University Of California Berkeley

NIH Research Projects · FY 2026 · 2008-02

PROJECT SUMMARY Inappropriate recognition of self nucleic acids (NA) by members of the Toll-like receptor (TLR) family can result in autoimmune diseases such as lupus and psoriasis. TLR7 (and TLR8 in humans) and TLR9 can be activated by self RNA and DNA, respectively, so defining the mechanisms that limit responses by these TLRs is highly relevant to human health and disease. There is also accumulating evidence that the mechanisms controlling TLR7 and TLR9 responses are distinct, but our understanding of the molecular bases for these differences and their relevance for disease remain poor. This application is a renewal of the grant that has funded our research studying the regulation of NA-sensing TLRs for 15 years. Our prior work helped to establish the paradigm that multiple mechanisms operate to restrict the function of NA-sensing TLRs to endosomes, which limits recognition of self NAs released from dead cells into the extracellular space. In the last funding period, we made a major breakthrough that revealed a new mechanism mediated by the TLR chaperone Unc93b1 that limits TLR7 responses to self RNA, and we showed that disruption of this mechanism results in TLR7-dependent autoimmunity in mice. Intriguingly, this mechanism controls TLR7 but not TLR9. Our prior discoveries raise many key questions that we aim to tackle in this renewal application. We do not yet understand the molecular steps controlling the new mechanism of TLR7 regulation we discovered. Moreover, we recently identified autoimmune patients with in-born coding variants in Unc93b1, but we do not know if/how these variants cause disease. In this proposal we will also expand our studies of NA-sensing TLR regulation beyond Unc93b1 based on recently completed genome-wide CRISPR screens for genes that limit TLR7 and TLR9 responses. Both screens identified genes and pathways involved in core cell biological processes, including endosome and lysosome regulation, underscoring the paradigm that the cell biology of NA-sensing TLRs is critical to their regulation. However, the hits from the TLR7 and TLR9 screens are almost completely non-overlapping, providing exciting mechanistic insights into how these receptors are distinctly regulated. Based on these results, we propose 3 Specific Aims. Aim 1 will define the key steps by which Unc93b1 limits TLR7/8 responses and will test whether the human coding variants we have identified disrupt these steps. Aim 2 will characterize results from a genome-wide CRISPR screen that identified the cellular machinery and pathways limiting TLR7 responses to self RNA. Aim 3 will focus on TLR9 and begin to define the mechanisms that limit TLR9 responses to self DNA. The overall impact of this application comes from the central role that NA-sensing TLRs play in autoimmunity and from the benefit gained by defining the mechanisms that limit responses to self NA. Our central premise is that defining the mechanisms that regulate TLR7 and TLR9 will uncover their distinct roles in autoimmune diseases and enable more effective therapies.

NIH Research Projects · FY 2025 · 2007-08

Genome sequencing is becoming cheaper and more powerful. However, a bottleneck to scientific progress using these data is the generation of high-quality genome annotations, describing the location and function of the genes in genomic DNA. In the past, these annotations were generated exclusively by professional biocurators, and these biocurators continue to be a critical source of expertise. However, the number of such biocurators is small compared to the amount of genomic DNA that is available. In recent years, professional biocuration has been supplemented by a growing volunteer force of interested biologists, each generally interested in one or two genes of interest. Although genome annotation is often done in bulk using computational tools, there is currently no substitute for a final pass of manual annotation. This is most commonly done using our Apollo software, which allows for live simultaneous collaborative annotation over the web. Our proposal here is to improve Apollo so as to empower both professional biocurators and crowdsourcing volunteers. We will empower professional biocurators by giving them the power tools they need to simultaneously annotate multiple genomes (by exploiting synteny), annotate variants, and annotate the function of genes. We will empower the crowdsourcing volunteers by lowering barriers to entry, making Apollo more usable. For all users we will train machine learning systems to automatically detect common annotation errors and suggest improvements. We will support Apollo users with maintenance, bugfixing, and various feature requests, as well as extensive outreach including outreach to developers.

