University Of California Berkeley

NIH Research Projects · FY 2026 · 2023-03

ABSTRACT Protein synthesis, or translation, connects genotype to phenotype in all forms of life. The Cate lab has a longstanding interest in the mechanisms of protein synthesis, from universal principles gleaned from bacterial translation to the basis of translation regulation in humans. This application tackles fundamental questions about how translation is regulated in humans. We propose to explore the regulation of translation initiation in specific cells and tissues, and mechanisms of translation elongation that affect the speed and accuracy of the ribosome. We think these two broad lines of investigation will lead to many discoveries about protein synthesis that could eventually be leveraged to treat human disease. The canonical mechanism of translation initiation in eukaryotes involves many general translation initiation factors. We recently discovered that one of these–eukaryotic initiation factor 3 (eIF3)–serves specialized roles to either activate or repress the translation of specific mRNAs. We also found that eIF3 unexpectedly includes its own 5’-m7G cap binding subunit. In this application, we will probe how and when eIF3 carries out its specific regulatory functions. We will use molecular and structural approaches to decipher how eIF3 and trans-acting factors interact with structured RNA elements to regulate the translation of specific mRNAs. We will also examine the role of eIF3 in regulating translation in activated T cells. Finally, we will determine how eIF3 regulation of T cell receptor translation affects T cell development. Answers to these questions will reveal fundamental insights into translational control and will provide a foundation for future engineering of improved cell-based immunotherapies. Protein targets for many human diseases remain “undruggable” due to their underlying biochemical functions and behavior. These limits to small molecule drug discovery hold back the promise of developing affordable therapeutics. We recently showed that small molecules that bind the ribosome can selectively stall the translation of human proteins, revealing an entirely new mechanism of action that could enable targeting previously “undruggable” proteins. These drug-like compounds directly and selectively modulate the translation of specific nascent polypeptides during translation elongation or termination. We also found these compounds impact ribosome quality control pathways. We will explore whether similar mechanisms are employed by cellular metabolites to regulate the translation of specific mRNAs. We will also map new ribosome quality control pathways that target translation frameshifting, a process sensitive to the mechanisms employed by the drug-like compounds to selectively stall translation. Taken together, these experiments will provide new molecular insights that could aid in the design of new small molecule modulators of human translation.

NIH Research Projects · FY 2026 · 2023-03

PROJECT SUMMARY Everyday experience requires humans to make plans in a hierarchical fashion, so they can anticipate visual events that might occur seconds, minutes, hours, or longer in the future. For example, when walking through a city, individuals must track their immediate surroundings (e.g., the movement of pedestrians around them), intermediate sub-goals (e.g., landmarks along their route), and long-timescale goals (e.g., their final destination). Despite the ubiquity of such hierarchical anticipation in behavior, it is unclear how the brain can simultaneously anticipate events at multiple timescales. Our aim is to uncover the mechanisms underlying hierarchical anticipatory signals in the brain’s visual system, by determining how these signals form, what they represent, how they are updated, and how they guide future-oriented behavior. This will be accomplished with functional magnetic resonance imaging (fMRI), neuropsychological studies, naturalistic stimuli, computational models, and sophisticated analytic approaches for characterizing the dynamics of brain activity. These methods will determine the conditions under which the visual system generates hierarchical anticipatory signals, the content and flexibility of those signals, how they arise, and their consequences for behavior. Aim 1 will establish how hierarchical anticipatory signals form and what they represent. We hypothesize that such hierarchical anticipation depends on input from memory systems, is informed by pre-existing schema, and is flexible in the visual features and timescales represented. Aim 2 will determine how hierarchical anticipatory signals may be affected by top- down goals to simulate the future, and how these signals relate to future-oriented visual behavior at a range of timescales. We hypothesize that the visual hierarchy differentially updates its anticipatory signals when the environment or goals change, and generates predictive signals in novel situations by linking separate episodic memories. Finally, Aim 3 will test competing theories of the structure of anticipatory representations. We hypothesize that anticipatory representations are influenced by both temporal and semantic relationships within an event sequence, and propose a computational model for predicting anticipatory event representations learned from a temporally-structured stimulus. Together, the findings will elucidate the mechanisms by which the visual system forms and flexibly updates anticipatory representations at multiple timescales, and how these representations relate to anticipatory behavior in naturalistic conditions. Such insights are important because expectations are instrumental in allowing individuals to behave adaptively, and disruption of visual anticipation might broadly impair goal-directed behavior. This work will therefore shed light on how the capacity to anticipate upcoming events to adaptively guide behavior might be impaired following damage to different parts of the visual system, including higher-order areas whose damage is not associated with primary visual deficits. Together, the results will provide empirical tests of the structure and development of anticipatory signals across the visual hierarchy, informing theories that consider the brain to be a fundamentally predictive organ.

NIH Research Projects · FY 2025 · 2023-02

Robert A. Saxton | K22 (PAR-18-467) | Project Summary / Abstract Although inflammation is essential for protecting organisms against infection, excessive or chronic inflammation is also associated with an increased risk of certain cancers. This is particularly true at epithelial barriers such as the colonic mucosa in the gastrointestinal (GI) tract, which are in frequent contact with the external environment and therefore particularly susceptible to damaging inflammatory responses. Indeed, over 20% of patients with inflammatory bowel disease (IBD) will go on to develop colitis-associated cancer (CAC). Moreover, most therapeutic options for autoinflammatory diseases like IBD involve the use of immunosuppressive drugs, which may also increase tumor incidence due to reduced immunosurveillance. An alternative approach is to exploit natural mechanisms of tissue protection and repair in order to reduce tumor-promoting inflammation without suppressing anti-tumor immune responses. Recently, several members of the IL-20 cytokine family have been shown to be upregulated in both IBD and GI cancers, but their functional roles in these contexts are not fully understood. This includes the cytokines IL-19, IL-20, and IL-24, all of which signal through the shared receptor subunit IL-20Rβ. However, whether this upregulation drives disease pathology or reflects a beneficial but insufficient homeostatic response remains unclear. This is largely due to the combinatorial and interconnected nature of receptor sharing within this family, resulting in a high degree of functional pleiotropy and redundancy that hinders experimental interrogation of these pathways. In this project, we will employ structure-guided protein engineering to deconvolute the pleiotropic functions of IL-20Rβ ligands in inflammation-associated colon cancer. We will first use a combination of directed evolution and structure-based rational protein design to develop a pharmacological toolkit, comprising IL-20 receptor agonists and antagonists with altered receptor specificities, allowing us to selectively modulate the activity of individual IL-20Rβ ligands. We will then use these tools in vivo to probe the effect of these engineered proteins in the development, progression, and gene expression changes over the course of colitis induction and tumor progression, using the well-established AOM/DSS mouse model of CAC. Together, these studies will provide important insights into the protective and pathogenic functions of distinct IL-20Rβ ligands in CAC, while also directly testing the therapeutic potential of our engineered cytokine variants in the prevention of inflammation associated cancer.

