Recent ucsf_etd items

Domain-Guided Machine Learning for High-Dimensional Multi-Modal Neuroimaging and Biomarker Integration in Alzheimer's Disease

Thu, 19 Mar 2026 00:00:00 +0000

Alzheimer's disease (AD) affects millions of individuals worldwide while imposing an escalating burden on healthcare systems and caregivers. The disease's complex pathophysiology is characterized by multiple concurrent pathological processes — including amyloid plaque deposition, neurofibrillary tangle accumulation, and progressive neurodegeneration — that unfold across multiple spatial and temporal scales with heterogeneous progression patterns and an often extensive pre-symptomatic phase. While advances in neuroimaging and fluid biomarkers have provided increasingly detailed in vivo windows into these disease mechanisms, the integration of high-dimensional, multimodal datasets presents significant computational and interpretive challenges that exceed traditional statistical approaches. This dissertation addresses these challenges by developing domain-guided machine learning methods that embed established neuroscientific knowledge — temporal biomarker dynamics, neuropathological...

DNA DAMAGE INDUCES A CONSERVED HSP70 PHOSPHORYLATION WITH ROLES IN CELL CYCLE CONTROL

Thu, 19 Mar 2026 00:00:00 +0000

Hsp70s are essential molecular chaperones that are increasingly recognized to be regulated by post-translational modifications. Here, we show that phosphorylation of a conserved threonine (T495), previously shown to be exploited by a Legionella pneumophila kinase to inhibit Hsp70, occurs endogenously in human cells in response to DNA damage, particularly when base excision repair is overburdened. This modification is cell cycle dependent, and in yeast, phosphomimetic or phosphonull Hsp70 variants disrupt G1/S progression under normal and DNA-damaging conditions. Biochemically, the phosphomimetic T495E mutation locks Hsp70 in an open-like conformation without blocking substrate engagement. Together, our results reveal a conserved mechanism by which dynamic Hsp70 phosphorylation regulates the G1/S transition, and delays cell cycle progression during DNA damage, highlighting how pathogen-derived insights can uncover fundamental cell biology principles.

Graph-Based Approaches for Exploring Chemical Space

Thu, 19 Mar 2026 00:00:00 +0000

Computational drug discovery is in a period of unprecedented abundance. Advances in high-throughput combinatorial chemistry have expanded the space of inexpensive, readily accessible compounds into the trillions. As these chemical libraries grow, so too does the success of their computational screening. Yet their sheer scale requires new methods capable of searching them efficiently and effectively. At the same time, this expansion marks a departure from the metabolites, natural products, and drugs that proteins have evolved to recognize. This raises an important question: do molecules from these libraries have not only improved on-target binding, but also greater selectivity and reduced off-target interactions? This dissertation approaches these questions through the unifying mathematical framework of a graph. After a brief introduction to graphs, computational drug discovery, and molecular docking, we present Retrieval Augmented Docking (RAD), a graph-based virtual screening...

Metabolic regulation of CD4⁺ T cell differentiation in cancer and infection

Thu, 19 Mar 2026 00:00:00 +0000

CD4⁺ T cell differentiation is essential for protective immunity against infection and cancer, yet the programs that enable productive effector differentiation across contexts remain incompletely understood. Emerging evidence implicates dynamic metabolic remodeling as a key regulator of T cell fate, but how these programs support effector differentiation and are disrupted in disease remain unclear. Here, we identify a transient CD4⁺ T cell state characterized by simultaneously high glycolysis and oxidative phosphorylation that serves as a critical metabolic intermediate during effector differentiation. During acute bacterial infection, CD4⁺ cells that enter this early-activated state exhibit elevated mitochondrial reactive oxygen species and sustained AP-1 activity, supporting Th1 effector programs even as proximal TCR signaling wanes. This program is conserved across CD4⁺ lineages, including Th2 cells, which similarly transit through an early-activated state with elevated AP-1...

Nitric oxide mediates interspecies interactions between Pseudomonas aeruginosa and Candida albicans

Thu, 19 Mar 2026 00:00:00 +0000

A fundamental aspect of life as a microbe is to live inside microbial communities, where constant interactions occur between members of different species and even different kingdoms of life. Massive changes in gene expression result from these interspecies interactions, with significant effects on both the microbial organisms involved, and the ways the microbial community as a whole interacts with its environment, such as that of an infection with the host. Despite the relevance to human health, genes mediating interspecies interactions are broadly uncharacterized. The study of microbes in multi-species communities, where the expression of such genes is induced, therefore, is an important and necessary way to investigate the molecular mechanisms behind interspecies interactions. The yeast, Candida albicans, is a normal resident of the human microbiome, but is also an opportunistic pathogen that can cause life-threatening bloodstream infections. The gram-negative bacterium, Pseudomonas...

Transcriptional Programming as a Determinant of Differential Drug Sensitivity in Breast Cancer

Thu, 19 Mar 2026 00:00:00 +0000

Cell states provide valuable information about the regulatory networks that dictate cellular function and behavior, thereby offering deeper insights into disease mechanisms. Identifying transcriptional programs that are functionally relevant and persist throughout disease progression remains a significant challenge, and addressing it is critical for developing therapies tailored to disease biology. Here, we present two case studies investigating the interplay between pre-existing transcriptional programs and drug response. In chapter 1, we leverage single-cell RNA sequencing to map cancer cell transcriptional states present in treatment naïve triple negative breast cancer models. Through integrated computational and experimental approaches, we characterize the functional consequence of a recurrent inflamed subpopulation and its contribution to chemotherapy resistance. In chapter 2, we explore MYC-driven transcriptional rewiring of mitotic processes to uncover a previously unrecognized...

Inflammatory switches in chemoattractant cues guide lymphocyte homing to responding lymph nodes and B cell evolution within germinal centers

Thu, 19 Mar 2026 00:00:00 +0000

In response to inflammatory insults, lymph nodes (LNs), major organs responsible for initiation of adaptive immunity, remodel themselves to produce an optimal response. Sustained lymphocyte migration from blood into LNs is one key aspect of this. The CC-chemokine receptor-7 (CCR7) ligand CCL21 is required for LN entry but is downregulated during inflammation, and it has been unclear how recruitment is maintained. Here, we show that LNs switch from total CCL21 dependency for lymphocyte recruitment to utilizing oxidized cholesterol, whose production is upregulated in LN high endothelial venules during viral infection. Lymphocytes also switch from CCR7 to the oxysterol receptor EBI2 for inflamed LN entry. Additionally, LN CCL19, a second ligand for CCR7 that is dispensable for LN homing in homeostasis, becomes critical in lymphocyte recruitment during inflammation. After entry into LNs, B cells then organize themselves into germinal centers (GCs), sites of antibody somatic mutation...

Leveraging Implementation Science and Innovation to Advance Equity in Cancer Detection and Diagnosis in Africa

Thu, 19 Mar 2026 00:00:00 +0000

Global inequities in early cancer detection and diagnosis continue to drive preventable mortality from breast and childhood cancers across low- and middle-income countries (LMICs). While high-income countries have achieved substantial reductions in cancer mortality through advances in diagnostics, therapeutics, and precision medicine, these gains have not been equitably extended to LMICs. Instead, limited diagnostic capacity, financial barriers, and fragmented care pathways contribute to delays in timely diagnosis and treatment. Using implementation science frameworks and methodologies, this dissertation examines multilevel barriers and facilitators to screening and diagnosis across two African health systems, and identifies opportunities to strengthen diagnostic delivery and support the implementation of diagnostic innovations.The first study in this dissertation (Chapter 2) quantitatively evaluates the performance of Morocco’s National Breast Cancer Screening Program (NBCSP)...