NIH Research Projects · FY 2025 · 2004-09

Project Summary/Abstract (Overall) This application is a competitive renewal of a program project grant entitled, “The intersection of innate and adaptive immunity to intracellular pathogens.” A major goal of this P01 is to identify and characterize innate immune pathways that are triggered, avoided, or manipulated by intracellular pathogens and to determine the role of these pathways during infection and immunity. More specifically, in this P01 we focus on the microbiology and immunobiology of three diverse facultative intracellular bacterial pathogens; Listeria monocytogenes, Legionella pneumophila, and importantly, M. tuberculosis. An overall theme of this application is that the innate immune system detects key metabolites and virulence activities of intracellular bacterial pathogens, including cytosolic invasion or access via dedicated bacterial secretion systems. For example, all three pathogens under investigation activate STING, either by direct secretion of a cyclic-di- nucleotide (CDN) or by activation of host cell cGAS in response to bacterial DNA, to activate STING, culminating in critical host responses including activation of a type I IFN and autophagy. In Project 1, Portnoy extends his studies on the roles of c-di-AMP and STING by examining how c-di-AMP secretion affects L. monocytogenes pathogenesis and dissemination to the placenta and brain during an oral model of infection. In Project 2, Cox asks how M. tuberculosis uses its ESX-1 type VII secretion system to perforate phagosomal membranes, activate STING and induce production of type I IFN, which promotes infection, but also activates ubiquitin-mediated autophagy responses, which serves to limit infection. However, while type I IFNs are generally accepted to play a crucial role in orchestrating anti-viral immunity, the roles of type I IFNs in the responses to bacteria are complex and often exacerbate infection by bacterial pathogens. In Project 3, Vance presents preliminary data suggesting that type I IFN-dependent induction of the interleukin-1 receptor antagonist (IL-1Ra) is an important mechanism by which type I IFNs exacerbate bacterial infections. We also explore the idea that CDNs are just one example of immunostimulatory bacterial metabolites by analyzing two other bacterial metabolites that lead to the activation of what are classified as innate or invariant T-cells, including MAIT cells and Vg9Vd2 T-cells. We will ascertain the relevance of these metabolites during L. monocytogenes and M. tuberculosis infection (Projects 1, 2 and 4). In Project 4, Stanley propose to follow up on her preliminary data showing the CDN-based protein vaccines result in a robust and durable tuberculosis vaccines especially when introduced intranasally that is associated with induction of a protective Th17 response. Stanley proposes to evaluate a number of vaccine strategies using CDNs in combination with modified BCG and L. monocytogenes-based vectors.

NIH Research Projects · FY 2024 · 2004-07

PROJECT SUMMARY This application seeks renewal of the Prevention Science Research Training Program (PSRTP). The PSRTP was established in 2004 as a collaborative effort of the Prevention Research Center (PRC) of the Pacific Institute for Research and Evaluation and the School of Public Health of the University of California Berkeley. The PSRTP is designed to prepare early career researchers to apply prevention science to the reduction of alcohol misuse, dependence, and problems. The PSRTP takes a trans- disciplinary approach that emphasizes the professional development of early career researchers by providing training that leads to greater (1) knowledge of the nature, etiology and consequences of alcohol misuse, dependence and problems; (2) understanding of the spectrum of prevention strategies and the science underlying these strategies; (3) knowledge of the methodologies and analytic strategies relevant to the study of prevention; and (4) sophistication in techniques associated with the implementation and evaluation of prevention programs. The overarching goal of the PSRTP is to provide early career scientists with the knowledge and skills necessary to succeed in the highly competitive research and academic environments that characterize prevention research. The PSRTP has the following specific aims: (1) to deliver a core curriculum to build expertise in prevention science as it relates to alcohol studies through a series of structured courses that address alcohol use and misuse, etiology, methodology, responsible conduct of research, and protection of human subjects; (2) to provide training within a trans-disciplinary environment through informal seminars structured around content and methodological areas and through participation in research in areas outside the trainees’ primary areas of expertise; and (3) to facilitate each post-doctoral trainee’s development as a researcher through intensive mentorship, undertaking an independent research project, participating in a grant writing practicum, publishing, and engaging in professional development activities. The PSRTP achieves these aims through: (1) formal seminars; (2) intensive individual mentoring by senior faculty; (3) development and execution of yearly Individual Development Plans; (4) integration into an ongoing funded research program; (5) completion of an independent research project resulting in at least two sole or senior authored papers; (6) specialized training in qualitative and quantitative research methods and data analysis through guided study groups, formal coursework at the University of California Berkeley, and workshops and seminars at other institutions; (7) attending regular presentations on current research methods, topics, and findings at seminars and roundtables at PRC that are independent of the PSRTP seminars, and (8) participating in professional development activities.

NIH Research Projects · FY 2026 · 2002-04

PROJECT SUMMARY/ABSTRACT Spontaneous activity is a hallmark of developing neural systems. Prior to the maturation of vision, immature retinal neurons spontaneously generate correlated activity. This activity propagates in the form of waves of action potentials that sweep across the retinal ganglion cell layer. Retinal waves persist from embryonic day 16 through two weeks after birth, a developmental period when functional circuits within the retina are emerging and retinal projections to the brain are undergoing a tremendous amount of refinement. Here we explore three Aims regarding mechanisms underlying the function of retinal waves. In Aim 1, we focus on understanding the circuits that mediate embryonic retinal waves. At this age, the retina is comprised of retinal ganglion cells, a few amacrine cells, and an extensive neuroblastic layer in which the other cell types are differentiating. Despite the lack of mature circuit elements, retinal waves are robust. Here we test hypotheses regarding the relative role of gap junction coupling and synaptic transmission in mediating these waves. In Aim 2 we focus on second postnatal week when retinal waves exhibit a profound propagation bias. During this time period, the majority of waves travel in the nasal direction, a firing pattern which mimics optic flow induced by forward motion. Here we explore the hypothesis that this asymmetry in propagating activity is due to asymmetric connectivity between a GABAergic interneurons that are well integrated into wave generating circuits. Finally, in Aim 3 we investigate the role of retinal waves and visual stimulation of light-sensitive retinal ganglion cells in the release of dopamine in the developing retina. Though dopamine plays a key role in several developmental processes, what controls release is unknown. We will employ a novel imaging method that allows for measuring phasic dopamine release in parallel with calcium transients. Using this method, we will explore the relative role of retinal waves and light stimulation in mediating dopamine release during development.”

