Iowa State University

NSF Awards · FY 2024 · 2024-08

This Research Experiences for Undergraduates (REU) site award to Iowa State University, located in Ames, IA, supports 10 students for 10 weeks during the summers of 2024-2026. In this program, funded by the Division of Chemistry, students will contribute to multidisciplinary cutting-edge research spanning chemistry, biochemistry, machine learning (ML), and computer science. Participants will gain hands-on research experience in software development, chemical simulation, data analysis, and responsible and ethical conduct of research. Professional development opportunities include weekly research seminars, bootcamps, and informal networking events. Ultimately, this REU site seeks to expose and better prepare more students for participating in STEM-related activities, particularly early career students who may not have had exposure opportunities otherwise. Predicting next generation enzymatic catalysts via simulations is an important, pressing, multidisciplinary problem that requires developments in the fields of computational chemistry, biochemistry, and computer science to develop software, simulation, and analysis techniques. The Sustainability Institute for Machine Learning and Collaborative Open-source Development of Enzymatic Simulations (SIMCODES) will provide individualized research projects for REU participants designed to (1) simulate protein and enzyme processes; (2) use ML methods to replace more expensive simulation methods; (3) use fragment-based quantum mechanics methods to quickly generate additional ML training data; (4) train ML models which can generalize results from one set of enzymes to another; and (5) develop interpretable ML models for predicting catalytic performance of enzymes. 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 · 2024-07

Organ formation in plants and animals relies on communication between cells. This project is focused on determining how organ size is influenced by communication between cells. This study will be carried out in the model plant Arabidopsis thaliana, which is closely related to crops such as canola and broccoli. Our experiments will be directed at roots, which are a critical plant organ for water and nutrient uptake. This research could result in agricultural advances based on tractable strategies to inform root growth. A key societal outcome of this project is broadening participation in STEM (science, technology, engineering, and mathematics) research. This project will provide hands-on research experiences for 400 high school students from diverse backgrounds via annual Science Bound Saturday workshops and 60 students via a 5-day summer short course at Iowa State University. These events will support the recruitment of underserved students to undergraduate STEM fields to improve equity and representation in STEM research. In addition, this research will be carried out by undergraduate students, two postdoctoral scholars, and one staff scientist using a mentored framework that sustains participation in cross-cutting research and strengthens partnerships between academia and non-profit research. Organ formation in multicellular organisms requires cellular communication and cell proliferation. An outstanding question in developmental biology is how cell proliferation is regulated in response to multiple growth cues, such as sugars and hormones. This project will identify the cellular basis of cell proliferation using the model plant Arabidopsis thaliana, which extensively relies on post-embryonic development for de-novo organogenesis. While it is known that in Arabidopsis roots the hormone auxin and sucrose play central roles in cell proliferation, the downstream cellular conduits of these growth cues are not well understood. This project will test the hypothesis that Arabidopsis thaliana myosin 1 (ATM1) influences sugar-driven cell proliferation in roots via an integrated and collaborative research plan. Objective 1 will focus on isolating ATM1-binding proteins to identify potential mechanisms for regulating cell division and intercellular trafficking. Objective 2 will measure cytoskeletal dynamics in roots without ATM1 to elucidate the relationship with cell cycle and cell division processes. Objective 3 will identify the function of ATM1 related to plasmodesmata to understand how intercellular trafficking influences cell division. These objectives will be achieved using interdisciplinary and complimentary approaches, including genetic, molecular, microscopic, and biochemical techniques. The experimental findings will be shared via preprints, publications, and via public datasets. The long-term goal of this work is to inform future strategies for organogenesis and plant resilience to nutrient stress. 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 · 2024-07

Small uninhabited aerial vehicles (UAVs) have become a part of everyday human activities like farming, sports, and zoon management. These UAVs have offered new ways to see the world, but looking is not enough for people; they need to see and touch things to fully understand them. This project will explore new ways for people to work safely and effectively with small UAVs. They will work to touch or interact with objects in dynamic environments. This project will feature a novel UAV. It will adapt using diverse human viewpoints to improve the precision of human-object interaction. There are two primary challenges in doing this. First, the preferred perspective for a person may not be the best perspective for UAV performance. Second, humans need specific viewpoints to do tactile tasks . The intersection of these challenges will result in guidelines for future UAVs to work with people to let them explore new environments. The design of the educational and outreach components will inspire and cultivate a new generation of human-robot interaction experts. This project will fix problems between humans and small uninhabited aerial vehicles (UAVs). These problems occur when small UAVs manipulate objects. The solution will include corrective approaches and interaction guidelines using visual perceptions. This work explores two main ideas. First, making the robot easier for users to understand through perceptible changes. Second, ensuring safety and efficiency. Interaction methods will adapt to fit the platform, users, and environment. The research goals of this project are: (1) to create a new computational framework. It will enable a shared visual interface between a small UAV and a human user. This will let the human and UAV share the same knowledge for tasks. (2) to develop a computational method. It will use synthetic visual data to get knowledge from human multi-modal inputs. These inputs have the abilities needed for manipulating real objects with UAVs. (3) to integrate the first two goals. This will improve the ability of the user and UAV to work together to manipulate objects. There will be a complete evaluation plan to support the three study aims. It will include formative assessments and continuous evaluation. This research will create new human-robot data sets. It will also produce technical knowledge and educational outcomes. It will do this by advancing the manipulation of physical objects by UAVs. This project is jointly funded by the Computer and Information Science and Engineering Directorate (CISE), Division of Information and Intelligent Systems (IIS), Human-Centered Computing cluster (CISE/IIS/HCC) and the Established Program to Stimulate Competitive Research (EPSCoR). 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 · 2024-07

