neocortex is its remarkable ability to change over a lifetime, particularly during early development. The development of cortical fields and their connections is highly dependent on the incoming sensory inputs they receive from the various sensory organs, such as the eyes and the skin. This input, together with the unique combinations of sensory information available in the environment shapes the neocortex to generate optimal behavior. We know from previous studies in our own laboratory that very early loss of input from the eyes leads to massive changes in the brain, such that all of what would normally be the primary visual cortex (V1) contains neurons that respond to somatosensory and auditory stimulation. This reorganized V1 receives ectopic input from thalamic nuclei and cortical fields associated with somatosensory and auditory processing. The current proposal addresses several fundamental questions raised by these previous findings: 1) How does the age of onset of blindness differentially impact cortical connectivity? 2) What are single-neuron response properties in reorganized V1 and S1, and does age of blindness onset impact these properties? 3) What is the relationship between functional and anatomical changes in V1 and S1 and compensatory behaviors mediated by the spared sensory systems? Our animal model, the short-tailed opossum, is highly altricial at birth (equivalent to embryonic day 11 in the mouse), allowing ex utero manipulations to the nervous system at developmental time points that would be in utero in other mammals. In these experiments, bilateral enucleations will be made at specific developmental milestones: 1) Prior to the onset of spontaneous activity in the retina, before retinal ganglion cells have reached their subcortical targets, and before thalamocortical axons have innervated the neocortex; 2) When spontaneous activity in the retina is present and retinogeniculate and thalamocortical axons have innervated their targets; 3) Just after eye opening, when sensory driven activity in the retina is present and thalamocortical and corticocortical connections have formed. Following enucleations, animals will be assessed at several different time points. These studies are novel in scope in that they interrogate how the of age of vision loss affects the reorganization of brain circuits and behavior, and if functional and anatomical changes to the neocortex are linked to compensatory behavior. These data can direct therapeutic interventions (e.g. tactile training based behavior), and even allow predictions for behavioral outcomes following retinal implants or gene targeted therapies performed at different ages.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT Obesity is associated with serious medical complications and responsible for a rising percentage of health care costs in the United States. While most anti-obesity drugs in the market work by suppressing appetite, increasing energy expenditure by stimulating thermogenesis is an alternative strategy. Humans and mice both possess constitutively active and inducible thermogenic fat, commonly called brown and beige fat. While Uncoupling Protein 1 (UCP1) has long been considered essential for non-shivering thermogenesis in adipose tissues, recent studies have demonstrated UCP1-independent thermogenic mechanisms, and they may be especially important in beige fat. We recently identified the endoplasmic reticulum (ER) membrane protein Nnat as a novel inhibitor of adipocyte thermogenesis and have shown that its effects on thermogenesis are UCP1-independent. We hypothesize that Nnat in adipose tissue plays a key role in controlling thermogenesis and glucose homeostasis. In Aim 1, we will characterize the regulation of systemic energy metabolism by adipose tissue Nnat. In Aim 2, we will investigate the mechanistic basis of Nnat action and will examine its interactions with the ER calcium pump SERCA and other possible ways that Nnat can impact thermogenesis. These studies will produce new insights into the control of adipose tissue thermogenesis and potentially lead to new strategies for anti-obesity therapy.

NIH Research Projects · FY 2025 · 2022-08

Project Summary/Abstract Rho family small GTPases are key regulators of activities such as cell migration, gene transcription, growth, and survival, processes initiated by signaling through diverse sets of molecules including cytokines, growth factors, and GPCRs. Dbl family Rho guanine-nucleotide exchange factors (RhoGEFs), including around 70 members, are critical activators of signaling by GTPases such as Rac, Cdc42, and Rho. RhoGEFs are multi-domain proteins that frequently function as signaling scaffolds at cell membranes and play roles in regulating other signaling pathways, a feature conferred by their complex architecture and the fact that each member has a unique domain composition. As major players in processes underlying cell migration and division, several RhoGEFs are strongly implicated in cancer. Despite their clinical importance, these proteins are vastly understudied at the molecular level from a whole-molecule, mechanistic perspective, and there are no therapeutic inhibitors that target these enzymes. Our laboratory is pioneering the study of full-length RhoGEFs and mechanisms in their regulation at lipid membranes, using cryo-EM as a major approach. Our long-term goal is to understand the complex, multi-component mechanisms behind Dbl RhoGEF signaling and regulation. Within this family, the phosphatidylinositol 3,4,5-trisphosphate (PIP3)-dependent Rac exchanger (P-Rex) subfamily, including P-Rex1 and P-Rex2, act as important regulators of cell migration. Both isoforms have been associated with human cancers, wherein they act as pro-metastatic factors. P-Rex2 is commonly mutated in breast cancer and melanoma, with mutations distributed throughout the protein. One study identified it as one of the most mutated genes in human metastatic melanomas. Altogether, data support that P-Rex is an important signaling molecule implicated in disease and a suitable therapeutic target. However, even though P-Rex was discovered over 15 years ago, the molecular details of its regulatory mechanisms are still not fully understood. P-Rex proteins are hypothesized to be autoinhibited in their inactive, non-signaling states and activated in multi- step mechanisms. They are activated by binding membrane-tethered G protein b and g subunits, downstream of GPCR signaling, and by binding cell membrane lipids, including the lipid PIP3. Additionally, P-Rex acts as a signaling scaffold in various cellular contexts by binding to signaling proteins like PKA and PTEN, resulting in changes in activities of P-Rex and the binding partner. Our long-term goal is to understand how different RhoGEFs transition between the basal and fully active states and how this transition is regulated, starting with the P-Rex subfamily. Furthermore, we will determine how these proteins act as signaling scaffolds at the cell membrane. Using nanodiscs, we will study the multi-valent interactions of RhoGEFs with lipids and regulatory molecules, giving us unprecedented insight into these signaling complexes. Mechanistic hypotheses will be tested in vitro and in cancer cell lines. Once important regulatory surfaces are identified, we will target these via rational design of therapeutic molecules.