NIH Research Projects · FY 2026 · 2002-02

Project Summary Genetic deficiency, environmental harmful stimuli, disease conditions, and aging can initiate various pathological processes in eye lens cells, ultimately leading to different types of cataracts. Previous studies of connexin 46 (Cx46) knockout (KO) mice at different genetic backgrounds have identified at least three genetic modifiers whose gene variants influence the development and/or severity of age-related cataracts. The three genetic modifiers are: a) the Prx gene on chromosome 7, which encodes periaxin, a PDZ-domain intrinsically disordered protein (IDP); b) the Bfsp2 gene on chromosome 9, which encodes beaded filament structural protein 2 (CP49 or phakinin), a key component of lens-specific intermediate filaments; c) a potential candidate, the PKIG gene on chromosome 2, which encodes the cAMP-dependent protein kinase inhibitor gamma, an effective inhibitor of PKA-mediated phosphorylase activation. This proposal aims to investigate how and why these three genetic variants modulate the severity of age-related nuclear cataracts in Cx46KO mice across different strain backgrounds. We will utilize cutting-edge technologies, including in vivo imaging with adaptive optics two- photon fluorescence microscopy and TMT-based quantitative mass spectrometry, to determine the molecular and cellular mechanisms underlying cataract formation. We will test novel hypotheses about the early pathological mechanisms of liquid–liquid phase separation (LLPS) in membrane associated cytosolic complexes that contribute to cataract formation. The proposed experiments will identify protein components and pathological cellular elements that cause lens light scattering and will determine the roles of secondary signaling molecules, such as calcium and cAMP, transported by lens gap junction channels in regulating membrane-associated cytosolic complexes in lens cells. Additionally, the study will characterize early pathological changes in LLPS-mediated protein aggregation caused by abnormal calcium and/or cAMP-PKA signaling in conjunction with genetic modifiers. This project will explore new knowledge and strategies for delaying or inhibiting cataract formation in vitro by manipulating secondary signaling molecules and/or genetic modifiers.

NIH Research Projects · FY 2025 · 2000-09

Project Summary/Abstract The GTP provides graduate training and research opportunities at the University of California, Berkeley, emphasizing the cross-disciplinary nature of this rapidly advancing field. The trainees and training faculty are drawn from Ph.D. programs in diverse departments and graduate groups, associated with a campus-wide Designated Emphasis that formalizes the requirements for a broad education in computational biology and genomics. The program has three principal thrusts: population and evolutionary genomics, functional genomics, and computational and statistical methods. Trainees will take advantage of a rich training environment of seminars, retreats, and group meetings as well as a diverse set of formal course offerings that range from introductory to advanced methods in genomic biology. Research training will typically begin by the end of the second year, following an introductory period of laboratory rotations, coursework, and preliminary examinations. Progress of the trainees is evaluated by annual thesis reviews and regular meetings with mentors. The Program will train between six and ten predoctoral students per year in genomics and computational biology.

NIH Research Projects · FY 2025 · 1997-08

Abstract The vision science community at UC Berkeley has a long and distinguished history, having contributed seminal discoveries in the fields of visual system development, physiology, genetics, psychophysics, and pathology over the past 50 years. UC Berkeley vision scientists come from diverse academic disciplines, increasing our understanding of vision at many different levels. Our group consists of 15 Principal Investigators holding 18 NEI R01 grants, along with more than 20 other Vision Scientists, ranging in interests from molecular mechanisms of retinal physiology and pathology to human visual perception. We request continued support for our CORE grant to ensure further success in vision research through shared resources and services. We seek funding for three modules which will support current faculty and attract new faculty to investigate the visual system. The modules are: (1) Gene Delivery (Xiaohua Gong & John Flannery, co-directors), designed to provide molecular biology expertise and support in the use of viral vectors for delivering genes into tissues of the visual system and for creating transgenic animal models of ocular disease. (2) Optical Imaging (Maria Feller and Austin Roorda, co-directors), which will apply and develop advanced imaging methods for visualizing cells in both animal and human eyes – designing, building, and facilitating the use of customized microscopes in individual labs and the Microscopic Imaging Center, and (3) Bioinformatics (Karthik Shekhar and Karsten Gronert, co-directors), which will facilitate the acquisition, organization, and analysis of large data sets obtained from genomic, transcriptomic and other -ohmic studies on the visual system, as well as high-density functional imaging data obtained with fluorescent reporters expressed in the retina or brain. UC Berkeley has demonstrated its strong commitment by hiring 6 new faculty members studying vision, with 4 more hires planned for the next several years, enabled by a $50 million philanthropic gift to the newly named Herbert Wertheim School of Optometry. The UC Berkeley central administration, and the academic centers for Vision Science on campus (Departments of Molecular & Cell Biology, Optometry, and the Helen Wills Neuroscience Institute) have all demonstrated their continued dedication specifically to the Vision Science Core by committing cost-sharing resources equivalent to more than $250,000 over the next 5 years.

