Vanderbilt University

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY We propose the construction of a three-dimensional (3D) multimodal molecular atlas of colorectal cancer (CRC) across different ages of onset of the disease. We aim to address the emerging clinical challenge of rising early-onset CRC cases by exploring molecular differences between early-onset and later-onset CRCs. We hypothesize that aberrant interactions between the carcinogenic microbes, tumor metabolic niche, and the tumor microenvironment lead to accelerated transitions of precancerous cell states to malignant states. Our atlas will focus on spatially mapping transitions from precancerous to cancerous components within the same tumor, utilizing a "phylogeographic" mapping approach to create individualized and global progression trajectories between tumor subtypes (early onset CRCs, later-onset microsatellite stable CRCs, later-onset microsatellite unstable CRCs). We employ cutting-edge technologies, such as customized spatial transcriptomics, co-detection by indexing highly multiplexed immunofluorescence microscopy, untargeted imaging mass spectrometry, and histological and autofluorescence imaging, to comprehensively characterize CRC tissue at various molecular levels and spatial scales. We employ a 3D multimodal strategy by reconstructing volumes from interleaving serial tissue sections evaluated by different technologies. Paired whole exome sequencing and single-cell RNA-sequencing data will anchor our spatial analyses to our previous Human Tumor Atlas Network (HTAN) data. We leverage our previous success in building colorectal atlases within the HTAN and ensure that data are released for open-access use to the research community. We have a strong team with expertise in genomic profiling, multi-omic spatial analysis, biostatistics, and artificial intelligence. Our proposal emphasizes our team's extensive track record in CRC research, with active programs in CRC, gut epithelial biology, CRC microbiome, epidemiology, and pathology. Our goal is to provide unprecedented insights into the genetic, transcriptomic, metabolomic, microbial, and architectural features of CRC in a spatially resolved manner to better understand CRCs across various age groups.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY Immune checkpoint inhibitors (ICIs) enable anti-tumor immunity by blocking immunoregulatory receptor-ligand interactions (e.g., programmed cell death protein 1 [PD-1] and its ligand [PD-L1]). Despite their widespread success as an anti-cancer therapy, ICIs function poorly in patients with bone metastases, and bone loss and elevated fracture risk are reported in patients receiving ICI therapy. My preliminary data indicate that PD-1 global knockout or pharmacologic blockade decreases bone mass in both tumor naïve mice and mice with bone-metastatic disease (E0771 tumor cells). Furthermore, PD-1 blockade reduces bone strength compared to IgG control treatment in mice with bone metastases. These data are consistent with reports of bone loss and fractures in patients treated with ICIs. I have also found that osteoclast activity and CD8+ T cell populations capable of secreting pro-osteoclastogenic cytokines are elevated in the bone marrow after PD-1 blockade. I therefore hypothesize that the detrimental effects of PD-1 blockade on bone stem from CD8+ T cell expansion, which promotes osteoclast-induced bone destruction, and that tumor resistance to ICIs in the bone microenvironment stems from T cell dysfunction. I propose to (1) determine how immune cells influence PD-1 blockade-induced bone loss, and (2) investigate the mechanism behind T cell dysfunction and tumor resistance to ICIs in the bone microenvironment. In Aim 1 (F99 phase), I will use T cell depletion and adoptive transfer studies to investigate the role of bone marrow immune cells on PD-1 blockade-induced bone loss in tumor-inoculated mice. I will also treat tumor-inoculated mice with α-PD-1 in combination with bisphosphonates to assess prevention of bone loss. In both of these studies, I will assess the bone phenotype via microCT and biomechanical strength testing, and the tumor and immune phenotypes via flow cytometry and histology. In Aim 2 (K00 phase), I will utilize digital spatial profiling and scRNAseq technology to characterize T cell infiltration into bone metastases and identify key signaling pathways between tumor cells, immunoregulatory cells (myeloid derived suppressor cells, tumor associated macrophages T regulatory cells) and cytotoxic T cells, which are important in escape of bone metastatic tumor cells from the T cell anti-tumor response. I will use de- identified human breast cancer samples to validate my findings and elucidate the mechanism(s) by which bone metastases escape T cell surveillance (e.g., T cell suppression, T cell exhaustion, lack of T cell infiltration into the tumor microenvironment, etc.). With the current lack of understanding of the mechanism behind bone loss in patients treated with ICIs and tumor cell resistance to ICIs after bone dissemination, this proposal will help manage bone health in the millions of patients receiving ICIs each year and confirm mechanistically whether anti-resorptives reverse ICI-induced bone loss. Furthermore, I will uncover novel mechanisms of bone metastatic immune evasion that, when targeted, may increase efficacy of ICIs in bone metastatic patients.

NIH Research Projects · FY 2025 · 2024-09

Project Summary We propose to further develop, refine, and validate our emerging free-solution assay (FSA) technology and our relatively new compensated Interferometric reader (CIR).1,2 The development of FSA-CIR addresses a significant void, a blind spot in cancer research because it represents the only label-free, solution-phase, ultra- sensitive, enzyme-free, technology compatible with essentially any matrix. Unlike existing tools, FSA-CIR has been shown to be useful for; a) mechanism of Action (MOA) studies on unadulterated/unmodified targets and probes with no relative mass sensitivity, b) full-length membrane protein interaction studies in native matrix, c) defining allosteric modulation and weak protein-protein interactions, d) accelerating quantitative assay development, e) potentially addressing biomarker discovery/validation bottleneck, f) performing quantitative interactions across the matrix spectrum on a single platform and g) enabling ex-vivo measurements to guide first-in-human dose determinations (FIHD) (see Pfizer letter). FSA-CIR is a paradigm shifting technology based on a novel molecular interaction transduction method with fluorescence-level sensitivity, and capabilities for targeting, probing, and assessing molecular and cellular features of cancer biology, as well as improving early detection and screening, clinical diagnosis. FSA is mix-and-read, agnostic to the molecular interaction pair and compatible with complex matrices, making it uniquely applicable in both the basic and clinical cancer research arenas. CIR represents a major advancement in interferometric sensing, due to an unprecedented level of sample-reference compensation CIR is operated without external thermal control, a unique feature for a refractive index (RI) sensor with <10-7 RIU sensitivity. The optical engine in CIR is unique, patented and quite simple, consisting of a diode laser, capillary tube, mirror and detector. When combining the interferometer with a droplet generator for sample introduction, CIR facilitates quantification of molecular interactions without relative mass dependence, at picomolar sensitivity and allows good sample throughput (50 serum sample-reference pairs run in quintuplet, [5 replicate droplet pairs], plus calibrations in a day. Feasibility of our assay methodology is demonstrated for mechanism-of-action (MOA) studies, quantification of drug target engagement as needed in theranostics and ultrasensitive, volume constrained, biomarker assay development, and target quantification. Data indicate FSA-CIR has the potential for widespread applicability and adoption throughout the scientific community and is mature enough to be an R-33 project. At project completion we aim to provide the scientific and medical community with a user-friendly platform technology for biochemical mechanism of action studies, to aid in improving cancer prognostics, and the ability to measure properties such as molecular and/or cellular mechanisms important in cancer.