CRISPR-based functional genomics for uncovering mechanisms driving neurodegenerative disease processes in neurons and astrocytes

Thu, 19 Mar 2026 00:00:00 +0000

Complex neurodegenerative diseases such as Alzheimer’s disease are characterized by the progressive, age-related death of neurons in the brain. This leads to cognitive decline, dementia, and ultimately death. Despite significant advances in our understanding of these diseases, our only treatments have a mild effect at slowing disease progression and there are no known treatments that stop, prevent, or reverse decline. However, recent advances in functional genomics technologies, such as CRISPR screening, have completely changed what is possible in the study of molecular mechanisms driving these diseases. Understating these fundamental mechanisms is an essential leap towards developing therapies that precisely target and ameliorate neurodegenerative disease processes. Using large-scale CRISPRi screening in human iPSC-derived astrocytes, two distinct reactive signatures were uncovered in a model of astrocyte reactivity: IL-1/IL-6-responsive and TNF/IFN-responsive states, differentially...

Extracellular targeted protein degradation expanded by a cytokine receptor–targeting chimera toolbox

Thu, 19 Mar 2026 00:00:00 +0000

Targeted protein degradation (TPD) has emerged in the past decade as a major new drug modality to remove intracellular proteins with bispecific small molecules that recruit the protein of interest (POI) to an E3 ligase for degradation in the proteasome. Unlike classic occupancy-based drugs, intracellular TPD (iTPD) eliminates the target and works catalytically, and so can be more effective and sustained, with lower dose requirements. Recently, this approach has been expanded to the extracellular proteome, including both secreted and membrane proteins. Extracellular targeted protein degradation (eTPD) uses bispecific antibodies, conjugates or small molecules to degrade extracellular POIs by trafficking them to the lysosome for degradation. Most eTPD receptors are expressed broadly or are restricted to the liver, limiting specific degradation in other tissues. Cytokine receptor targeting chimeras (kineTACs) are genetically encoded bispecifics for eTPD that fuse a natural ligand...

Integrated epigenetic and genetic programming of primary human T cells

Thu, 19 Mar 2026 00:00:00 +0000

Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable, and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations, and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Finally, we successfully combined genetic and epigenetic-engineering using orthogonal CRISPR Cas12a/dCas9 systems for targeted CAR knockin and CRISPRoff silencing of therapeutically...

Engineering a Molecular Dimmer Switch to Quantify Temporal Gene Dosage Sensitivity and Essentiality

Thu, 19 Mar 2026 00:00:00 +0000

Studying dynamic biological processes requires tools that can control gene expression with both precision and reversibility, a challenge that static gene editing methods cannot fully address. This thesis explores the development and application of inducible CRISPR interference (CRISPRi) systems that integrate degron-mediated control to achieve high-resolution temporal regulation of target genes. By fusing catalytically inactive Cas9 (dCas9) to transcriptional effectors tagged with degrons, effector CRISPRi protein stability can rapidly and reversibly be modulated, enabling the study of the phenotypic consequences of hypomorphic gene expression levels in mammalian cells. I review inducible strategies for their ability to fine-tune genetic perturbations in diverse cellular contexts. I provide experimental data demonstrating the utility of these temporally-gated systems for tackling key questions in functional genomics and cancer biology, such as defining windows of gene essentiality,...

Dissecting mechanisms of medulloblastoma growth and metastasis in vivo

Thu, 19 Mar 2026 00:00:00 +0000

Medulloblastoma (MB) is the most common malignant brain tumor in children, and Group 3 (G3) MB—frequently driven by MYC amplification—is the most aggressive subgroup, with limited targeted therapies and a strong propensity for metastatic dissemination. In this thesis, I discuss the generation of a novel, MYC-driven G3 model of MB derived from human neuroepithelial stem cells (NESCs), enabling systematic interrogation of the regulatory programs that sustain tumor growth and metastasis. In Chapter 2, I establish that a MYC-expressing NESC model aligns transcriptionally with human G3 MB. Using this platform, I perform the first in vivo genome-wide CRISPR interference (CRISPRi) screen in MB, nominating epigenetic regulators as key oncogenic dependencies. In particular, the chromatin modifiers SIN3B and MTA3 emerge as functional drivers of G3 MB growth, and their knockdown impairs proliferation in vitro and tumor growth in vivo, implicating the histone deacetylation complexes Sin3...

Deep learning strategies for representation learning and generative modeling in the biosciences

Thu, 19 Mar 2026 00:00:00 +0000

Representation learning is a subfield of machine learning dedicated to extract useful representations of data for downstream, domain specific tasks. This class of workflows is particularly important in modern computational biology and bioinformatics, where the large scale of datasets makes manual human interpretation and analysis infeasible. Though the representation learning field is increasingly concerned with general techniques to extract representations with desirable characteristics, its optimal application in the biosciences has not yet been established. In particular, diversity and scale of data modalities observed in the field, not limited to images, sequences, and timeseries, may require more tailored workflows. This thesis aims to describe methods by which prior biological knowledge can be incorporated into the representation learning workflow resulting in significant performance improvements.Chapter 2 focuses on the development of new methods for analysis of large-scale...

Interrogating the gene-regulatory function of human-specific non-coding DNA in the developing human cortex

Thu, 19 Mar 2026 00:00:00 +0000

Humans have evolved multiple specialized traits compared to other non-human primates (NHP), including human cognition, complex social behaviors, and susceptibility to certain neuropsychiatric disorders. The neocortex of the human brain plays a primary role in cognition, behavior, and disease. Human neocortex has disproportionately expanded about three-fold compared to our closest living evolutionary relative chimpanzee, since our divergence 6-8 million years ago.Despite clearly observable phenotypic differences, identifying causative genetic changes underlying human-specific traits including cortical expansion remains challenging. The remarkable sequence similarity of protein coding sequences between humans and chimpanzees, highlights the importance of studying non-coding sequences to better understand the evolution of human-specific traits. Importantly, non-coding regulatory elements provide context-specific means of altering gene expression patterns such as in different cell...

Tumor Diversity and Therapeutic Vulnerabilities: Scalable Platforms for Drug Response Profiling, Cancer-Emergent Biomarkers, and Metabolic Intervention

Thu, 19 Mar 2026 00:00:00 +0000

Cancer heterogeneity, between and within tumors, remains a central obstacle to durable therapeutic responses. Addressing this challenge requires scalable experimental systems that capture the genetic and phenotypic diversity of human tumors, and molecular tools to monitor disease progression and identify new therapeutic strategies. This dissertation develops and applies integrative approaches to interrogate tumor biology across diverse genetic backgrounds, identify cancer-emergent molecules with diagnostic and functional relevance, and uncover metabolic vulnerabilities amenable to therapeutic intervention.In Chapter 1, we introduce GENEVA (Genetically Diverse and Endogenously Controlled Phenotypic Variation Assay), a platform enabling scalable, single-cell resolution profiling of drug responses across multiplexed tumor models. By combining patient-derived and cancer cell lines into mosaic 3D cultures and xenografts, GENEVA captures inter- and intra-population heterogeneity in...

Simultaneous Encoding of Multiple Locations in Distinct Hippocampal Networks

Thu, 19 Mar 2026 00:00:00 +0000

Future behavior is guided by current experience, memory of the past, and imagination of possible futures. A major hippocampal subfield, CA1, encodes spatial information about present location as well as previously visited and potential future locations. CA1 is often described as a single structure that alternates between these representational modes; however, the hippocampal formation is organized along a dorsoventral (longitudinal) axis into anatomically distinct subregions. The dorsal and ventral poles of CA1 serve different roles in spatial navigation and emotional processing, but whether the intermediate subregion is functionally distinct from dorsal CA1 remains unclear. Although sharp gene-expression boundaries divide CA1 into dorsal, intermediate, and ventral subregions, electrophysiological signatures vary gradually along the dorsoventral axis, suggesting that function may also change in a graded manner.We leverage these gradual electrophysiological changes to test whether...