NIH Research Projects · FY 2025 · 2023-02

PROJECT SUMMARY Identifying just one new clinical candidate for the treatment of human disease usually requires the design, synthesis, testing, and redesign of thousands upon thousands of organic compounds. Improvements to synthetic technologies therefore have a major impact on the time required to identify clinical candidates by maximizing the number of compounds that can be accessed from a single precursor. In particular, adjusting key properties such as bioactivity, solubility, metabolism, and stability are best accomplished by methods that are capable of preparing a wide variety of new compounds with a minimal number of steps. Late-stage functionalization of carbon-hydrogen bonds offers medicinal chemists this coveted opportunity by facilitating the introduction of numerous types of functional groups into a given lead structure. Recent efforts have demonstrated that transition- metal catalysts can enable the diverse functionalization of strong alkyl C–H bonds within organic compounds via the intermediacy of an organoboron compound. However, methods to achieve control over the site- and stereoselectivity of alkyl C–H bond functionalization are limited by their strength and ubiquity in complex molecules. The proposed research focuses on the development of a broadly applicable strategy to achieve selectivity in the functionalization of C(sp3)–H bonds that is independent of inherent substrate preferences. The impact of this work is to enable practitioners to make precise structural edits to bioactive compounds without lengthy synthetic manipulation. The proposed approach converts a major challenge in complex molecule functionalization, the presence of potentially intervening groups, into an opportunity to localize reactivity of a transition metal catalyst to convert specific C–H bonds into C–B bonds. Specifically, the proposed research will create catalysts and reagents that bind an existing polar functional group, such an alcohol or amide, thereby guiding functionalization to an adjacent site. Synthetic routes are presented to access a suite of catalysts and reagents. In conjunction with experiments to evaluate their suitably for guided functionalization, they will be refined iteratively for application to target structures. Subsequent studies of the functionalization of complex, biologically active compounds will demonstrate the applicability and generality of the proposed method to lead optimization. To control stereoselectivity, a key consideration in alkyl C–H bond functionalization, chiral diborane reagents derived from readily available precursors will be employed. By differentiating the energies of diastereomeric intermediates and transition states en route to the alkylboronate products, new derivatives can be accessed with well-defined three-dimensional structures. An integrated component of the proposed research program are mechanistic experiments that will form the basis of informed improvements to the overall approach, as defined by metrics that include reaction efficiency, site-selectivity, and stereo-selectivity. Achieving the specific aims of the proposed research will expand the opportunities available to scientists to make precise edits to complex organic compounds at alkyl C–H bonds, facilitating access to new bioactive compounds.

NIH Research Projects · FY 2025 · 2023-02

PROJECT SUMMARY Parvalbumin (PV) neuron hypofunction and increased excitation-inhibition (E-I) ratio in feedforward cortical circuits likely contribute to abnormal sensory processing in Autism Spectrum Disorders, but the origins and molecular mechanisms of PV hypofunction, and its generalizability beyond feedforward circuits, remain unclear. Here, I will test the hypothesis that PV circuit hypofunction arises because of impaired homeostatic plasticity of PV circuits, that normally acts to maintain cortical excitability during periods of shifting sensory input. In L2/3 of whisker primary somatosensory cortex (S1), PV circuit homeostasis is robustly engaged by brief whisker deprivation, which reduces intrinsic excitability of PV neurons, decreasing feedforward inhibition. In Aim 1.1, I will use in vitro electrophysiological measurements of PV cell excitability to test for impaired PV circuit homeostasis in two ASD mouse models (Fmr1-/y and Tsc2+/-). These models share PV hypofunction but differ in several molecular and synaptic phenotypes, making them a powerful test case for whether the PV hypofunction may arise from a common source. Previous physiological studies have primarily focused on dysfunction in bottom-up feedforward circuits in ASDs, but recent reports in people with ASDs suggest that sensory processing issues may result from a functional deficiency in top-down feedback pathways, resulting in overreliance on feedforward input. Top-down pathways provide strong input to S1, but it is unknown whether the physiology of feedback pathways is altered in ASD mouse models and whether their alteration may also result from a failure of homeostasis in PV cells. In Aims 1.2 & 1.3, I will assess changes in baseline function and homeostatic plasticity of S2->S1 inputs to L2/3 pyramidal and PV cells in S1 using optogenetics. Understanding the molecular mechanisms that underlie impaired PV circuit homeostasis in ASDs may enable therapeutic interventions to restore PV circuit function. These molecular mechanisms are currently unknown. I will identify the molecular mechanisms underlying deprivation-induced weakening of PV intrinsic excitability, the key initial step in PV homeostasis. This is known to involve an increase in voltage-gated potassium (Kv) channel currents. The molecular mechanisms likely involve activity-dependent protein synthesis, which is reportedly dysregulated in both the Fmr1-/y and Tsc2+/- mice, though potentially in opposite directions. A promising candidate signaling pathway that could mediate PV circuit homeostasis is activity- dependent synthesis of transcription factor ER81 leading to increased Kv1.1 expression in PV cells. In Aim 2, I will use novel cell-specific genetic strategies to test the hypothesis that PV circuit homeostasis requires protein synthesis in vivo and involves activity-dependent synthesis of ER81 and increased Kv1.1- and this is impaired in ASD mice. I will also develop CRISPR tools to modulate Kv1.1 levels to rescue PV homeostasis in ASD mice, potentially leading to therapeutic approaches for ASDs.

NIH Research Projects · FY 2026 · 2023-02

Abstract Astrocytes are the most abundant cell types in the brain and have long been thought as primarily passive support cells. Studies in the past two decades leveraging modern techniques have revealed crucial roles for astrocytes in neuronal circuit assembly, synaptic function and behavior. Aberrant astrocytic function is implicated in neuropsychiatric and neurodegenerative diseases, and astrocytes hold great promises as novel therapeutic targets for improving treatment efficacy. Despite this progress, a deeper mechanistic understanding of astrocytes' causative and correlative roles in operating neural circuitry and their contribution to behavior is still lacking. This knowledge gap is largely due to the lack of technologies to effectively manipulate astrocyte activity with cell-type and temporal precision. The physiological hallmark of astrocytes is their complex spatiotemporal patterns of intracellular and intercellular calcium signaling crucial to their bidirectional interaction with neurons. The objective of this project is to develop a non-invasive, wireless and genetically encoded actuator to modulate astrocytic activity with cell-type and temporal precision in vivo. Our approach, named FeRIC (Ferritin iron Redistribution to Ion Channels), combines the use of radiofrequency (RF) waves and ion channels to control membrane ion permeability non-invasively and wirelessly. The FeRIC technique utilizes RF waves to activate membrane proteins that are coupled to the endogenous cellular iron storage protein ferritin. Our preliminary studies have demonstrated the feasibility of FeRIC-mediated RF stimulation to modulate calcium activities in astrocytes and astrocytic networks that resembles those observed under physiological conditions. Further, FeRIC-mediated RF stimulation of astrocytes has been able to elicit neurotransmitter release and evoke action potentials in connected neurons. We aim to develop a set of molecular tools and characterize their abilities 1) to modulate global calcium signaling in astrocytes, 2) to modulate microdomain calcium activities in astrocytes and 3) to modulate astrocyte-neuron interactions at the tripartite synapses in vivo. If successful, the project will develop a non-invasive and genetically encoded molecular tool to modulate astrocytic activity with cell-type and temporal precision. We will elucidate the biophysical underpinnings of the mechanism. The project will have a broad impact to the study of the roles of astrocytes in health and disease.