NIH Research Projects · FY 2024 · 2024-09

PROJECT SUMMARY Aging is a complex process characterized by many hallmarks, such as DNA instability, epigenetic changes, and loss of protein homeostasis. Cellular rejuvenation, which aims to restore cells to a youthful state, offers hope to counteract aging and its associated diseases. Recent advances in epigenetic reprogramming using Yamanaka factors (a set of four transcription factors) have rejuvenated aged cells to youthful states and extended lifespan in mice. However, the clinical use of Yamanaka factors is limited due to their tumorigenic risk and full reprogramming potential. Therefore, it is important to find new rejuvenating transcription factors that are safer and more potent than the Yamanaka factors. The Li lab has recently developed a systematic approach and identified ~30 potential rejuvenation transcription factors. They have identified ~30 transcription factors that can restore youthful gene expression patterns in aged human fibroblasts in vitro. Critically, they also validated a few top hits with cellular and molecular phenotyping of aging hallmarks. However, the underlying mechanisms by which these transcription factors/chromatin modifiers rejuvenate aged cells, and the ability of these transcription factors to rejuvenate other types of aged cells (such as post-mitotic cells) are unknown. To better prepare me for such research, I propose to continue my training in cell/molecular biology by investigating how BRWD3 regulates DNA replication and epigenetic modifications (F99 Aims). This will not only enhance my comprehensive skill set for mechanistic studies, but also deepen my understanding and investigative strategies for chromatin-associated proteins, which are central to my proposed F00 aging research. During the K00 phase, I will leverage my molecular research expertise and the Li lab's system-level approaches to advance our understanding of cellular rejuvenation. I propose to dissect the mechanism of a top rejuvenation candidate and identify its key targets responsible for rejuvenation (K00 Aim 2.1). I will also use the induced neurons with the system-level approaches developed by the Li lab to explore the rejuvenation potential of the top 30 transcription factors in aged neurons (post-mitotic). Collectively, these experiments will not only deepen our understanding of the rejuvenation mechanism, but also shed light on rejuvenation approaches for overlooked post-mitotic cells, leading to the discovery of safer and more universal rejuvenation solutions for both mitotic and post-mitotic cells.

NIH Research Projects · FY 2026 · 2024-09

PROJECT SUMMARY/ABSTRACT Today’s sexual minority (SM) youth are coming out at increasingly younger ages, with the average age of disclosure at 13 years old and 35% coming out as preteens. SM preteens experience up to 6 times higher risk for suicidal thoughts and behaviors (STBs) compared with their heterosexual peers. SM preteens’ social and developmental contexts likely contribute to significant risk and protective factors for STBs. For example, they must simultaneously navigate preteen developmental stressors and supports (like peer relationships and first romantic experiences) while also managing an emerging SM identity and associated exposure to stigmarelated stress and resilience. Yet, several knowledge gaps remain. The field of SM preteen research is in its infancy, without consensus on best practices for sampling and recruiting high-risk SM preteens. The field also lacks psychometrically valid assessments for SM preteens as well as longitudinal studies assessing risk and resilience trajectories during this sensitive developmental period. The overarching goal of this rigorous multimethod project is to address these gaps. Youth and parent advisory boards will be assembled to enrich our research and ensure its cultural responsiveness, ethical soundness, and ultimate benefit to SM preteens and families. Our research will address three aims. First, we will use a five-step Delphi process to develop consensus among a diverse panel of experts (including researchers, clinicians, legal experts, parents, leaders of SM community youth groups) on best practices for safely, ethically, and effectively sampling, recruiting, and retaining SM preteens at risk for suicide into research. Second, we will create and pretest an assessment of stigma-related stress and resilience for SM preteens using a three-phase approach (developing an initial item pool; refining items; establishing content validity with SM preteens). Last, we will enroll a national cohort of preteens at risk for suicide with one parent/caregiver, which we will call the SPARK (SM Preteens Advancing ouR Knowledge) Cohort. SPARK participants will be administered an online assessment battery of SM status, developmental stressors and supports, stigma-related stress and resilience, and STBs every 6 months for 2 years. Analyses will use rigorous weighted generalized estimating equations to estimate trajectories of risk and protective factors for STBs. Subgroup analyses will examine how trajectories of STBs and associated risk and protective factors differ by sexual minority status as well as race and ethnicity and other theoretically informed intersectional factors among preteens. This research is guided by an innovative conceptual model integrating advances in developmental science with the NIMHD Health Disparities Framework and involves community partners at SM youth organizations nationwide to enhance feasibility. Findings from this project will advance best practices for sampling SM preteens, measuring stigma-related stress and resilience, and mapping trajectories of risk and protective factors for STBs, aligning with key NIMH priorities.

NSF Awards · FY 2024 · 2024-09

In January 2022, the largest submarine explosive volcanic eruption recorded by modern instruments occurred at Hunga volcano in Tonga. This research will collect samples and new observations of volcanic sediment to understand how underwater volcanic eruptions transport material. The research uses this recent eruption to learn about underwater volcanic landslides that have been impossible to study directly until now. The results will help predict hazards from submarine eruptions. This project will include public outreach by a science communication professional. The project also involves international collaboration with the Kingdom of Tonga and the training of four graduate students. In 2022, Hunga Tonga volcano erupted explosively producing a widely studied stratospheric ash cloud and an estimated 10 cubic kilometers of much less well studied submarine volcaniclastic deposits. This project seeks to characterize the large-scale submarine volcaniclastic density currents produced by this eruption in order to better understand these understudied volcanic products globally. Systematic sampling and mapping in a field campaign using remotely operated submersible Jason, autonomous underwater vehicle Sentry, and ship-based gravity and slow coring will sample the eruption deposits at multiple spatial scales. These new data will enable computational modeling aimed at better understanding transport mechanisms, mobility, and rheology of submarine volcaniclastic flows. The 2022 Hunga Tonga eruption illustrated how vulnerable communication cables and other seafloor infrastructure are to these density currents. Similar volcanoes and similarly vulnerable infrastructure exist around the globe and particularly in the island arc systems around the Pacific. Broader impacts of this work will include four U.S. graduate students, involve public outreach from the ship and subsequent events hosted at the Smithsonian Institution. Extensive international collaboration is planned, with scientists, students, and a science communicator from Tonga included in the fieldwork and lab analysis. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-09