Mechanical forces have long been implicated in regulating basic cellular and molecular processes such as cell proliferation, differentiation and DNA-protein bonding. Understanding the basic working mechanism of these processes can lead to breakthrough improvements in biochemical and biomedical sciences and engineering. Atomic force microscopy (AFM), by far, is the most suitable platform for nanomechanical characterization of biological materials owing to its capability to exert precisely controlled force at desired locations and sense the sample response. However, such a technique is subject to substantial workload and biases of human experimentalists. It heavily relies on constant human supervision and human insight for execution and analysis of problems such as AFM probe breakage after prolonged functionalization, and sample damage due to lack of optimization of the loading forces. To address these challenges, this project will build a transformative new cyber physical system (CPS) by leveraging recent advances in artificial intelligence (AI) and machine learning (ML) towards high-throughput, scalable, and ultra-precise AFM. This will lead to a key enabling tool to create new knowledge of life science materials. This project will develop and validate a novel closed-loop framework with AI-based sensing & characterization, modeling interactions between the AFM probe and soft biological samples via physics-aware neural surrogates, and AFM navigation & control algorithms via real-time learning that will lead to a next-generation AI-enabled AFM (namely, AI-AFM). The key intellectual merits extend beyond conventional AFM applications in biomechanical and biomaterial studies. Specific innovations will include: (i) large multimodal models for bioimaging and AFM data characterization; (ii) generative models for enhancing AFM images (iii) AFM probe–sample contact dynamics modeling using physics-aware ML for optimizing the AFM mechanical stimuli design; (iv) ML-based closed-loop+feedforward predictive control in an adaptive manner for the AFM material mapping; and (v) software and hardware implementation and demonstration of the sensing, modeling and control modules in a commercial AFM setup. The research outcomes will go beyond live cell AFM studies and impact other CPS sectors such as biomedical devices, materials, and manufacturing. This project will incorporate the research outcomes at all educational levels by enriching the graduate/undergraduate curriculum, providing undergraduate research experience and K-12 outreach activities, and broadening the participation of women and underrepresented minorities in computing and engineering. 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 / ABSTRACT Highly pathogenic and low pathogenic strains of avian influenza continue to circulate and infect birds in Asia with occa- sional spread into the North American flyway. These necessitate the culling of any poultry farms that test positive for these strains. Furthermore, through continued circulation, humans remain under constant threat that one of these strains will reassort and infect humans. While the current strategy for combating these strains is surveillance and biosecurity, these strategies clearly do not work in many parts of the world, as they are hot zones for these viruses. As an alternative, vaccinations for poultry and waterfowl would certainly be a boon for human health as they would restrict the number of influenza strains in these flu reservoirs. Here, we seek to use mRNA vaccines that code for a universal flu Hemagglutinin antigen we have developed. In tandem with polyanhydride delivery vehicles that impart thermostability to mRNA and serve as antigen depots, we will vaccinate chicken eggs to determine efficacy against highly pathogenic and low patho- genic avian influenza strains. We will also develop transgenic mealworms to use as booster or as primary vaccines for poultry, but eventually waterfowl, for future use as flu vaccine bait stations.

