Cornell University

NSF Awards · FY 2024 · 2024-07

This research project will advance statistical modeling and computing strategies for dependent data. Dependent data are widespread and important. Many socioeconomic, cultural, and political data are measured on spatial areal units, most economic data are time-ordered and co-dependent, and modern monitoring systems record social, environmental, and economic exposure data at near-continuous resolutions. However, this growing abundance of dependent data has outpaced the development of statistical methods and algorithms for such data. The project will develop new statistical tools that will allow researchers to extract reliable information and make decisions from such dependent data. The methods to be developed will be motivated by specific, timely, and important problems in the following areas: local elections and redistricting; inflation modeling and forecasting; spatial pattern extraction for economic, health, and urban data; and modeling of monitoring and exposure data. The project will provide training and mentoring for undergraduate and graduate students, develop publicly available software and visualization tools, and showcase local, state, and federal government data. This research project will develop new statistical tools to adequately capture a broad array of data dependencies, provide computational scalability for massive datasets, and leverage the dependence structures for more adaptive and localized estimation, uncertainty quantification, and imputation of missing data. Unmodeled dependence renders inferences suboptimal or invalid, resulting in underpowered analyses and erroneous conclusions. In addition, dependent data are often high-dimensional with substantial missingness, leading to significant computational and statistical challenges. Within a Bayesian framework, the project will simultaneously integrate the dependence in (i) the model for the signal to provide smoothness and regularization, (ii) the accompanying shrinkage or sparsity prior for enhanced local adaptivity, and (iii) the computational and numerical strategies for scalable posterior inference. Dependence will be encoded as a graph that links together observational units, such as consecutive observations for time-ordered or functional data, adjacent pixels for image or lattice data, and neighboring areal units for spatial data, among many other examples. This graph-based formulation will lay the foundation to unify and advance a broad collection of models, shrinkage and sparsity priors, and inference algorithms for dependent data. The tools to be developed will be customized for a variety of settings, including trend estimation and imputation, shrinkage or sparsity priors, graph-informed regression analysis, factor models, and discrete data, among others. 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 · 2024-06

This research investigates collective action problems to better understand the extent to which groups can solve them. Society faces many challenging collective action problems. A broad goal of the research is ultimately to help society by contributing to the improvement of existing institutions for solving these problems. Many fundamental theoretical and empirical questions remain unresolved about how to efficiently aggregate preferences and information in the face of individual free riding incentives, especially when side payments are not possible. There are many open questions about actual human decision making and behavior under different institutional environments. The theoretical arm of this research is aimed at better understanding the efficient aggregation of preferences and information, using an organizational design approach. The experiments provide information on actual behavior in these institutions, pointing to how they may be modified to improve decision making; and how the theory might be modified in light of behavioral findings from the experiments. The empirical research is aimed at better understanding the forces underlying voter turnout in mass elections. More specifically, the theoretical research addresses specific questions about the relative performance of different organizational structures, or mechanisms, where measures of performance may include the probability of group success at overcoming the free rider problems, or, more generally, economic efficiency. The research team first investigates these questions taking a mechanism design perspective that differs from the usual approaches to study “public goods.” The new perspective studies honest and obedient communication mechanisms, which coordinate the actions of group members without commitment, coercion or monetary transfers. These “Volunteer Based Organizations” (VBOs) require only very simple binary communication in which members express a willingness to either volunteer or free ride. The research goes on to explore: (1) the efficiency properties of VBO mechanisms; (2) a “mechanism equilibrium” when there are multiple competing groups, each of which solves collective action problems which can crowd each other out; and (3) an application of VBO mechanisms to a group-based model of voter turnout. The application to voter turnout also involves an empirical project to structurally estimate the VBO model of group turnout with a new voter-turnout dataset. The researchers then go beyond this static setting and study the dynamics of collective action problems, where individual volunteering or free riding decisions evolve sequentially over time. In many applications, for example international environmental agreements (IEAs), grass root campaigns or uprisings against authoritarian regimes, collective action evolves over time, starting with a small core of activists/volunteers. Individuals who are most willing to volunteer (lowest cost) commit earlier, which in turn can create a bandwagon effect inducing higher cost individuals to follow. This fosters coordination and improves efficiency, allowing individuals in the group to be screened sequentially. Behavior in this environment can be studied as a dynamic participation game; or as a dynamic mechanism design problem if the group can design an honest and obedient mechanism that takes advantage of the dynamic structure. The research studies both approaches and then proceeds to investigate two further extensions: (1) the effect of size asymmetries across the group members; and (2) the effect of non-stationarities, reflecting changes in the value of group success or costs of participation as time unfolds. The third arm of the research is experimental and involves four laboratory experiments and one large-scale online experiment. Three of the laboratory experiments are directly motivated by the static model of VBOs; the fourth is motivated by the dynamic theory. The large-scale online experiment explores group sizes an order of magnitude large than is possible in the laboratory. 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 · 2024-06

Non-technical description The classification of a drug substance as a medicine or poison depends on several factors including the amount given, how rapidly it is given, where it is given, and drug specificity. This proposal focuses on the latter, that is, enabling the drug to go directly to a desired location so that it can specifically kill the cells that are causing a specific disease. The drug in this case is a tiny protein called a peptide, akin to a short, beaded necklace where each bead is an amino acid. These peptides can be designed, by stringing the beads together in a specific order, to delete bad disease-causing proteins in cells. However, peptides are not specific and are not terribly efficient at getting inside cells. One way to improve their specificity is to attach the peptide to a large targeting protein that transports the drug to the site where it needs to go. To improve their cell entry, another short polymer strand is attached that allows the peptide to slip inside the cell when it gets there. While this sounds like a good plan, the only way it works is if the peptide can detach from the targeting protein at the right time. If it detaches too early before it reaches the cell where it needs to be, it might go to undesired locations and lead to toxic or poisonous effects. If it detaches too slowly, it will be ineffective. This NSF proposal will study how to attach peptide drugs to the targeting protein and how the speed of detachment affects the ability of peptide to exert its functional effect. Studying the mode of attachment and speed of release will be beneficial for scientific progress and will have a significant impact in several biotechnology fields such as antibody-drug conjugates, peptide-conjugation, and peptide delivery, where effective delivery strategies can be used to build better drugs and advance national health. Furthermore, educational and outreach activities will be integrated throughout this research through a common theme focused on promoting peer-to-peer learning and empowering young aspiring scientists to take up leadership positions in communicating STEM ideas to the broader public. Education and outreach goals will include the development of interactive modules for the CATALYST Academy workshop and the 4H Focus for Teens Program. Technical description This NSF project will develop a new class of bioconjugates to improve the intracellular delivery of Peptide-based proteolysis TArgeting Chimeras (PepTACs) toward their use in proteome-editing applications. PepTACs are bispecific peptide-based ligands that induce targeted protein degradation via the ubiquitin proteosome system. By employing a peptide ligand that recruits an E3 ubiquitin ligase and another that targets a protein of interest (POI), PepTACs facilitate the formation of a ternary complex, POI ubiquitination, and subsequently rapid catalytic POI degradation by the proteasome. However, these heterobifunctional peptide-ligands are not cell-specific and their potency is limited due to inefficient intracellular delivery. Building on the benefits of peptide-based ligands and the clinical success of antibody-drug conjugates, this NSF project aims to improve cell-specific PepTAC delivery using antibody carriers and cell-penetrating oligothioetheramides (CPOTs) for efficient cytosolic delivery. The resulting optimized product, an antibody-PepTAC conjugate (APC), will be designed to enable rapid and efficient intracellular protein degradation mediated by PepTACs. The proposal outlines several experiments to study the impact of conjugation site on APC transport and the release kinetics of PepTAC-CPOT constructs from the antibody within the endosomal compartment. Parameters from these studies will be correlated to APC intracellular transport and protein degradation. By studying these critical design features, this project will lay the groundwork for the effective delivery of PepTACs, unlocking their vast potential as invaluable tools for cell-specific targeted protein degradation. The ability to rapidly engineer and deliver high-affinity protein degraders against any intracellular target will be of great significance to experimental chemical biology researchers seeking to decipher protein interactions and unravel biological networks. This project is particularly impactful as a biological tool, providing an alternative method for achieving protein degradation (knockout) without the need for genetic materials or alterations to the cells genetic content. 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 · 2024-06

