Grants

NIAID - National Institute of Allergy and Infectious Diseases

To support the advanced development of candidate therapeutics for antibiotic resistant pathogens. The supported research and development activities will progress the therapeutic product development and may include lead optimization, candidate selection, preclinical and IND enabling studies, Chemistry, Manufacturing, and Controls (CMC), IND submission, clinical safety and efficacy assessment.

NSF

Most structural biology methods examine proteins at one moment in time, as if their structures were static. In recent years, however, we have come to understand that the dynamics of a protein are essential to its function. More tools are needed to examine protein dynamics. In this research, the investigator will seek to apply a method of time-resolved cryo-electron microscopy developed in his lab to diverse biological molecules of eminent interest in medicine, in collaboration with three renowned scientific laboratories, thus broadening the utility of this important tool for studying protein dynamics. The method involves rapidly mixing two components of a reaction, allowing the reaction to proceed for a controlled length of time, then rapidly freezing the sample for cryo-electron microscopy (cryo-EM). Time-resolved cryo-EM will show the progression of a biochemical reaction as a sequence of intermediate states, like successive frames of a movie. The application of this method in the life sciences will greatly expand our understanding of molecular interactions in the cell in healthy persons, as well as their disruption in disease. This research is truly interdisciplinary as it is at the intersection of biology, biomedical engineering, nanofabrication, microfluidics and high-performance computing. As such it will inform molecular medicine and inspire projects for graduate students in the labs of the collaborators and nation-wide as it opens avenues of research and training in health science research never explored before. Using newly designed PDMS-based microfluidic chips, the PI's team will apply the time-resolved cryo-EM sample preparation method, which his lab has developed and demonstrated with the ribosome, to a diverse range of other molecules: (1) RNA polymerase, a large molecule that copies the genetic information from DNA to make mRNA; (2) GLP1R, a G-protein coupled receptor found on beta cells of the pancreas and neurons of the brain; and (3) multi-drug efflux transporter AcrB, to be isolated and inserted into proteoliposomes. Although the structures of these molecules are known, their mode of action involving domain motions in the time range of 10 to 1000 milliseconds cannot be explored with normal methods of structure research. Time-resolved cryo-EM can fill this knowledge gap. Samples will be supplied by three collaborating labs, and feasibility of determining intermediate states in the functional cycle will be explored. The experience gained will guide the decisions of the PI’s team on necessary design modifications, desired ranges of control parameters, and the addition of other features required to make the device generally applicable. 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.

NIGMS - National Institute of General Medical Sciences

PROJECT SUMMARY/ABSTRACT Precision genome editing presents opportunities for treatment of disease and for use in biotechnology. Tyrosine family site-specific DNA recombinases (Y-SSRs), such as Cre, are uniquely positioned as chemical biology tools for genetic engineering because they are capable of excision, integration, and inversion of DNA sequences without requiring exogenous co-factors. A major focus in tyrosine recombinase research is the retargeting of these enzymes to new DNA sites, primarily using substrate-linked directed evolution (SLiDE). Although successful in many regards, SLiDE has two substantial drawbacks that limit its use: limited capacity for negative selection can lead to promiscuous recombinases, and lack of selection tunability limits the ability to select for highly active recombinases. Off-target activities could have serious negative consequences in the human genome, limiting the use of evolved recombinases as probes or eventual therapeutics against human disease. Rigorous characterization of the activity of evolved recombinases towards off-target sites and the development of methods to lower or eliminate these off-target activities is a high-priority enabling technology. Likewise, development of a directed evolution scheme that can select for high recombination efficiency would enable the production of recombinase libraries with higher average efficiency in less time. Here, we aim to address both specificity and efficiency of recombination during evolution by developing novel SLiDE methodology. First, to combat promiscuity in evolved recombinases, we will develop a SLiDE method that leverages simultaneous positive selection at a desired target site and negative selection against a library of off- target sequences. We will use this method to evolve novel recombinases for activity against loxHTLV, the target of the previously-engineered RecHTLV. The activity of novel recombinases with the off-target library will then be quantified and compared to that of wild-type Cre and RecHTLV to observe differences in their promiscuity profiles. Second, to enable selection for higher efficiency recombinases, we will establish a bacterial system by introducing toxic “kill switches” into evolution vectors that are temperature controlled. Recombinase-expressing E. coli that have been transformed with these vectors will select for enzymes that can excise the toxic gene from all plasmid copies before timed activation of the kill switch. We will validate this system with existing recombinases and then evolve a new recombinase for activity on loxHTLV to compare to the activity and evolutionary timeline of the previously evolved RecHTLV. We hypothesize that this novel selection for recombination efficiency will rapidly produce an enzyme with improved efficiency in fewer rounds of evolution. Development of these selection systems will accelerate the development of specific, efficient evolved recombinases, streamlining the timeline for development of novel tools and potential therapeutics.