NIH Research Projects · FY 2026 · 2023-01

PROJECT SUMMARY The goal of this project is to understand the mechanistic basis for gating and function in channelrhodopsins, retinal-binding proteins that are similar to vertebrate visual proteins and form light-gated ion channels to control phototaxis in motile algae. In the nearly two decades since they were first cloned, channelrhodopsins have become important models for understanding membrane protein structure, function, and biophysics and widely utilized molecular tools in optogenetics, in which their heterologous expression in genetically targeted cells enables control of membrane potential and electrical excitability with light. Here, we will apply cryo-electron microscopy to determine structures of channelrhodopsins in different functional states and electrophysiological recordings of structure-based variants to understand the basis for channel gating and determinants for key channel properties. We aim to capture structural snapshots of different open and closed conformations by identifying combinations of stimulation conditions and channel variants that promote different states. We will leverage these structural insights to interrogate the molecular basis for diverse kinetics, conductance, and spectral sensitivity among channelrhodopsins and derive physical models for gating and functional properties. We will focus our efforts on two channelrhodopsins that are the most potent members of the two depolarizing channel families widely used in optogenetics, the cation channelrhodopsins (CCRs) and bacteriorhodopsin-like cation channelrhodopsins (BCCRs). CCRs and BCCRs share a common architecture, but are structurally, evolutionarily, and mechanistically distinct. Comparative analyses of these two channelrhodopsin families will therefore provide additional insight into how light energy is converted into gating conformational changes and the molecular basis for channel activity. Since the initial characterization and cloning of channelrhodopsins, the optogenetic toolbox has been greatly expanded by the engineering of novel channelrhodopsins with varied and improved properties. Still, these efforts have been limited to date by an incomplete understanding of the structural and mechanistic basis for channel function. Therefore, in addition to providing fundamental mechanistic insight into channelrhodopsin gating and activity, this work will serve as a basis for the rational design of new channelrhodopsin variants with modified properties that further expand the potential of optogenetic manipulations. Such tools could enable new experiments at larger scale, in deeper tissue, in larger organisms, and with higher precision. They could also lead to new clinical approaches for treating disease including those of the nervous and cardiovascular systems.

NIH Research Projects · FY 2025 · 2023-01

Measles: A Global History Project Summary Measles is caused by a notably stable virus and has been vaccine preventable since the 1960s, following commercialization of the first effective measles vaccine in the U.S. But after the first several years—and then decades—of measles vaccination, U.S. medical and public health experts began to remark on how distinctly vaccination was changing measles's epidemiology, altering the geographic, racial, age, and income groups most and least affected by the disease. This oft- made observation, however, overlooked measles' long history. Extant for thousands of years, measles had always been shaped by the times and places in which it made its appearance. Urbanization, colonization, trade, war, schooling patterns, treatment, and other social, cultural, political, scientific, and economic factors shaped and reshaped measles over and over, changing it from epidemic to endemic to eliminated and back again, from “severe” to “mild” and vice versa, and from a universal scourge to a commonplace feature of childhood. In the era of modern biomedicine, measles has repeatedly been described as one of the deadliest and most contagious diseases, as well as one of the most eradicable—a scientific belief resting on assumptions about measles' stability that are in fact a small part of its centuries-long story. This project will construct a global history of measles by following the disease from medieval Islamic clinical descriptions to contemporary battles over its elimination. The project has three specific aims. First, it will produce the first book on the global history of measles, with a focus on how conceptions and perceptions of measles rooted in space and time have long made measles both a stable and dynamic illness. Second, it will analyze measles' historical roles in the emergence and development of what is now called global health. Third, it will examine and elucidate measles' practical and symbolic historical significance in efforts to manage other infectious diseases over time, from smallpox to COVID. The book will be published by Polity Press and written for an audience of academics, policymakers, advocates, and the public. Research methods for this historical project include both secondary source synthesis and primary source location and analysis. The project draws on a broad secondary literature on the histories of infectious disease, epidemics, medicine, and global health. Its primary source base consists of evidence from databases of periodicals, government reports, and scientific papers; digitally accessible documents, archives, and manuscript collections; and brick-and-mortar archival collections. These range from Index Medicus to the African Online Digital Library and from the records of the U.S. CDC to the archives of the WHO.