CD38 expression by neonatal human naïve CD4+ T cells shapes their distinct metabolic state and tolerogenic potential

Thu, 19 Mar 2026 00:00:00 +0000

Neonatal life is marked by rapid antigen exposure, necessitating establishment of peripheral immune tolerance via conversion of naïve CD4+ T cells into regulatory T cells (Tregs). Here, we demonstrate heightened capacity for FOXP3 expression and tolerogenic function among cord blood versus adult blood naive CD4+ T cells and that this is linked to their unique metabolic profile and elevated expression of the NADase, CD38. Early life naïve CD4+ T cells demonstrate a metabolic preference for glycolysis, which directly facilitates their differentiation trajectory. We reveal an age-dependent gradient in CD38 levels on naïve CD4+ T cells and show that high CD38 expression contributes to both the glycolytic state and tolerogenic potential of neonatal CD4+ T cells, effects that are mediated at least in part via the NAD-dependent deacetylase SIRT1. Thus, the early life window for peripheral tolerance in humans is critically enabled by the immunometabolic state of the naïve CD4+ compartment.

Mechanisms of Intestinal and Enteric Nervous System Development: Insights from Mouse and Human Models

Thu, 19 Mar 2026 00:00:00 +0000

The gastrointestinal tract is a complex organ system whose function depends on coordinated activity of epithelial, mesenchymal, and neural compartments. During embryonic development, these compartments undergo orchestrated morphogenetic events to establish the architectural and functional features of the mature intestine. This thesis integrates developmental biology, stem cell biology, and human genetics to elucidate mechanisms governing intestinal morphogenesis and enteric nervous system (ENS) development, and to identify genetic and cellular pathways underlying disorders of gut-brain interaction (DGBIs).Chapter 1 provides an introduction to intestinal villus morphogenesis, ENS development and patterning, motor neuron specification, and the genetic susceptibility to DGBIs, establishing the context for the experimental work presented in subsequent chapters.Chapter 2 investigates the role of extracellular matrix (ECM) adhesion and remodeling in intestinal villus morphogenesis....

Investigating Neuronal APOE4-Driven Toxicity in Alzheimer’s Disease Pathogenesis

Thu, 18 Dec 2025 00:00:00 +0000

Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimer’s disease (AD). Within the CNS, APOE is produced by a variety of cell types under different conditions, each of which differentially influences disease progression. While astrocytes are the primary producers of APOE in the CNS, neurons exhibit a striking upregulation of APOE expression in conditions of stress and aging. Here, we asked whether neuronal APOE4 alone is sufficient to drive AD pathologies. We generated a PS19 tauopathy mouse model selectively expressing APOE4 in neurons, and found that neuronal APOE4 expression alone proved sufficient to promote pathological tau accumulation and propagation, neurodegeneration, and neuroinflammation at levels comparable to tauopathy models with human APOE4 knocked-in to all cells. Single-nucleus RNA sequencing further revealed similar neuronal and glial disease signatures between the two models. Together, these findings demonstrate that neuronal...

Cellular, biochemical, and structural characterization of anti-immune factors in the phage-bacteria arms race

Thu, 18 Dec 2025 00:00:00 +0000

Bacteria are subject to predation by bacteriophages, leading to an evolutionary arms race where bacteria-encoded immune systems and phage-encoded anti-immune factors evolve to counteract each other. A classic example of this evolutionary arms race dynamic is bacterial CRISPR-Cas immune systems, which are inhibited by phage-encoded anti-CRISPR proteins (Acrs). While CRISPR-Cas and Acr interactions have been characterized in vitro, their impact on fitness, and the evolutionary benefits and drawbacks of the mechanistic diversity in the Acr family, are best investigated in the native context of phage infection, which I explore in Chapter 1. On the other hand, for anti-immune factors that are less well-characterized than Acrs such as the jumbophage nucleus, in vitro biochemistry can aid in establishing molecular mechanisms of protein import, which I present preliminary work for in Chapter 2. Altogether, my thesis characterizes anti-immune factors at different scales, from molecular...

At the Interface: Unlocking Enzyme Partnerships in Bacterial Cell-Wall Remodeling

Thu, 18 Dec 2025 00:00:00 +0000

Gram-negative bacterial pathogens rely on a dynamic peptidoglycan (PG) cell wall to maintain viability, withstand antibiotic stress, and interface with their hosts. Although numerous PG-active enzymes and PG-sensing proteins have been identified, the principles that govern how their activities are structurally coordinated, acutely perturbed, and encoded in primary sequence remain incompletely defined. This dissertation addresses these questions by integrating high-resolution structural biology, nanobody-based perturbation, and machine learning to elucidate mechanisms of PG remodeling and recognition across multiple scales, from a single enzyme complex to proteome-wide families of PG-binding domains.Chapter 1 delineates the structural and biochemical basis of conformational gating in the LtgA–Ape1 PG-remodeling complex from Neisseria meningitidis. Single-particle cryo–electron microscopy, structure-guided mutagenesis, and kinetic analyses reveal how Ape1 binding reorganizes the...

Protease-Gated Programmable Fusogenic Nano-Encapsulations for Spatially Selective Targeted Delivery

Thu, 18 Dec 2025 00:00:00 +0000

Targeted intracellular delivery remains limited by poor the rate-limiting nature of endosomal escape for most lipid nanoparticles. We developed enzyme-triggered Fusogenic Nano Encapsulations (eFugene), a protease-gated, membrane-fusogenic nanoencapsulation that converts local proteolysis into a switch that drive cell selective rapid delivery. eFugene operates through a peptide-gated interfacial charge switch, maintaining an mildly anionic “off” state in off-target environments that limit uptake while rapidly unmasking a fusogenic core that drives plasma-membrane merger and direct cytosolic release near target microenvironments. Using high-throughput, on-particle peptide screening enabled by rapid TCO–tetrazine coupling, we optimized eFugene to tune activity to the urokinase plasminogen activating system (uPA) via uPA-responsive surface (denoted u-eFugene). In 2D cocultures, u-eFugene showed a selectivity between uPA-high and uPA-low contexts and defined an operational window....

Bacterial chemoprotective mechanisms rescue host anticancer drug toxicity

Thu, 18 Dec 2025 00:00:00 +0000

Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment coupled to cell culture and mouse experiments. We show that the gut microbiome impacts anticancer drug toxicity through two mechanisms: drug inactivation and the biosynthesis of chemoprotective metabolites. Leveraging a cohort of CRC patients treated at UCSF, we found that the gut microbiota was altered during oral fluoropyrimidine chemotherapy, increasing the abundance of a bacterial operon (preTA) capable of inactivating 5-fluorouracil (5-FU). Colonization of mice with preTA+ bacteria decreased intestinal 5-FU levels and rescued drug toxicity. Bacterial preTA abundance predicted fluoropyrimidine toxicity in patients. We then performed longitudinal metagenomic...