NSF Awards · FY 2024 · 2024-06

Evolutionary trees provide information about the relationships among lineages of emerging pathogens and cancer cells, as well as plants, animals and other organisms. To study evolution and the diversity of life on Earth, researchers need high-quality software for constructing evolutionary trees from DNA sequence data. RevBayes is a freely available and popular software package for constructing evolutionary trees. It achieves high flexibility through the use of an interpreted programming language that allows users to construct evolutionary trees from a variety of different types of data under many different scenarios. The community of scientists currently using and developing RevBayes is distributed across many different universities and countries. The RevBayes community develops and maintains a variety of resources, including inference software, visualization tools, and detailed user tutorials. As an open-source project, RevBayes benefits from free contributions from users and developers around the world. A major goal for this Pathways to Enable Open-Source Ecosystems (POSE) project is to assess how to transition this community into a self-sustaining and self-governing ecosystem that can ensure continued growth and stability by making use of free contributions from an increasing number of users and developers. These efforts and experiences will help inform other teams in the field. Training opportunities for junior researchers to learn transferable software development skills will be offered. Junior researchers will also be provided with networking opportunities both within and outside the RevBayes team. This project will investigate and test strategies to improve the experience of community members at all levels (user, contributor, developer) in order to increase the rate at which people join the community and transition to higher levels of involvement. The OSE will facilitate this collaboration by establishing a deliberate dialog with potential, new, and veteran developers to identify where the project is succeeding and where it can be improved. The team will organize an in-person meeting to obtain feedback from community members and discuss community organization. They will also conduct a poll to incorporate feedback from community members from a variety of backgrounds and career stages. Based on this feedback, the OSE will improve the clarity and depth of existing RevBayes user tutorials and developer documentation, which will ultimately empower RevBayes users to make new biological discoveries and RevBayes developers to innovate new models and methods. A comparative database of software for estimating evolutionary trees and a review how RevBayes is used in published scientific studies will be conducted. These assessments will provide a multifaceted view of the breadth of the RevBayes community, as well as their research interests and needs. These activities will be combined with efforts to understand and improve the current governance structure of the RevBayes project and create new venues for communication between users and developers. By establishing the foundation for RevBayes to function as an open-source ecosystem, the team will ensure that the RevBayes project and its products are viable for long-term stability and growth. 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 Hematophagous arthropods transmit numerous viruses, many of which are serious human pathogens. To combat the growing public health impact of arthropod-transmitted viruses, many metagenomics studies have been performed to characterize the arthropod virome. The importance of proactive virus discovery cannot be understated because it allows risk assessments to be performed and viral diagnostic assays and control strategies to be developed before virus spillover occurs. Most metagenomics studies designed to identify novel arthropod- associated viruses have focused on mosquitoes, with other hematophagous arthropods being largely neglected. Another limitation of many previous studies is that virus isolation was not attempted, with newly discovered viruses known only from sequence data, which has impeded their phenotypic and serological characterization. The overall goal of this grant application is to define the virosphere of understudied hematophagous arthropods and to identify and characterize novel viruses capable of vertebrate cell replication. Two specific aims have been designed to achieve this goal. In specific aim 1, a diverse range blood-feeding arthropods (ticks, midges, sandflies, blackflies, and fleas) will be assayed for novel and previously recognized viruses by unbiased high-throughput sequencing (UHTS). These experiments will be performed using homogenates already in our possession and prepared from >37,000 arthropods from North America. Total RNA will be directly extracted from every homogenate and viral sequences will be identified using UHTS and an established bioinformatics pipeline, allowing the virosphere of the arthropods to be defined. Additionally, the codon and dinucleotide frequencies of every novel virus will be determined to provide insight into their host ranges and to identify those most likely to replicate in vertebrate cells. In this regard, vertebrates and invertebrates preferentially have certain codon and dinucleotide usage biases and the preferences of RNA viruses often mimic those of their hosts. In specific aim 2, an aliquot of each homogenate will be inoculated onto human and nonhuman primate cells then two blind passages will be performed. Total RNA will be extracted from all final culture passages and analyzed by UHTS and bioinformatics in order to specifically identify vertebrate-infecting viruses. If an isolate is not recovered but the homogenate is predicted to contain a vertebrate-infecting virus, as determined in the codon and dinucleotide frequency analysis, virus isolation will be attempted using additional vertebrate cell lines. The in vitro replication kinetics and yields of every novel virus capable of vertebrate cell replication will be determined. The studies proposed in this grant application provide the groundwork for future in vivo experiments, where viruses capable of vertebrate cell replication will be further characterized. Experimental infections will be performed with vertebrate animals and arthropods to assess viral virulence and to identify competent vector species, respectively. Future experiments will also be performed to determine the incidence and seroprevalence of select viruses in human and vertebrate animal populations.