NEI - National Eye Institute

PROJECT SUMMARY/ABSTRACT Glaucoma is a leading cause of irreversible blindness worldwide, resulting from progressive damage to retinal ganglion cells (RGCs). Current diagnostic methods detect disease only after significant structural and functional loss, and existing metrics for disease progression require extended monitoring periods, limiting the feasibility of clinical trials for neuroprotective therapies. There is an urgent need for robust, mechanistically relevant biomarkers to enable earlier detection of glaucoma progression and facilitate the development of novel therapeutics. This project aims to refine and validate advanced imaging biomarkers using Adaptive Optics-Optical Coherence Tomography (AO-OCT), a high-resolution imaging modality that permits direct visualization of RGC soma and vascular mural cells, including pericytes, in both animal models and human subjects. Preliminary data indicate that AO-OCT can detect early morphological changes in RGC soma and pericytes associated with glaucoma progression. However, further validation and improvement of these biomarkers are necessary before larger-scale clinical trials can be conducted. The proposed study consists of two specific aims. In Aim 1, we will utilize transgenic mouse models to confirm the specificity of AO-OCT biomarkers for RGCs and pericytes and to longitudinally assess cellular changes in two established glaucoma models. This work will provide critical validation of AO-OCT imaging against gold- standard histological techniques. In Aim 2, we will conduct a two-year longitudinal study of 50 human subjects with mild glaucoma to assess the relationship between AO-OCT biomarkers and conventional clinical measures of disease progression. Additionally, we will develop AI-based vessel segmentation techniques to enhance the precision of pericyte identification and characterization. This research will yield highly sensitive and specific biomarkers for glaucoma progression, enabling more efficient and cost-effective clinical trials for neuroprotective therapies. Ultimately, these advancements will improve early diagnosis, facilitate the development of novel treatments, and reduce the global burden of blindness due to glaucoma.

NINDS - National Institute of Neurological Disorders and Stroke

PROJECT SUMMARY The precise formation of circuits in the cerebral cortex, involving both excitatory pyramidal neurons (PNs) and inhibitory interneurons (INs), is crucial for proper brain function, with disruptions in this process being implicated in neurodevelopmental disorders such as autism, epilepsy, and schizophrenia. Recent work from the Fishell Lab has revealed that the connectivity of neurons in layer 5 (L5), a critical region for top-down information processing, follows a highly specific targeting pattern that arises during postnatal development. Specifically, in primary visual cortex (V1), L5 is comprised of two distinct excitatory populations—intratelencephalic (IT) and extratelencephalic (ET) neurons—both of which are modulated by inhibitory somatostatin-expressing cortical interneurons (SST cINs). Notably, specific subtypes of SST cINs, such as Chrna2 and Calb2, selectively target ET populations in adulthood. However, it remains unclear whether these targeting patterns are innate or develop over time. Preliminary findings suggest a novel hypothesis: SST cINs may initially target IT neurons and later shift their targeting specificity to ET neurons after eye-opening (P14) in mice, implying a dynamic developmental switch. This transition could be influenced by changes in excitatory drive, considering that retinotopic maps in V1 are shaped by spontaneous waves of activity both prior to and during eye-opening, while feedforward excitation from visual experience appears necessary for the proper maturation of visual responses. The goal of this proposal is to investigate the mechanisms driving this developmental switch and its functional implications. To do this, the study will (1) examine activity patterns of L5 SST cINs, IT, and ET populations across key developmental timepoints (P10, P15, P30) using 2-photon calcium imaging, (2) determine whether the switch in SST cIN targeting influences activity within L5 circuits or the ability of the animal to detect visual stimulus through use of targeted expression of Kir2.1 in SST cINs which prevents the switch in synaptic targeting, and (3) assess whether visual experience is necessary for the proper development of these circuits by rearing mice in darkness and analyzing the effects on L5 activity and circuit formation. By elucidating the activity-dependent processes that regulate the development and refinement of cortical circuits, this project aims to improve our understanding of how disruptions in these processes contribute to neurodevelopmental disorders.

NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development

PROJECT SUMMARY Epilepsy affects over 50 million people worldwide, with developmental and epileptic encephalopathies (DEEs) representing the most severe and treatment-resistant forms. DEEs are characterized by early-onset seizures and developmental delays, often caused by pathogenic variants in genes critical for brain function. Understanding these genetic underpinnings has revolutionized epilepsy research, paving the way for precision medicine—therapeutic strategies tailored to specific genetic and molecular mechanisms. Among these disorders, EEF1A2-related neurodevelopmental disorder (EEF1A2 syndrome) stands out as a rare yet compelling example, highlighting the need for targeted research to understand and treat epilepsy. Mutations in the EEF1A2 gene, which encodes the eukaryotic elongation factor 1A2 (eEF1A2), have been identified as a cause of severe neurodevelopmental disorders, including DEEs. eEF1A2 facilitates protein synthesis by delivering aminoacyl-tRNAs to ribosomes in a GTP-dependent manner. Approximately 50 distinct missense mutations have been reported, with recurrent variants such as G70S, E122K, and D252H associated with severe intellectual disability. These mutations map to key functional domains of eEF1A2—GTP binding (G70S), tRNA binding (E122K), and actin binding (D252H)—and exhibit distinct clinical phenotypes. While G70S and E122K are linked to early-onset epilepsy, D252H is associated with milder or no epilepsy. The role of eEF1A2 in actin dynamics through its third functional domain is also unclear, suggesting potential additional roles in neurons. This project aims to address these gaps through two specific aims: 1. Determining how EEF1A2 mutations alter protein synthesis in human neurons. 2. Determining how EEF1A2 mutations alter actin dynamics, neuronal morphology, and development. Previous studies have been limited by the species-specific isoform switch between eEF1A1 and eEF1A2 that occur in humans but are not fully replicated in mouse models. By utilizing human-induced pluripotent stem cells (hiPSCs) differentiated into cortical neurons, this research will overcome these limitations by determining the alterations due to these mutations on protein synthesis, elongation rate, translatome profile, and translational efficiency (Aim 1). Additionally, alterations in actin mobility and subcellular structure, as well as neuronal morphology, synapse number, and neuronal electrophysiological properties will be determined (Aim 2). The findings will advance our understanding of eEF1A2's neuron-specific roles and inform precision medicine strategies for EEF1A2 syndrome treatment.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

Abstract Atopic dermatitis (AD) is a chronic skin condition characterized by T cell-driven Type 2 inflammation. The MC903- induced dermatitis model has enabled dissection of pathways driving acute AD-like disease such as keratinocyte TSLP production and Th2 signaling; however, its ability to model persistent disease states remains unexplored. Using a repeated-challenge protocol with MC903, we found that adult mice undergoing a primary bout of AD-like inflammation develop persistent, tissue-specific inflammatory memories in skin that manifest as exaggerated pathologic responses during secondary MC903 challenge. This aligns with the emerging idea that AD chronicity stems from local memories of inflammation that persist in healed lesions and exacerbate future disease flares. However, AD in childhood follows a distinct course, with a unique immune composition and lower incidence of chronic disease. We thus tested our model in neonatal mice, and despite observing similar primary response kinetics to MC903-treated adults, we strikingly saw no signs of aggravated pathology during secondary MC903 challenge. This suggests that AD-like inflammatory memory fails in early life. Characterizing the cellular and molecular mediators of these divergent skin phenotypes will be the focus of our proposed work. Our data suggests that inflammatory memory in adults is driven by the emergence of Type 1 (T1) immune features in skin such as T1 tissue-resident memory T cells (Trms), mirroring recent findings in human AD. Transcriptional profiling suggests fibroblasts help to organize these networks by supporting T cell positioning and Trm development within inflamed adult skin. Given emerging data to suggest that neonatal T cells and fibroblasts exhibit distinct inflammatory behaviors from their adult counterparts, we hypothesize that inflammatory memory is impaired in neonatal skin due to age-related differences in T cell and fibroblast function. To test this, we will first use lineage tracing to define the fates and phenotypes of adult and neonatal T cells during AD-like inflammation in developing and adult skin (Aim 1). Subsequently, we will interrogate fibroblast-T cell interactions in the atopic skin of adult and neonatal mice using in vivo profiling via scRNA-seq and immunofluorescence staining as well as in vitro functional assays involving fibroblast-T cell co-cultures. Our work is conceptually innovative and clinically relevant, especially given the growing incidence of chronic AD in adults. Completion of the proposed work will clarify the basic mechanisms by which neonatal skin escapes inflammatory memory, potentially aiding in the identification of new therapeutic interventions for chronic AD.