The goal of our proposed research program is to develop new spectroscopic methods capable of providing enhanced insight into protein structure and dynamics within complex environments that impact human health. We will apply these methods to study structural changes induced by protein-protein and protein-surface interactions under conditions that are not accessible by other experimental approaches. Our first research direction focuses on advancing the use of unnatural amino acids (UAAs) beyond probes of local environment by taking advantage of the unique spectral features provided by two-dimensional infrared (2D IR) spectroscopy to measure vibrational couplings between UAA labels. These couplings depend sensitively on the distance and relative orientation between UAA vibrational modes and thus can be used to map protein structure. We will select UAAs modified with functional groups that have vibrational modes within a biologically transparent region of the infrared spectrum, allowing us to probe the structure of protein complexes and aggregates in biological media. We will use the Alzheimer’s β-amyloid (Aβ) protein, the most studied self-assembling protein, in cerebrospinal fluid as a prototypical system to develop and refine our approach into a broadly applicable method that will enable the study of dynamic protein interactions that result in formation of protein complexes and aggregates involved in a range of diseases. The Aβ studies will also allow us to bridge the gap between in vitro aggregation studies and ex vivo fibril structures and gain unprecedented new insight into physiologically relevant self-assembly pathways in Alzheimer’s disease. Our second research direction aims to understand, for the first time, the detailed residue-level changes to protein structure that occur when proteins interact with nanoparticle (NP) surfaces. NPs are ubiquitous in our lives and are increasingly being considered for biomedical applications. However, the effect of nanomaterials on living systems remains unclear. One concern is that proteins readily adsorb onto the surfaces of NPs, which can result in changes to protein structure and thus function. Our initial studies will examine the differing effects of NPs on the secondary structure of model peptides and lysozyme, first with metallic NPs as a model system to understand the effects of NP size and concentration, and then with silica NPs to examine the role of surface chemistry in affecting structural changes. Machine learning-based approaches to enhance the sensitivity of 2D IR spectroscopy to site-specific labels will be developed to further improve structural resolution. Ultimately, these studies will be expanded to understand the interactions between a broader range of both nanomaterials and proteins in biologically relevant media.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY Insulin-binding B lymphocytes contribute to type 1 diabetes (T1D) through B cell receptor (BCR) recognition of insulin and autoantigen presentation to T lymphocytes in the mouse model of T1D. Insulin is a key autoantigen targeted by B and T lymphocytes in human and murine T1D. Heterogeneity in diabetes onset and response to immunotherapy in humans has significantly hindered development of successful T1D immunotherapies. The first immunotherapy for T1D was recently approved, yet responses were incomplete and non-durable. Therefore, a better understanding of how immune cells implicated in pathology arise and evolve with T1D progression is critical to improve immunotherapy development in the future. A major knowledge gap exists regarding how insulin-binding B lymphocytes acquire insulin reactivity and persist in the repertoire to support T1D pathology. Autoreactive BCRs are often polyreactive against other antigens, but the functional consequence of this polyreactivity, and how it changes with autoimmune disease progression, is not clear. My preliminary data show 67% of stage 1 at-risk T1D B cell receptors (BCRs) were polyreactive, which dropped to 29% in stage 2 at-risk T1D BCRs measured by Hep-2 reactivity. When the only amino acid mutation in one anti-insulin BCR was reverted back to germline, the insulin-binding area under the curve (AUC) was reduced by ~84%. In contrast, germline reversion of 22 amino acid mutations in another anti-insulin BCR resulted in only an ~11% reduction in AUC. Therefore, I hypothesize that insulin-binding B lymphocytes in at-risk T1D individuals will lose polyreactivity with disease progression and increased BCR somatic hypermutation, but the number of BCR mutations will not correlate with increased affinity for insulin. To test this hypothesis, I will take advantage of our unique Type 1 Diabetes TrialNet cohort, which consists of 2+ islet autoantibody-positive participants across three stages of T1D: Stage 1 (normal oral glucose tolerance), Stage 2 (impaired glucose tolerance), and new-onset Stage 3 (clinical diabetes), all of whom are insulin therapy-naive. I will use advanced human hybridoma technology that can capture rare antigen-specific B lymphocytes in peripheral blood, in combination with single cell technology, to identify insulin-binding B lymphocytes from at-risk individuals. I will investigate how affinity and polyreactivity shift across disease stages and with increased BCR somatic hypermutation. These studies will build a foundational understanding of B lymphocyte recognition of insulin, a major T1D autoantigen, and will clarify the impact of affinity maturation on this recognition. These findings will identify insulin-binding B lymphocyte changes that can be monitored as early indicators of immunotherapy response in the future to improve clinical trial evaluation and inform clinical management. The technical skills and professional development proposed in this training plan, paired with strong, multidisciplinary mentorship, will support my future career goal to be an independent scientist and leader in immunotherapy design.

NSF Awards · FY 2024 · 2024-09

This project will probe fundamental geometric and dynamical phenomena in several mathematical contexts centered around the notion of symmetry. Mathematically, symmetry (as can appear in molecules and in rigid motions of space) is formalized in the construct of a group, a foundational concept in many branches of mathematics. This project focuses on groups that arise in the study of low-dimensional topology and geometry that concern both the structure of the space itself, such as its curvature, distance and volume, and the structure of their associated parameter spaces, which capture the geometric structures supported on the space, or the configurations of points on the space. For the purposes of this project, the two most important classes of examples are graphs and surfaces, and the groups that that can be obtained by combining these objects in basic ways. This project will identify and study how the inherent structure of these groups reveals important geometric and dynamical phenomena. The research activities in this project will be integrated with graduate and postdoctoral training and the development of structured avenues for undergraduate students to engage in mathematical experimentation and exploration. Specifically, this project investigates the geometry of groups and the dynamics of free group automorphisms. There are several distinct but interrelated goals: Firstly, the project will develop a new theory of geometric finiteness for subgroups of mapping class groups that is tested against examples and understood from the dual perspectives of the intrinsic geometry of surface group extensions and the extrinsic structure of mapping class groups. This is motivated by the theory of Kleinian groups and builds on the PI's recent work in studying surface group extensions associated to lattice Veech groups. Secondly, the project will study the asymptotic behavior of least pseudo-Anosov dilatations and prove that, up to normalization, these numbers accumulate on only finitely many values. This will be accomplished by carefully analyzing the fibrations of individual hyperbolic 3-manifolds and using the fact that all least dilatation pseudo-Anosovs arise as monodromies of only finitely many 3-manifolds. Thirdly, the project will further develop a new theory of orientability of fully irreducible free group automorphisms and study how this interacts with branched covers, stretch factors in finite covers, and polynomial invariants of free-by-cyclic groups. In particular, it will utilize train track theory to show that each fully irreducible automorphism has a canonical orientation double cover. Fourthly, the project will study the Cannon-Thurston maps that encode the boundary structure of hyperbolic group extensions and prove that these maps are uniformly finite-to-one. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-09