NIH Research Projects · FY 2025 · 2022-12

Abstract White adipose tissue (WAT) is a metabolically active organ that is adaptive and undergoes changes throughout the human lifespan. While adipocyte number can increase via recruitment of precursors in the stromal vascular fraction (SVF) of WAT to differentiate into adipocytes, the total number of adipocytes in WAT is set mainly during adolescence, and thus changes in WAT mass, adiposity, mostly reflect alterations in lipid storage. In obesity, WAT may become severely dysfunctional and does not expand properly to store the excess energy, resulting in ectopic fat deposition and lipotoxicity in other tissues. Unhealthy expansion of WAT by adipocyte hypertrophy (increasing cell size) may also result in deleterious effects, such as insulin resistance and type 2 diabetes. In addition, SVF populations may drastically change and be contributing factors towards disease progression. Hence, maintaining white adipose tissue with balance between adipocyte hypertrophy and hyperplasia (increasing cell number) is important for whole-body metabolism and energy balance. In general, WAT is categorized as either subcutaneous (SAT) or visceral (VAT) adipose tissue. SAT provides insulation and cushioning and serves as a long-term energy storage depot. VAT cushions and maintains distance between organs and is critical for lipid storage during hyperphagia. While VAT is associated with pathological conditions, such as insulin resistance and cardiovascular disease, SAT is protective against these diseases. During aging, VAT tends to increase while SAT decreases significantly. VAT expansion occurs as lipid storage is shifted from SAT to VAT and visceral adipocyte hypertrophy increases. However, the explanation behind the decrease in metabolically protective SAT mass during aging has been more elusive. Although the developmental origin and function of VAT and SAT are known to differ, in general, the proliferation and differentiation capacities of adipose precursor cells (APCs) in each depot are believed to drastically decline during aging. I have recently reported that aging-dependent regulatory cells (ARCs) emerge and accumulate as a unique subpopulation of SAT during aging. ARCs arise from APCs but exhibit impaired differentiation capacity and express high levels of proinflammatory cytokines. By secreting cytokines, such as Ccl6, ARCs inhibit the proliferation and differentiation of neighboring bona fide APCs. Thus, the emergence of ARCs is responsible for the drastic decrease in adipose precursors and defects in adipogenesis, resulting in the loss of SAT during aging. Interestingly, the transcription factor PU.1 is the driver for the development of ARCs in SAT during aging. Though I have shown PU.1 to be responsible for the development of ARCs, the exact mechanism by which PU.1 alters the transcriptome of ARCs is currently unknown. Therefore, the objective of the proposed study will be to 1) identify the mechanism by which PU.1 alters gene expression in ARCs and to 2) characterize the role of PU.1 on SAT function in vivo.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract This project will study the long-term effects of a child health program on recipients’ living standards, labor supply, health, marriage and fertility and other life outcomes. The project extends a longitudinal (panel) dataset of participants in a randomized health intervention (primary school-based deworming) when they were 8-15 years old. A novel aspect of the project is its intergenerational linkages: the dataset, the Kenya Life Panel Survey (KLPS), contains detailed information on health, nutritional, educational, demographic, and labor market outcomes for over 6,500 Kenyans during 1998-2021, and the health, behavioral and cognitive development of their 3-9 year old children (collected 2018-2021). The resulting 28-year longitudinal dataset will allow the study team to exploit experimental variation to estimate the long-run and intergenerational impacts of a child health intervention. Critically, the most recent KLPS round had an effective survey rate of 84% among adults 20 years after the start of the deworming program, with balance across treatment arms, alleviating leading concerns about differential attrition and bias. We will make use of the panel data structure to estimate the effects of major parental life events and shocks -- such as migration, marital separation, job loss -- on the cognitive and development outcomes of their children. Having access to repeated measures of both parents and children over time is unusual in any context but especially in low and middle income countries (LMICs), and we aim to create the premier intergenerational longitudinal dataset in Sub-Saharan Africa. The matched parent-child data will also allow us to estimate the correlation between performance on the same cognitive tests taken by parents (when they were in primary school) and their own school-age children. We propose to collect KLPS Round 5 with 6,500 adult survey respondents (aged 35-43) and a second round of surveys and assessments with over 5,000 of their children (aged 6-13). The KLPS sample contains individuals who participated in the Primary School Deworming Program (PSDP) mentioned above, and some who participated in an unconditional cash grant program. Previous research shows that deworming had substantial positive impacts on the health, schooling, living standards, urban residence and earnings of beneficiaries 10-20 years later; the cash grant program had positive short-run impacts on earnings. We also implemented two parent-child interventions (reading promotion and sleep promotion), and will estimate the medium-run (4-5 year) impacts of these interventions on child learning and development. The randomized design of all of these interventions addresses the key methodological problem of confounding. Causal long-run effects of health on life outcomes have rarely been demonstrated due to the near absence of experimental variation in combination with detailed longitudinal data on recipients and children. Accurate information on long-term direct and intergenerational impacts is essential for assessing the cost-effectiveness of child health programs.

NIH Research Projects · FY 2025 · 2022-09

Project Summary Background Single-cell sequencing data has enormous potential to improve our understanding of human health, with direct applications in the areas of diagnosis and therapeutic selection. Single- cell sequencing of mRNA expression levels (scRNA-Seq) initially focused on understanding fun- damental biological systems at the single-cell level, but there is an increasing emphasis on using scRNA-Seq to understand the role of single-cell variability on human health outcomes. While the exploration of single-cell human variability and its relationship to disease is advancing, the cor- responding statistical methodology to handle this type of data at the human population level lags behind. Project Objectives Broadly, the long-term goal of this proposal is a coherent methodological framework for the analysis of the effect of single-cell variability on patient phenotypes. This pro- posal considers the setting of population scRNA-Seq studies, where scRNA-Seq data is collected from many patients representing populations with differing health outcomes. The proposed re- search consists of the development and evaluation of statistical methodologies for these kinds of scRNA-Seq population studies. The methodology developed by this proposal will fill a critical gap, helping to unlock the potential of scRNA-Seq data for improving human health. Project Methods The proposed research program focuses on three specific aims that target the most common analysis needs in scRNA-Seq population studies. Aim 1: Patient-level represen- tation for scRNA-Seq data. This Aim will develop a summary representation of the scRNA-Seq profile of a patient and create statistical methods that allow comparisons of this summary profile between different patient populations. Aim 2: Predicting patient phenotypes based on scRNA-Seq data. This aim will develop models that can predict health phenotypes based on the scRNA-Seq measurements on a patient. Aim 3: Identifying cell-level and gene-level biomarkers for patient phe- notypes. The methods developed in this aim will allow for identifying genes and cell populations that differ at the single-cell level between patient populations. The biomarkers identified from these methods will generate testable hypotheses for future exploration of the mechanistic relationship between single-cell variability and patient outcome.

NIH Research Projects · FY 2025 · 2022-09

ABSTRACT / PROJECT SUMMARY Spatial navigation requires working memory for the ability to flexibly update an internal representation of position as one moves through the world, yet also stably hold “in mind” one’s position during periods of rest. Despite the critical importance of working memory for a wide range of cognitive processes, we currently lack basic understanding of how working memory circuits balance the fundamental tension between flexibility and stability. This gap is due to three major challenges: (1) defining a complete network that holds internal representations during working memory; (2) the ability to causally test how fluidly networks can transition between distinct representations; and (3) a conceptual framework for how transition probabilities are modulated at a biophysical level. This proposal will overcome these challenges by investigating how dopamine modulates the stability of internal spatial representations in a tractable experimental system: the central complex of the fruit fly, Drosophila. We have developed methods to measure how dopaminergic modulation shapes synaptic, cellular, and network dynamics of genetically identified neurons that code for spatial orientation. First, we will measure when dopamine modulates navigational circuits using whole-cell electrophysiology from the brains of flies walking in virtual reality. Then we will define how dopamine levels shape network dynamics by using optogenetics to explore how dopamine alters the ease of overwriting spatial representations. Finally, we will use cell-type specific perturbations of dopamine receptors with in vivo electrophysiology and calcium imaging to define how changes to synaptic and intrinsic properties shape network fluidity. The ultimate goal is a biophysical-level description of how neuromodulation shapes working memory processing online. Due to the difficulty of interpreting and perturbing population activity that is distributed across large mammalian brains, these experiments have been previously out of reach. By using Drosophila, we can focus on a compact navigational circuit comprised of only a few hundred neurons with known connectivity and unmatched genetic access. Although there are clear differences between flies and mammals, dopamine signaling and spatial coding properties (head direction networks) are strikingly conserved across species. These similarities argue that the principles we discover in the fruit fly will be relevant to cognitive processing in other animals. A mechanistic understanding of working memory fluidity is essential for the top-down design of therapeutic strategies to treat cognitive disorders.