NIEHS - National Institute of Environmental Health Sciences

PROJECT SUMMARY Obesity and type-II diabetes are a pandemic, causing grave social and economic burdens in the United States. Epidemiological and animal studies showed that the flame retardants polybrominated diphenyl ethers (PBDEs) and a most widely used current PBDE-alternative – tetrabromobisphenol A (TBBPA) are linked to obesity and diabetes. However, mechanisms governing early life exposure to flame retardants and obesity/diabetes remains unknown; no studies have compared the effect of PBDEs vs. TBBPA, and little is known regarding how early life flame retardant plus additional risk factors (e.g. dietary factors) later in life modulate obesity. The liver- and intestine-enriched pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are novel regulators for obesity. Intestinal inflammation, as triggered by dysbiosis of the gut microbiota, is an early mediator of obesity and type-II diabetes. In the previous grant cycle, we have demonstrated that: 1) early life exposure to the PBDEs and TBBPA produces a pro-inflammatory/pro-obese microbial signature later in life; 2) PXR and CAR are necessary in maintaining the basal healthy gut flora to prevent the blooming of pro-inflammatory microbes; 3) the presence of gut microbiome promotes immunotolerance in the liver, whereas early life exposure to PBDEs produced gut dysbiosis associated with enhanced immune cell hepatic mobilization, reduced PXR/CAR signaling, and predicted liver injuries in adulthood; Early life exposure to an industrial PBDE mixture persistently disrupted the microbial tryptophan metabolism. We also showed that the microbial tryptophan metabolite indole-3- propionic acid (IPA) mimicry FKK6 compound protected against intestinal inflammation associated with increased anti-inflammatory short-chain fatty acids (SCFAs) and the SCFA-producing microbes. Building on our findings, the objective of the renewal is to determine how the host nuclear receptors, gut microbiome, and early life flame retardant exposure interact to modulate the adult onset of obesity and type-II diabetes. Our central hypothesis is: early life flame retardant exposures upset the physiological functions of PXR/CAR, leading to pro- inflammation and pro-obesity microbial metabolites and elevated AhR signaling, which augmented obesity following a 2nd hit (e.g. a high fat diet [HFD]) later in life; whereas the microbial mimicry is a novel remediation strategy. We will test this hypothesis in 3 Aims: Aim 1 will determine to what extent PXR and CAR modulate the inflammation- and obesity-related host and microbial signatures following early life exposure to PBDEs and TBBPA. Aim 2 will determine how early life flame retardant exposure and PXR/CAR interact to modulate the high fat diet-induced obesity later in life. Aim 3 will determine how gut microbiome mechanistically contributes to the divergent roles of PXR and CAR in obesity following the “two-hit” exposure paradigm. The overall impact of this research is that we will determine how TBBPA vs. PBDE exposure in early life, especially in the combination of a high-risk obesogenic adult diet, results in adult obesity. This perspective will be shown through the lens of the important host nuclear receptors, which are well-established mediators of endocrine response.

NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development

PROJECT SUMMARY/ABSTRACT During development, neurons that are generated at a single location can go on to innervate different targets and carry out different functions. A fundamental question in developmental neurobiology is to understand how this functional diversification occurs. The developing brainstem gives rise to facial branchiomotor neurons (FBMNs), which innervate different sets of muscles in the face and collectively control all facial movements. While the developmental programs specifying FBMNs are well understood, differences between FBMNs that enable them to wire to different upstream neurons and muscle targets to control different behaviors remain poorly understood. Agenesis, miswiring, and other developmental anomalies of FBMNs cause Congenital Cranial Dysinnervation Disorders (CCDDs), characterized by clinical presentations including facial paralysis, depending on which neurons are affected. A better understanding of FBMN development will also advance our understanding of the etiologies of CCDDs. The evolutionary conservation of FBMNs enables investigation in the transparent zebrafish embryo. To identify transcriptional heterogeneity among developing FBMNs, single-cell RNA sequencing and in situ hybridization were used, identifying two transcriptionally distinct populations in the facial motor nucleus, the brainstem structure composed of FBMN cell bodies. The positions of the two transcriptional populations correlate with developmental age: earlier-born neurons migrate to ventral positions and express different genes than later- born neurons, which migrate to dorsal positions. While previous studies have identified some topography in the facial motor nucleus, the relationship between topography, birth order, and gene expression remains unclear. These observations raise the possibility that birth order specifies distinct gene expression programs, which specify innervation targets. Aim 1 proposes to use high-resolution live imaging to uncover the organization of the facial motor nucleus and determine whether this organization is a product of developmental timing. Aim 2 proposes to combine rapid reverse genetic screening and multiplexed single-cell transcriptomic phenotyping to identify functional regulators of facial motor nucleus development, with specific insight into the etiology of the CCDD, Hereditary Congenital Facial Paresis.

NIAID - National Institute of Allergy and Infectious Diseases

PROJECT SUMMARY/ABSTRACT HIV-1 infection remains a global health crisis. While highly active antiretroviral therapy (ART) allows most people to live with HIV, ART is not curative. HIV-1 exists within a reservoir of latently-infected cells as an integrated provirus DNA that is rekindled for virus gene expression and viral recrudescence upon ART cessation. The field of HIV Cure is accordingly constantly developing new ways, on the one hand, to permanently silence HIV-1 gene expression (block and lock), or, on the other hand, to enhance gene expression and then to eliminate HIV+ cells from the body (shock and kill). HIV-1 structural proteins and replication enzymes are expressed from proviral DNA as Gag and Gag-Pol polyprotein precursors, respectively, which are cleaved into constitutive components by the viral protease (PR) enzyme during virus assembly and maturation. Retroviral PRs are quasi site specific enzymes, and retroviruses have accordingly evolved to regulate PR activity to limit the extent of cellular proteolysis, which otherwise could be leveraged to detect the virus as a foreign invader. Indeed, the field has in recent years described effective small molecule kill modulators, called RT-TACKs, because they work by engaging the reverse transcriptase (RT) domain within Gag-Pol to effect premature Gag-Pol dimerization, which in turn prematurely activates the viral PR to cleave cellular inflammasome modulators and elicit pyroptotic cell death. In addition to protease and RT, the integrase domain encompasses part (the C-terminal portion) of Gag- Pol. Integrase has previously been implicated in regulating PR activity during HIV-1 maturation, but the underlying molecular mechanisms have remained unclear. In this study, we have assessed if integrase-targeting compounds might also elicit pyroptotic cell death. The work described in this application will determine the developmental potential of integrase-targeted activator of cell kill (IN-TACK) compounds for elimination of HIV+ cells.