NIH Research Projects · FY 2025 · 2024-06

Project Summary/Abstract Organophosphate (OP) nerve agents (OPNA) are increasingly used to attack civilians worldwide. OPNA poisoning is a global health problem. There is no effective treatment for OPNA survivors. The life-long health consequences of OPNA survivors are beginning to emerge. However, the mechanisms of OPNA-induced long-term brain injury are largely unknown. Acute exposure to OPNA induces seizures (neural excitability) and status epilepticus (SE). In the long term, SE-induced brain changes alter the signaling molecules in neurons and glia. We hypothesize that OPNA-induced SE promotes key molecular interactions and exacerbates neurodegeneration, reactive gliosis, and the development of epilepsy. In recent years, novel pathways of neuroinflammation and neurodegeneration are emerging as mechanistic targets for therapeutic development. Our current findings and others suggest that a non-receptor Src family tyrosine kinase Fyn and a serine/threonine cyclin-dependent kinase 5 (CDK5) are the critical kinases activated in both neurons and glia in response to status epileptics (SE) that promote neuroinflammation, hyperexcitability, and neurodegeneration. The activated Fyn and CDK5 can trigger a self-perpetuating pathway in the glia and interact with phosphorylated tau, NR2B, and PSD95 in neurons to promote and maintain the disease state. Therefore, our overarching hypothesis is that the seizures induced by acute exposure to OPNA facilitate Fyn-tau interactions in neurons and CDK5 and Fyn activation in both glia and neurons. These, in turn, activate NR2B-PSD95 interactions to cause neuronal hyperexcitability (epileptiform spiking and spontaneous seizures), reactive gliosis and the production of proinflammatory cytokines (neuroinflammation), nitrooxidative stress and neurodegeneration (“disease promoters”), and promote brain pathogenesis in the long term. We will test the hypothesis in a well-characterized OPNA (diisopropylfluorophosphate (DFP)) rat model. In Specific Aim 1 (SA1), after acute exposure to DFP, we will characterize the changes in Fyn, tau, and CDK5 and their interactions at various time points in key brain regions. We will fractionate brain lysates to isolate synaptosomal membranes, cytosol, and nuclear fractions and conduct co-immunoprecipitation (co-IP)/WB. We will use brain sections for proximity ligation assay (PLA) to determine interacting complexes and immunohistochemistry for cell-specific localization of signaling molecules, gliosis, and neurodegeneration. In SA2, we will validate these interactions using Fyn-tau interactions blocking peptide and a CDK5 inhibitor. We will investigate the interactions of Fyn and CDK5 with NR2B and PSD95 and their impact on hyperexcitability, neurodegeneration, and protection by pathway inhibitors and blocking peptides. We will investigate peripheral biomarkers of neurodegeneration in the serum and CSF. This proposal is in response to the CCRP initiative FOA (PAR-23-027), “which is expected to generate data that elucidate the mechanisms of OPNA-induced brain toxicity and potential new targets for therapeutic development.”

NIH Research Projects · FY 2026 · 2024-06

Training the next generation of biomedical researchers is essential for our society as they play a critical role in advancing new breakthroughs to improve health outcomes and transform health care (AAMC, 2023). A growing number of biomedical research training programs, housed in research institutes, universities, and teaching hospitals, have been established with the goal of equipping aspiring researchers with the necessary knowledge, skills, and resources to contribute to the continuous progress of biomedical research and its potential to positively impact society. A barrier to the sustained success of such training programs is that they lack the knowledge, skills, and resources to effectively assess and evaluate the training programs. This creates a major loophole in the training cycle that fails to inform stakeholders about how well these training programs position their trainees in integrating interdisciplinary approaches to answer key biomedical research questions. This project addresses NIGMS’ Enhancing Program Evaluation Capacity at institutions with biomedical research training programs by developing online modules to inform program directors and administrators about effective and practical approaches to evaluate biomedical research training programs. Through this project, we aim to increase awareness of the importance of evidence-based decision making and enable biomedical science administrators and other stakeholders with the tools and skill sets to make program evaluation an on-going, integral component of research training programs from the beginning rather than a one-time event. Our proposed solution highlights the strength of decision-making based on systematically collected evidence that improves the quality of biomedical research training programs and therefore contributes to the development of biomedical research and global health. The overall goal in this proposal is to equip participants with the competencies (knowledge, skills, and attitudes) necessary to conduct high-quality evaluations and make evidence-based decisions to improve program effectiveness and learning outcomes in biomedical research training programs. To achieve this, we will pursue three specific training goals: 1) design and develop a comprehensive online training program; 2) pilot test and refine the educational modules; and 3) disseminate knowledge and strategies on evaluation through a website, content management system, publications, and presentations. The training will include seven modules covering main components of program evaluation, from foundational practices to quantitative and qualitative methods, and to communication of evaluation results.

NSF Awards · FY 2024 · 2024-06

The traditional chemical process for producing plastic and other polymeric products from natural gas starts with the thermal steam cracking of ethane or propane to produce ethylene and propylene. For ethane, in particular, the overall process is extremely energy-intensive resulting in huge emissions of the greenhouse gas carbon dioxide (CO2). Catalytic processes offer opportunities to reduce the energy demands and associated CO2 emissions, but are hampered by the formation of carbon deposits (i.e., coke) on the catalyst surface, and coalescence of the small platinum (Pt) catalyst particles into larger particles – both of which decrease the catalyst performance and require frequent catalyst regeneration. The project addresses both deactivation modes via a novel class of catalysts known as MXenes. Recently, the investigators developed an atomically thin Pt nanolayer catalyst supported on a molybdenum-titanium-carbon MXene. The catalyst was evaluated for the catalytic dehydrogenation of ethane and propane into ethylene and propylene, and, as compared to Pt nanoparticles, the Pt nanolayer catalyst showed superior coke-resistance, sinter-resistance, high activity and selectivity toward ethylene and propylene. Nevertheless, further advances in catalyst design are needed for commercial use. The project will advance the basic science of heterogeneous catalysis by addressing a critical gap in understanding the stability of the unique Pt nanolayer/Mo 2TiC2 MXene catalyst. A multidisciplinary research approach will be undertaken, involving materials synthesis, in situ/operando characterization, theoretical computation, kinetics measurement, and reaction-diffusion model development. Collectively, the research thrusts will provide foundational insights related to the stability and coking resistance of MXene-supported Pt-group catalysts, thus providing a basis for improved catalyst formulations and designs. Beyond the technical aspects, the knowledge gained from this project will foster the development of a skilled technical workforce and drive innovation in the chemical and petroleum industries. The multidisciplinary research and the integration of research and education will provide both undergraduate and graduate students with a unique training experience in materials science, catalysis science, reaction engineering, computational chemistry, and kinetic modeling. The research results will be integrated with chemical engineering curricula at both Louisiana Tech University and Iowa State University, and also support K-12 STEM outreach at local schools. 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 2026 · 2024-05