Analytical approaches to fatty acid oxygenases and their lipid mediator products Project Summary/Abstract This program focuses on technically challenging questions related to lipoxygenases, their associated enzymes and proteins, and an unprecedented higher-resolution analysis of mechanisms of biosynthesis and fate of the oxidation products. These pathways are conserved widely in evolution and ubiquitous in higher animals. A major thrust is uncovering the mechanistic basis of how a 12R-lipoxygenase (12R-LOX) metabolic pathway functions to secure formation of the water permeability barrier in the epidermis. Pathway genetic deficiencies have devastating consequences, being neonatal lethal in mice and in humans causing congenital ichthyosis (scaly skin), an extremely socially challenging condition. We identified 12R-LOX, epidermal-LOX-3, and the dehydrogenase SDR9C7, as working in series to oxidize linoleic acid (18:2w6) that is esterified in a skin-specific acylceramide. Such oxidations are essential for covalent binding of ceramides to barrier protein, forming sub- structures visible by EM: the corneocyte lipid envelopes. We will apply a singular combination of technical resources (recombinant enzymes and barrier proteins, novel LOX products, unique collection of oxidize acylceramides, access to mouse knockout epidermis, quantitative LC-MS assays, proteomics) to uncover how 12R-LOX oxidations lead to sealing the permeability barrier. Our hypothesis rides on the nature of the linoleate- ester oxidation, which forms an epoxy-enone-linoleate, reactive with nucleophiles and capable of adducting to protein. Understanding these mechanisms will have long-term impact on treatment of skin barrier-related diseases as well as optimizing artificial skin production for treating burns and severe diabetic ulcers. In a second arm of the program, we address technical questions in the field of lipoxygenase product biosynthesis. First, defining the biochemical mechanisms of forming the oxygenated derivatives of “fish oil” fatty acid EPA and DHA, products currently cited as pro-resolving in inflammation, the biosynthesis remaining controversial over the past 20 years. Second, the mechanisms in cyclization of fatty acid allene oxides (highly unstable epoxides) to cyclopentenones. The latter is relevant to heme-protein chemistry and to synthetic chemistry of cyclopentenones and other 5-membered carbocycles. Summing up the vision and suitability for the freedom afforded by MIRA funding: we address mechanistically important and challenging projects, apply unparalleled technical abilities including analysis of extremely unstable pathway intermediates, and leadership in exemplifying the highest standards in the fields of lipoxygenases and related lipid oxygenases.

NIH Research Projects · FY 2024 · 2024-09

Structural investigation of biological complexes at near atomic resolution is essential to illuminating the molecular mechanism of biological systems under physiological and pathological conditions; these efforts ultimately lead to developing therapeutics and improving human health. Understanding lipid-protein interactions, protein-ligand interactions, multi-subunit protein assembly, and physiologically relevant conformational ensembles require experimental measurement and structural determination, because these are questions too complex to solve in silico even with today’s most advanced structural prediction and simulation software. Single particle analysis (SPA) cryo-EM is used extensively for structural determination at Vanderbilt investigators to illuminate novel mechanism underlying DNA replication (Chazin and Eichman), nuclear export of mRNAs (Ren), calcium signaling (Karakas), host-pathogen interaction (Cover, Crowe, Lacy, and Wan), therapeutic antibody development (Crowe), membrane trafficking (Jackson), neuronal signaling (Nakagawa and Zhou), biomimetic polymers (Duvall), energy homeostasis (Lepesheva), and membrane protein biology of GPCR, ion channels, and transporters (Hamm, Karakas, and Nakagawa). Furthermore, technological advance in cryo-electron tomography enabled visualization of macromolecules in subcellular compartments in situ, providing access to intact ultrastructure of synapses (Zhou) and viral assembly mechanism in host cells (Wan). Essential to these discoveries are the extensive trial-and-error efforts to optimize and identify specimens most suitable for high resolution analysis using the state-of-the-art Titan Krios. This process is often referred to as specimen screening, which requires visualization of negative stain specimen by a 100-200kV transmission electron microscope (TEM) equipped with a detector suitable for image acquisition and subsequent data processing to address specimen quality. We have been extensively using two old TEMs equipped with outdated technologies, 100kV Morgagni and 200kV Tecnai-F20 (TF20), for screening. However, all components of Morgagni and the detector of TF20 are out of replacement parts. Adding a modern detector to TF20 will not add usage hours, yet be prohibitively costly. Considering the low cost-benefit of upgrading TF20 and our inability to repair the Morgagni, we propose to retire the two old TEMs and acquire the modern 120kV TEM, Talos L120C, as a replacement. Talos L120C will provide additional ability to image vitrified samples at cryogenic temperatures in the instance where our cryo- TEM Glacios, used for screening vitrified specimen, is temporarily down for repair. Collectively, the Talos L120C, which will be housed in the cryo-EM core facility and used by the investigators from four Schools and Colleges at Vanderbilt, will fulfill the needs currently met by the retiring TEMs and further establish a robust cryo-EM workflow pipeline to advance the NIH funded projects aimed to improve human health.

NIH Research Projects · FY 2025 · 2024-09

PROJECT SUMMARY Worldwide, the number of adults over the age of 60 will double to 2.1 billion by 2050, leading to an enormous rise of age-related, non-communicable diseases (NCDs) such as dementia, type 2 diabetes, and cardiovascular diseases. Previous work with small-scale, subsistence-level groups suggests that these “diseases of aging” may be avoidable and not an inevitable part of getting older. For example, age-matched samples of Tsimane forager-horticulturalists in Bolivia exhibit the lowest levels of coronary artery disease in the world and slower brain atrophy than Americans and Europeans. The ability of subsistence-level groups to “escape” age-related diseases has been hypothesized to be partially driven by differential immune investment across the life course: these groups are highly physically active, often resource constrained, and constantly exposed to immune threats–all factors which are predicted to keep the runaway sterile inflammation associated with many NCDs in check. However, no study to date has used modern ‘omics tools to understand age effects on immune investment in subsistence-level contexts, or how lifestyle change may directly alter these patterns. The central objective of this study is to use a multi-omic approach to understand the effect of lifestyle on immune activity across aging. Using within and between-population comparisons, I will test how immunological aging varies between individuals experiencing diverse lifestyles, ranging from traditional subsistence-level to highly urban lifestyles. To do so, I will work with the Tsimane of Bolivia, the Turkana of Kenya, the Orang Asli of Malaysia, and with public data generated from US individuals. I will focus on three molecular phenotypes from peripheral blood that are known to be age-associated in post-industrial contexts–gene expression, DNA methylation (DNAm), and clonal hematopoiesis of indeterminate potential (CHIP)–and I will characterize these features in subsistence-level Tsimane, Turkana, and Orang Asli. I will then explicitly ask how lifestyle variation impacts patterns of aging and immune function using (i) cross-population comparisons between these subsistence-level groups and a highly urbanized population (i.e., the US) and (ii) within-population comparisons, as subsets of the Turkana and Orang Asli have recently moved to urban city centers while others still practice their traditional pastoralist (Turkana) or hunter-gatherer (Orang Asli) lifestyles. I predict that the energy excess characteristic of sedentary, calorie dense urban lifestyles will be associated with age-related changes in somatic mutation rates as well as inflammatory DNAm and gene expression, while in subsistence-level settings immune variation will primarily track pathogen responses with blunted age effects. Importantly, I will assess these predictions using both within- and between-population comparisons to reveal robust, generalizable results. Together, this study will illuminate how urbanization impacts immunological aging typical of NCDs and will generate extensive ‘omics and health knowledge for historically marginalized groups that are chronically under-represented in genomic studies.