NIH Research Projects · FY 2025 · 1997-07

The UC Berkeley Center on the Economics and Demography of Aging (CEDA) provides an outstanding infrastructure to develop and pursue research that shapes scholarly understanding of the social science determinants of population-level older adult health, and research that informs public policy on aging. CEDA has earned an international reputation as one of the leading research centers in the world for the economics and demography of aging, drawing on the Berkeley Department of Demography as a leading research and training program in these fields. CEDA’s mission is to promote and disseminate path-breaking theoretical, methodological, and empirical research focused on four signature themes: (1) Mortality measurement, (2) Policy and behavioral determinants of adult health, (3) Biodemography of aging, and (4) Macro consequences of global aging. Cross-cutting these themes will be an expanded emphasis on understanding the drivers of and remedies for socioeconomic disparities in aging. CEDA’s mission will be advanced via 5 cores: administrative and research support, program development (pilots), communication and dissemination, external networks, and external research resources support. The efforts proposed here are designed to lead to fundamental field-shaping research, innovative external grant applications to NIA and other agencies, valuable publicly available research tools and data sets, and translational research disseminated to inform aging-related policy.

NIH Research Projects · FY 2025 · 1997-04

OVERALL: SUMMARY The UC Berkeley Superfund Research Center, in consultation with the Center’s key stakeholders and advisory boards, has identified six complex and intractable problems associated with hazardous waste sites, namely how to: 1) better assess risks to pregnant women, the fetus and young children; 2) protect disadvantaged communities; 3) understand the totality of chemicals communities are exposed to; 4) account for interactions between mixtures of chemicals; 5) perform on site in situ remediation without depleting valuable resources or transporting contaminated soil to other locations; and, 6) destroy persistent chemicals that are resistant to remediation. Four interactive projects (2 biomedical and 2 engineering) and 4 required cores are proposed to address these six problems though original research. Our proposed research and community engagement efforts aim to provide information and tools that will help solve these complex problems associated with Superfund contaminants and address the four mandates of the Superfund Research Program (SRP). The proposed interdisciplinary projects and cores of the UC Berkeley Center are all designed to address one or more of the four mandates as applied to chemicals high on ATSDR’s Superfund priority list, of importance to the US EPA’s Programs, and of concern to other stakeholders, including arsenic, chromium and other metals, PFAS and other halogenated contaminants. Our overall goal is to improve the remediation and understanding of the health effects of mixtures of Superfund contaminants. To achieve this, we propose to take a systems approach, a problem-solving paradigm grounded in public health concepts. Together with our Stakeholders, we will collectively form an understanding of some of the issues they face and create a bidirectional dialogue between us. We will attempt to perform basic research that informs action, learning and refining as we go. This ‘systems’ approach is central to improving public health. It is an approach that has been widely used in many public health settings and will be used as the central paradigm within our Center. Biomedical Projects 1 and 2 with the DMAC will study the effects of mixtures of contaminants on perinatal outcomes and the developing immune system. Engineering Projects 3 and 4 will develop a complementary treatment approach consisting of in situ chemical treatment in combination with biological radical systems to remediate a broad range of PFAS and other highly persistent halogenated pollutants. With Core A they will also assess the fate of the transformation products generated by the treatment process and their potential for toxicity. Core B in collaboration with Projects 1, 4 and the DMAC will address drinking water quality problems in California that exist despite sophisticated statewide water infrastructure and federal water quality laws. Core C (DMAC) will manage, store and share data from all projects and cores using FAIR guidelines and assist in the biostatistical analysis of all project-generated data. Core D will provide all trainees with trans-disciplinary education, and training in environmental health, toxicology and environmental engineering.

NIH Research Projects · FY 2024 · 1995-07

Summary: P. aeruginosa is a leading cause of blinding eye disease. Contributing to disease pathogenesis is invasion of corneal epithelial cells, as we have demonstrated in vitro and in vivo. Here, we report that P. aeruginosa can establish multiple niches inside corneal epithelial cells, some colonizing the cytoplasm and other vacuoles – often in the same cell. Reporter expression results show different phenotypic states in these alternate locations, the pattern suggesting “acute” infection mode for cytoplasmic bacteria and “chronic” (biofilm forming) mode for those in vacuoles. While genetic regulation of the switch between these two states has been extensively studied in vitro, how this might work inside a cell is unknown. Our published and preliminary data show that “acute” and “chronic” modes cooperate to determine corneal epithelial cell responses, to allow P. aeruginosa to penetrate the multilayered corneal epithelium, to colonize the cornea, and to cause pathology. Here, we will test the hypothesis that their unique intracellular niches contribute to their cooperative efforts during corneal infection. The three aims will explore significance of intracellular diversification to the bacteria, to the host corneal epithelial cell, and to disease pathogenesis. Approaches will utilize multiple novel tools developed using funding from this grant, including bacterial constructs, imaging technologies, and infection models. The two consultants are leading experts in bacterial gene regulation, respectively covering both phenotypes. Importantly, our data suggest that vacuolar P. aeruginosa transition into biofilms, which can be difficult to kill or even to culture. A vacuole would enclose a biofilm inside two host membranes - vacuolar and plasma. This intracellular phenotype alone could explain why P. aeruginosa infections are notoriously difficult to manage and why disease can continue despite apparent sterilization of the ulcer.