Many flaviviruses are adapted to dual-host transmission and maintained in cycles between hematophagous arthropods (i.e. mosquitoes and ticks) and vertebrates. An example of mosquito-borne flavivirus (MBFV) is Zika virus (ZIKV), which is a human pathogen of global concern. Other flaviviruses, such as Long Pine Key virus (LPKV), replicate in mosquitoes and phylogenetically affiliate with MBFVs, but lack the capacity to infect vertebrate cells. These viruses are known as dual-host affiliated insect-specific flaviviruses (dISFs). The precise sequence elements and virus-host interactions that modulate the differential host ranges of MBFVs and dISFs have not been defined. Identification of these sequences and virus-host interactions would provide key insight into why some flaviviruses infect and cause devastating disease in humans while others are insect-specific. In the initial funding period, we identified the broad genetic determinants that modulate the differential host ranges of MBFVs and dISFs. Through the construction and characterization of chimeric viruses, we demonstrated that ZIKV loses its vertebrate-infecting tropism when its 5’ untranslated region (UTR), adjacent capsid protein (C) gene, and 3’ UTR are replaced with those of LPKV, while its mosquito-infecting phenotype is retained. The UTRs contain highly structured elements that interact with NS3 (the viral helicase) and NS5 (the viral RNA polymerase) to regulate genome replicate. The UTRs, NS3, and NS5 of MBFVs also interact with many host proteins, but the host proteins that comprise the dISF replication complex are unknown. The overall goal of this continuation is to dissect the 5’- and 3’-terminal ends of the flavivirus genome to pinpoint the precise sequences responsible for flavivirus host-specificity and to compare the virus-host interactions that occur during MBFV and dISF replication through the identification and functional characterization of host proteins that bind to their UTRs, NS3, and NS5. Three independent aims have been designed to achieve this goal. In aim 1, we will dissect the 5’ UTR, C gene, and 3’ UTR of the genomes of LPKV and ZIKV to identify the specific sequences responsible for their differential host ranges. Chimeras of LPKV and ZIKV will be created and the abilities of the resulting viruses to replicate in vertebrate and mosquito cells will be assessed. We will initially focus on each secondary structure (e.g. stem-loops, hairpins, dumbbells), either alone or together with others, then target specific sequences in structures of greatest interest. Subsequent experiments will be performed using additional dISFs and MBFVs to determine whether the genetic determinants that modulate host-specificity are shared among flaviviruses of the same group. In aim 2, we will identify and functionally characterize host proteins that bind to the 5’- and 3’-terminal ends of the dISF and MBFV genomes. Biotinylated RNAs containing the 5’ UTR, C gene, and 3’ UTR sequences of select dISFs and MBFVs will be transfected into mosquito and vertebrate cells. The cell cultures will be inoculated with virus then RNA-binding proteins (RBPs) will be recovered using streptavidin beads and identified by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis. We will pinpoint the precise viral sequences that interact with RBPs of greatest interest by reversible RNA-protein crosslinking, immunoprecipitation, and RNAseq. Select RBPs will be further analyzed in overexpression and knockdown experiments to determine whether they are positive or negative regulators of viral replication. In aim 3, we will identify and functionally characterize host proteins that bind to NS3 and NS5 of select dISFs and MBFVs. A novel proximity-based protein labeling technique known as TurboID will be used to recover mosquito and vertebrate hosts that associate, either directly or indirectly, to NS3 and NS5 of the selected viruses. Recovered proteins will be identified by LC-MS/MS analysis and a subset will be characterized in overexpression and knockdown experiments to determine whether they enhance or suppress viral replication. Data generated from the experiments outlined in the aforementioned aims will allow us to define the genetic and molecular determinants of flavivirus host-specificity.