Prostate-Specific Membrane Antigen Targeted StarPEG Nanocarrier for Imaging and Therapy of Prostate Cancer

Thu, 18 Dec 2025 00:00:00 +0000

Prostate Cancer remains a major cause of cancer-related death in men, and many patients with prostate cancer will eventually progress to a metastatic, resistant disease. Prostate-specific membrane antigen (PSMA) is highly overexpressed on prostate cancer cells and has been successfully used for both nuclear imaging and radiotherapy purposes using small-molecule radiopharmaceuticals. However, small PSMA ligands clear rapidly and often require multiple high-dose treatments in order to achieve a therapeutic effect. Nanomedicine platforms have been developed to deliver imaging or therapy payloads passively by the enhanced permeability and retention (EPR) effect or actively using targeting agents. This enables nanocarriers with a longer biological half-life to accumulate and be retained in the tumor for a longer period. Passive nanocarrier delivery alone has shown limited and heterogeneous tumor penetration in EPR-low prostate cancer models. Building on prior work with ⁸⁹Zr-labeled...

Developmental origins and molecular mechanisms of sacrococcygeal teratomas: Insights from primordial germ cells, X-chromosome biology, and epigenetic reprogramming

Thu, 18 Dec 2025 00:00:00 +0000

Sacrococcygeal teratomas (SCTs) are the most common neonatal tumors, yet their developmental origins, molecular mechanisms, and female-sex bias remain poorly understood. This thesis integrates spatial transcriptomics, single-cell RNA sequencing, and experimental models to investigate SCT biology and its hypothesized origins from primordial germ cells (PGCs). We first examined female primate ovarian reserve establishment, showing that rhesus macaque primordial follicles arise from two pre-granulosa cell subtypes, with PG2 cells predominating and supporting early hormone production before birth. We then generated a cellular atlas of SCTs, revealing epithelia-rich and epithelia-poor subtypes, marked inter-tumor heterogeneity, and evidence that X-chromosome inactivation failure in female tumors may contribute to observed sex biases. Finally, using iPSC-derived PGC-like cells, we modeled germ cell reprogramming to pluripotency, identifying transcriptional, metabolic, and epigenetic...

Approaches, resources and tools (ART) for the development and discovery of cysteine-reactive covalent molecules

Thu, 18 Dec 2025 00:00:00 +0000

Cysteine-reactive covalent molecules have emerged as powerful therapeutic agents in the clinic and as useful chemical tools in the lab, but their successful development requires both strategies to enhance their selectivity and resources to better understand cysteine reactivity across biological contexts. This dissertation presents complementary approaches that advance both fronts. First, I describe a steric tuning strategy for electrophilic warheads that improves covalent inhibitor selectivity independent of the intrinsic electrophile reactivity. We demonstrate the utility of this approach by exchanging the acrylamide warhead on the Bruton’s tyrosine kinase (BTK) inhibitor, Ibrutinib (Ib), for fumarate-based electrophiles. The incorporation of a tert-butyl fumarate electrophile onto Ib (IbtBu) preserved on-target BTK engagement while markedly reducing time-dependent and time-independent off-target reactivity, decreasing proteome-wide labeling from 247 proteins to 7, with BTK as...

Dissecting mechanisms of immune self-tolerance via bioinformatic analysis of cellular and molecular states

Thu, 18 Dec 2025 00:00:00 +0000

Multicellular organisms rely on complex immune systems that initiate innate and adaptive responses to invading pathogens to survive. A crucial challenge for adaptive immunity is distinguishing self from invading non-self. For T cells, this self-education is established through central tolerance in the thymus, mediated largely by Aire-expressing medullary thymic epithelial cells (mTECs), and is reinforced through peripheral tolerance in the host’s tissues. While some aspects of central tolerance are well characterized, peripheral tolerance remains less well-defined; however recent work implicates an MHCII expressing, RORgt⁺ antigen-presenting cell in tolerance to food antigens and the gut microbiome. Because of the complexity of these tolerance mechanisms and the cellular diversity of their mediators, integrative bioinformatic analyses of large multi-modal ‘omics datasets can provide key insights to help unravel these biological processes. Using single-cell transcriptomics to investigate...

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets

Thu, 18 Dec 2025 00:00:00 +0000

Cell surface proteins represent critical targets for cancer immunotherapy, yet most discovery efforts rely solely on differential expression rather than structural features. This dissertation advances "structural surfaceomics"—a methodology integrating surface-selective biotinylation with crosslinking mass spectrometry (XL-MS)—to systematically map conformational landscapes of tumor cell surfaces and identify epitopes suitable for therapeutic targeting. Chapter 1 establishes quantitative surfaceomics workflows for multiple myeloma, developing confidence scoring approaches for cell surface protein identification and enrichment validation. This proteomic foundation enables robust surfaceome characterization in myeloma. Chapter 2 presents AlphaCross-XL, a computational platform bridging experimental crosslinking data with AlphaFold-predicted structures. This visualization tool enables systematic structural validation and identification of conformational deviations from predicted...

Remak bundle size, structure and function are regulated by the Schwann cell basal lamina

Thu, 18 Dec 2025 00:00:00 +0000

Remak bundles are groups of small-diameter unmyelinated nociceptive axons ensheathed by Schwann cells (SCs). Whereas the development and maturation of myelinating SCs has been extensively studied, the formation of Remak bundles remain poorly understood. By preventing the secretion of type IV collagen from SCs, we observe normal myelin but abnormal Remak bundles. There is a decrease in the density of Remak bundles, an increase in bundle size, improperly ensheathed axons, and a decrease in mechanosensitivity. While Remak bundle formation appears to be independent of integrin signaling, loss of type IV collagen leads to a decrease in postnatal SC proliferation. Inducing the emergence of supernumerary SCs rescues Remak bundle architecture and mechanosensitivity. Taken together, our results demonstrate that SC-secreted basal lamina critically regulates Remak SC number, bundle size, and structure. Our findings provide insight into the functional role of Remak bundles and highlight their...

Exploring the Experiences of Women Forcibly Displaced by Climate-Driven Flooding: Health, Livelihood, and Policy Implications

Thu, 18 Dec 2025 00:00:00 +0000

Background: Climate change is an escalating public health emergency that increasingly drives forced displacement, particularly through flooding. Although climate-driven disasters disrupt entire communities, their consequences are profoundly gendered. Women often shoulder disproportionate caregiving burdens, face barriers to healthcare access, and experience economic and psychological strain during and after displacement. In California’s Central Coast, recurrent flooding in the Watsonville and Pájaro region has repeatedly displaced agricultural, largely Latino, and low-income populations. Yet, little research has examined women’s lived experiences within these recurring climate events and the structural conditions that shape their recovery. Objectives: This dissertation aimed to (1) examine the health, safety, and recovery experiences of women displaced by flooding in the United States; (2) identify social, economic, and policy factors that influence women’s health and well-being...

OPTIMIZATION OF ANTIGEN-TARGETING STRATEGIES FOR CHIMERIC ANTIGEN RECEPTOR T-CELL THERAPIES

Thu, 18 Dec 2025 00:00:00 +0000

Chimeric antigen receptor (CAR) T-cells are a powerful therapeutic technology that has shown exceptional efficacy in B-cell cancers and multiple myeloma, but only limited effects in other hematological malignancies or solid cancers. A major challenge has been developing and optimizing strategies for targeting cancer-specific cell surface targets without targeting healthy tissues, especially given the heterogeneity of cell-surface protein expression in most tumors.Here, I first develop a dual-antigen targeting CAR T-cell therapy against the antigens CD70 and the active conformation of integrin β2 (aITGB2), two antigens known to be expressed in acute myeloid leukemia (AML) but on very few healthy tissues. I show that an OR-gated approach for these antigens significantly increases the proportion of AML blasts that can be targeted. I identify dual-targeting CAR-T constructs with superior anti-tumor cytotoxicity in vitro against AML cell line and patient-derived xenograft models. I...