NIH Research Projects · FY 2025 · 2022-09

Project summary. The gut microbiome plays important roles in host health and fitness. In the human gut, microbes are estimated to have ~100-fold more genes than in the host genome, and throughout animal evolution, bacterial biochemical diversity has been instrumental in enabling hosts adapt to new diets and environments. The current Anthropocene is posing new challenges to ecosystems and the communities living in them. Among those is xenobiotic usage and pollution, including antibiotics and pesticides, some of which are tightly regulated for known toxic effects, the toxicity of others is still debated. The gut microbiome has been shown to respond to xenobiotic exposures, and anecdotal evidence demonstrates that microbiome adaptation and exchanges with the environment can help animals adapt to the new stress within one generation. However, microbiome adaptation may have trade-offs as changes to microbiome composition, or dysbiosis, are often associated with pathology. We hypothesize that the pressure of human-made xenobiotics promotes pervasive microbiome-assisted adaptation and that the associated changes are a yet underappreciated cause for human variation and pathology. We propose to use the C. elegans model to explore the pervasiveness of microbiome-assisted adaptation to pesticides, the underlying mechanisms and the long-term consequences for host health throughout its life. We have established C. elegans as a model for microbiome research, enabling work with natural-like microcosms, synthetic communities and fluorescently-labeled commensals, and showed that similar to vertebrate models, worms harbor characteristic microbiomes that reflect the environmental availability of bacteria, which are further shaped by host genetics. Preliminary experiments with an antibiotic (to ensure effects on bacteria) that is also toxic to worms, readily demonstrated gut microbiome adaptation that protected the host, and further showed that adapted microbiomes were not simply enriched with the most environmentally-available strain, but that host filtering, modulated by the toxin, shaped them. The proposed plan will start with a characterization of this example of adaptation, to gain insights into pivotal mechanisms of microbiome-assisted adaptation. However, the bulk of the proposed work will focus on adaptation to commonly used herbicides and insecticides (toxic to worms too), which are associated with pathology in humans, but are poorly understood. We will identify protective bacteria, study the course of adaptation and the role of the host in determining it, and characterize long-term consequences focusing on phenotypes associated with altered metabolism, immunity and lifespan. Recent efforts are invested in looking into the effects of various pesticides on the gut microbiome, assuming that those may have detrimental consequences. Our hypothesis is that this is far more common than currently appreciated, and that this is part of the broader process of host adaptation to xenobiotic pressure. The proposed plan will explore how readily this happens, how it happens, and what are the trade-offs.

NIH Research Projects · FY 2025 · 2022-09

Project Description/Summary Mitochondrial DNA (mtDNA) encodes RNAs and proteins critical for cell function. However, the pathways that regulate mtDNA synthesis and segregation in animal cells are not well understood. The goals of this work are to identify the protein components of mitochondrial DNA nucleoid complexes, to investigate how mitochondrial replication and dynamics are coordinated to homeostatically maintain mtDNA nucleoid segregation and abundance, and to probe the mechanisms underlying selection against mutant mtDNAs in somatic cells. These experiments will provide fundamental insights into the maintenance of the essential mitochondrial chromosome in animal cells and how maintenance processes are regulated, potentially leading to the discovery and characterization of novel pathways that regulate the inheritance of mtDNA disease alleles. We will employ cutting-edge microscopy of living cells and whole animals, proteomics, and single cell transcriptional analyses to interrogate the molecular functions of candidate proteins implicated in the maintenance of mtDNA integrity. These experiments will reconcile inconsistencies in the mitochondrial biology literature, provide fundamental insight into the mechanisms of mtDNA copy number control, and identify novel pathways that regulate the tissue-specific manifestations of mitochondrial dysfunction.

NIH Research Projects · FY 2025 · 2022-09

The wide-reaching impacts of the COVID-19 pandemic highlight the extreme threat posed by the cross-species emergence of zoonotic pathogens. Bats (order: Chiroptera) are the natural reservoir hosts for the majority of the world’s most virulent zoonotic viruses, including Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and SARS, MERS, and now SARS-CoV-2 coronaviruses. Remarkably, bats exhibit little demonstrable disease upon infection with viruses that cause extreme pathology in other mammals, likely in part due to their unique anti-inflammatory molecular adaptations, which are thought to have evolved to mitigate the accumulation of physiological damage accrued during flight. Surprisingly, isolated island bat communities around the world support the endemic circulation of numerous viruses in populations below the critical community size required for persistence of related pathogens in other hosts. Since cross-species spillover of several bat-borne viruses bears a distinctive seasonal signature, coincident with the timing of reproductive and nutritional stress for the bat hosts in question, disentangling the mechanisms governing the transmission, circulation, and persistence of these viruses in wild bat populations is of critical public health interest. In part with the research initiatives proposed here, we will use molecular and serological tools to develop a longitudinal time series of immunological and infection data for henipaviruses and coronaviruses circulating in wild fruit bats in Madagascar, leveraging samples collected in our longterm wildlife surveillance effort. Bats are widely consumed as a source of human food in Madagascar, and preliminary data from our research group demonstrates serological signatures of prior human exposure to these zoonotic viruses across the island. We propose to fit disparate dynamical models to the resulting population-level data in order to distinguish mechanisms underpinning seasonal viral shedding pulses and concomitant transmission in these bat hosts. In addition to population-level studies, we will also construct within-host models of viral control in a single bat immune system, which we will fit to experimental infection data from Betacoronavirus-challenged bats in the laboratory, with the aim of deciphering the mechanisms which motivate viral shedding. Our project aims to simultaneously develop molecular tools of bat cell lines and viruses with which to support within-host studies in our own Madagascar system. Finally, we will build on population-level and within-host studies to model and implement a vaccine intervention designed to eradicate circulating henipavirus from a test-population of Madagascar fruit bats. Broadly, our project aims to use a uniquely integrative combination of field, molecular, and modeling tools to enable the prediction and prevention of bat virus spillover events before they occur.

NIH Research Projects · FY 2024 · 2022-09

Project Summary Dysfunction of the prefrontal cortex (PFC) and the hippocampus (HPC) has been implicated in many neuropsychiatric disorders, including schizophrenia, major depression, and post-traumatic stress disorder. Many of the behavioral symptoms of these disorders can be modeled as dysfunctional reinforcement learning (RL) processes. For example, a failure to optimally balance goal-directed (“model-based”, or MB) and habitual (“model-free”, or MF) control can explain rumination in OCD. An overarching goal of our research is to inform the future development of devices that will interact with neural circuits in a principled way to treat neuropsychiatric disorders. One impediment to this approach is that the neural coding in many of these circuits remains poorly understood. The aim of the current grant is to investigate the neuronal properties of HPC and PFC, and how these structures interact with each other. The HPC-PFC circuit may play an important role for reward-based learning processes that depend on a model of the environment. The HPC has long been associated with representing a ‘cognitive map’ that encodes the structure of the environment. It is bidirectionally connected with medial PFC (mPFC), which has been implicated in reward-based learning and value-based decision-making. Our hypothesis is that the HPC-PFC is critical for MB RL, via the HPC representing a predictive map of task, and communicating this map to mPFC to allow value inferences that guide behavior. Our theoretical construct for modeling this process is the successor representation (SR), which learns a map of the task in parallel with reward contingencies, and then evaluates potential actions by integrating the predictive map with the learned reward contingencies. To test this hypothesis, we have developed an abstract foraging task that requires the subject to navigate a hidden state space to find a reward. To solve this task optimally, the subject must engage in MB RL and develop an internal map of the state space. This map allows the subject to store the location of the most recent reward and then correctly select the necessary actions to reach the rewarded location. First, we will record from single neurons in mPFC and HPC, then record simultaneously from mPFC and the hippocampus to examine how these regions communicate with each other during MB RL. Taken together, the results of this proposal will expand our understanding of the roles and interaction of HPC and PFC in the primate brain. This knowledge will not only inform efforts to improve diagnostic tools in clinical psychiatry but can also lay the groundwork for the development of neuroprosthetic devices that will interact with neural circuits in a principled way to treat neuropsychiatric disorders.