NIH Research Projects · FY 2025 · 2024-05

PROJECT SUMMARY Antimicrobial resistance (AMR) is a significant challenge for human health, especially with the emergence of multi-drug resistance bacteria and the lack of new antibiotics development. In the United States alone there are over 2.8 million cases each year with over 35,000 deaths. Worldwide annual deaths are over 700,000 and this number is expected to grow to 10 million by 2050. There is a great concern that the COVID pandemic may have increased AMR risk. While the next generation ASTs have been actively under development in the last decade and some automatic tools were approved by the FDA, they are mostly based on morphological changes with limitations in sensitivity and selectivity, mostly requiring overnight cultures and long turn-around-time. Additionally, a separate capital investment is necessary for automatic AST instruments. In vivo isotope labeling with heavy water (D2O) has been used to monitor microscale cellular responses such as protein synthesis and turnover, DNA replication, and de novo lipogenesis. When bacteria are cultured in D2O, newly synthesized bacterial lipids are labeled by deuterium and can be readily detected by mass spectrometry (MS). We are developing a new antibiotic susceptibility test (AST) using deuterium-labeling mass spectrometry (DLMS), in which AMR bacteria can be rapidly detected by a bench top matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF) that is commonly available in many clinical labs for bacterial species identification. Based on previous success on resistant E. coli and methicillin-resistant Staphylococcus aureus (MRSA), our DLMS AST will be now applied to all ESKAPE (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter) pathogens using a bench top MALDI-TOF, the Bruker Biotyper. The minimum inhibitory concentration (MIC) measured by DLMS will be compared with a traditional broth dilution method, which is expected to be comparable but achieved in only a few hours instead of one or two days. To further accelerate the adoption of this DLMS AST assay by clinical bacteriologists, an on-agar assay will also be developed using ETESTÒ and D2O agar. Furthermore, we will explore the discovery of new AMR metabolite biomarkers using DLMS, which will not only shorten the turn- around-time but also provide information about resistant mechanisms. Our long-term vision is to have both global markers (deuterated lipids) and specific AMR biomarkers (deuterated small metabolites) simultaneously detected by DLMS using a bench-top MALDI-TOF, allowing prompt prescription of the most appropriate antibiotics and reducing antibiotic overuse.

NIH Research Projects · FY 2025 · 2024-05

Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant mortality. SMA is caused by deletions of or mutations in the Survival Motor Neuron 1 (SMN1) gene that codes for the multifunctional SMN protein. SMN2, a nearly identical copy of SMN1, fails to fully compensate for the loss of SMN1 due to predominant skipping of exon 7. Prevention of SMN2 exon 7 skipping is a proven approach for the treatment of SMA. Among many regulatory elements that modulate SMN2 exon 7 splicing, intronic splicing silencer N1 (ISS-N1) has been extensively validated as an antisense oligonucleotide (ASO)-directed therapy for SMA. Nusinersen, an ISS-N1-targeting ASO (abbreviated as “N1ASO”), became the first FDA-approved drug for SMA. Risdiplam, a small molecule capable of preventing SMN2 exon 7 skipping, is also approved for SMA therapy. Gene replacement is an additional therapeutic avenue for the treatment of SMA. Current therapies of SMA do not fully meet the needs of SMA patients, as most severe SMA patients remain wheelchair-bound even after several years of treatment. One of the likely causes of low efficacy of available drugs for SMA is the off-target effects at concentrations used for clinical applications. Phosphorothioate (PS) backbones present within ASOs are known to produce off-target effects. However, off-target effects of 2¢O-Methyl (OMe) or 2¢O- Methoxyethyl (MOE) incorporations in the sugar moiety of RNA oligonucleotides remain largely unknown. Additional off-target effects of ASOs could be expected due to tolerance for mismatch base pairing with the target. High concentration of a 20mer N1ASO encompassing PS/OMe modifications has been recently reported to cause massive perturbations of the transcriptome in SMA patient cells. However, similar study has not yet been done with Nusinersen, an 18mer N1ASO encompassing PS/MOE modifications. Also, there is no comparative study on the concentration-dependent chemistry-specific off-target effects of N1ASOs. Unlike PS/OMe and PS/MOE ASOs that contain negatively charged backbones, morpholino ASOs have neutral backbones. We performed RNA-Seq on transcripts generated from SMA patient cells treated with N1ASOs encompassing PS/OMe, PS/MOE and morpholino modifications. Our preliminary analysis and pilot validations of RNA-Seq data reveal chemistry-specific perturbations of the transcriptome. Here we propose to fully analyze and validate the results of RNA-Seq. In Aim 1, we will determine the nature of genes and pathways impacted by an N1ASO encompassing three chemistries. We will determine the extent to which small, large, coding, non-coding genes are affected by the chemistry of an N1ASO. We will validate upregulated and downregulated genes as well as seven types of aberrant splicing events, including exon skipping, exon inclusion, enhanced intron retention, enhanced intron removal, alternate 5ʹ splice site usage, alternate 3ʹ splice site usage and mixed splicing events. We will analyze promoters and upstream sequences of upregulated and downregulated genes to determine the presence of common motifs responsive to N1ASOs. We will examine if the off-target effect on splicing is associated with splice site strengths of the affected exons. We will determine if ISS-N1-like sequences within the affected exons and/or their flanking introns are associated with the off-target splicing. We will examine if transfection conditions also affect the nature of off-target effects of N1ASOs. We will determine if some of the off-target effects of N1ASOs are cell-type specific. In Aim 2, we will determine primary and secondary targets of N1ASOs by capturing the antisense effects at early and late timepoints of the treatment with N1ASOs, respectively. We will examine both sequence-dependent and sequence-independent targets. We will employ minigenes to uncover the nature of sequences associated with the aberrant splicing triggered by N1ASOs encompassing different chemistries. We will interrogate the role of ISS-N1-like sequences in the affected exons and/or their flanking introns. Our results will reveal the required minimum complementarity between ASO and its target for the antisense response. We will determine if the chemistry-specific off-target effect of an N1ASO is due to a common motif within the target sequence. Outcomes of our proposed study will have high significance for developing future ASO-based therapies for SMA as well as other diseases amenable by ASOs encompassing PS/OMe, PS/MOE and morpholino modifications.