PROJECT SUMMARY The goal of this exploratory work is to elucidate the evolutionary history of symbiotic associations between the Mucoromycotina fungi and their endosymbiotic bacteria (EB), focusing on population-level processes, including fungal adaptation to human hosts and contributions of shared 6-methyladenine (6mA) DNA epigenetic modifications as means of communication between the partners. We expect that this work will establish foundations for future treatment of mucormycoses, which are human infections caused by Mucoromycotina. Mucormycoses are increasingly frequent, highly destructive, and often fatal in immune-compromised individuals. While bacteria-free asymbiotic Mucoromycotina are responsible for many infections, EB are often detected in clinical isolates and known to affect Mucoromycotina virulence in humans. Therefore, elucidating population-level processes that govern these Mucoromycotina-EB symbioses is important for developing novel mucoromycosis therapies. One of the mechanisms contributing to the establishment and maintenance of such symbioses may be sharing of 6mA DNA modifications by Mucoromycotina and bacteria. Importantly, these modifications and the contributing enzymes are nearly absent from mammals and potentially could be targeted by pharmacological inhibitors for mucormycosis therapy. To test the hypothesis that EB manipulate their fungal hosts through epigenomic reprogramming, we propose functional characterization of candidate bacterial symbiosis factors, including adenine-specific DNA methyltransferases. To gain insights into population-level processes shaping fungal-bacterial symbioses, we plan to conduct a population genomic study of a model fungal-bacterial symbiosis complemented by a population-level analysis of genome-wide 6mA modification and transcriptional landscapes in fungi differing in the symbiotic status and source of isolation (natural versus clinical settings). Expected outcomes of the project include insights into population-level processes, including fungal adaptation to mammalian hosts and the role of epigenetic reprogramming in the initiation and functioning of fungal- bacterial symbioses important for human health as well as 6mA methylome data for a leading causal agent of mucormycosis. The findings are expected to be instrumental in developing future mucormycosis therapies relying on 6mA DNA modification inhibitors.

NIH Research Projects · FY 2025 · 2024-06

Project Summary/Abstract The NYS Veterinary Diagnostic Center/Cornell Animal Health Diagnostic Center at Cornell University (AHDC) is a full-service multidisciplinary veterinary diagnostic laboratory and the only of its kind in the northeastern United States. The AHDC received over 300,000 client accessions in 2023. The Bacteriology section has MALDI-TOF analyzers, Sensititer systems, veraTREK® blood culture instruments, a BSL3 upgradable workspace, and 16S DNA sequencing capabilities, making it a full-service bacteriology laboratory. Additionally, the AHDC has the capacity to perform whole genome sequencing. The Bacteriology laboratory of the AHDC performed over 100,000 tests in 2023 on clinical samples, tissues, serum, bacterial isolates, environmental, food, and feed samples, including over 5,000 antimicrobial sensitivity panels. The AHDC has partnered with the FDA and played an active role in pet food and animal feed contamination investigations many times over the past two decades. We hope to continue our participation with the FDA Vet-LIRN program and other network laboratories to: 1. Continue to participate in VPO designated sample analyses and surveillance activities to promote animal health and welfare and add to the Vet-LIRN Network’s surge capacity to assist in emergency and large-scale outbreak testing. 2. Provide analytical data to support regulatory actions by developing and using standardized methods, equipment platforms, and reporting methods. Continuing to participate in proficiency testing provided by the VPO, continue investigating consumer reported cases as requested by the VPO, and continuing to improve and implement standardized quality management systems as designated by the VPO. 3. Continue to participate in small-scale antibiotic susceptibility testing studies to address emerging antimicrobial resistance issues, acting as a source laboratory for the FDA Vet-LIRN AMR monitoring project to collect and submit bacterial isolates and associated antimicrobial susceptibility data.

NIH Research Projects · FY 2026 · 2024-06

Project Summary Opioid alternative analgesics that would kill pain potently without the respiratory side effect will be of specific importance in addressing the opioid crisis. The medicinal herb kratom (Mitragyna speciosa) produces natural products (mitragynine and 7-hydroxymitragynine) that selectively activate analgesia only, which are promising “biased” opioid alternatives. Elucidating the kratom biosynthetic pathway composed of enzymes catalyzing sequential reactions toward the syntheses of mitragynine, 7-hydroxymitragynine, or other kratom products is important to the development of “biased” non-opioid analgesics. We propose to identify and reconstruct both the kratom biosynthetic pathways and the plant enzyme complexes organizing plant biosynthesis in yeast by integrating plant functional genomics analysis and synthetic biology. The research will provide new chemical and plant biology knowledge to a broader community, develop a post-translational level understanding of plant pathway regulation in yeast, and highlight the possibility of using synthetic biology to understand how nature achieves complicated natural product biosynthesis. This proposal will develop the conceptual framework to understand how nature organizes the specialized metabolism in plant toward high efficiency and complexity. The development of high-throughput protein-protein interaction method in yeast for plant complex identification will provide new methods and knowledge for plant pathway discovery and reconstruction. The methods and knowledge we develop toward these goals will also enable the structural elucidation, biological activity evaluation, and microbial production of biased opioid alternatives, leading to the development of next-generation painkillers to address the opioid crisis.