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

PROJECT SUMMARY Early life exposures play a significant role in shaping health and disease susceptibility. Yet, our understanding of the developmental programming of adult stem cells that maintain tissue homeostasis is limited. Mature adult intestinal stem cells (ISCs) sustain continuous life-long adaptations to diet and the intestinal microbial milieu to preserve tissue stability and prevent sequelae leading to diseases such as inflammatory bowel disease (IBD) or sporadic cancer. ISC’s developmental trajectory is influenced early in life by a maternal environment that provides extrinsic patterning cues and nutrients to influence cell, tissue, and system maturation. Despite the fundamental nature of these developmental phases, we do not understand how durable programmable molecular mechanisms are established or how adverse maternal environmental exposure is maintained in a stable and homeostatic manner within ISCs. There is a critical need to establish how the environment contributes to intestinal homeostasis and long-term disease risk. Using genetically engineered mouse and organoid models, this project aims to distinguish ISC developmental programming and determine both early intrinsic adaptations and extrinsic environmental interactions that promote establishment of a stable pre- pathological ISC ground state. Our central hypothesis is that offspring exposure to an obesogenic maternal environment during pre- and postnatal development establishes a maladaptive pre-pathological ground state ab initio. In Aim1 we will characterize the extent of altered ISC changes in offspring exposed to maternal pro- obesity high-fat Western diet (HFD) during pre- and postnatal phases of maternal dependence, and test the duration that these features exist as offspring age. We will further challenge offspring with the reintroduction of the HFD and test for pathological states. In Aim2, we will investigate how lipid metabolism drives ISC- programming by testing for necessity of lipid regulators, Ppar-d and Ppar-a, and for sufficiency with increased PPAR-d activity. In Aim3, we will explore the role that external signaling from the immune system contributes to developmental programming and later risk of disease. We will test the necessity of pro-inflammatory cytokine IL-17 and the influence in tumorigenesis and inflammatory states. In summary, these efforts will enhance our understanding of how developmental programming in early life leads to health and disease disparities as we age.

NIGMS - National Institute of General Medical Sciences

Biological oscillators, the rhythmic and regular increases and decreases of gene expression or protein activity, drive many dynamic molecular and morphological processes. Probably the most familiar is the circadian clock, but there are also ultradian clocks that operate on the order of minutes and/or hours. Examples of ultradian clocks are those that regulate periodic root branching in Arabidopsis, molting cycle in C. elegans, timing of mitosis to tightly coordinate cell proliferation and tissue morphogenesis, stem cell maintenance, bulk protein degradation and re-synthesis in proliferating mammalian cells, and tissue patterning during somitogenesis, a fundamental vertebrate developmental process that we have studied for many years. Somitogenesis is the anterior to posterior sequential segmentation of the vertebrate embryonic mesoderm into blocks of tissue called somites, which later give rise to axial skeletal muscle, vertebrae, and dermis This rhythmic and regular process is controlled by a molecular oscillator called the segmentation clock which operates in the unsegmented presomitic mesoderm (PSM) and is characterized by rapid cycles of mRNA and protein expression with a species-specific periodicity. Like many cell-autonomous oscillatory networks, the segmentation clock is regulated by a self-sustaining negative feedback loop, where a core oscillatory factor, a transcriptional repressor, inhibits expression of downstream oscillatory genes, including itself. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short- lived. In all vertebrates examined to date, transcriptional repressors of the Hes/her gene family are considered the evolutionarily conserved pacemakers of the segmentation clock. For proper somite formation, rates of each oscillatory step, from transcription to translation to decay, must be regulated to ensure correct somite size and number. Computational modeling and experimental perturbations have shown that transcriptional and translational time delays (the amount of time from transcription or translation initiation to the emergence of a mature mRNA or protein, respectively) and degradation rates of both transcript and protein are parameters having the largest influence on clock period and evidence from in vivo studies assessing the impact of timing of mRNA and protein processing and decay mirrors modeling predictions. Transcriptional regulation alone is not sufficient to produce genetic oscillations and we are focusing on understanding the post-transcriptional regulatory mechanisms that promote proper oscillatory expression. The two key questions that we address in this proposal are: (1) What are the key targets of the core Hes/Her oscillators that carry out oscillatory output? and (2) What are the post-transcriptional regulatory mechanisms driving rapid decay of oscillatory gene transcripts. Answering these questions will address how oscillatory gene expression regulates pattern and fate.