NIH Research Projects · FY 2024 · 2023-09

PROJECT SUMMARY / ABSTRACT Vaccination is an effective public health measure, yet host factors including advanced age, sex, obesity, physical or mental health status may influence vaccine efficacy. Adjuvants improve immunogenicity to vaccination but often result in greater side effects. As an alternative to the inclusion of adjuvants in the vaccine formulation, evidence suggests physical exercise performed at the time of immunization may serve as an effective non-pharmacological approach with the potential for greater impact in individuals with suboptimal immune response and reduced reactogenicity. The effect of host factors on immune response to SARS-CoV-2 and long-term protection remains to be established, and positive findings for an adjuvant-like effect of physical exercise would have an immediate translational impact. However, major barriers to the implementation of exercise are inconsistent findings and a gap in the knowledge of the mechanisms that underlie such effects. Our recent publication shows that we have identified an exercise protocol that consistently increases antibody response to vaccines that is reproducible across several different vaccines. This finding holds the potential to transform vaccine efficacy and address questions on the breadth and durability of immune response and underlying mechanisms. The goals of this application are to determine the extent to which physical exercise exhibits an adjuvant-like effect across long-term antibody and T cell-mediated immune responses to COVID-19 mRNA-based vaccines and establish the degree of immune enhancement in individuals who may have suboptimal vaccine response due to high psychological stress. An additional goal is to identify potential operative mechanisms, and compelling preliminary data show promise for metabolism-related mechanisms, a new direction in this field of study. Aim 1 will identify the extent to which a single exercise session applied at the time of initial immunization shapes the magnitude, breadth, and durability of immune response to SARS-CoV-2 mRNA vaccine. Outcome measures are serum anti-spike receptor-binding domain (RBD) IgG titer, neutralizing antibody, antigen-specific CD4+ and CD8+ T cell response measured up to one-year post-immunization. Aim 2 will determine the influence of psychological stress on antibody and antigen-specific CD4+ and CD8+ T cell immune response to SARS-CoV-2 immunization and the extent to which exercise may override any potential effect of stress. Aim 3 will apply transcriptomic (RNA-Seq) and metabolomic (Raman) measures to identify pathways by which exercise influences immune response to vaccination. The long-term goals of this research direction are to refine and develop behavioral interventions that optimize immunity and more broadly apply the findings learned with respect to critical pathways of immunogenicity to optimize vaccine development for currently underserved populations.

NIH Research Projects · FY 2024 · 2023-08

Project summary Lymphatic filariasis is a mosquito-transmitted disease caused by filarial nematodes, including Brugia malayi, B. timori, and Wuchereria bancrofti, that affect millions of people in the poverty- stricken regions of Sub-Saharan Africa and Southeast Asia. The filarial worms are located in the host lymphatic system, blocking lymphatic drainage, resulting in gross swelling of the limbs (elephantiasis) and skin infections. These infections result in physical disability and disfigurement, mental stress, and reduced productivity, hampering social-economic development in endemic regions. Control and treatment of lymphatic filariasis rely on the mass drug administration (MDA) of antiparasitic drugs, ivermectin, diethylcarbamazine, and albendazole. This strategy has been successful to a certain extent, but the parasitic infections persist, mainly attributed to the limited adulticidal effect of current anti-filarial agents. Besides, there are no vaccines available for use, and concerns about developing drug resistance in humans. There is an accepted need to identify novel chemotherapeutic targets and macrofilaricidal therapeutics for more efficient control of filarial infections. Here we propose to investigate and characterize the pharmacological properties of UNC-49 γ- aminobutyric acid (GABA) channels in B. malayi to contribute to the search for novel drug targets. The majority of the commercially available anthelmintic drugs target cys-loop ligand-gated ion channels (LGICs), including the recently introduced emodepside (SLO potassium channels), monepantel (nAChRs), and derquantel (nAChRs). However, nematode ion channels are an underexploited chemotherapeutic target with a limited number already explored. Ionotropic GABA channels are the major inhibitory chloride-gated channels at the neuromuscular junction of invertebrates and are essential for coordinated movement. And yet, GABA receptors serve as the target of only one antiparasitic drug, piperazine. UNC-49 GABA channels have been characterized from Caenorhabditis elegans and Haemonchus contortus. These channels were distinct from the vertebrate receptors in subunit composition, in vivo function, and pharmacological properties and displayed species-based diversity. It is essential to gain insights into the molecular mechanisms of species-based diversity among nematode ion channels to understand drug targets better. We propose to perform cloning and heterologous expression of the previously uncharacterized UNC-49 GABA channels from B. malayi. We will use electrophysiological methods to conduct pharmacological characterization on the channels expressed in a heterologous system, Xenopus oocytes, and HEK293 cell lines. We will also use RNAi techniques on B. malayi worms to knock down GABA subunit encoding genes to validate GABA as a drug target. The results generated through these experiments will help develop preliminary data concerning the biology and pharmacology of GABA channels in the filarial nematode. Upon completing this project, we will have broadened our understanding of the filarial UNC-49 channels and identified the contribution of UNC-49 isoforms to the endogenous GABA function. The project has two specific aims: Aim 1: To study the role of UNC-49 channels' physiological function in adult B. malayi. Aim 2: Cloning of UNC-49 subunits from B. malayi and functional expression to characterize the channels' pharmacology.