Correcting van der Waals Overestimation in Docking: A Solvent-Compensated, MD–ML Framework for Ultra-Large Screening

Thu, 18 Dec 2025 00:00:00 +0000

This dissertation addresses a long-standing issue in molecular docking: why do docking scores, particularly for hydrophobic ligands in buried pockets, reach unphysically large magnitudes? After testing alternative force field parameters and scoring models, I traced the problem to a missing physical term. The Lennard-Jones potential in docking captures favorable protein ligand van der Waals interactions but neglects the dispersion stabilization that ligands experience in water. Unlike rigorous free energy methods, which account for this via a thermodynamic cycle, docking double-counts dispersion inadvertently in favor of binding.To resolve this, I introduce a physically grounded correction: the solvent compensated van der Waals model. It estimates each ligand’s dispersion stabilization in water via explicit solvent molecular dynamics and subtracts this term from the protein ligand van der Waals score. This adjustment preserves pose ranking while restoring score magnitudes to experimentally...

Cross-language speech computations in the human temporal cortex

Thu, 18 Dec 2025 00:00:00 +0000

Understanding speech is a rapid and seemingly effortless feat that humans perform every day. Yet this ability relies on complex neural computations that integrate language-specific knowledge in order to transform external acoustic signals into internal linguistic representations. This dissertation investigates how neural computations in the human temporal cortex, particularly in the superior temporal gyrus (STG), support speech processing across languages. In the first chapter, we introduce the theoretical and empirical foundations for studying speech processing in the STG and describe how high-resolution intracranial brain recordings, such as electrocorticography (ECoG), have enabled its functional description. Based on prior work, we argue that the STG performs fundamentally nonlinear and dynamic speech computations, including categorization, normalization, and the extraction of temporal structure. Open questions remain as to the extent to which speech computations in...

Elucidating the role of Vif-RNA and arms race interfaces in binding and promoting A3G ubiquitination

Thu, 18 Dec 2025 00:00:00 +0000

Human APOBEC3G (A3G) is a potent cellular restriction factor against HIV-1. The viral protein Vif hijacks a Cullin5 RING (CRL5) E3 ubiquitin ligase to polyubiquitinate A3G for proteasomal degradation, neutralizing its antiviral potency. An ancient Molecular Arms race between lentiviruses and primate hosts modulates the Vif-A3G protein interface. Recently, we demonstrated in a cryo-EM structure that HIV-1 Vif also uses an RNA oligonucleotide as a molecular glue to bind A3G for polyubiquitination. Vif binds RNA and A3G in a manner that is compatible with polyubiquitination by coenzymes in the CRL5 complex. Vif utilizes RNA-binding to bind conserved residues in A3G, limiting its ability to escape antagonism. We demonstrate that RNA acts as a molecular glue, promoting the complex assembly of Vif and A3G. The role of RNA in promoting A3G ubiquitination is investigated using quantitative pulse-chase assays that monitor A3G mono-ubiquitination. The study of Vif-A3G binding, mediated...

Learning Without a Brain: Molecular Pathways and Patterns of Habituation in the Single Cell Stentor coeruleus

Thu, 18 Dec 2025 00:00:00 +0000

How can a single cell learn without a brain? Although learning is often viewed as a unique feature of animals with complex nervous systems, single-celled organisms also demonstrate basic forms of learning and memory. The single cell Stentor coeruleus contracts in response to mechanical taps, but habituates and learns to ignore the taps after repeated stimulation. Here, we explored the molecular changes that occur during the formation of this cellular memory in order to improve our understanding of non-synaptic learning. We impaired cellular protein synthesis with cycloheximide and puromycin and found that, contrary to the effects of such treatments on metazoa, these drugs accelerate habituation and prolong memory retention in Stentor. Exploratory proteomic and transcriptomic analyses identified candidate proteins and genes that change over the course of learning and forgetting. These candidates, including EF-hand domain-containing proteins, metal-dependent protein phosphatases,...

Cellular and molecular mechanisms of blood-brain and blood-spinal cord barrier heterogeneity during development

Thu, 18 Dec 2025 00:00:00 +0000

The blood-brain barrier (BBB) and blood-spinal cord barrier (BSCB) regulate exchange between the peripheral circulation and the central nervous system (CNS). During development, these barriers have a selective permeability that differs from adult states, creating both vulnerabilities and therapeutic opportunities. This dissertation addresses fundamental questions about blood-CNS barrier during development. (1) What endothelial and mural cell subtypes are present during early CNS vascular development? (2) How do these subtypes map to regions of differing barrier permeability? (3) What molecular signatures distinguish these regions? Chapter 2 presents a single-cell atlas of mouse brain and spinal cord vasculature at embryonic day (E)13.5 and E18.5, identifying endothelial and mural subtypes that establish arteriovenous zonation. Trajectory analysis revealed maturation programs progressing from proliferation through angiogenesis to transporter-rich barrier states, with region-specific...

Non-invasive prediction in glioma using machine learning and multi-parametric MRI

Thu, 18 Dec 2025 00:00:00 +0000

Glioma is a highly heterogenous brain tumor, with the most aggressive subtype serving, essentially, as a death sentence. Many have investigated glioma from various angles, from biomarker discover to better target and develop therapies, to implementing machine/deep learning to improve diagnose and disease monitoring. Glioma’s location within the brain and heterogeneous nature create a unique challenge in the quest towards improved outcomes and a full cure. Currently, diagnosis and treatment methods fail to encapsulate full tumor heterogeneity, which can lead to over and under diagnosis and subsequent over or under treatment. This provides a ripe landscape for individualistic precision medicine implementation. Magnetic resonance imaging (MRI) is routine in the diagnosis and monitoring of glioma. Many recent studies have established links between this non-invasive imaging and histopathological metrics used to diagnose and grade glioma; helping to illuminate a path for artificial...

Exploring Molecular Glues for 14-3-3 Protein-Protein Interactions

Sat, 20 Sep 2025 00:00:00 +0000

14-3-3 regulates the activity of thousands of client proteins in various biological pathways through physical occlusion, structural conformations, and scaffolding protein-protein interactions (PPIs). Utilizing the role of 14-3-3 to regulate client proteins, the Arkin lab has developed molecule glues (MGs) that stabilize native 14-3-3/client interactions, harnessing the negative regulatory interactions to “turn off” client proteins’ functions in disease. By targeting PPIs as opposed to singular proteins, selectivity can be enhanced through selective MGs that bind the unique composite interfaces for a PPI of interest. This also allows for unstructured proteins/regions that were previously difficult to target to gain new induced binding pockets for modulators for the development of novel therapeutics. The work presented in this dissertation showcases the work on exploring MGs for various 14-3-3/client interactions, with focus on the 14-3-3/ERα and 14-3-3/CRAF complexes. These...

Computational Models of Molecular Recognition: Principles and Applications in Ligand and Protein Design

Sat, 20 Sep 2025 00:00:00 +0000

The ability of proteins to specifically interact with other molecular species—including small molecules, lipids, and metal ions—is known as molecular recognition. In this dissertation, I develop computational models of such interactions across diverse contexts, using design applications to assess and extend our understanding of molecular recognition principles. Chapter 1 introduces the concepts of molecular recognition and de novo design that recur throughout the thesis. In Chapter 2, I validate a newly developed symmetric docking algorithm using the many-body neural force field ANI-2x, enabling the design of ligands that bind symmetrically to screw-symmetric protein targets such as amyloids. Chapter 3 presents a model of helical peptide behavior during translocation through the endoplasmic reticulum (ER) membrane, using data from an in vitro assay to construct a predictive scale for transmembrane, interfacial, or aqueous outcomes. Chapter 4 investigates an engineered histidine...