NSF Awards · FY 2024 · 2024-09

The Standard Model of particle physics has been a remarkably successful theory, agreeing with several decades of experimental observations involving weak, electromagnetic, and strong interactions. The LHC discovery of the Higgs boson in 2012 was further confirmation of this success. However, the Standard Model remains an incomplete theory as it fails to explain dark matter and it does not provide an explanation for the mass of light neutrinos. Interestingly, these insufficiencies appear to be part of an intriguing overlap in the sciences describing the largest and smallest scales of the universe: proposed extensions of the Standard Model also shed light on our understanding of the evolution of our universe and the dark matter relic density measured by astronomers. This work exploits the rich particle physics program at the Large Hadron Collider at CERN in Geneva, Switzerland to search for dark matter and other physics beyond the Standard Model. The expanding LHC data set collected by the CMS experiment offers significant opportunity for new discovery, providing greater sensitivity for new physics signatures which would address questions in both particle physics and cosmology. This research program is aimed at questions motivated by the synergy between these two disciplines, for example, by using events produced through vector boson fusion processes to search for dark matter and supersymmetry. In addition, this effort leverages searches for TeV-scale particles using tau lepton reconstruction and identification, which combined with other techniques, enables targeted searches for interesting new physics such as dark matter, compressed spectra SUSY, heavy neutrinos, leptoquarks, and new heavy neutral gauge bosons such as Z-prime. This research is also enabled by hardware operations and development work on the CMS pixel detector and on development of advanced machine learning data analysis techniques. In addition, the group will undertake multiple education and outreach activities, including the national initiative Quarknet, research experiences for Vanderbilt undergraduates, hosting intern days for local secondary school students, and hosting a "Dark Matter Fest" for students. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

The National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) is a highly competitive federal fellowship program. GRFP helps ensure the quality, vitality, and strength of the scientific and engineering workforce of the United States. The program recognizes and supports outstanding graduate students who are pursuing research-based master's and doctoral degrees in science, technology, engineering, and mathematics (STEM), including STEM education. GRFP provides three years of financial support for the graduate education of individuals who have demonstrated their potential for significant achievements in STEM. This award supports the NSF Graduate Fellows pursuing graduate education at this awardee institution. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

2420676 (Tong) and 2420677 (Lin). Climate change is threatening water sustainability by causing more droughts and limiting water access to people around the world. For example, the Western United States has suffered from severe droughts and heat waves, and the Colorado River has recently experienced record low water levels. Brackish water desalination (BWD) is a promising approach to produce more freshwater, but it is inhibited by the lack of effective strategies for brine management. The goal of this research is to develop cost- and energy-efficient brine treatment technologies that enable decarbonized BWD for climate-adaptive water supply. This goal is targeted to be achieved through interdisciplinary research that integrates fundamental interfacial processes and thermal transport to achieve a solar driven zero liquid discharge (ZLD) system. The environmental impacts of this system will be evaluated by techno-economic analysis, life-cycle assessment, and assessing public acceptance. Further benefits to society will result from research training of college students from underrepresented groups, curriculum enrichment, and outreach and public engagement activities. The accelerating global effects of climate change have resulted in an immediate need of adapting water supplies to the rapidly intensified drought conditions. The nationwide adoption of BWD as a feasible strategy to augment freshwater supply is hindered by the challenge of brine management. Minimizing brine volume via ZLD is the key to render BWD a practical and viable means to mitigate the adverse impact of climate change on water security and resiliency. The overarching goal of this project is to achieve solar driven ZLD for decarbonized inland freshwater production as part of a strategy to address climate change. Specific objectives of the project are to 1) develop a novel process integrating nanofiltration and reverse osmosis to enable cost-effective brine volume reduction; 2) design an innovative interface enhanced crystallizer for energy-efficient and robust brine crystallization, guided by fundamental understanding of interfacial salt crystallization, 3) develop a novel high-efficiency heat pump to power ZLD with interface enhanced crystallizer; and 4) evaluate the sustainability of off-grid, decarbonized inland BWD with ZLD with concurrent techno-economic, lifecycle, carbon flow, and social acceptance assessments. To achieve these objectives, this project will integrate and converge knowledge and approaches from multiple disciplines including environmental engineering, environmental sustainability, interfacial engineering, thermal transport processes, systems engineering, and social science. The successful completion of this project has the potential for transformative impact through enabling decarbonized ZLD to support the wide adoption of climate-resilient inland desalination that improves water resilience against a changing climate. The project will provide undergraduate and graduate students from underrepresented groups with opportunities of preforming interdisciplinary, convergent research to solve an environmental and sustainability challenge of global concern. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY / ABSTRACT Funds are requested to purchase a Leica EM ICE high-pressure freezer to prepare electron microscopy samples for projects focused around mental health research within the Vanderbilt Brain Institute (VBI), a multi-disciplinary research institute comprised of faculty at Vanderbilt University (VU) and Vanderbilt University Medical Center (VUMC). The requested instrument will be integrated into and managed by the Vanderbilt Cell Imaging Shared Resource (CISR), a microscopy core with a 20+ year history of successful microscopy management, training, and acquisition of new technology. This instrument capable of fast-freezing live or fixed samples in vitreous ice for downstream applications including freeze-substitution TEM, cryo-FIBSEM, and cryo-ET. This equipment is essential to progress the research of the 7 Major Users within Vanderbilt and the VBI with projects surrounding neuronal cell biology, synapse assembly and plasticity, synaptic signaling, glutamate receptors, and communication between cell populations. These molecular and cellular investigations will advance already funded NIMH and NIH projects totaling over $4M in FY23 in the areas of psychiatric disorders, Alzheimer’s, ALS, learning and memory, Rett syndrome (RTT), childhood neurodegenerative diseases and more. The proposed high-pressure freezing system is based on the needs of the VBI and Major Users to capture neuronal processes with the highest resolution and fidelity possible to understand fundamental advance these NIMH and NIH funded projects. The Leica EM ICE high-pressure freezer includes: 1) The base unit high- pressure freezing that uses pressurized liquid nitrogen to both generate pressure and cool samples simultaneously; 2) Electric and light stimulation modules to capture synaptic events at the point of freezing 3) A cell and tissue incubator system to load live samples into the EM ICE; 4) Sapphire based freezing modules to allow correlative light and electron microscopy either before or after freezing, and conventional flat carriers for freeze-substitution and freeze-fracture/etch applications. This system would be housed in renovated electron microscopy suite in Medical Center North which is directly adjacent to the VBI and the majority of the User labs. Vanderbilt University is providing financial support to promote the long-term operation of the instrument. If awarded, the Office of the Dean of Basic Sciences is committed to providing $75,896 for CISR service contracts, staff salary, computer purchases and upgrades, and reduction in user fees over the first 5 years. Technical support and training of new users will be facilitated by the exceptional staff within the CISR, which has a greater than 20-year history of assisting over 300 labs on campus in both sample preparation and imaging. Moreover, this equipment will be housed in newly renovated electron microscopy space that is centrally located near the Major User group. Collectively, the proposed high-pressure freezing system, together with outstanding institutional and core facility support, will enable the long-term objective of supporting and advancing neuroscience and mental health research Vanderbilt.