U.S. National Science Foundation

Developmental Sciences

NIDCR - National Institute of Dental and Craniofacial Research

PROJECT SUMMARY The objective of this proposal is to elucidate the complex genetic, transcriptional, and histological landscape underpinning palate morphogenesis by leveraging a systems genomics approach in genetically diverse mice. Craniofacial morphogenesis involves the outgrowth and fusion of facial prominences, which must be coordinated with skeletal specification and differentiation to generate a functional craniofacial complex. Underscoring the sensitivity of this intricate choreography, orofacial clefts (OFCs) are the most common facial anomaly in humans, affecting 1/700 births worldwide. Mouse models provide a key platform for human disease allele discovery owing to recent developments in gene editing that enable rapid validation of novel variants. However, multiple published examples demonstrate the profound effect that mouse genetic background can have on the penetrance and expressivity of craniofacial phenotypes. Thus, our limited understanding of the effect of natural strain variation on developmental processes presents a major challenge to validation of disease variants and our ability to model human congenital malformations. While individual genes are critically required for normal development, it is the collective function of genes and their interactions, modularly organized into gene regulatory networks (GRNs), that control the transcriptional dynamics and timing of morphogenesis and differentiation. Variation in these dynamics likely accounts for normal variation in facial shape but can also underpin craniofacial birth defects. However, feasibility limits studies of genetic variation in developing embryos to only a few genes at a time and experimental models that accurately relate genomic sequence variation to variation in transcriptional dynamics are critically lacking. These challenges complicate a systematic address of genome-scale mechanisms that drive morphogenesis and the potential for pathological outcomes. The complementary Collaborative Cross (CC) recombinant inbred strains and Diversity Outbred (DO) heterogeneous stock combine the genetic and phenotypic diversity of 8 common inbred founder strains of mice in a design optimized for systems-level genetic dissection of complex traits. It has been demonstrated that QTLs for facial shape in adult DO mice are enriched for genes with established function in craniofacial and skeletal development. However, these studies do not address mechanisms of where, when, or how QTL candidate genes influence facial shape. The proposed aims will apply a developmental systems genomics approach to map the influence of genetic variation within a model of palate morphogenesis. Aim 1 will define the temporal dynamics of morphogenetic networks within the segmentally organized upper jaw and identify QTL/eQTL underlying strain differences in developmental timing and palate morphogenesis. Aim 2 will employ single-cell and spatial genomics to genetically dissect the molecular signatures of QTL/eQTL with cellular and histological resolution. Aim 3 will leverage quantitative phenotyping to relate differences in morphogenetic dynamics and resulting morphology to variation in underlying genotype and thereby derive mechanistic insight into the integration of genomic regulatory systems.

NCCIH - National Center for Complementary and Integrative Health

ABSTRACT: Obesity is prevalent among adults (>40%) and children (~20%) in the U.S. and is expected to increase dramatically in the next 25 years. Addressing the obesity epidemic is vital for public health because of its wide range of comorbidities including deadly conditions such as stroke, hypertension, diabetes, heart disease, liver disease, sleep apnea, pregnancy complications, and cancer. Most clinical interventions for obesity target individuals who are already obese. However, a growing body of research demonstrates that obesity can be caused by adverse events during development that drive irreversible effects on metabolic programming. This work highlights a critical need for preventative measures to address the obesity epidemic. Vitamin D is an essential nutrient that has recently been implicated in obesity. This has the potential to impact a large population since up to 80% of pregnant women are deficient in vitamin D (VDD) and emerging studies implicate this may disrupt developmental programming of metabolism and increase offspring susceptibility to obesity later in life. This proposal will leverage our novel mouse model of VDD-induced adiposity (a naturally genetically divergent Collaborative Cross (CC) mouse lineage) to model the human condition so we can better understand the developmental mechanisms driving obesity and target them for effective interventions. The mouse serves as a vital model for studying this important question not only because of its conserved vitamin D biology but also because mouse research allows us to avoid ethical limitations that inhibit studying VDD in human pregnancy and provides control over environmental and genetic confounders present in human populations. The proposed study aims to: (1) Determine the importance of vitamin D sufficiency during pre-, peri-, or post-conceptional windows of development in driving the accumulation of adiposity and risk of obesity-related comorbidities later in life; and (2) Define the developmental timing of VDD-induced transcriptional dysregulation and investigate its role in disruption of metabolic programming. Addressing these gaps in our understanding of the role of VDD in developmental mechanisms of obesity will help determine the relative importance of VitD monitoring and timely interventions for VDD during pregnancy to protect offspring metabolic health so that effective guidance can be developed.