PET/MRI Assessment of Patellofemoral Osteoarthritis Pain Induced by Exercise

Sat, 20 Sep 2025 00:00:00 +0000

Background: Patellofemoral Joint Osteoarthritis (PFJ OA) is a chronic articular disease in the knee joint characterized by the degradation of cartilage and pain. Previous studies have found degraded cartilage in asymptomatic individuals while others suggest a correlation between inflammation and pain. 18F-fluorodeoxyglucose ([18F]-FDG), a glucose analog radiotracer, reflects glucose hypermetabolism and may suggest an influx of proinflammatory cells due to the need of oxygen consumption during the inflammatory process. This study aims to highlight the anatomical structures in the PFJ that experience hypermetabolism which may indicate the presence of inflammation before and after exercise using positron emission tomography (PET) with [ 18F]-FDG and magnetic resonance imaging (MRI). Methods: Five subjects were enrolled: one control subject and four subjects diagnosed with PFJ OA. Images were acquired before and after subjects performed 25 single-legged squats. Eight knee regions...

The molecular logic of lamellipodia formation

Sat, 20 Sep 2025 00:00:00 +0000

Cells manipulate the shapes of their plasma membrane to execute different cellular functions, ranging from endocytosis, developmental morphogenesis to the protrusions that drive cell migration. All those processes are dependent on the rearrangement of the actin cytoskeleton, whose patterns of organization are controlled by proteins known as nucleation-promoting factors (NPFs). Cells use different NPFs to orchestrate dramatically different actin networks. For example, N-WASP controls the finger-like actin networks that comprise invadopodia, filopodia, and sites of endocytosis. In contrast, the WAVE regulatory complex organizes sheet-like protrusions known as lamellipodia that are ancient highly conserved engines of cell motility. The multivalent interactions that generate N-WASP organization are relatively well-understood and have been reconstituted with purified proteins in vitro. But how the WAVE complex oligomerizes into lines is not understood and has not proven amenable to...

A convergent approach to resorcinolic macrolides to expand structural diversity

Sat, 20 Sep 2025 00:00:00 +0000

Resorcinolic macrolides (RMs) are a structurally diverse class of natural products characterized by a conserved resorcinolic ester core linked to a highly variable macrocyclic bridge. Their ability to interact with ATP-binding sites, particularly in heat-shock protein 90 (Hsp90) paralogs, has garnered significant interest for developing selective inhibitors with therapeutic potential. Despite their structural diversity, limitations in efficient synthetic routes have hindered the comprehensive exploration of their structure-activity relationships (SAR) and the development of analogs with enhanced binding and selectivity. This dissertation presents a modular, enantioselective synthetic framework to access novel RMs, enabling a thorough investigation of their biological activity and selectivity profiles.The first chapter describes the development of a protecting group-free synthesis of (±)-de-O-methyllasiodiplodin, a structurally minimal RM derived from the fungus Lasiodiplodia theobromae....

Improved prediction of structurally diverse de novo proteins

Sat, 20 Sep 2025 00:00:00 +0000

Nature uses structural variations on protein folds to fine-tune the geometries of proteins for diverse functions, yet deep learning-based de novo protein design methods generate highly regular, idealized protein fold geometries that fail to capture natural diversity, limiting the complexity of protein functions that can be designed using these methods. In this dissertation, I describe my work in improving protein structure prediction for geometrically diverse de novo proteins (Chapter 2), analyzing what this improved model learned (Chapter 3), and predicting thermodynamic stability from protein sequence (Chapter 4). In Chapter 2, using physics-based design methods, we generated and experimentally validated a dataset of 5,996 stable, de novo designed proteins with diverse non-ideal geometries. We show that deep learning-based structure prediction methods applied to this set have a systematic bias towards idealized geometries. To address this problem, we present a fine-tuned version...

Engineering a Silicon Membrane Oxygenator for an Artificial Placenta

Sat, 20 Sep 2025 00:00:00 +0000

Extracorporeal membrane oxygenation (ECMO) is a life support therapy used in patients with severe respiratory or cardiovascular failure, where gas exchange occurs outside the body via a membrane oxygenator. However, current clinical oxygenators are limited by poor hemodynamics, large blood priming volumes, and the need for continuous anticoagulation, which can lead to bleeding and clot formation. These complications, in turn, increase the risk of embolism and device failure. Microfluidic oxygenators have emerged as a promising alternative, offering improved gas exchange efficiency and hemocompatibility by incorporating biomimetic features, physiological pressures, and reduced shear stresses. Here, we describe the development of a microfluidic oxygenator composed of semipermeable silicon membranes, consisting of a semiconductor silicon backbone and a thin, gas-permeable silicone layer. First, two silicon membrane designs were evaluated, both demonstrating strong mechanical robustness,...

Diffusion MRI Biomarkers of RNS Efficacy in Epilepsy

Sat, 20 Sep 2025 00:00:00 +0000

Rationale: Responsive neurostimulation (RNS) is a promising therapy for medically refractory epilepsy (MRE), yet clinical outcomes remain highly variable and difficult to predict. Identifying preoperative biomarkers that forecast treatment response could improve patient selection and inform neuromodulation strategies. We investigated whether structural and diffusion MRI features from limbic white matter pathways and mesial temporal structures could predict seizure reduction with hippocampal-targeted RNS.Methods: We retrospectively analyzed 41 patients who underwent hippocampal-targeted RNS implantation at UCSF. Diffusion tensor imaging (DTI) metrics and volumetric measures from mesial temporal and limbic regions were analyzed. Clinical response was quantified as time weighted percent seizure reduction across follow up visits. ElasticNet regression was employed to identify imaging features associated with response, with performance assessed using leave-one-out cross-validation...

MRI Changes in Presymptomatic Genetic Prion Disease Patients

Sat, 20 Sep 2025 00:00:00 +0000

Purpose: Early detection of symptomatic prion disease (PrD) is critical because it allows for earlier intervention, management, and treatment of symptoms. The goal of this project is to evaluate the utility of imaging biomarkers in identifying microstructural abnormalities within genetic prion disease (gPrD) patients prior to symptom onset. This was accomplished by comparing cross-sectional and longitudinal MRI (standard T1-weighted (T1w) and diffusion tensor imaging (DTI)) of healthy controls (HC) and presymptomatic (presymptomatic) gPrD carriers to assess for group-wise and individual-level abnormalities; and further analysis evaluated correlations between imaging abnormalities and clinical abnormalities of disease progression to investigate imaging’s potential as an early biomarker. Materials and Methods: This project utilizes standard structural T1w MRI and DTI images of HCs (recruited by the UCSF Memory and Aging Center) and presymptomatic gPrD participants (recruited by...

Oral Regeneration in Stentor coeruleus: Cytoskeletal Patterning and Cell Cycle Control

Sat, 20 Sep 2025 00:00:00 +0000

Regeneration and wound healing are essential biological processes that restore cellular and tissue integrity following injury from external perturbations. Central to these processes is the interpretation of positional cues which include chemical or mechanical signals that instruct cells on what to rebuild and where to place structures. While the mechanisms underlying tissue and organ regeneration have been extensively studied, the molecular and spatial logic of regeneration at the subcellular level remains less understood. The giant single-celled ciliate Stentor coeruleus offers a powerful model for uncovering how cells interpret positional information to reconstruct complex intracellular architecture. With a highly polarized body plan, anterior-posterior axis, and an oral apparatus critical for feeding, Stentor can regenerate entire structures from fragments, provided a part of the macronucleus is intact.Here, we explore how cytoskeletal patterning and cell cycle regulators support...