NSF Awards · FY 2024 · 2024-06

Recent years have seen incredible progress in Artificial Intelligence (AI), largely thanks to improvements in the training and use of deep models. However, much of the progress in AI has come from training on massive publicly available datasets, such as, all of the images and text found on the Internet. By contrast, many important real-world problems depend on scarce or highly specific data that still must be captured manually. For example, consider the task of monitoring a crack in the foundation of an aging bridge, where the goal is to predict whether and when repairs should be made to ensure the safety of travelers. Or the case of monitoring a patient's wound outside of hospital settings. Solutions to these problems cannot be found on the internet; they require specific knowledge about a specific subject at a specific time. This project focuses on developing mobile applications to help regular users capture information that experts - e.g., doctors, scientists, and engineers - need to make important decisions. The project will also integrate research with education and outreach to high school students and teachers. This research focuses on the development of applications for domain-specific data capture on ubiquitous devices. The project will combine novel interaction design with adaptive tracking and registration strategies to build systems that help users capture target distributions of field data important to different downstream tasks. These systems will include tools that make it easy for experts to define target distributions of important observations, which can then be used to guide the collection of field data by non-experts using custom mobile applications. These applications will also allow the capturing users to update and adapt target distributions according to evolving field conditions. The project will further leverage guided capture systems to enable new types of visualization and analysis and develop tools to efficiently label captured data. The research integrates three key components into the design of these novel systems: (1) mobile tracking and registration; (2) reconstruction, visualization, and analysis; and (3) user interaction design and real-time guidance through Augmented Reality (AR). The integration of these components will help enable new applications. For example, new mobile tracking and registration abilities make it possible to register mobile devices against more complex target distributions, allowing us to offer more precise guidance for a broader range of downstream tasks. This integration makes the work highly interdisciplinary, with contributions in computer vision, computer graphics, and human-computer interaction, as well as collaboration with domain experts in downstream application domains. 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 · 2024-05

PROJECT SUMMARY The immune system is a rapidly evolving defense mechanism against threats both internal: cancer, and external: viruses, bacteria, and other pathogens. Intraspecific sequence variation in both mice and humans can dramatically change infection responses, raising the question: What is driving these regulatory changes in immune responsiveness between individuals? Transposable elements (TEs) are mobile genetic elements that comprise nearly half of the human and mouse genomes, represent a potent source of inter- and intra-species genetic diversity, and can act as cis-regulatory elements by regulating nearby genes. However, the full regulatory contribution of TEs in intraspecific variation within the immune system is understudied. Preliminary analyses in naïve and activated mouse CD8+ T cells, an immune cell responsible for killing infected or cancerous cells, highlight TEs as key sources of cis-regulatory activity. In particular, I have predicted regulatory links between TEs and 1668 genes, of which 178 are differentially expressed across genetically distinct mice strains. Although these results suggest that TEs contribute a sizable number of intraspecific regulatory interactions in mouse CD8+ T cells, it remains unclear whether TEs provide a similar regulatory contribution in human intraspecific variation of CD8+ T cell activation. I propose an interdisciplinary project that will characterize the intraspecific cis-regulatory impact of TEs in both human and mouse CD8+ T cells. Specific aim 1 will use scATAC-seq, scRNA-seq, long-read Nanopore sequencing, and in vitro phenotypic assays on CD8+ T cells from genetically distinct mice lines to validate the intraspecific regulatory activity of candidate TEs from preliminary analyses. The results of aim 1 will – for the first time – identify the phenotypic impact of candidate TE enhancers on CD8+ T cell activation in mouse. Specific aim 2 will utilize publicly available and in-house anonymized human CD8+ T cell genomic data to quantify and compare the gene targets of TE-derived intraspecific variation to those identified from preliminary data in mouse. The results of aim 2 will provide – for the first time – a direct characterization of the cis-regulatory activities of TEs and their contribution to intraspecific variation between human and mouse CD8+ T cell activation. I will utilize prior bioinformatics experience in complex single-cell analyses alongside extensive training in molecular biology to perform the proposed experiments. Further refinement of critical thinking and scientific communication skills will ensure my development into a well-rounded scientist and facilitate a smooth transition into a postdoctoral position post-graduation. The Feschotte and Grimson labs, alongside collaborators in the Rudd lab and Genomics Innovation Hub at Cornell University, have access to considerable experience and resources that will ensure mastery of these skills. Together, this proposal will further our understanding of how TEs facilitate the rapid evolution of the immune system within and between human and mouse.

NIH Research Projects · FY 2026 · 2024-05

PROJECT SUMMARY Nearly one-third of US reproductive aged women have obesity prior to pregnancy and similar numbers have vitamin D insufficiency (25(OH)D< 20 ng/mL). Both vitamin D deficiency and obesity may impact the intrauterine and maternal environment to increase the risk of adverse birth outcomes. Risk of obesity and D deficiency are significantly higher among Black women compared to White women. In addition, well-described differences in vitamin D metabolites, calcitropic hormones, and vitamin D binding protein (DBP) genotype are evident in Black women compared to White women. Despite a dramatic increase in awareness of the multiple roles of vitamin D in human health, little is known about regulation of vitamin D metabolism during pregnancy. Maternal concentrations of the prohormone 25(OH)D remain constant across pregnancy but concentrations of the hormone calcitriol (1,25(OH)2D) more than double in early pregnancy and, despite the rapid t1/2 of calcitriol (~4 h), this hormone remains elevated across the 9-month gestation period. These changes are unique to pregnancy and do not occur at any other life stage. Marked metabolic changes in D absorption and/or utilization must occur to support these physiological changes, but these pathways remain largely unexplored at this key life stage. Obesity increases the risk of vitamin D deficiency but it is unknown if this is due to sequestration in body fat, obesity-driven changes in the hormone activation or inactivation pathways, or to other unidentified differences in D absorption and utilization. We recently developed a novel ultra-high performance liquid chromatography tandem mass spectrometry method capable of measuring the absorption of trideuterated-vitamin D3, its conversion into 25(OH)D3 and the subsequent serum half-life of 25(OH)D3. We will use this innovative approach to examine vitamin D kinetics in non-pregnant and pregnant women. This approach allows us for the first time in humans, to evaluate metabolic utilization of vitamin D3 and how it is impacted by pregnancy (Aim 1). Genetic variants in the DBP gene that affect DBP concentration, as well as genetic variants in other key genes that are directly involved in vitamin D3 and 25(OH)D3 production and utilization, and their contribution to the differences in vitamin D kinetics will be characterized between White women and Black women whose genetic ancestry will be confirmed with ancestry-informative genetic markers (Aim 2). The impact of adiposity on outcomes will be addressed by recruiting both normal weight women and women with obesity in each ancestry group. Body composition will be measured, and subcutaneous abdominal fat will be collected to 1) evaluate how this storage depot of vitamin D3 and 25(OH)D3 is impacted by obesity, genetic ancestry, and pregnancy and 2) determine how variability in the mass of this storage depot impacts D kinetics (Aim 3). The proposed research will provide novel data on the maternal metabolic pathways that impact vitamin D utilization and will identify both modifiable and non-modifiable factors that can be targeted to improve maternal vitamin D status and fetal vitamin D availability across pregnancy.