NIH Research Projects · FY 2025 · 2022-09

For decades, diagnostic errors have constituted a blind spot in the effort to improve health care quality. Compared with the multitude of metrics available to assess the quality of treatment, clinicians and policymakers have few tools with which to measure and improve the quality of diagnostic decisions. Without better methods to systematically measure the quality of diagnostic decisions at the clinician level, it will continue to be difficult to identify patterns in diagnostic errors, categorize types and causes at scale, and develop and evaluate interventions to prevent them. Our long-term goal is to develop tools to measure diagnostic quality across clinical providers from large-scale data, and to build frameworks and knowledge to translate those measures into appropriate interventions. The objective of this application is to apply and validate a system for measuring diagnostic quality across radiologists in the setting of pneumonia diagnosis among 5.5 million visits with chest X-rays in Veterans Health Administration (VHA) emergency departments (EDs). In this project, we will address three challenges fundamental to any data-driven approach to measuring quality of diagnostic care. The first is a lack of observable ground truth against which to benchmark diagnoses, particularly in large-scale data. This challenge is particularly problematic when policies seek to balance type I errors (false positives) against type II errors (false negatives). Second, rates of diagnostic errors depend on the underlying prevalence of disease in the patient population, which may be incompletely observed. Third, small case numbers per clinician can complicate comparisons between clinicians, since measured differences may reflect underlying diagnostic quality or may arise from random noise. We will address these challenges with a novel combination of methods from statistical classification and applied economics, building on prior work. We propose the following specific aims: (1) We will validate data-driven measures of pneumonia diagnoses and diagnostic outcomes. In prior conceptual work building on the econometric literature of selection, we show that we may infer relative differences in diagnostic quality—as differences in type I error rates and type II error rates—even if individual type I errors are unobservable, under quasi-experimental assignment of cases to radiologists; (2) We will interpret provider-level rates of type I error and type II error in a receiver-operating curve (ROC) framework in which diagnostic errors may arise from incorrect diagnostic thresholds (trading off type I and type II errors) or poor diagnostic accuracy (incurring both too many type I errors and type II errors); and (3) To explore the determinants of clinician diagnostic quality, we will correlate our measures of radiologist diagnostic quality with their characteristics and actions across thousands of radiologists. To assess the potential consequences, we will study health outcomes of patients quasi-experimentally assigned to radiologists of differing diagnostic quality. Our project will lay the groundwork for data-driven measurement of diagnostic quality across clinical providers, a necessary first step in understanding and improving the diagnostic performance of our health care system.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract Peroxiredoxin 6 (Prdx6) is a multi-functional enzyme that expresses glutathione peroxidase, phospholipase A2 (PLA2), and lysophosphatidylcholine acyltransferase (LPCAT) activities in separate catalytic sites. Prdx6 can reduce phospholipid hydroperoxides and hydrolyze and re-acylate phospholipid fatty acyl bonds. Prdx6 is, therefore, a complete enzyme for the repair of peroxidized cell membranes. Prdx6 has been implicated in several pathophysiological conditions, including acute lung injury, inflammation, carcinogenesis, various chronic central nervous system diseases, retinal disease, type 2 diabetes, muscle atrophy, and male infertility, but basic questions about the biology of this unique enzyme remain unanswered. Our preliminary data strongly suggest that Prdx6 suppresses ferroptosis, an iron-dependent form of regulated cell death driven by the accumulation of phospholipid hydroperoxides. Emerging evidence implicates ferroptosis in several degenerative diseases, carcinogenesis, stroke, traumatic brain injury, and ischemia/reperfusion injury, among others. Hence, establishing the mechanisms and physiological relevance of ferroptosis regulation by Prdx6 is crucial. My lab is interested in studying the role of the glutathione peroxidase, PLA2, and LPCAT activities of Prdx6 on the regulation of ferroptosis induced by inhibition of cystine uptake, hypoxia/reoxygenation, and oxygen toxicity. We will use mice and cells with single point mutations that inactivate each of the activities of Prdx6 without affecting the others, along with state-of-the-art analytical tools to dissect the role of this enzyme on the regulation of ferroptosis. In a second project, I propose to study the role of Prdx6 in the maintenance of mitochondrial function. Our preliminary data show that Prdx6 deficiency alters transcriptional signatures of mitochondrial metabolism and reduces mitochondrial respiration. We will study the effects of the catalytic activities of Prdx6 on mitochondrial morphology, dynamics, and function using extracellular flux assays and three-dimensional imaging techniques. The results of this proposal will contribute to our understanding of one of the critical mediators of cellular redox balance. These results will also provide essential information for future translational strategies for the prevention and treatment of diseases associated with dysregulated redox homeostasis.