NIH Research Projects · FY 2026 · 1994-05

PROJECT SUMMARY Support is requested for 12 optometry (OD) students per year to participate in short-term training in vision research during the summer following successful completion of their first year. The training will be conducted by established vision science and clinical science researchers in the Herbert Wertheim School of Optometry and Vision Science. The training program is designed to attract talented students to careers involving clinical and/or translational research. Training will be provided within the laboratories of 26 mentors in the School, where currently 28 pre-doctoral Vision Science students and 21 postdoctoral fellows are involved in eye and vision-related research. The Vision Science PhD graduate program is interdisciplinary, in existence for nearly 80 years, with the majority of its graduates remaining actively engaged in research. Training is broad, encompassing many disciplines among which are neuroscience, computational modeling, psychology, molecular and cell biology, neurophysiology, immunology and infectious diseases, with both basic science and clinical translational emphases. By serving as hosts for T35 trainees, the Vision Science research community provide ideal role models for trainees in line with the program goal of fostering interest in clinician scientist careers. A wide range of basic science, as well as clinical research projects are on- going in the laboratories of the mentors and open to trainees. To-date, this short-term training program has provided for many clinicians a conduit to the Vision Science PhD program, which has long been supported by a T32 Training Program grant. Students attending Optometry schools from across the country are targets of our recruitment efforts aimed at attracting a diverse pool of talented health professional students to our program, with outreach to individual schools and to pre-Optometry career education programs, e.g., Opto-camp, supplemented by web-based and social media promotion. A recently added, zoom-based, research career-focused event will also be made generally accessible, i.e., beyond the trainee cohort, to further support the program's long-term goal of encouraging OD students to pursue advanced research training and/or maintain involvement in research beyond their professional training.

NIH Research Projects · FY 2025 · 1989-06

7. Project Summary / Abstract Copper (Cu) is an essential micronutrient for nearly all forms of aerobic life because of its participation in key redox reactions and reactions of O2 chemistry. Cu deficiency, accordingly, has an impact on multiple metabolic and developmental pathways. Cu deficiency in animals and humans occurs because of genetic defects or in situations of malnutrition. In previous work, Merchant and co-workers, using a model organism, Chlamydomonas (an alga in the green lineage), discovered fundamental mechanisms and regulatory circuits for maintaining Cu homeostasis that are broadly relevant. Specifically, the group showed that an abundant Cu protein, plastocyanin, is replaced by an iron-containing heme protein, cytochrome (Cyt) c6, when Cu is scarce. The Cu that is spared by this replacement is “upcycled” for use in Cyt oxidase in respiration. This switch allows maintenance of two important bioenergetic pathways – photosynthesis and respiration. Genetic analysis identified a Cu-response regulator (CRR1), a transcription factor that activates the CYC6 gene encoding Cyt c6 through associated Cu response elements (CuREs) as well as ~64 other genes that form the nutritional Cu regulon, including assimilatory Cu(I) transporters CTR1 and CTR2, enzymes of heme biosynthesis, and other factors that enable Cu allocation to Cyt oxidase and that adjust thylakoid membrane properties to accommodate the substitute protein. In this project period, the focus is on how CRR1 is turned off for tight homeostatic regulation of Cu metabolism. In the working model, supported by substantial preliminary data, CRR1 activates the Cu regulon in deficiency, while upon Cu supplementation, the protein is post-translationally modified, which marks CRR1 for recognition and ubiquitylation by CEHC1/FBXO3, a newly discovered F-box protein, followed by proteasome- dependent degradation. In this context, there are 3 aims. 1) Post-translational modifications of CRR1 in +Cu cells will be captured by LC-MS following immunoprecipitation of CRR1 under specific conditions where the protein accumulates, as in the cehc1 mutant. The site(s) of modification will be tested for their impact on Cu- responsive degradation of CRR1, individually and in combination, by site-directed mutagenesis of CRR1. 2) Physical interaction between CEHC1 and CRR1 will be tested by co-localization and captured by co- immunoprecipitation, and the substrate binding domain of CEHC1 will be identified by mutation and tested in vitro for binding to the Cu dependent degron. Candidate CRR1 modification enzymes or other components in this regulatory circuit, such as a Cu sensor, will be discovered by exploiting a powerful gain-of-function classical genetic screen for constitutively active CRR1 using CuRE-reporter constructs. 3) The operation of a post- translational mechanism to regulate Cu uptake by CTRs will be evaluated by using quantitative proteomics to measure Cu-dependent changes in half-life and by monitoring sub-cellular localization as a function of Cu supply. The execution of this project will complete our picture of nutritional Cu signaling and homeostasis through discovery of the feedback loop that keeps CRR1 off in the Cu replete cells.