NIH Research Projects · FY 2026 · 2024-05

Project Summary /Abstract Viruses present one of the most efficient mechanisms for intracellular cargo (i.e. viral genome) delivery in which interactions at the virus-host cell interface dictate the delivery pathway. For instance, enveloped viruses- those that are 'wrapped' in a lipid bilayer, deliver their genetic cargo by first interacting with extracellular receptors, triggering a reaction cascade that results in fusion of the virus- and host cell lipid membranes and cargo release into the cytosol. Harnessing the efficiency of this translocation mechanism would drastically improve cellular uptake of therapeutic and bioactive cargo, currently a major obstacle in both agricultural and pharmaceutical communities, each with major impact on human health. The research proposed in this fellowship aims to repurpose viral fusion machinery for delivering user-defined cargo to cells containing the appropriate receptors. More specifically, several virus-derived proteins have been chosen including Hemagglutinin (HA) - from Influenza, glycoprotein G (NiV-G) and fusion protein F (NiV- F) - from Nipah virus, and Spike protein - from SARS-CoV-2. These proteins represent a small selection of model proteins, all of which interact with different receptor types found on the cellular surface, providing a potential handle for targeting cells that abundantly display the specific receptors. To circumvent challenges associated with using infectious viruses or isolating membrane proteins, we will concurrently adapt existing cell-free synthesis (CFPS) techniques to produce membrane proteins and efficiently insert them into our delivery vehicles of choice- liposomes. The short-term goals of this project are to demonstrate 1) virus fusion-protein activity and delivery, and 2) improved efficiency of virus membrane insertion into liposomes using the adapted CFPS methodologies. The long-term goals include tuning the biodistribution capabilities, afforded by the virus-derived proteins, to deliver cargo to discrete and specific locations within the human body or other organism. This fellowship will provide the applicant with the financial support needed to design and test the proteoliposome-based delivery system and develop ideas that will aid the applicant's independent research program in the field of virus-inspired biomaterials.

NIH Research Projects · FY 2026 · 2024-04

PROJECT SUMMARY/ABSTRACT Vocal communication is essential for human social relationships, and deficits in vocal communication that characterize autism spectrum disorder (ASD) have devastating impacts on the affected individuals and on society. Despite the importance of vocalization to social behavior, the brain circuits that allow animals to vocalize appropriately according to behavioral context remain poorly understood. This proposal seeks to apply powerful intersectional tools in the mouse to (1) identify and characterize forebrain-to-midbrain circuits that underlie the context-dependent control of social vocalizations and (2) to understand the midbrain circuits that underlie the production of distinct acoustic categories of vocalization. Prior work has shown that midbrain- projecting neurons of the preoptic hypothalamus regulate courtship vocalizations in male mice. Aside from these neurons, the forebrain inputs to the midbrain that regulate social vocalizations, and whether the relevant inputs differ according to social context, remains unknown. Aim 1 will combine in vivo calcium imaging, neuronal silencing, and mapping of axonal projections to test the hypothesis that midbrain-projecting preoptic neurons regulate social vocalizations produced during affiliative female-female interactions. In Aim 2, retrograde tracing from the midbrain will be combined with Fos mapping and light sheet imaging of optically cleared brains to identify novel populations of midbrain-projecting forebrain neurons that are active during and may regulate vocal communication during courtship, during female-female interactions, or in both contexts. In Aim 3, activity-dependent labeling in the midbrain will be combined with neuronal ablation and retrograde tracing from hindbrain vocal premotor neurons to test the hypothesis that distinct sets of midbrain neurons control the production of different acoustic categories of vocalization. This work will delineate brain circuits that underlie the context-dependent control of vocalization in the mammalian brain, and more broadly, that link the encoding of social information to the flexible and appropriate execution of social behaviors. By identifying core mechanisms of healthy vocal communication, this work will provide a foundation to understand neural circuit alterations the contribute to vocal communication differences in mouse models of ASD and other neurodevelopmental disorders.

NIH Research Projects · FY 2026 · 2024-04

Project summary Drosophila (fruit flies) are an exceptional model for evolutionary genetics, with many species that can be subjected to the full suite of modern genetic and genomic methods that have been developed in the model species D. melanogaster. Hybrids between D. melanogaster and its sibling species D. sim- ulans are a long-standing model of speciation and our group has made several key contributions to understanding the genetic basis of hybrid incompatibilities between them. One major effort here will be to identify the maternal factors in D. simulans that interact with a large satellite block specific to D. melanogaster to cause F1 hybrid lethality. This will allow us to obtain a mechanistic understanding of how rapidly evolving non-coding DNA can lead to chromosome instability and lethality between spe- cies. Drosophila have also played a major role in the discovery of the phenomenon of meiotic drive, where different alleles segregate non-randomly from heterozygous parents in violation of Mendel’s first law of equal segregation. Meiotic drive can cause reductions in organismal fertility, drive rapid changes in karyotypes including of sex chromosomes, and contribute to species isolation. Yet little is known about fundamental questions such as the prevalence of meiotic drive in natural populartions or the differences in frequency between male and female meiotic drive. In a second project we will con- duct a high-throughput and sensitive screen for meiotic drive across all chromosomes in D. melano- gaster and D. simulans populations. In a third project we will investigate evolution of the primary sex determination signal. This signal comprises a group of positive and negative regulators of a central switch gene, that allow the developing Drosophila embryo to distinguish whether it has one or two X chromosomes and thus develop as a male or female. Surprisingly, there is substantial variation within D. melanogaster populations affecting the fidelity of the sex determination signal, which we will genet- ically map and characterize. We will also identify gains and losses of the signaling elements in ~100 fully sequenced species from across the Drosophila phylogeny. These approaches will provide data essential for understanding the evolutionary forces that drive changes in sex determination signals across animals. Our experience along with many reagents and methods we have previously devel- oped position us to accomplish these projects in Drosophila evolutionary genetics with the flexibility provided by the MIRA funding mechanism.