NIH Research Projects · FY 2026 · 2022-09

Project Summary Nearly 40% mammalian genome originates from retrotransposons. Most mammalian retrotransposons are strictly silenced in development and physiology, yet induction of specific retrotransposons can be observed in normal oocytes and preimplantation embryos. Interestingly, a subset of retrotransposons confer a gene regulatory role, at least in part, by acting as alternative promoters, exons and polyadenylation signals to regulate proximal protein-coding genes. Such retrotransposon-dependent gene regulation frequently alter gene structure and/or gene expression, and have been shown in our preliminary studies to play important developmental functions in oocyte biology and preimplantation development. Female reproductive aging presents an excellent experimental system to probe the functional importance of retrotransposons in aging. Unlike somatic tissues which strongly repress retrotransposon expression, oocytes and preimplantation embryos exhibit a strong induction of specific retrotransposons, possibly due to extensive epigenetic reprogramming during these unique developmental stages. Our preliminary studies show that aged oocytes exhibit expression alteration of specific retrotransposons, as well as RT:gene isoforms. Interestingly, the IAPEy4 family, which is retrotransposition-competent, is strongly induced in aged oocytes. IAPEy4 induction could lead to DNA damage and innate immune response in aged oocytes, as a result of its retrotransposition. In addition, the MII oocyte specific MTC-Dicer1 isoform is strongly repressed in aged oocytes. The MTC-Dicer1 encodes an N-terminally truncated Dicer isoform that governs the transposon surveillance through post-transcriptional silencing by RNAi. These findings suggest that altered retrotransposon expression and retrotransposon mediated gene regulation in aged oocytes could functionally promote reproductive aging. Using genomics, mouse genetics, cell and molecular biology, we proposed to investigate the importance of retrotransposons in female reproductive aging. We will 1) profile retrotransposons and retrotransposon-dependent gene regulation in young and old oocytes and somatic granulosa cells; 2) Investigate the importance of aberrant retrotransposon induction and retrotransposition during reproductive aging; 3) investigate the importance of retrotransposon mediated gene regulation in reproductive aging. Taken together, the proposed studies will provide new insights into the cellular and molecular mechanisms that govern female reproductive aging, and will add a new dimension to our understanding of retrotransposon functions in development and disease.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY The microbiota of the mammalian gut is a complex community of individual strains shaped in part by microbial competition over diet components. Despite computational analyses predicting enzymatic capacity of diverse bacteria, this knowledge is not sufficient to determine how diet influences bacterial abundance in the gut. In particular, little is known about regulation of carbon utilization enzymes in gut bacteria. Do they have mechanisms similar to E. coli carbon catabolite repression to consume preferred nutrients sequentially? Or do they consume all available nutrients simultaneously? How do these different strategies contribute to microbial abundance in the gut? We have identified a mechanism resembling carbon catabolite repression in Collinsella aerofaciens that may be a disadvantage when there is an abundance of secondary carbon source in the gut. Our laboratory seeks to characterize regulatory mechanisms governing carbon consumption in Collinsella species, in culture and in the mouse gut. Collinsella species are poorly studied Actinobacteria that are linked to chronic human diseases including type 2 diabetes and atherosclerosis. We have studied a group of closely related species and strains that vary in their regulation of carbon consumption. We will use this existing variability and experimental evolution to identify a common pathway of carbon catabolite repression in these bacteria. We will measure the heterogeneity of this pathway and related metabolic functions using single-cell RNA-seq. Finally, we will characterize the impact of this regulation on bacterial growth and competition in the mouse gut. Together, this research will define regulatory pathways that contribute to advantageous strategies in the complex nutrient environment of the mammalian intestine. Despite the vast number of correlative studies implicating a role for the gut microbiome in human disease, there remains much to explore in identifying bacterial metabolic pathways governing bacterial abundance and function in the gut. This gap limits both our understanding of the basic biology of these community interactions as well as the ability to design effective microbial therapeutics for human diseases characterized by complex microbial dysbiosis.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY SYNGAP1-related intellectual disability is a neurodevelopmental disorder caused by mutations in the SYNGAP1 gene. SYNGAP1 encodes SynGAP, which is a highly abundant protein in the post- synaptic density of excitatory synapses. At synapses, SynGAP functions to repress downstream NMDAR signaling and AMPAR trafficking through its inhibition of small GTPases. Translocation of SynGAP out of the post-synaptic density is required to allow NMDAR-dependent long-term potentiation (LTP) in cultured neurons. In the absence of SynGAP, NMDAR-dependent plasticity is unrestrained leading to alterations in synapse strength, spine structure, and plasticity. While the functions of SynGAP have been well- studied in the cortex and hippocampus, the striatum also exhibits high levels of SynGAP expression. Striatal projection neurons are GABA-ergic neurons covered in a dense array of dendritic spines, which receive excitatory inputs from the cortex. SynGAP is therefore positioned to play a key role in gating transmission and plasticity at striatal synapses. Despite this, SynGAP’s functions in striatal neurons have not yet been defined. Importantly, several of the major symptoms of SYNGAP1 disorder are likely to involve alterations in striatal activity including motor developmental delay, repetitive and restrictive behaviors, and other behavioral problems. In this project, we will elucidate the consequences of SynGAP loss on striatal synaptic function and determine whether loss of SynGAP from striatal neurons is sufficient to induce behavioral alterations relevant for SYNGAP1 disorder. Specifically, we will determine how loss of SynGAP impacts striatal synaptic development, transmission and plasticity. In addition, we will use imaging approaches to investigate how SynGAP deficiency affects spinogenesis, spine number and morphology. To determine whether deletion of Syngap1 from striatal neurons is sufficient to alter disease-relevant behaviors, we will investigate how haploinsufficiency of Syngap1 in cell type-specific knock-out mice affects motor function, habit learning, and behavioral flexibility. Finally, we will test whether restoration of Syngap1 expression selectively in striatal projection neurons can improve synaptic and behavioral abnormalities using genetic rescue strategies. Together, this work will 1) further our understanding of SynGAP’s functions at striatal synapses, 2) identify the striatal cell type(s) most relevant for the manifestations of SYNGAP1 disorder, and 3) define critical periods for the onset and rescue of disease-related phenotypes.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY This project aims to understand the function and regulation of three ion channels that conduct K+ across cell membranes and belong to the two-pore domain K+ channel family. We will apply cryo-electron microscopy to determine structures of the channels in different functional states within lipid environments that mimic the cellular membrane and electrophysiological recordings to characterize their activities in order to derive physical models for channel gating and modulation. We aim to capture structural snapshots of the different open and closed conformations for each channel by varying conditions that alter channel function including solution composition, lipid composition, and presence of small molecules or interacting proteins. The three channels are members of different branches of the two-pore domain K+ channel family. While they share a common structural architecture, each channel is regulated by pH in a different way; one is inhibited by protons on both sides of the membrane, the second is inhibited only by extracellular protons, and the third is both inhibited and altered in its ionic selectivity by extracellular protons. The underlying molecular mechanisms by which pH is sensed and converted into a change in channel activity are correspondingly different between the channels. Each channel is further regulated by a distinct set of factors including signaling lipids, interacting proteins, solution ion composition, and small molecule drugs. Comparative analyses of the three structurally and evolutionarily related K+ channels will therefore provide additional insight into their functional properties and biological roles. Two-pore domain K+ channels mediate cellular electrical signaling by establishing and maintaining the resting membrane potential and opposing excitability. The channels under study here are involved in respiratory regulation, cardiac rhythm generation, blood pressure control, central chemoreception, and systemic pH homeostasis among other processes. Their dysregulation is implicated in cardiac arrythmia, kidney disease, and hypertension in humans and they are targets of anesthetics, antiarrhythmics, and drugs under investigation for obstructive sleep apnea. Therefore, in addition to providing fundamental mechanistic insight into the physical and chemical basis for channel function, this work will serve as a basis for the development of more potent and specific pharmacological agents targeting ion channels to promote health and treat disease. Importantly, the technical and methodological advances developed here for structural characterization of small membrane proteins in lipid environments are expected to be widely applicable and will facilitate insights across the breadth of biology in which membrane proteins play important roles.