NIH Research Projects · FY 2026 · 1988-06

Project Summary/Abstract Listeria monocytogenes is facultative intracellular food-borne pathogen that provides an extremely amenable model for basic studies on host-pathogen interactions. During past funding periods, genetic screens led to the discovery that L. monocytogenes upregulates the expression and synthesis of glutathione synthase (GshF) during infection and that glutathione is an allosteric activator of the major virulence transcription factor, PrfA. Mutants lacking GshF fail to fully activate PrfA and consequently form small plaques in tissue culture cells and are approximately 200-fold less virulent in mice. However, virulence of gshF mutants was fully rescued by mutations that locked PrfA in its active configuration, referred to as PrfA* mutants. During the current funding period, we designed a genetic screen with the goal of identifying additional transposon mutants that formed small plaques in tissue culture cells, but were restored to a wild- type phenotype when the mutation was transduced into a PrfA* background. In addition to finding the expected gshF mutants, we found mutants in gloA, which encodes glyoxalase A, the primary component necessary for the glutathione-dependent detoxification of the reactive electrophilic species (RES), methylglyoxal (MGO), which is a toxic side-product of glycolysis in both bacteria and host cells. Mutants lacking gloA were approximately 1000-fold less virulent in mice and like gshF mutants, were restored to full virulence in a PrfA* background, suggesting that MGO is an in vivo cue leading to GshF synthesis and activation of PrfA. MGO reacts with both amino acids and guanine causing DNA damage and mutations. In preliminary data, we confirmed that gloA mutants had a 10-fold increase in their mutation rate when exposed to MGO in vitro, but strikingly, the mutation rate of gloA mutants was approximately 100-1000-fold higher in the spleens and livers of infected mice, suggesting that the in vivo environment encountered by L. monocytogenes is enriched in MGO and consequently highly mutagenic. Double gloA/prfA* mutants were not only fully virulent, they did not suffer increased mutation rates in vivo, suggesting that in the absence of GloA, activated PrfA protects against DNA damage by a yet-to-be discovered mechanism. Based on the literature, we hypothesized that DNA damage caused by MGO was repaired by UvrAB-dependent nucleotide excision repair pathway. Astonishingly, a uvrAB mutation rescued the virulence defect of gloA mutants, but unlike PrfA* mutants, gloA/uvrAB mutants still had an extremely high mutation rate. These data suggest that gloA mutants suffer severe DNA damage in vivo and are killed by the resultant DNA repair process. In this renewal, we propose to characterize the in vivo environment that causes such a high rate of mutations in gloA mutants, determine how PrfA mediates GloA-independent protections from MGO, and lastly explore the hypothesis that gloA mutants are killed by their own DNA repair process.

NIH Research Projects · FY 2026 · 1985-09

Abstract Prefrontal cortex (PFC) plays a pivotal role in distributed neural networks orchestrating human behavior. Notably, PFC dysfunction is observed in numerous debilitating developmental, neurological and psychiatric disorders. This emphasizes the need for improved knowledge of the physiology implementing goal-directed behavior to better understand these devastating neuropsychological impairments. The last two decades have seen an exponential increase of PFC research in animals and humans but numerous questions remain. Intracranial EEG recording (iEEG) in humans provides a powerful method to assess the spatial-temporal structure of network activity enabling imaging of both local and inter-areal dynamics. Local neural activation is measured with high frequency activity (HFA; 70-200 Hz) and single-unit activity (SUA). Inter-areal interactions are assessed using connectivity metrics including phase slope index, directional phase amplitude coupling, Granger causality, mutual information and single-trial HFA latency onsets. We combine these local and network approaches with iEEG recordings to address four core areas of PFC dependent function including attention, working memory, learning and interpersonal communication. Aim 1 draws on our prior iEEG work documenting lateral PFC-hippocampal theta band engagement in working memory (WM) and rhythmic PFC- Parietal attentional sampling in the theta range. Here we test the hypothesis that shared and distinct theta networks support WM and attention. Critically, we record from the same individual utilizing identical stimuli differing only in task requirements. In a second study, we employ a naturalistic slot machine gambling task positing that orbital PFC-insular- anterior cingulate interactions track wheel-spinning expectations determining both satisfaction and the motivation to spin again. The slot machine expectation manipulation we employ is banned in casinos given its powerful drive to continue gambling. Aim 2 assesses feedback- based learning in two studies. One posits lateral PFC-hippocampal interactions in rule-based concept learning, the other proposes a central role for orbital PFC-hippocampal interactions in flexibly responding to changing outcome contingencies. Aim 3 proposes novel dual iEEG studies examining how interacting humans exchange knowledge. One task requires transferring knowledge about items and a second examines non-verbal social communication. Dual iEEG involves recording from two interacting patients and preliminary data indicates synchrony between patients in PFC-hippocampal-anterior cingulate circuits during knowledge exchange. Taken together, the proposed work will advance our understanding of how PFC dependent networks support goal-directed human behavior.