NIH Research Projects · FY 2026 · 2024-03

Environmental issues like exposure to air pollution or pesticides and their link with cancer development are at the forefront of current public health research. Animals have long been recognized as sentinels for environmental pollutants that can be hazardous for human health. Interestingly, and despite the fact that domestic animals like horses and dogs share comparable habitats, and thus, are exposed to similar environmental risk factors as humans, their susceptibility to develop certain types of cancer, like mammary cancer, differs greatly. The overarching goal of this research is to use a comparative species approach to identify the responses of horses (a species resistant to mammary cancer) and dogs (a species susceptible to mammary cancer) to environmental carcinogens, such as polycyclic aromatic hydrocarbons (PAHs) that are linked with increased breast cancer risk. Published work from our lab has shown that equine mammary cells undergo apoptosis while canine mammary cells continue to proliferate when exposed to 7,12-dimethylbenz[a]-anthracene (DMBA), a synthetic PAH derivate commonly used to induce mammary cancer in rodents. These data led to our hypothesis that mammary cancer-proof mammals eliminate DNA-damaged cells through apoptosis, while damaged cells from mammary cancer-susceptible mammals are repaired and persist, allowing for the accumulation of potential malignant mutations. However, it is difficult to test this hypothesis in vivo due to logistical challenges of treating horses and dogs with DMBA. To address this, we established a mammary xenograft model by transplanting mammary tissue fragments from equine or canine donors into the cleared mammary fat pads of immunodeficient mice. We confirmed that these transplanted tissue fragments are proliferative, hormone-responsive, and recapitulate the architecture and function of the donor gland. We now propose to use this novel model to assess the effects of DMBA on equine and canine mammary xenografts to further evaluate mammary cancer resistance and susceptibility mechanisms in vivo. Following DMBA treatment, the mammary xenografts will be assessed for histopathological features, DNA damage, and necrotic/mitotic rate. Activation of apoptotic and tumor-associated pathways will be assessed using a spatial transcriptomics approach, which maintains spatial context of the tissue while providing complete transcriptomic data. Successful outcome of this proposal will (i) improve our understanding of histopathological responses of mammary glands from sentinel species to DMBA and (ii) corroborate whether increased apoptosis is indeed a mechanism driving mammary cancer resistance in equine mammary glands. Evaluation of this potentially conserved mechanism of mammary cancer resistance in response to PAH exposure will help define important regulatory mechanisms that can ultimately result in the identification of biomarkers of exposure and breast cancer risk.

NIH Research Projects · FY 2025 · 2024-03

Summary/Abstract The poor suffer disproportionally from poor mental and physical health. Many causes for these disparities have been considered, including low income. But, poor families' incomes are not only low, but also often unstable and unpredictable. This instability creates uncertainty about whether they will be able to safeguard their future wellbeing. According to the allostatic load framework, prolonged activation of physiological stress responses will cause “wear and tear” on the body, heightening risks of cardiovascular disease and of age-related metabolic diseases, promoting cognitive decline and dementia, and accelerating cellular aging. This R01 will study the causal effects of income instability on the psychological and physical health of the poor. Our specific aims are to: 1) Identify the causal effect of income instability on psychological health (e.g. depression, anxiety), biomarkers of stress (e.g. cortisol), and physical health (e.g. blood pressure), 2) Decompose the effects identified in aim 1 into the effects of predictable and unpredictable instability and compare to the impact of increasing the average level of income, and 3) Investigate the channels through which effects on health occur, including both economic and behavioral channels and estimate the impact of key moderating factors (e.g. age, gender, baseline mental health). The trial will be conducted in southwestern Bangladesh. We will manipulate income instability by varying the number of work hours (and hence earnings) of participants in a cash-for-work program. Participants in the first treatment arm will have a fixed work schedule, with the same hours and earning each period. The hours and earnings of a second treatment arm will vary over time, but the fluctuations will be known in advance. Finally, the number of work hours and earnings of a third treatment arm will fluctuate unpredictably. Each of these arms will be compared to a control group that is surveyed, but not offered additional work. Importantly, we will vary income instability while holding the average level of income constant in order to disentangle the impact of instability from the level-effect. The study will create 1,867 new jobs that would not otherwise be available during the lean season when jobs are scarce. The intervention has been designed so that the job opportunity cannot make them worse off than they would otherwise have been in the absence of research.

NIH Research Projects · FY 2026 · 2024-03

Project Summary The nucleus is the defining feature of eukaryotic cells; it is also the largest and stiffest cell organelle. Increasing evidence suggest that these physical properties of the nucleus can affect diverse cellular functions, and that mechanical forces acting on the nucleus conversely modulate nuclear structure and function, including chromatin organization, gene expression, and genomic integrity. This ‘nuclear mechanobiology’ is particularly relevant in the context of cell migration in 3D in vivo environments, where cells frequently move through tight interstitial spaces that require substantial deformation of the cell nucleus. Examples include cell migration during development, wound healing, inflammation, and cancer metastasis. Our laboratory previously demonstrated that the required deformation of the nucleus limits the ability of cells to migrate through tight spaces, with highly migratory cells often having more deformable nuclei, and that nuclear deformation associated with confined migration can lead to transient nuclear envelope rupture, DNA damage, and changes in chromatin organization. These findings point to an exciting new concept in which the deformation of the nucleus as cells move through tight spaces could activate or suppress transcriptional programs that further enhance migration and modulate other functions, or that could lead to the selection of cells particularly adept at such confined migration. Nonetheless, many questions remain. Over the next five years, we will focus on three complementary and synergistic overarching research areas: (1) investigate how cells generate, apply, and coordinate the large cytoskeletal forces required to move and deform the nucleus through confined spaces; (2) identify the mechanism(s) responsible for confined migration induced changes in chromatin organization, and (3) determine the functional consequences of confined migration on cellular fate and functions, along with the underlying mechanisms. Towards this goal, we have developed several novel experimental platforms that enable extended live-cell imaging of cells migrating through precisely-defined microenvironments while visualizing nuclear deformation, nuclear envelope rupture, DNA damage, and chromatin modifications, and that allow collection of cells after confined migration for subsequent analysis. We will pair these platforms with molecular biology approaches and assays for genome-wide analysis of changes in 3D chromatin organization and gene expression in a range of different cell types, reflecting physiological and pathological scenarios. Our ultimate goal is to uncover general principles in nuclear mechanobiology that will lead to an improved understanding of the impact of migration through tight spaces on cellular function and fate, including the activation or suppression of specific transcriptional programs that may further enhance cell migration or modulate other cellular functions. Insights gained from these studies may help guide therapeutic approach for a variety of clinical conditions, from wound healing and immune-responses to therapies targeting metastatic tumor cells.

NIH Research Projects · FY 2026 · 2024-02

PROJECT SUMMARY The immunogenicity of nanomaterials is directly related to their performance and toxicity. However, there is still a lack of systematic studies of how nanomaterials interact with the immune system. In this work, we will focus on the immunogenicity of lipid nanoparticles (LNPs). Various studies have raised concerns about the adverse event of LNPs from PEG lipids, ionizable lipids, and even helper phospholipids, such as anti-polyethylene glycol (PEG) antibodies found in BioNTech/Pfizer and Moderna COVID vaccines. During our recent studies of LNP- based mRNA cancer vaccines, the side effects, including ulcerative dermatitis, were also found on vaccinated mice after subcutaneous administrations. Most studies of LNPs via screening or design today have mainly focused on LNP efficacy while few on LNP immunogenicity. Very limited human data on very limited formulations in the context of COVID-19 vaccines following intramuscular administration have very limited scope in immunogenicity such as accessing the overall outcome of immunogenicity only. The investigations have not extensively delved into the underlying causes of the widely reported adverse effects associated with LNP-based mRNA vaccines, the specific immunological pathways of immunogenicity, and the underlying relationship between immunogenicity and components of LNPs. Currently, the mechanism of how LNPs induce adverse events is yet to be fully understood. Here we will formulate three libraries of LNPs covering widely used lipids and vary chemical properties of each component. We will perform immunological assays on primary murine cells to evaluate cytokine secretion and profile inducible gene expression. Similar tests will be performed in human peripheral blood mononuclear cells (hPBMCs). Toll-like receptor (TLR) and NOD-like receptor (NLR)-dependent immune response will be evaluated by reporter assays and validated in deficient mouse primary cells. Furthermore, the immunogenicity of LNPs will be profiled in the setting of intramuscular injections by assessing local inflammatory responses at the injection sites, and intravenous injections by evaluating the systemic response including accelerated blood clearance effects. Through these studies, we will identify key components that are responsible for LNP immunogenicity, understand how the chemistry of each LNP component alters the level of immune activation, and discover any synergistic effects on the immunogenicity among the components. The success of this work will advance current LNP technologies and provide clinical benefits for applications from vaccines to therapeutics.