NCATS - National Center for Advancing Translational Sciences

ABSTRACT There is a need in the market for a true platform technology that automates the tissue processing experience. Syntr Health Technologies has dedicated the last nine years to developing the technology that can streamline tissue processing. Our FDA-cleared SyntrFuge System and SyntrFPU360, is a platform technology that can process a variety of different tissue types such as cancer tumors of kidney, liver, brain, and breast tissue by dissociating them into single cells to better understand tumor tissue heterogeneity, of which the single cell analysis market is valued at $3.3 Billion and expected to grow to $6.3 Billion by 2026. Additionally, our platform can be used to microsize autologous adipose tissue to be used for reinjection back into the patient to treat medical conditions of the aging population such as diabetic foot ulcers, knee osteoarthritis, and breast cancer reconstruction surgery. Syntr Health successfully completed an SBIR Phase I grant where we utilized microsized adipose tissue to heal diabetic ulcers in an animal model. This study had an important role in developing a treatment modality that translated successfully into humans. Preliminary human clinical data shows significant diabetic foot ulcer wound closure within 28 ± 4 days using autologous adipose tissue processed in our platform. The diabetic foot ulcer market is currently valued at $1.98 Billion with a CAGR of 8.2%. This high growth potential is attributed to the increase of the diabetic population. Moreover, the use of microsized adipose tissue is showing great promise in intra-articular injections to knee joints for the treatment of osteoarthritis (OA). The knee OA market in North America is currently valued at $5.9 Billion and growing at a CAGR of 8.8%. Over 88% of individuals with OA are 45 or older. The high growth potential of this market is largely attributed to the increase of the aging population along with the increase in obesity rates. Our platform technology for the rapid processing and/or microsizing of tissues can disrupt these markets in a major way. The full automation and market readiness of this technology in this Phase II SBIR is paramount to increase favorability in the adoption of this much needed technology in various medical fields..

Full Life Care

Conduct workshops to teach low-income Seattle Housing Authority residents about smart speakers and other Internet of Things devices that can enhance daily living for people with disabilites.

City of Richmond

Outback in the Temple of Venus

Dewitt Medical Foundation

Dewitt Medical Foundation is an active grantmaking foundation based in Cuero, TX. Focus: health. Contact the foundation directly for current funding opportunities.

New York Works 12-13

Dey's Plaza Apartments Capital

NSF

Slime molds have inspired and enabled a wide range of biotechnology and bioengineered applications. They are unusual organisms since as a single-celled organism they multinucleate, are capable of movement, memory-like behavior, decision-making, and efficient network formation. Biological highways built by the slime mold Physarum polycephalum experience similar goals and tradeoffs to human-built networks, including needing to efficiently allocate the matter the highways are built from, handling fluctuating levels of traffic, and resisting damage or outages. In building highways and its other behaviors, Physarum shows itself capable of intelligence and memory, while having no central organizing body and only limited ability to transmit information between different parts of the organism. Here, collaborating researchers at UCLA (USA) and TUM (Germany) will work to build experimental and theoretical models of Physarum’s ‘behavioral space’. The central hypothesis of this work is that slime mold highways can be reduced to finitely many modes. These modes are derived from physical constraints upon the long-range flows that can be created within the network as well as feedback between flows on the slime mold highways and the bio-motor driven pulsations of the network that create and shape them. The research team will map out Physarum’s behavioral space, relating the modeled flow modes to the biophysical processes that the slime mold uses to piece together its highways, including tube sprouting and pruning, and to the migration of the organism. Because of its size and the speed of its internal flows, Physarum contends with an extreme version of the physical challenges encountered by all single-celled organisms: how to allocate resources and coordinate behaviors across the entire cell. Work to understand its repertoire of intelligent behaviors will have expansive impacts on understanding of the extents to which cell behaviors emerge from biophysical constraints or from choices. Combined with the peculiar charisma of intelligent slime molds, the project creates a rich trove of broader impact activities. These include a workshop to fertilize discussions of multinucleate cell organization across organisms and ecosystems, and a joint US-German Research Experience for Undergraduates (REU) in which each year, three undergraduates from each country collaborate, make integral contributions to the project, and learn key physics skills. Additionally, the team will design and disseminate standards aligned lesson plans for K-12 students on maze-solving, to foster inquiry and curiosity about algorithms and information-use. This collaborative U.S.-German project is supported by the U.S. National Science Foundation (NSF) and the German Research Foundation (DFG), where NSF funds the U.S. investigator and DFG funds the partners in Germany. 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

This project explores new ways to control and stabilize quantum systems that are not in equilibrium, which is an essential step for advancing quantum technologies. One leading technique for realizing new phenomena is periodic driving with external sources, such as lasers, which can be combined with other methods such as optimal control. This research aims to overcome current limitations in cooling and controlling these systems, which are crucial for simulating complex quantum behaviors. Robust control of quantum matter is a fundamental building block of quantum computers, sensors, and devices, with potential applications in energy, superconductivity, and precision measurement. This project tackles a major challenge in quantum simulation: how to reliably prepare and stabilize exotic quantum states that arise when systems are driven out of equilibrium. By leveraging tools like Floquet engineering—where periodic driving creates new effective Hamiltonians—and advanced control techniques, the research aims to overcome current limitations in cooling and manipulating quantum systems such as ultracold atoms and superconducting qubits. The project focuses on three key areas: understanding how topological order emerges during non-equilibrium transitions, developing optimal control strategies in open systems, and managing resonances in periodically driven systems. These efforts promise to deepen our theoretical understanding of quantum dynamics while also offering practical protocols for experimental platforms. The broader impact includes advancing technologies relevant to quantum computing, materials science, and precision measurement. 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