NSF Awards · FY 2024 · 2024-08

National frameworks for science education in the United States advocate for bringing science, technology, engineering, mathematics, and computer science (STEM+CS) disciplines together in K-12 classrooms. Although curricular materials are emerging to support STEM+CS integration, research demonstrates that teachers need support to engage students in authentic STEM+CS practices that leverage and sustain student and community assets. This project aims to support middle school teachers in their enactment of an integrated science, engineering, and computational modeling curriculum unit and understand how teachers customize computationally-rich, Next Generation Science Standards (NGSS)-aligned curricular materials to their own schools and classrooms. Through this work, the project team seeks to develop a better understanding of the supports that teachers need to successfully adapt science curricular materials to different classroom, school, and community contexts. The project involves collaborating with school districts to implement the Water Resource Challenge (WRC), developed based on existing NSF-supported curricular materials, and revise it to enable customization for different teachers and school settings. As more NGSS-aligned STEM+CS materials are developed for teachers, this work is important for understanding how teachers adapt and customize curricular materials to meet the needs of their students. The project leverages a participatory design paradigm to engage middle school teachers in professional learning experiences focused on the development of STEM+CS curricular materials. Through design-based research, the project examines the kinds of support teachers need to customize STEM+CS curricular materials for their specific contexts. Researchers will investigate implementation integrity and explore factors that shape teachers' enactment and adaptation of STEM+CS curricular materials, including use and customization of educative materials and teacher guides, teacher characteristics (e.g., STEM+CS experience, beliefs, and perceptions of students), and classroom contexts (e.g., student assets and resources, community resources, district, and state requirements). Specifically, the project will investigate: (1) the kind of supports teachers need to be able to customize STEM+CS curricular materials; (2) how teachers customize and enact STEM+CS curricular materials in their classroom; and (3) students' learning of STEM+CS concepts and practices and their STEM+CS identity when teachers use customized and non-customized materials. The project will involve 18 teachers and impact up to 4,800 students in school districts in Virginia and Tennessee. Project outcomes include co-designed STEM+CS curricular materials, a computational modeling environment, and teacher resources to support STEM+CS integration in curricular materials and practice. The Discovery Research preK-12 program (DRK-12) seeks to significantly enhance the learning and teaching of science, technology, engineering and mathematics (STEM) by preK-12 students and teachers, through research and development of innovative resources, models and tools. Projects in the DRK-12 program build on fundamental research in STEM education and prior research and development efforts that provide theoretical and empirical justification for proposed projects. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

Many children in the U.S. struggle in math due to difficulty understanding place value and calculating with two-digit numbers (11-99). Playing number board games is a fun, commonly used and effective way to improve children’s numeracy knowledge. Consequently, this project will explore children’s numeracy learning in both the commonly used 0-100 number board game layout as well as an innovation modifying the game board’s layout to support children looking for and making use of predictable patterns in numbers (a “patterning lens”). In the modified board condition, children will play with a 0-100 game board with the numbers increasing from bottom-to-top and left-to-right, such that decades are in the far-right column and numbers ending in the same ones digit are in the same column (similar to a hundreds chart). Support for recognizing patterns will also be provided using visual cues to highlight numeric patterns. This study will advance understanding of a feature of games that can enhance learning and provide evidence for the benefits of a hundreds chart as a tool for promoting numeracy learning in primary grades. This study will provide essential evidence to refine a theory about how supporting a patterning lens promotes early numeracy learning, including the causal contribution of this malleable factor to early numeracy learning. It will utilize an experimental design involving pretest, 4 game-playing sessions that will vary across conditions, and posttest. Participants will be 100 students (ages 5-7 years) attending racially- and economically-diverse public schools. Three aspects of base-10 knowledge for two-digit numbers will be assessed: place value, number comparison, and arithmetic. All children will play a 0-100 number board game that will vary in the spatial organization of the numbers. In the experimental condition, implicit support for a patterning lens will be provided by organizing numbers in a 10 x 10 matrix with numbers from left to right so that numbers ending in the same ones digit are in the same column (similar to a hundreds chart), and with visual cues to highlight numeric patterns (e.g., the ones digits repeat in each decade). In the control condition, the numbers will be organized to snake back and forth, as is typical for board games. This study will provide a rigorous test of the effects of implicit support for using a patterning lens for numeracy learning by controlling for all other aspects of board game play (i.e., the same range of numbers, playful interactions, etc.). Furthermore, the study will use a microgenetic design, making it possible to examine the process (e.g., rate of learning) as well as the products of change, which will allow for greater understanding of the components of change for theory refinement for the role of a patterning lens in numeracy development. This study will also advance understanding of a feature of games that can enhance learning by promoting relevant cognitive processes and provide empirical evidence for the benefits of a hundreds chart as a tool for promoting numeracy learning. This project is supported by NSF's EDU Core Research (ECR) program. The ECR program emphasizes fundamental STEM education research that generates foundational knowledge in the field. Investments are made in critical areas that are essential, broad and enduring: STEM learning and STEM learning environments, broadening participation in STEM, and STEM workforce development. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT Staphylococcus aureus is an opportunistic pathogen that is critical to public health and a top cause of infectious death worldwide. To infect humans and cause disease, S. aureus is dependent on the availability of nutrient metals, including zinc (Zn). In response to infection, host factors including the S100 protein calprotectin (CP) act as effectors of nutritional immunity and sequester nutrient metals. Vertebrate proteins of the COG0523 family have been identified as bona-fide Zn metallochaperones that equip downstream metalloprotein effectors with Zn ions. COG0523s in bacteria are predicted to perform a similar role in maintaining cellular metal homeostasis and supporting cellular function, particularly in the setting of Zn starvation. This proposal aims to evaluate S. aureus COG0523 orthologs crzA and zigA, define the impact that these genes have on pathogenesis, and elucidate their role in Zn transfer to predicted interaction partners. Preliminary data suggest that crzA and zigA are regulated by Zn via the transcriptional repressor Zur, that high confidence interaction partners exist for both CrzA and ZigA, and that loss of either COG0523s or predicted binding partners increases sensitivity to DNA damage. This phenotype is pronounced in crzA and zigA mutants exposed to both Zn stress and specific DNA damage. The central hypothesis of this proposal is that S. aureus COG0523s transfer Zn to metalloproteins involved in DNA damage repair in a Zn- and GTP-dependent manner and that this process is important to S. aureus pathogenesis. To test this hypothesis, biochemical, genetic, and microbiological techniques will be used to define a model of CrzA and ZigA function in S. aureus. In Aim 1, I will define the mechanism for interaction between COG0523s and their clients and evaluate how metal, candidate clients, and GTP/GDP affect the dynamics of CrzA and ZigA Zn transfer. To accomplish this, I will express and purify COG0523s and their clients, and define the function and required co-factors of ZigA and CrzA by co-immunoprecipitation, client- specific biochemical assays, and inductively coupled plasma mass spectrometry (ICP-MS). In Aim 2, I will test the hypothesis that COG0523s regulate client activity and affect S. aureus DNA maintenance and that conserved COG0523 Walker and CXCC motifs are required for ZigA and CrzA function in S. aureus. I will conduct growth curves and survival assays in the presence of DNA damaging agents and in bone-marrow derived macrophages to elucidate the impact of Zn, DNA damage, COG0523s, and the metal/GTP-binding motifs of these proteins on S. aureus growth and mutagenesis. In Aim 3, I will test the hypothesis that CrzA and ZigA enable S. aureus to circumvent host-imposed Zn restriction. Manipulation of Zn-handling both in the host and pathogen will demonstrate the impact of COG0523s on infection and increase the rigor of our approach. Taken together, the proposed work will have broad implications for the study of S. aureus pathogenesis. This work has the potential to establish CrzA and ZigA as the first experimentally confirmed bacterial Zn-metallochaperones and continue to develop an understanding of the role of nutritional immunity in therapeutics and clinical practice.