NIH Research Projects · FY 2026 · 2024-02

Project Summary / Abstract Transposons are mobile genetic elements that provide an important mechanism for the acquisition of pathogenesis functions and antibiotic resistance in bacteria. A family of these elements, Tn7 and Tn7- like elements, tightly control transposition allowing them to be particularly successful across diverse bacteria. On five distinct occasions discovered by the lab and collaborators these elements have coopted CRISPR-Cas systems. CRISPR-Cas systems typically function as adaptive immune systems in prokaryotes that utilize an RNA-based system to recognize and cleave viruses and other invading DNA elements. In coopting CRISPR-Cas systems they were naturally adapted for guide RNA-directed transposition suggesting promising new tools for programable editing. As an editing tool, CRISPR-Cas transposons (CASTs) direct a single cargo DNA into a pre-programmed position in one orientation without the negative side effects of inducing a double strand break in the target DNA. CAST enable genome editing of bacteria, individually and in communities. They also have future potential for human therapeutic gene editing. Despite the potential promise with the CAST systems, major questions remain about how they function, which limits their broad application. By advancing our understanding across diverse CAST systems we provide foundational knowledge to enable important genome and population editing applications. Each of the four projects focuses on CAST systems based on different families of Tn7-like elements that use different mechanisms of transposase assembly and activation. This mechanistic understanding will be critical for optimizing these systems and adapting them to new hosts. Understanding the basic features of all CAST systems will bring the field closer to the aspirational goal of setting up a system where associations between a transposon and any CRISPR- Cas system could be engineered de novo. Our work will additionally provide insight into canonical CRISPR-Cas systems and the unappreciated widespread use of atypical guides for gene regulation. The mechanistic understanding we gain with diverse CAST elements will allow also allow us to understand the outsized role of Tn7 and Tn7-like elements in pathogens for the acquisition of antibiotic resistance and virulence factors. Relevance to Public Health: Public health will be served because we will provide the framework for developing important new genome modification techniques that will be broadly applicable for gene editing, especially for future human therapeutic gene editing. Fundamental information about these systems will also help us understand molecular mechanisms that allow the evolution of pathogens and multidrug resistant bacteria though the transfer of genetic information.

NIH Research Projects · FY 2026 · 2024-01

Abstract Reactive oxygen species (ROS) perform dual roles in cells, acting as both destructive and constructive agents. At high levels, intracellular ROS facilitate irreversible macromolecular damage and are associated with a range of disease pathologies. At lower physiological levels, ROS play important roles in the activation of beneficial signaling events through the reversible post-translational modification of cysteine and methionine residues. Despite the emerging appreciation for ROS as constructive signaling agents, and the importance for functional redox signaling in managing cellular ROS, relatively few redox-signaling pathways have been characterized. Many proteins susceptible to oxidation have been cataloged. However, the consequences of oxidation and the physiological outcomes have been established for only a limited number of these targets. We argue this central knowledge gap limits larger efforts towards the development of effective therapeutics to help manage cellular ROS. Since its inception, our research program has focused on broadening our knowledge of ROS-based signaling events. Our overarching goal is to elucidate individual pathways activated by the modification of protein cysteine and/or methionine by ROS. Our intent is to uncover and to characterize redox-signaling components, including ROS sources, redox targets, and oxidation regulators, as well as the consequences (outcomes) for signaling at the protein and physiological level. Our research efforts center on two focus areas: (1) an analysis of the role for cysteine oxidation in managing ROS within the endoplasmic reticulum (ER) and (2) the study of the consequences of protein methionine oxidation (MetO) formation and reduction. Our prior work established that oxidation of a conserved cysteine in the Hsp70 BiP alters its chaperone activity to sustain ER function under elevated ROS conditions. Our ongoing work intends to broaden our understanding of redox signaling at the ER and BiP oxidation, answering the questions: What are the local endogenous sources of ROS in the ER that are sensed by BiP? How does BiP oxidation influence known ER stress response pathways? In addition, we intend to bolster the fundamental understanding of MetO formation and resolution in cells, focusing in parallel on what we consider the most prominent gaps in our knowledge of MetO: What are the physiological targets of MetO? What is the role for methionine sulfoxide reductases in regulating individual protein MetO events throughout the cell? By answering these questions, we intend to provide insight into the basic cell functions used to manage cellular ROS and avert cellular damage. We anticipate that our experience and expertise, coupled with a diversity of personnel and scientific approaches, will allow us to make sustained research progress over this MIRA award.

NIH Research Projects · FY 2026 · 2024-01

Project Summary. Rapid evolution lies at the core of some of the greatest challenges humanity faces today, ranging from the evolution of drug and antibiotic resistance to the rapid emergence of new Covid variants. Researchers are now envisioning even faster evolutionary dynamics brought about by CRISPR gene drives. This fascinating new technology could be used to directly suppress wild populations, or to rapidly spread an engineered allele through a population, for example a gene that reduces pathogen transmission in mosquitoes. Unfortunately, current population genetic models are not well-suited to describing such rapid processes, because they are often still grounded in simplistic assumptions such as a homogeneous, randomly mating population. Research in my lab centers on the development of new population genetic models and computational tools for studying rapid evolutionary processes such as CRISPR gene drives that allow us to better predict their expected outcomes. Over the past five years, my lab has developed a comprehensive modeling framework for gene drive dynamics. Here, we propose to incorporate increasing levels of biological realism into this framework to address three broad questions: (1) How can we systematically identify the features and parameters that are most critical for determining the outcome of a drive release in our simulations? (2) Is it possible to reliably confine a gene drive to an intended target population, and how could this be achieved? (3) Could a suppression drive in a mosquito population eradicate diseases such as malaria or dengue even when it does not achieve complete suppression of the mosquito vector? As gene drive technology comes ever closer to field experimentation, answers to these questions will be essential for a realistic evaluation of the expected outcomes of a drive release into a wild population. Motivated by insights from our modeling work on gene drives, we propose a second line of research focusing on the question of how continuous space can affect the dynamics of other rapid evolutionary processes, such as strong selective sweeps, which conceptually resemble the spread of a gene drive in many ways. We hypothesize that similar to what we found for gene drives, continuous spatial structure could also have a profound impact on the population dynamics of strong selective sweeps, and thus the signatures they leave in population genomic data. We plan to study this question using forward genetic simulations together with recently developed methods for inferring sweep parameters based on supervised machine learning. Finally, we plan to implement critical improvements in our SLiM evolutionary simulation framework, enabling forward simulation of populations of billions of individuals, so that we can predict the outcomes of the release of a CRISPR gene drive into a mosquito population with sufficient accuracy and robustness to facilitate a well-informed discussion about the feasibility, reliability, and risks of such approaches.