NIH Research Projects · FY 2024 · 2022-08

Project Summary Sjögren’s Disease (SjD, previously known as Sjögren’s syndrome) is a chronic, multisystem autoimmune disease that causes significant morbidity. Experts estimate that 1.3 million individuals have SjD in the United States alone. Previous research, particularly Mendelian randomization (MR) analyses, has provided strong evidence for low vitamin D as a risk factor contributing to several autoimmune conditions. Vitamin D is important for dozens of biological processes. The gene transcription that occurs with the binding of vitamin D to vitamin D receptors (VDRs) produces downstream effects implicated in immunomodulation, calcium metabolism, cellular growth, proliferation and apoptosis, and other important immunologic functions. Single nucleotide polymorphisms (SNPs) associated with genetic variation in VDR binding affinity (VDR-BVs) have been previously identified in lymphoblastoid cell lines (LCLs); these VDR-BVs are enriched in genomic regions associated with several autoimmune diseases, cardiovascular disease, osteoporosis, depression, and cancer. To date, available research on vitamin D in SjD has been limited to small studies of serum vitamin D levels in SjD cases and controls which observed lower vitamin D levels in cases. There have been no published studies investigating: 1) low vitamin D as a risk factor for SjD using MR analysis, or 2) genetic variation within individual VDR binding sites as a risk factor for SjD. VDR-BVs are therefore strong candidates to investigate for their genetic contribution to SjD. The overall objective of this F31 application is to identify VDR-BVs across the genome and characterize their association with SjD susceptibility, severity, and related clinical outcomes. We hypothesize that altered VDR binding disrupts downstream gene regulation by vitamin D and increases the risk of developing SjD or results in more severe disease. Our approach will use an assembled dataset with more than 1,500 SjD cases and 27,000 controls (for which the data are already available) matched on race/ethnicity, with whole genome SNP profiles and demographic and clinical data from the Sjögren’s International Collaborative Clinical Alliance (SICCA) registry. For this project, we will use VDR-BVs previously identified through ChIP-seq analysis in LCLs and conduct subsequent analyses in primary CD4+ and CD8+ T cells. The proposed study will: 1) Identify VDR binding sites through ChIP-exo analysis in primary CD4+ and CD8+ T cells using the SICCA cases and controls; 2) Estimate the association between VDR-BVs and vitamin D-related SNPs and SjD susceptibility among SICCA study subjects using MR methods; and 3) Estimate the association between VDR-BVs and vitamin D-related SNPs and clinical SjD phenotypes among SICCA study subjects using MR methods. Results from the proposed aims will identify genetic risk factors for SjD related to vitamin D and identify new genes and regulatory pathways involved in the development of SjD. Ultimately, the goal of this work is to understand the mechanisms by which vitamin D affects this immune-mediated disease.

NIH Research Projects · FY 2025 · 2022-08

Project Summary / Abstract Problems in scientific practice have generated widespread concern about the reliability of findings in behavioral and social science research (BSSR), including work related to aging. These problems arise from a lack of transparency on the part of researchers, as well as incentives in publishing and academia that encourage the presentation of results in ways that are newsworthy, but not necessarily reproducible or rigorous. Training on transparency and reproducibility is critical for equipping the BSSR workforce to conduct credible research. But while it is becoming more widely available, it is not yet the norm in graduate curricula. Led by the Berkeley Initiative for Transparency in the Social Sciences (BITSS), the Research Transparency and Reproducibility Training (RT2) is designed to strengthen the integrity of BSSR by increasing awareness of problems driven by opacity and providing exposure to and practice with tools designed to improve openness. In addition to providing an overview of problems and solutions in transparency, RT2 will provide space for practice with open science tools, as well as feedback on ongoing work in which participants are applying openness practices. BITSS has developed curricular materials for and delivered seven RT2 events and dozens of related workshops since 2014. This project will first adapt these for application in BSSR focused on aging topics, and integrating applied and discourse-based approaches to improve their effectiveness. This curriculum will be delivered through annual short courses for graduate students, postdocs, and other junior researchers. We will further facilitate long-term adoption of technical and transferable skills by investing in “‘champions” who provide support to peers and collaborators. We will provide access to funding and other guidance to help them integrate new practices into their research and teaching activities. Finally, we will evaluate the effectiveness of RT2 and its impact on learners through pre- and post-training surveys and in-depth interviews with randomly selected participants. Feedback from previous participants and applicants have demonstrated RT2’s effectiveness, as well as growing demand for training of this kind. In broadening its methodological focus and integrating applied and discursive approaches, RT2 can further transform research culture, equipping participants to lead, teach, and collaborate on transparent and reproducible aging research, laying the groundwork for better informing the decisions of policymakers, practitioners, and the public, and for facilitating collaboration and equity in BSSR.

NIH Research Projects · FY 2025 · 2022-08

Project Summary Alzheimer’s disease (AD) pathology begins to emerge in the brain and drives cognitive decline before the onset of clinical symptoms. It has been known for decades that the basal forebrain (BF) is vulnerable to early tau accumulation, and yet neuroimaging research of early, preclinical AD has largely focused on tau accumulation in the temporal lobe, beginning in entorhinal cortex (ERC), and subsequent memory decline. An overarching goal of the current proposal is to reinvigorate interest in BF research, especially in cognitively healthy older adults where the earliest, preclinical AD pathological changes can be observed. The broader implication of a better understanding of how preclinical AD unfolds across the brain is the opportunity to detect the disease before the emergence of symptoms when interventions can be most effective. Research Project: In this proposal, BF and ERC will be examined side-by-side to test the hypothesis that a common, preclinical AD process is unfolding in both regions. Atrophy and tau accumulation in BF and ERC will be explored, including how tightly correlated these changes are and whether there is evidence of temporal ordering of these changes (e.g., BF first or ERC first). Cognitive consequences of BF tau burden and atrophy will be assessed and compared to memory changes associated with ERC tau and atrophy. Specific gaps in the field will be addressed by exploring relationships of BF and ERC volume/atrophy with PET biomarkers and longitudinal, domain-specific cognition (Aim 1), determining how patterns of seed-based functional connectivity of BF and ERC relate to tau pathology burden and spread (Aim 2), and establishing correlated gene expression relationships across BF, ERC and connected regions to identify common pathways that may underlie their vulnerability to AD (Aim 3). These experiments will help uncover common drivers of AD vulnerability in BF and ERC and elucidate the role of BF in preclinical AD, including associations with generalized cognitive decline. Candidate Development and Environment: This proposal will promote the candidate’s ultimate career goal to build an independent research program that takes multimodal, innovative approaches to characterizing cognitive aging and preclinical AD. During the K award, the candidate will extend her expertise in neuroimaging of preclinical AD by integrating novel PET tracers and datasets while also acquiring new expertise in several key areas: the anatomy of the BF and cholinergic system, analysis of genetic expression data in concert with neuroimaging data and advanced statistical approaches grounded in causal inference. The candidate’s training plan outlines her approach to engage the rich resources available in her lab and the broader UC Berkeley community, including access to unique datasets, community-building seminars and retreats and world-renowned faculty across many disciplines. The diverse team of collaborators and advisors the candidate has assembled for this project will ensure she is successful in leveraging her unparalleled environment toward gaining independence.