NIH Research Projects · FY 2026 · 2024-08

PROJECT SUMMARY Cytochromes P450 (CYP) form one of the largest enzyme superfamilies on Earth and can be divided into two groups based on their substrate preferences: those metabolizing a vast array of xenobiotic molecules (e.g., drugs and pollutants) and those with very strict requirements towards their physiological substrates (e.g., steroids and vitamins). Sterol 14α-demethylases (CYP51) represent a very special P450 family, which is currently regarded as the evolutionary progenitor for all existing P450s. CYP51 enzymes are found in all kingdoms of life. With sequence identities across phyla as low as 22-25%, they catalyze the same three-step regio- and stereo-specific reaction that involves two successive hydroxylations followed by the C-C bond cleavage. The CYP51 reaction is an essential step in the biosynthesis of sterols and serves as the major drug target for the treatment of fungal infections in humans and plants. We have validated CYP51 druggability across phylogeny, including protozoa (trypanosomes, leishmania, amoebas) and human. We determined 35 CYP51 X-ray structures and successfully applied structure-based drug design to build an in-house chemical library of novel pathogen-selective inhibitors, which are non-toxic and have favorable pharmacokinetics. Our work has revealed the conserved molecular basis for CYP51 catalysis, species-specific variations substrate preferences and sensitivity to inhibition, and has enabled identification of CYP51 orthologs in >1000 bacterial organisms, justifying prokaryotic ancestry of the enzyme. We have also discovered that, as part of conservation from bacteria to human, CYP51 catalysis involves large-scale conformational rearrangements in the P450 molecule. The goals of our research under MIRA support will be to combine the strength of different techniques of biochemistry, molecular and structural biology (crystallography, cryo-electron microscopy, computational approaches) in order to understand how conformational dynamics governs CYP51 throughout the catalytic cycle, mediates allosteric regulation, specificity in molecular recognition and intermolecular assemblies of multi-component electron transfer systems. We will gain new mechanistic insights into CYP51 enzyme function and inhibition, as well as uncover the structural basis for its possible role in P450 diversification. The current set of proteins available for comparative analysis comprise CYP51s form endoplasmic reticulum of higher and lower eukaryotes (vertebrates, fungi, and protozoa), their endogenous electron donor partners cytochrome P450 reductases, and the natural CYP51-ferredoxin fusion protein from the cytoplasm of a sterol- making bacterium. Enzymes from plants that contain multiple CYP51 genes will be added as the research program progresses.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY For viruses with multi-segmented double-stranded RNA (dsRNA) genomes, the correct assortment of segments must be selectively packaged into an assembling viral capsid to form an infectious particle, but packaging mechanisms are incompletely understood. This gap in knowledge limits the ability to genetically modify segmented dsRNA viruses for vaccines and therapies. The packaging mechanisms of oncolytic dsRNA virus mammalian orthoreovirus (reovirus) remain largely understudied. Thus, genetic modification to increase its oncolytic potential has been limited. Packaging of reovirus RNA is thought to be a highly ordered process. Signals required for packaging are thought to be located at the segment termini, which are predicted to interact and form RNA secondary structures. The observation that reovirus can package defective viral genomes (DVGs) presents new opportunities to identify minimal reovirus packaging determinants, since DVGs are nonfunctional forms of the viral genome that retain packaging and replication signals. The goal of my proposed research is to elucidate mechanisms of reovirus RNA packaging and identify elements within the viral genome that play a role in this process. Preliminary and published data indicate that reovirus can package deletion DVGs that lack most of the internal region of a segment but retain both termini. I will take advantage of reovirus DVG selection to elucidate minimal packaging requirements. I hypothesize that reovirus DVGs contain minimal RNA recognition elements and that structures at the viral RNA segment termini mediate packaging. To test this hypothesis, I propose two specific aims. In Specific Aim 1, I will use ClickSeq, Illumina next-generation short-read sequencing, Oxford nanopore third-generation long-read sequencing, and molecular virology approaches to define DVG characteristics that allow preferential RNA packaging. In Specific Aim 2, I will use 2’-hydroxyl acylation followed by primer extension (SHAPE) and reverse genetics to determine the structures of reovirus RNA segments and identify components within the viral RNA that are essential for selective reovirus segment packaging. The findings generated by the proposed aims will reveal selective reovirus RNA packaging mechanisms, which may apply to other segmented viruses. Continued studies building on these findings will facilitate reovirus genetic modification to improve its effectiveness as an oncolytic therapy.