NIH Research Projects · FY 2026 · 2024-01

PROJECT SUMMARY In both mammals and invertebrates, initiation of post-mating responses in the female post-copulation is known to contribute to reproductive success. Seminal fluid proteins (Sfps) have been shown to initiate many of these responses. However, male x female interactions are underexplored as contributors to infertility. Investigating the mechanisms and evolution of male x female interactions is critical for understanding the complexities of reproduction. I will use D. melanogaster as a model system for investigating post-copulatory male x female interactions via characterization of male and female contributions to the Drosophila mating plug’s (MP) formation and ejection. In Drosophila, the MP forms in the uterus of the female via coagulation of male- ejaculated Sfps and some female reproductive tract proteins. Genetic disruption of the MP impacts reproductive outcomes by affecting sperm retention; however, little is known about the male and female proteins (and their interactions) that modulate mating plug ejection (MPE) rates either directly by contributing to MP composition/degradation or indirectly by regulating female ejection behavior. In Aims 1 & 2 I will respectively use female or male phenotypic variation in the Drosophila Genomic Reference Panel to perform a GWAS on MPE timing. I will then functionally investigate how top gene candidates mediate MPE timing. I have concluded a GWAS on female MPE timing and have so far identified 4 neuronal genes that regulate female MPE (Aim 1). Using highly tissue- and cell type- specific knockdown of gene candidate expression via RNA interference, I will more deeply characterize neuronal regulation of female MPE timing. After also identifying and characterizing male genes regulating MPE timing (Aim2) I will perform a 6x6 grid cross of males and females with disrupted function of MPE genes to investigate the presence of complex non-additive male x female MPE interactions. Finally, I will investigate the molecular evolution and function of male and female genes contributing to MP composition (Aim 3). I discovered that many male and female MP genes are closely paralogous to each other and evolving under positive selection, potentially suggestive of evolution under sexual conflict. After fully characterizing the evolution and coevolution of these male and female MP paralogs, I will investigate their sex-specific functions in MPE and MP formation. Observation of opposing functions for paralogous male and female MP genes would point to sexual conflict driven evolution caused by opposing sex-specific optimal mating strategies. Observation of complementary functions would indicate similar evolutionary pressures acting on male and female paralogs to cooperatively ensure optimal reproductive outcomes.

NIH Research Projects · FY 2026 · 2024-01

Abstract: Research in my laboratory has centered on the development and application of multi-disciplinary approaches to study signal transduction pathways important in normal physiology and, when de-regulated, contribute to a number of diseases. This began with our discovery and cloning of a novel signaling partner for the epidermal growth factor receptor, the human Cdc42 protein, a small GTPase highly conserved from yeast to humans, and continued with the identification of many Cdc42 regulatory proteins and signaling targets. The conservation of Cdc42 throughout evolution accounts for the many fundamentally important roles it plays in cell biology and organism development, including the regulation of cell growth and migration, and the establishment of cellular polarity. We then discovered an unanticipated but highly significant function of Cdc42 in directing the upregulation of glutamine metabolism and metabolic activities that generate building blocks for biosynthetic processes required in a wide range of cellular functions. This also provides a mechanism for connecting the various intracellular processes regulated by Cdc42 to the surrounding environment by directing the biogenesis of extracellular vesicles (EVs), which have been implicated by our laboratory and others in mediating intercellular communication across the evolutionary spectrum from bacteria to higher organisms. Recently, we found that Cdc42 activates these metabolic activities through the assembly of large protein complexes. Understanding how these metabolic/signaling nodes are assembled holds important clues to their regulation and function, as well as sheds light on a long-standing question of how Cdc42 activates a critically important protein kinase, mTOR (mechanistic Target of Rapamycin), which is a necessary step for cap-dependent mRNA splicing, the neuronal differentiation of embryonic stem cells (ESCs), and the survival of cancer cells under stressful conditions. Elucidating the biochemical and structural features of these large complexes that activate glutamine metabolism and mTOR, which are essential for cell growth and survival, and helping to move forward the field of EVs represent major research goals for our laboratory in the next 5 years. Key gaps in our knowledge surrounding these broad areas of study will be addressed. We want to understand how Cdc42 directs the formation of metabolic/signaling nodes that not only play such important roles in cell biology but also have significant implications for disease, define the mechanisms responsible for their regulation, and determine their 3D structures. We also will set out to address challenging questions to further the development of the EV field, by identifying the biochemical determinants and signaling cues that dictate the loading of essential EV cargo and determining the structural features of EVs that enable their various biological functions. To achieve these goals, we will leverage our expertise in signal transduction and benefit from a strong group of collaborators.

NIH Research Projects · FY 2025 · 2023-12

SUMMARY Breast cancer accounts for nearly a quarter of all cancers in women and it remains the second leading cause of cancer deaths in the US, despite substantial changes in standard of care treatments. Identifying evolutionary mechanisms that naturally protect species from developing cancer is becoming an increasingly appreciated approach to develop therapeutic strategies that are both efficient and non-toxic. We recently identified a cancer- suppressing mechanism based on the secretion of bioactive factors with anti-cancer activity by mammary cells (aka. mammosphere-derived epithelial cells or MDECs) from domesticated mammary cancer-proof mammals. Specifically, these bioactive factors were shown to (i) induce triple negative breast cancer (TNBC) cell death, without affecting normal human breast cells, in vitro and (ii) reduce tumorigenicity in a xenograft TNBC mouse model in vivo. These findings led to our central hypothesis that the MDEC secretome from mammary cancer- proof mammals has significant potential for the development of novel effective and non-toxic therapies to treat and/or prevent breast cancer, especially the aggressive and hormone therapy-unresponsive TNBC. We now propose to follow up on these interesting findings by further characterizing the anti-cancer activity of the MDEC secretome in greater depth (Aim 1) and evaluating the therapeutic and/or preventative effects of the MDEC secretome in mouse models of TNBC (Aim 2). The significance of this application lies in the novelty of the approach being used to identify non-toxic efficient breast cancer therapeutic and/or preventative interventions by focusing on bioactive anti-cancer factors produced by normal mammary cells from mammary cancer-proof mammals. The proposed experiments will increase our knowledge of novel cancer-suppressing mechanisms and will provide a solid basis for the design of effective and non-toxic therapies that can be used to fight aggressive TNBC and/or for the development of protective factor-based therapeutics to eliminate or reduce TNBC in high-risk populations.