Genes, Omics, and Justice: Bridging the Gaps in Computational Precision Medicine

Sat, 20 Sep 2025 00:00:00 +0000

Precision medicine seeks to tailor healthcare based on individual genetic and molecular profiles. However, most existing tools and datasets were developed using Eurocentric cohorts, limiting their accuracy and equity across diverse populations. This dissertation addresses disparities in precision medicine through the development and application of computational approaches rooted in evolutionary theory, population genetics, and multi-omic technologies. I first introduce py_ped_sim, a simulation tool to evaluate the performance of kinship inference methods across varied ancestry backgrounds. I then apply untargeted metabolomics to examine postnatal metabolic changes linked to respiratory disease in extremely premature infants. In a large-scale genome study using data from the TOPMed consortium, I assess ultra-rare variant patterns and show how genetic ancestry shapes trait architecture and variant discovery. Finally, I reflect on my efforts to foster equity in science through mentorship,...

Brainstem circuits that control appetite

Sat, 20 Sep 2025 00:00:00 +0000

Nutrients are essential for sustaining life as we know it. Therefore, organisms, including humans, have evolved complex brain networks to control the decision to seek food, consume it, and when to stop eating. Importantly, the desire to overeat and store excess energy for scarce times must be weighed against the harmful effects of overloading our digestive systems.The satiation of hunger has traditionally been viewed as a gradual process triggered during a meal by gastrointestinal feedback, which is relayed by sensory nerves to the caudal brainstem to suppress appetite. Therefore, brainstem circuits – namely, the caudal nucleus of the solitary tract - are thought to be activated over tens of minutes to promote satiety. However, this assumption has not been directly tested due to the challenge of studying such a deep brain structure. To address this longstanding question, we developed new methods for recording the activity of distinct cell types in this brain region and determined...

A genome-wide CRISPR screen highlights cationic amino acid homeostasis as a regulator of lysosomal pH

Sat, 20 Sep 2025 00:00:00 +0000

Lysosomes are critical organelles for maintaining proteostasis in cells. One of the defining characteristics of lysosomes is their relative acidity compared to other subcellular compartments. This acidic pH is critical for the efficient breakdown of macromolecules and cellular homeostasis, and disruptions in lysosomal pH homeostasis have been linked to aging and disease. The mechanisms through which lysosomal pH is maintained are incompletely understood, a question important in neurons which are susceptible to age associated decline in proteostasis. Supporting this, we found neuronal lysosomes have a unique pH optimum for tau degradation. To better understand neuronal lysosomal pH regulation, we conducted a genome-wide CRISPRi-based screen in iPSC derived neurons for modifiers of lysosomal pH. We validated several previously known regulators of lysosomal pH and discovered novel pathways capable of modifying lysosomal pH including the protein UFMylation and mitochondrial integrity....

Validation and Optimization of a Quantitative Susceptibility Mapping (QSM) Pipeline for Paramagnetic Rim Lesions in Multiple Sclerosis

Sat, 20 Sep 2025 00:00:00 +0000

Quantitative Susceptibility Mapping (QSM) provides valuable sensitivity to paramagnetic rim lesions (PRLs) in multiple sclerosis, but the influence of algorithmic choices within the processing pipeline remains unclear. This study systematically compared two phase unwrapping methods (ROMEO and PRELUDE), two background field removal strategies (V-SHARP and RESHARP), and dipole inversion with iLSQR to assess their impact on lesion visibility and contrast stability.ROMEO achieved rapid phase unwrapping (20–40 seconds per dataset) compared to the several hours required by PRELUDE, yet PRELUDE produced clearer boundaries for small lesions, particularly in anatomically complex regions. For background field removal, V-SHARP provided greater global stability across brain regions, while RESHARP enhanced local lesion-to-background discrimination, especially within the corpus callosum and basal ganglia. Case-specific analyses further revealed that lesion distribution strongly influenced outcomes:...

Cdc37's C-terminal platform stabilized by Hectd3 in complex with Raf1 and Hsp90, visualized by Cryo-EM

Sat, 20 Sep 2025 00:00:00 +0000

Hsp90 is a well conserved and highly expressed molecular chaperone that interacts with 10% of the proteome to facilitate folding and activation. These interacting partners, dubbed clients, interact with Hsp90 throughout their entire lifetime and not just in the stages of initial folding. This continual interaction with this clientele makes Hsp90 a hub of proteostasis regulation which includes folding, activation, and degradation triage decisions. Hectd3 has been shown to degrade Raf1 in an Hsp90 dependent manner, here we show Hectd3 in complex with Hsp90:Cdc37:Raf1 in a closed Hsp90 state. Hectd3 reveals a C terminal platform on Cdc37 providing a potential scaffold for Hectd3 ubiquitination. We show Hectd3 can mono ubiquitinate the kinase domain of Raf at multiple lysines when Hsp90 is not in a molybdate trapped closed protective state. This mono ubiquitination of Raf1 upon Hsp90 opening could potentially bias the kinase toward a degradative end when subsequent E3 ligases could...

A Large Language Model for Liver Lesion Characteristic Extraction and Longitudinal Tracking from LI-RADS Reports

Sat, 20 Sep 2025 00:00:00 +0000

Background: Large language models (LLMs) can be utilized to summarize radiologist-written reports for abdominal MRI and CT scans of liver lesions suspicious for hepatocellular carcinoma (HCC), and identify and track the growth of lesions over time. The standardized liver lesion reporting method, Liver Imaging Reporting and Data Systems (LI-RADS), allows for consistent representation of lesion characteristics which aids in the consistency of feature extraction.Objective: This study evaluates the ability of an LLM to compile qualitative radiologist reports into a structured database containing liver lesion identification and developmental features, and subsequently using those features to identify and track specific lesions across scans. Methods: This retrospective study included patients at risk for HCC who underwent abdominal CT or MRI scans that contained a LI-RADS 5 lesion. The radiologist reports of 108 scans from 15 patients were inputted to an LLM (GPT-4.1) alongside...

Design and Synthesis of C4-modified Group A Streptogramin Analogs

Sat, 20 Sep 2025 00:00:00 +0000

Natural products and their derivatives have long served as powerful tools for treating bacterial infections, but the rise of antibiotic resistance threatens their continued effectiveness and has significantly depleted the current antibiotic pipeline. Structural modifications to natural product antibiotics have proven to be effective in overcoming certain resistance mechanisms and extending their clinical utility. The development of C4-modified group A streptogramins that overcome acetyltransferase resistance, a pervasive resistance mechanism to the class, is an example of successful implementation of this strategy. However, the synthetic chemistry to reach these new analogs was inherently limiting, enabled access to only two analogs with modifications at the desired position on the scaffold.In chapter 1, we report the development of a modified route to group A streptogramins that enables access to a broad diversity of functionality at C4. Using cryo-EM binding data to guide structural...

Prefrontal neurocardiac networks during approach-avoidance behaviors

Sat, 20 Sep 2025 00:00:00 +0000

Animals engage in approach-avoidance behaviors when confronted with potentially threatening cues. These behaviors are supported by neural computations and peripheral reactions in the body, such as autonomic signals that give rise to the classic “fight-or-flight” response. Significant changes in heart rate during these situations are a hallmark of this response. Importantly, the brain exerts top-down control over cardiac activity and heart rate can also influence brain function. Fluctuations in heart rate modulate neural activity in the medial prefrontal cortex (mPFC), a region involved in evaluating social environments, anxiogenic contexts, and guiding adaptive decisions. However, how cardiac signals are mapped in the mPFC during approach-avoidance behaviors remains unclear. To address this, we developed a multidisciplinary approach to simultaneously record heart rate and measure single-cell calcium signals from mPFC neurons in freely moving mice navigating social and anxiogenic...