NIH Research Projects · FY 2025 · 2024-08

Project Summary A fundamental question in cell biology is how this crowded space can be organized to enable the control of biochemical processes and reactions in space and time. Biomolecular condensates have emerged as a potential universal solution to how activities and functions are organized within cells. Condensates by nature are formed via collective interactions between biomolecules which together form concentrated assemblies. These collective biochemical interactions govern both condensate regulation and function within cells. The interface of the condensate with the cytosol (interfacial surface) has emerged as a critical molecular determinant for condensate regulation, and function. Biological Pickering agents absorb the interfacial surface of condensates and offer a versatile solution for how cellular functions can be compartmentalized. As interest in biomolecular condensates as an organizing principle in the cell has increased, so have the criticisms of the quality of evidence supporting the biological significance of condensates in native cells. To overcome these valid criticisms a key challenge moving forward for the field is the development of technical approaches to measure and manipulate the collective interactions within these assemblies in native cells. The molecular mechanics that underpin condensate regulation, dynamics, and function in native cells is not well understood. During C. elegans embryogenesis, RNA granules called P granules undergo a dramatic stereotyped polarization within the zygote. Using P granule as a model condensate this proposal aims to define the core biochemical principles that underpin the spatial and temporal regulation of P granule polarization. The goals of this proposal are to 1) identify key biochemical determinants that facilitate P granule assembly 2) define the molecular mechanism by which DYRK kinase regulate P granule disassembly 3) define the biochemical mechanism by P granule assembly and disassembly is spatially regulated 4) determine the biochemical mechanism by which biological Pickering agents are removed from the interfacial surface of P granule 5) define the molecular mechanics that underpin the kinetic arrest of P granules. To accomplish these goals, we will use a multifaceted approach that includes biochemistry, cell biology, and genetics. Leveraging our unique in vivo and in vitro assays we will define the collective biochemical grammar that facilitates the regulated assembly and disassembly of P granules.

NIH Research Projects · FY 2026 · 2024-08

Project Summary The objective of this proposal is to create a novel ciliary stent integrated with wirelessly actuated artificial cilia for treating cilia dysfunction in various diseases such as Chronic Obstructive Pulmonary Disease (COPD). Significance: This work is motivated by the prevalence of Central Airway Obstruction (CAO) due to various lung diseases especially COPD where 53% of the patients developing airway collapse and resulting in excessive mucus accumulation even with an implanted airway stents. Our objective in this proposal is to create a novel airway stent that provides the radical support in airway collapse, does not have the issue of tissue in-growth, and provide the function of transporting mucus with artificial cilia. This approach is clinically innovative because it will potentially overcome the limitation of existing airway stents by reducing the frequency of bronchoscope operations and blind suction of conventional silicone airway stents, and reducing the risk of open-surgery due to tissue ingrowth of conventional metal airway stents. Innovation: Technical innovation comes from 1) a novel artificial cilia blanket design and fabrication which can transport mucus efficient by mimicking the non-reciprocal motion and metachronal coordination of biological cilia, and 2) a novel magnetic actuation and control system which can wirelessly actuate the artificial cilia safely with minimal invasion. Magnetically actuated cilia have been reported for transporting liquids in microfluidics but has not been designed and integrated on airway stents for treatment of COPD. Approach: This proposal proposes to create our airway stents with artificial cilia through three specific aims. Aim 1 involves the design of the magnetically actuated artificial cilia, the integration of the artificial cilia on existing meshed airway stents, and the magnetic actuation systems. Aim 2 focuses on validation experiments including experiments of the airway stents with artificial cilia in phantoms, ex vivo tissues, and porcine lungs to evaluate the mucus pumping performance and overall system functionality. These Aims will be carried out by a multidisciplinary team of investigators combining expertise in lung surgery, mechanical design and control of airway stents, and design and control of the stent delivery and remove tools using a flexible bronchoscope. The goal of this R21 project will be the demonstration of accurate spatial deployment, efficient mucus transporting, and an-trauma removal of the stent to enhance the treatment of COPD. We hypothesize this R21 project will bring a potentially curative treatment for COPD to many more patients. Broad impact includes paving the way for an innovative medical device with minimal invasion, long-term, and out-of-hospital treatment of cilia impairment due to multiple diseases in multiple organs in the human body. Further research will be initiated on translating the stent mechanism for various lung diseases such as Cystic Fibrosis and lung cancer. In the long term, this proposed technology will have a giant potential to clinical trials for patients with cilia dysfunction in general.

NSF Awards · FY 2024 · 2024-08

The mismatch hypothesis states that past lifestyles selected for genes that are now, in modern urbanized groups, detrimental to human health. The presence of these past-selected genes in modern human populations account for the current surge of non-communicable diseases such as obesity, type-II diabetes, and cardiovascular disease. To date, most studies that test this idea are limited because they compare genetically distinct groups. This dissertation project addresses this issue by focusing on a group of individuals that share a similar genetic background but live in environments that are a “match” (subsistence-level) or a “mismatch” (urban) to their previous lifestyle. The study informs genome-environment interactions in humans, human adaptation, and health, as well as the tempo of evolution in modern human populations. The study involves the participating community through multiple strategies and uses community-driven techniques in the production of public information. The study provides training opportunities for graduate and undergraduate students of diverse backgrounds and deepens the interaction and communication among researchers interested in this topic. A total of ~700 participants, with approximately even sex-ratios, are included in the study. A composite continuous lifestyle index (traditional-to-non-traditional) is calculated for each individual based on data collected through structured interviews. Putatively beneficial genomic sites are identified using whole genome sequencing (WGS). Signatures of past-selection are recognized using selection statistics that examine patterns of allele frequency and/or haplotype homozygosity. These analyses include population branch statistics (PBS), integrated haplotype score (iHS), and cross population extended haplotype homozygosity score (XP-EHH). Two outgroups are used to calculate allele-frequency-changes in each single nucleotide polymorphism (SNP). RNA extracted from the participants is analyzed with mRNA-seq analyses. The expression of the identified previously-selected genes will be assessed to characterize genotype-environment interactions and evaluated in relation to lifestyle-associated diseases. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

The archaeological record of human history is vast, spanning most of the planet's land masses, and mostly unrecorded, with knowledge derived from a tiny fraction of sites around the world. The lack of data from larger connected regions makes it difficult to understand how fieldwork-derived data from small sites fit within the bigger picture of the human past. This project pursues this big picture through a combination of fieldwork and artificial intelligence to produce an archaeological survey that uses high resolution multi-spectral satellite imagery. The datasets produced by this survey enable research on past human adaptation and social networks on a continental scale. Mapping how human populations and settlements are distributed within geographic regions is a critical step for understanding how societies change and adapt to their surroundings. Archaeology is often the only source of information about human settlement patterns before the Early Modern era, but it is extremely challenging to use the field’s traditional methods to map sites across regions. This project meets that challenge by developing artificial intelligence models to identify archaeological features in high resolution satellite imagery, over an area of nearly two million square kilometers. The project develops new deep learning models that are tuned for feature detection and deployed to identify abandoned structures across vast areas. These models are important for research in diverse fields such as earth and environmental sciences, infrastructure planning, and emergency response. The models' results are combined and audited with observational data from fieldwork in different regions. The models and data are open-source and available to the research community to study long-term trends in human adaptation, settlement, and demography. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.