NIH Research Projects · FY 2026 · 2023-12

PROJECT SUMMARY / ABSTRACT Tissue regeneration is the process through which damaged tissue is restored to its original structure and function. There is wide variation across species in their regenerative ability. For example, zebrafish can regenerate all retinal neurons after injury while humans and mice cannot. Understanding the genetic basis and molecular underpinnings of complex tissue regeneration in model species holds the promise to enhance human regenerative medicine. Here I am using zebrafish to test the novel hypothesis that the control of transposable elements (TEs) is a necessary checkpoint for complex tissue regeneration. TEs are mobile DNA elements capable of self-replication that are ubiquitous and abundant in eukaryotes. Uncontrolled TE activity leads to accumulation of TE-encoded nucleic acids and proteins that interfere with cell homeostasis and can result in DNA damage, disrupting genome integrity. TE upregulation has been reported during tissue regeneration in salamanders, sea cucumbers, and worms. I hypothesize that TE activation is a hallmark of tissue injury that must be suppressed for successful regeneration, and an inability to suppress TEs will stall regeneration. Supporting this hypothesis, my preliminary analyses of bulk RNA-seq data reveal TE upregulation during early stages of eye regeneration that are later restored to control levels prior to tissue repair. I predict that zebrafish and other organisms with a strong regenerative capacity deploy specific control systems to suppress TE activity during regeneration. Here I will directly test the role of the Piwi pathway in suppressing TE activity during zebrafish eye regeneration. The Piwi pathway is known to repress TEs in animal gonads, including zebrafish, but there is growing evidence that the pathway is active in somatic tissues and required for regeneration in planarians. Furthermore, I have detected piwil1 expression in the zebrafish eye, raising the testable hypothesis that it functions during eye regeneration. I will utilize a model of zebrafish retinal regeneration and a 2-pronged approach combining multimodal genomics and manipulative experimentation. First, I will further establish that TE upregulation is a hallmark of tissue injury by profiling TE expression changes across five regenerating tissues using publicly available single- cell transcriptomic data. Second, I will generate a multi-omic single-cell dataset to assess TE expression changes during cone regeneration from the onset of injury through to functional recovery. These data will provide the most comprehensive and precise view of TE expression dynamics during regeneration for any species. Lastly, I will directly test whether TE repression is required for regeneration by modulating TE activity using Piwi pathway mutants and chemical inhibitors of TE activity. Together the outcomes of this project will be the first to directly assess the role of TE activity and regulation during complex tissue regeneration. Moreover, these studies will lay the foundation for new testable hypotheses surrounding differences between regeneratively competent versus incompetent organisms and lead to the development of novel regenerative therapies.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY Appropriately recognizing and responding to social partners is a fundamental principle guiding every social interaction from single cells to humans. Social environment is known to interact with development to give rise to typical behavioral responses, however the mechanisms by which social experience shapes the development and tuning features of the nervous system to give rise to these behaviors remains poorly understood. How does the social environment throughout development interact to shape how the brain encodes and discriminates social information? The proposed research addresses these questions in a novel experimentally tractable system for investigating social development of a neural circuit, the northern paper wasp, Polistes fuscatus. P. fuscatus females have highly diverse color markings on their face which they use to discriminate social partners via vision alone. Like humans, P. fuscatus wasps treat faces as special visual objects and the development of this specialized recognition ability is dependent on social experience. The social lives of these wasps are rich and complex, allowing for highly refined social memory and even transitive inference of social relationships. Conveniently, wasps do not possess image forming eyes prior to adult emergence. This key feature allows for the ability to precisely control both the timing and diversity of social experience, while maintaining normal larval development. Further, we have recently discovered a common population of socially responsive neurons in the central brain of P. fuscatus, which show selective tuning to visual stimuli of forward- facing wasps above other visual objects, analogous to the ‘face cells’ in the primate brain. These cells encode both social detection and identity discrimination, providing a clear neural target to study how social experience shapes the tuning features of a socially selective circuits. The proposed experiments take advantage of the unique strengths of this system to address this question at three levels. First, we will assess how these circuits are impacted by long-term social isolation. Second, we will track the developmental tuning trajectory of these circuits to identify how these circuits develop and are refined through maturity to give rise to the highly selective features found in mature adult wasps. Third, we will investigate how both individual neural and population-level tuning features are affected by the diversity of social experiences wasps have, via manipulation of facial diversity among groups. These experiments will aid in discovering fundamental features of how social circuits are tuned via social experience and guide future experiments to identify shared principles guiding social cognition. Further this award will also support the awardee’s transition to an independent research career at a research-intensive university and support the establishment of their laboratory studying how social experience shapes the development of circuits underlying social cognition.

NIH Research Projects · FY 2025 · 2023-09

PROJECT SUMMARY Learning and memory are fundamental cognitive functions that allow us to learn from the environment around us. Memory is the ability to store and recall information essential to everyday life. An indispensable property of memory is its stable storage, allowing for the recall of memories over extended periods of time. Yet the physiological mechanisms underlying the stable storage of memories for such a long-lasting time remain to be elucidated. Memory formation involves two stages, encoding, and consolidation. After encoding, the consolidation process solidifies these neuronal traces into long-lasting memories. Consolidation is a progressive process, starting with immediate consolidation that, over time, becomes long-term consolidation. The hippocampus (HPC) is a brain region fundamental to memory formation and immediate consolidation. As consolidation continues, the HPC offloads memories to the cortex, eventually becoming independent of the HPC. The HPC consolidation of memories involves a highly synchronous network event called a sharp-wave ripple (SWR). During SWRs, memory traces that represent a particular experience are replayed in a compressed manner, which is thought to consolidate these neuronal representations through synaptic plasticity. Yet, it is unknown how information from the HPC is transferred to the cortex during SWRs during immediate consolidation. A cortical region also involved in memory is the prefrontal cortex (PFC). Both the HPC and PFC are involved in spatial memory, making it an ideal behavior to investigate the transfer of HPC information to the PFC during immediate consolidation. The respective contribution of SWRs and local cortical circuit dynamics for immediate memory consolidation remains unknown. Furthermore, the circuit and cellular changes during immediate consolidation are not fully understood. This proposal targets these exact questions by 1) directly testing whether SWRs transfer information to the PFC necessary for immediate consolidation; 2) identifying the PFC neuronal assembly modifications during SWRs underlying immediate consolidation; and 3) elucidating the local PFC circuitry mechanisms that regulate these neuronal assembly changes during immediate consolidation. The aims of this proposal will directly test whether communication between HPC and PFC that occurs during SWRs is crucial for immediate memory consolidation and how local processes in the PFC evolve during memory consolidation. This work aligns with NIMH’s mission to understand the mechanisms of learning and memory at a system level by investigating the interactions between brain regions that might underlie these functions.