Identification of Novel CD46-Binding Peptides for PET Imaging of Prostate Cancer Using Phage Display

Sat, 20 Sep 2025 00:00:00 +0000

Prostate-specific membrane antigen (PSMA) PET is central to prostate cancer imaging, yet it shows reduced sensitivity in PSMA-low disease, including neuroendocrine variants. To develop CD46-targeted peptide tracers suited for faster imaging, we carried out four rounds of phage display with a Ph.D.-12 library against recombinant CD46. Rounds alternated between bead-based (1, 3) and plate-based (2, 4) formats, with antigen reduced from 25 to 10 µg and wash stringency increased (Tween-20 from 0.1% to 0.5%). Phage enrichment was evident by titer: amplified outputs rose from 1.8×10¹⁰ pfu/mL in round 1 to 9×10¹¹ pfu/mL in round 3, then measured 6×10⁹ pfu/mL in round 4. Next-generation sequencing showed contraction of library diversity from 6,623 unique peptides (50,804 total reads) in round 1 to 427 (3,873 reads) in round 4. Normalized-frequency trends highlighted strong enrichment of Peptide A (2.08%→17.84, rounds 1→4) and a late rise of Peptide B (0.44% in round 3 to 6.82% in round...

Single-cell lineage tracing in clinically relevant lung cancer models informs actionable programs to delay EGFR-targeted therapy resistance.

Sat, 20 Sep 2025 00:00:00 +0000

Lung cancer is the leading cause of cancer related deaths worldwide. Although mutation driven cancers, such as those harboring activating EGFR mutations, show a high rate of initial response to targeted tyrosine kinase inhibitors (TKIs), all patients eventually develop acquired resistance. This dissertation aims to investigate the residual disease state (RD) to better understand the responding, yet persistent, tumor and identify potentially targetable features of the tumor landscape.The first chapter leverages static genomic barcoding paired with single-cell RNA sequencing (scRNA-seq) to identify pre-existing features of two distinct TKI-resistant preclinical EGFRm models. The static genomic barcoding enabled the identification of cell lineages that were either susceptible or resistant to TKI therapy. scRNA-seq analysis of these lineages enabled identification of pre-treatment features, as well as the mapping of transcriptional changes over treatment time. First, in our patient-derived...

How to compartmentalize signaling: lipids, Hedgehog, and ciliary PKA

Sat, 20 Sep 2025 00:00:00 +0000

Cells coordinate nearly countless numbers of signaling reactions within them at any given time. To distinguish between different signaling inputs and outputs, cells utilize spatially compartmentalized signaling hubs to regulate their biochemical processes. We review how the primary cilium, an organelle specialized in intracellular signaling, utilizes lipids to create a specialized microenvironment. Hedgehog (HH) signaling in vertebrates is dependent on the primary cilium, an organelle that scaffolds signal transduction. HH signals induce Smoothened (SMO) enrichment in the cilium and indirectly triggers the conversion of GLI proteins into transcriptional activators of HH target genes. Recently, SMO has been shown to inhibit protein kinase A (PKA). To test the hypothesis that SMO specifically inhibits PKA at cilia to activate the HH signal transduction pathway, we developed a ciliary PKA biosensor. Activation of the HH signal transduction pathway by either Sonic hedgehog (SHH) or...

Resting state functional magnetic resonance imaging in presymptomatic and symptomatic genetic prion disease

Sat, 20 Sep 2025 00:00:00 +0000

Genetic prion diseases (gPrDs) are rare, fatal neurodegenerative disorders caused by pathogenic variants in the PRNP gene. Identifying early markers of network dysfunction is critical for advancing early detection and intervention strategies. This study investigates default mode network (DMN) functional connectivity alterations in presymptomatic gPrD carriers, with a focus on differences between faster- and slower-progressing subgroups. Resting-state fMRI data was acquired from presymptomatic carriers, symptomatic participants, and matched healthy controls. Seed-to-voxel analyses were performed to compare DMN connectivity across groups, with statistical significance determined after correction for multiple comparisons. Presymptomatic carriers exhibited distinct connectivity alterations based on progression rate. Faster-progressing individuals showed reduced posterior DMN connectivity, centered in the posterior cingulate and precuneus, while slower-progressing carriers displayed...

An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA

Sat, 20 Sep 2025 00:00:00 +0000

Lysine demethylase 5A (KDM5A) plays a key role in the regulation of chromatin accessibility by catalyzing the removal of trimethyl marks on histone H3K4 (H3K4me3). KDM5A is also an oncogenic driver, with overexpression of KDM5A observed in various cancers, including breast, lung, and ovarian cancer. Past studies have characterized the functions of KDM5A domains, including KDM5A interactions with the histone H3 tail, but have yet to identify the broader mechanisms that drive KDM5A binding to the nucleosome. Through investigation of binding and catalysis on nucleosome substrates, we uncovered multivalent interactions of KDM5A with the H2A/H2B acidic patch and DNA that play crucial roles in the regulation of catalytic activity. We also identified an intrinsically disordered region (IDR) containing bifunctional arginine-rich motifs capable of binding to both the histone H2A/H2B acidic patch and nucleosomal DNA that is necessary for catalysis on nucleosome substrates. Our findings...

The intracellular domain orchestrates Notch1 polarization and activation by shear stress

Sat, 20 Sep 2025 00:00:00 +0000

Hemodynamic shear stress regulates endothelial phenotype through activation of Notch1 signaling, yet the mechanistic basis for this activation is unclear. Here, I establish a fluid shear stress-dependent mechanism of Notch1 activation in blood endothelia that is distinct from canonical ligand trans-endocytosis. Application of laminar flow triggers the rapid spatial polarization of full-length Notch1 heterodimers into downstream membrane microdomains. Unlike canonical transactivation, I find that this response occurs independently of ligand redistribution, and Notch1 receptors are cis-endocytosed into the receptor-bearing cell within polarized microdomains prior to proteolytic activation. Furthermore, I discover that the Notch1 intracellular domain (ICD) critically orchestrates receptor polarization and proteolytic activation in response to flow but is dispensable for canonical ligand trans-activation. Shear stress increases ICD interaction with annexin A2 and caveolar proteins...

RISK FACTORS ASSOCIATED WITH THE CO-OCCURRENCE OF SEVERE PAIN AND SLEEP DISTURBANCE IN ONCOLOGY OUTPATIENTS RECEIVING CHEMOTHERAPY

Thu, 17 Jul 2025 00:00:00 +0000

Background: Pain and sleep disturbance frequently co-occur in oncology patients. Little is known about inter-individual variability in their co-occurrence and associated risk factors.Objective: The aims of this study were to identify subgroups of patients with distinct joint pain and sleep disturbance profiles and to evaluate for differences among the subgroups in a number of demographic and clinical risk factors.Methods: Oncology outpatients undergoing chemotherapy completed questionnaires six times over two chemotherapy cycles. Of the patients who reported any pain (n = 972), worst pain intensity was assessed using a 0 (no pain) to 10 (worst pain imaginable) numeric rating scale (NRS) and pain characteristics using the Brief Pain Inventory. Self-reported sleep disturbance was evaluated using the General Sleep Disturbance Scale (GSDS). Latent profile analysis (LPA) was used to identify subgroups of patients with distinct joint pain and sleep disturbance profiles.Results: Two...

Cardiovascular Disease in Women Veterans: Examining the Influence of Posttraumatic Stress Disorder, Depression, and Health Behaviors