NIH Research Projects · FY 2025 · 1984-07

This project seeks to continue providing high quality, interdisciplinary training in demography, with a focus on the relationships between population dynamics, socio-cultural systems, and human health and welfare. Our objective is to continue with our successful recruiting, training, and placement of high-quality trainees across a range of disciplines. Demographic analysis offers a distinct and critical perspective on the health and development of children, as many of the most important issues influencing child and family well-being in the contemporary world are demographic in nature, including declining and postponed fertility, declining and postponed marriage, and the divergence of child welfare by social class. Berkeley is widely recognized as one of the leading centers of demographic training and research in the US and the world. Berkeley has long occupied a unique niche in the population studies training ecosystem, with a strong focus on the analysis of population systems and how they relate to cultural, economic, and political systems. Our graduates hold academic positions at leading universities and demographic research centers in the departments of sociology, economics, anthropology, demography, history, public health and statistics, with recent trainees accepting tenure-track positions at Princeton, NYU, Michigan, Stanford, and others. This training grant complements our other NIA- and NIH-funded initiatives, including the P30 Center for the Economics and Demography of Aging, the R24/P2C Berkeley Population Center, the R25 Summer Workshop in Formal Demography, the NIA T32 Training in the Demography of Aging; and the newly funding NICHD T32 Training in Data Science. Berkeley demography has deep tradition of formal demography, increasingly complemented by computational demography, as well as its cultural, critical, and theoretical approaches. The program is deeply interdisciplinary, drawing students and trainees from demography, sociology, public health, and economics. Our trainees will continue to (1) learn core demographic methods and theory, with a focus on formal aggregate and computational approaches; (2) learn to think in critical and theoretically rich ways about population processes and dynamics; (3) apply their knowledge of population processes and dynamics to substantive areas, including family, migration, and health; and (4) take a broad array of supplemental courses. Some trainees received their PhD in Demography or in Sociology and Demography, and others do so in different disciplines, learning demography supplemental to their other discipline. Time from entry to PhD is typically 5 to 6 years. Trainees typically receive T32 support for up to four years for the Demography PhD, and up to two years for trainees from other departments, and most are recruited for the T32 in their first or second years. Support is requested for six predoctoral trainees, consistent with the past.

NIH Research Projects · FY 2025 · 1983-07

Project Summary In eukaryotic cells, the packaging of genomic DNA into nucleosomes represents the basic barrier to transcription by RNA polymerase II (Pol II). The dynamic modulation of the magnitude of this barrier and the degree of chromatin compaction constitute fundamental mechanisms of regulation of gene expression. Having previously characterized the magnitude and mechanical properties of the nucleosomal barrier and their effect on Pol II transcription, we aim to investigate the modulation of this barrier and its regulation of genome accessibility to Pol II by environmental and cellular factors. We will do this by combining single-molecule optical tweezers/fleezers (SM-OT) methods with high-resolution single particle cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), and quantitative in vivo fluorescence imaging. We have determined that nucleosomes display a trimodal distribution of unwrapping forces corresponding to alternative nucleosome states that we hypothesize represent different barriers to transcription by Pol II. We will investigate this intrinsic plasticity of nucleosomes and its modulation by factors that promote their interconversion, including histone variants, post-translational modifications, and specific transcriptional regulators (pioneer factors, elongation factors, and histone chaperones). Next, we will use our SM-OT assay to investigate how specific transcriptional regulators (e.g., FACT, Spt4/5, Chd1) affect the dynamics of Pol II as it transcribes through the nucleosomal barrier. We will also explore how histone PTMs, that have either activating or repressive roles on transcription, modify the molecular trajectories and dynamics of individual Pol II molecules. Moreover, we will study how Pol II crosses hexasomes and tetrasomes, both generated during moderate and intense transcription and that have been proposed to play important roles in vivo. We will structurally characterize the nucleosome remodeling during passage of Pol II by cryo-ET both in the presence or absence of transcription regulators. In eukaryotic cells, gene expression requires the passage of Pol II through arrays of nucleosomes organized as chromatin. These arrays can adopt higher-order and more compacted structures that impose a greater barrier to transcription by Pol II. Therefore, to understand how nucleosome arrays regulate genome accessibility, we will study their mechanical stability using SM-OT unwrapping assays and characterize the energetics of internucleosome interactions in these structures. We will also investigate the impact of nucleosomal arrays on the transcription dynamics of individual Pol II using SM-OT in the absence and presence of transcription regulators, and under different conditions that modulate chromatin compaction. We will compare the dynamics of Pol II obtained in these in vitro experiments, with its dynamics in vivo. To this end, we will introduce the strong nucleosome position sequence 601 into Drosophila embryos and monitor the effect of single vs multiple nucleosomes on the rate of transcription by Pol II via quantitative live-cell imaging.