High energy collisions between atomic nuclei are known to produce a novel state of matter, called a quark-gluon plasma and containing unbound constituents, quarks and gluons, that has unusual properties. Existing descriptions of the formation and decay of this state are based on statistical concepts that ignore essential aspects of quantum physics, such as quantum entanglement and microscopic preservation of information. This project will develop descriptions of these processes that exactly respect the laws of quantum physics using a two-pronged approach: (i) The formation of a thermal gluon plasma is studied by exact numerical simulations of gluon dynamics starting from a highly excited quantum state and following it up to the formation of a thermal gluon plasma. (ii) The decay process, in which the quark-gluon plasma decays into many individual particles, is modeled extending ideas from string theory to systems of relevance to nuclear physics and enabling a study of quantum entanglement between emitted particles. The methods and insights developed in this project have broad relevance for the quantum description of dynamical processes in isolated quantum systems, utilizing heavy ion collisions as near-ideal prototype to the mutual benefit of nuclear physics and quantum information science. Dynamical processes involving quarks and gluons at strong coupling are beyond the reach of perturbation theory and Euclidean lattice gauge theory. An important phenomenon of this type is the process of thermalization, which is pervasive in cosmology and high-energy nuclear and particle interactions but conceptually at odds with the microscopic reversibility ensured by the unitarity of quantum evolution. Another process that is usually described by statistical, rather than quantum mechanical techniques is multi-fragmentation as it occurs, e.g., during the deconfinement-confinement transition of a quark-gluon plasma. This proposal follows three interrelated tracks: (a) Delineation of the limits of feasibility of exact real-time lattice calculations with digital computers in the context of the simplest non-abelian gauge theory realized in nature, SU(2). (b) Identification of observable deviations from full thermal equilibrium due to quantum entanglement in exactly solvable low-dimensional models of strongly coupled non-abelian gauge theories using techniques derived from string theory. (c) Exploration of the capabilities of available quantum computers to study the thermalization and fragmentation processes that are accessible to digital computation within certain system size limits. The results obtained with digital computers serve as benchmarks for simulations on quantum computers and help determine the threshold for quantum supremacy. 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

The collisions between neutron stars and between neutron stars and black holes are among the most energetic phenomena in the Universe. These events can be studied using gravitational-wave observatories, such as NSF's Laser Interferometer Gravitational-Wave Observatory (LIGO), and ground-based and space-based observatories, such as NSF's Vera Rubin Observatory and NASA's James Webb Space Telescope. Through these cosmic collisions it is possible to study, among others, the nature of matter at supernuclear densities, testing quantum chromo dynamics in a regime that cannot be probed on Earth, the nuclear physics involved in the formation of rare-earth elements, gold, and alkali metals, and the outcome of the evolution of massive stars. This project aims to develop the theoretical framework necessary to interpret upcoming observations and advance research in these areas. In particular, the team will construct a large template of synthetic neutron star merger observations, leveraging new national computing resources to perform sophisticated general-relativistic simulations. These data will then be used to develop statistical and artificial intelligence models that can be used to interpret real observations. This project will train one US graduate student and three US undergraduate students at the interface between high-performance computing, computational fluid dynamics, and machine learning, thus strengthening the US STEM workforce. This project will also develop new simulations and data analysis techniques and produce open-source code for the benefit of the broader STEM community. This work will be performed in collaboration with researchers at the Friedrich-Schiller-Universität, funded by the German science agency DFG, and will include a research exchange program with Germany, thereby strengthening bilateral ties with Germany. The project will assemble a comprehensive, publicly accessible database of double neutron-star and black-hole neutron-star merger simulations and leverage it for multimessenger astronomy. The database will contain about 1,000 simulations, varying in the binary masses and spins, as well as in the equation of state used to describe neutron-star matter. For each simulation, the team will release the multipole-decomposed gravitational-wave signal, mass ejecta, and remnant properties, including 3D snapshots that could be used as initial conditions for longer-term postmerger simulations. The team will use the data to inform and calibrate 1) merger and post-merger gravitational-wave waveform models; 2) understand the critical physical dependencies of the post-merger evolution of binary neutron-star and black-hole neutron-star mergers; 3) data-driven models of the ejecta; and of 4) the expected thermal and non-thermal counterparts to mergers. These data and models will be the theoretical foundation for the interpretation of future merger observations. The database will also support independent theoretical and observational investigations by other teams. 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.