NIH Research Projects · FY 2025 · 1982-07

Project Summary Thirty-two Vision Science preceptors, members of the Vision Science Graduate Group from 7 different departments/11 programs on the U.C. Berkeley campus (optometry and vision science, psychology, molecular and cell biology, neurobiology, neuroscience, infectious disease and immunology, bioengineering, computer science, physics, electrical engineering, chemical and biomolecular engineering), seek support for 10 predoctoral trainees and 1 postdoctoral trainee. Support is sought for 2 years of graduate training toward the PhD for the predoctoral trainees and for 3 years for the health-profession degree seeking trainee (OD, MD etc.) The interdisciplinary program in Vision Science has been in existence for over 80 years. The first PhD graduated in 1950. There are currently 1 postdoctoral (OD) and 32 predoctoral students engaged in studies leading to the PhD in Vision Science. In addition, there are 30 post-doctoral fellows currently training in the laboratories of the faculty of the Vision Science Graduate Group. Of the 284 trainees who have received research degree training in Vision Science (almost all PhD), the majority are now active vision researchers. Many have successfully competed for independent research funding. Our purpose is to attract outstanding trainees who will develop independent and productive vision research careers. Pre-doctoral and health profession degree trainees, most with additional formal basic science training (e.g., cell biology, immunology, neurobiology, epidemiology, or biostatistics), will earn Ph.D. (Vision Science) degrees. Each predoctoral trainee will receive stipend support during the first two years from the NIH Training Grant, supplemented by the Departmental and University fellowships. During the final three years, support will be provided entirely from resources of the University of California (primarily through individual faculty research grants). Health profession trainees will be supported for the first three years followed by other funding. Trainees will complete the formal course and teaching requirements and will be trained in laboratory research techniques in both basic sciences and vision science. The training is augmented by the extensive resources of the Berkeley campus and the technical support provided to the Vision Science Graduate Group and the NEI Core Grant.

NIH Research Projects · FY 2026 · 1978-07

This proposal reflects the renewal of an NIAAA-funded alcohol training program at the Alcohol Research Group (ARG) in operation since 1971, which has provided 279 fellows with training and support. The main goal is to continue to support a program designed to prepare trainees for a path of active research in alcohol studies. This will be accomplished by offering applicants with backgrounds in public health, epidemiology, psychology, sociology, social welfare, economics, and related professional disciplines the opportunity to carry out their own research and grant-writing with the support of a collegial and highly interactive environment of researchers and faculty actively working in the alcohol field. The Director of Training is Dr. William Kerr, a Senior Scientist at ARG and Director of NIAAA National Alcohol Research Center Epidemiology of Alcohol Problems. Our program focuses primarily on training in the incidence, prevalence, and etiology of alcohol use, use disorders and related problems and secondarily on alcohol-related health services and alcohol policy research. Fellows learn from an intensive period of residence and involvement in the research environment and activities of the Alcohol Research Group and it’s long-standing NIAAA National Alcohol Research Center. ARG’s research focii reflect the Program aims and include the social epidemiology of alcohol problems and alcohol-related health services and policy research. Fellows also benefit from participation in mentorship, research, and training opportunities at the School of Public Health at UC Berkeley, where the program resides and at collaborating institutions UCSF, UCLA and San Jose State University. Three postdoctoral and 3 predoctoral fellows are supported by the program annually, with most in residence for 2 years. Predoctoral fellows complete a dissertation on an alcohol-related topic, while postdoctoral fellows publish papers, conduct new research, and submit NIAAA grant applications. Fellows are advised and actively mentored by our 16 Training Faculty at ARG, UC Berkeley and collaborating institutions. All trainees attend and contribute to a weekly Advanced Alcohol Research Seminar, a formal course offered at ARG via UC Berkeley’s School of Public Health. Other program components include graduate courses at UC Berkeley, a Grant-Writing Seminar, visiting speakers, in-house statistical and other trainings and training in the responsible conduct of research. The proposed renewal would continue the only NIAAA-funded T32 training program to focus broadly on the epidemiology of alcohol-related problems.

Other NSERC · FY 2024

somatosensory cortex, perceptual learning, neural population coding, 2-photon microscopy, voltage imaging, computational neural modelling

Other NSERC · FY 2024

Computational biology, Machine learning, Sequence-to-activity models, Long read sequencing, Deep neural networks, Functional genomics, Epigenetics, Gene regulation, Nuclear lamina, CpG methylation

Other NSERC · FY 2024

Excited state dynamics, Materials science, Transport, Semiconductors, Photovoltaics, Optics, Statistical mechanics, Microscopy / imaging

Other NSERC · FY 2024

Optimal Power Flow, Control of Renewables, Online Convex Optimization, Algorithms, Machine learning

Other NSERC · FY 2024

Differential Geometry, Symplectic Geometry, Gauge Theory, Low Dimensional Topology, Floer Theory, Contact Geometry, Mathematical Physics

Other NSERC · FY 2024

computer vision, machine learning, video understanding