NIH Research Projects · FY 2026 · 2023-08

As SARS-CoV-2 continues to wreak havoc across the globe, it is imperative to understand the mechanism and regulation of the viral genome replication and transcription, which are essential processes in coronavirus life cycle and represent important targets for therapeutic interventions. Coronavirus genome replication and transcription are carried out by a dynamic replication-transcription complex (RTC), assembled from an array of viral non-structural proteins (nsps). Within the RTC, a unique proofreading exoribonuclease (ExoN) complex, nsp14-nsp10, boosts replication fidelity by excising mis-incorporated nucleotides and many antiviral nucleotide analogs. In addition to its role in proofreading viral RNA synthesis, the ExoN complex is also involved in viral RNA 5′ capping, which is critical for immune evasion by coronaviruses. Despite extraordinary efforts in studying coronavirus biology and replication, major gaps remain in our understanding of the key roles ExoN complex plays in various fundamental aspects of coronavirus life cycle. First, it is unclear how ExoN complex coordinates with the low-fidelity viral polymerase to proofread RNA synthesis. Second, it is poorly understood how ExoN complex is modulated by viral cofactors. Third, it is unknown how the two different enzymatic functions, RNA cleavage and capping activities, of ExoN complex are coupled in the virus life cycle. The central objective of our proposed experiments is to fill these gaps in understanding through a systematic dissection of the structural basis and functional roles of ExoN complex and its dynamic interlay with viral cofactors in viral RNA synthesis and processing. We will use SARS-CoV-2 as a model system and employ a combination of cryo-electron microscopy, single-molecule biophysics, protein-RNA biochemistry, and cell virology to achieve this central goal through the following aspects: Project 1, coordination of polymerase and exoribonuclease during mismatch correction. We will define the mechanism by which RNA mismatches are transferred from polymerase to ExoN and identify the molecular determinants for their functional interplay. Project 2, modulation of ExoN complex by viral cofactors. We will elucidate the molecular details of the interaction between ExoN complex and a key RTC subunit, nsp8, and determine how this interaction modulates the proofreading activity of ExoN complex during mismatch correction. Project 3, coupling of RNA exonucleolytic digestion and 5′ capping activities of ExoN complex. Building on our newfound cryo-EM structure of a dimeric form of the ExoN complex in which its RNA digestion and capping activities are coupled, we will determine the molecular and biochemical underpinnings and establish the physiological significance of the functional link between the two enzymatic activities of ExoN complex. Through this research program, we will reveal the principles and molecular details governing the multifaceted roles of this unique viral RNA proofreader and provide new insights into the mechanisms and regulation of coronavirus genome replication and transcription. More broadly, the established tools and experimental platforms are readily applicable to studying other RNA viruses.

NIH Research Projects · FY 2026 · 2023-08

Project Summary/Abstract Inter-organelle communication plays an essential role in maintaining cellular homeostasis and animal aging. Mitochondria, as a highly dynamic organelle and the metabolic hub of the cell, frequently interact with other cellular organelles to coordinate metabolic processes and maintain cellular homeostasis. Although it is well known that mitochondrial dynamics are often altered during animal aging, it remains largely unanswered whether and how inter-organelle communication plays a crucial role in age-dependent alternations of mitochondrial dynamics. Like mitochondria, peroxisomes play an important role in redox and lipid metabolism (e.g., ether phospholipid biosynthesis). However, peroxisome aging research is an understudied area. In this proposal, we will combine CRISPR genome editing, organelle proteomics, metabolomics, and cutting-edge imaging tools to investigate the important role of peroxisome-mitochondrion communication in animal aging. The proposal is based on our previous exciting findings showing that activation of peroxisomal receptor protein Pex5 not only rescued age-dependent decline of peroxisomal import, but also preserved mitochondrial structure and function. We further show that peroxisomal ether phospholipid biosynthesis is involved in the regulation of mitochondrial dynamics. Furthermore, we uncovered a novel positive feedback loop that regulates the ether phospholipid synthesis pathway under oxidative stress. In this proposal, we will address two outstanding questions: 1) Why and how does peroxisomal import decline with age? 2) How does peroxisomal dysfunction contribute to cellular aging? Could inter-organelle communication be a core mechanism? The proposed work will provide novel insights into the significant role of peroxisome-mitochondrion communication in animal health aging and longevity. Three specific aims are proposed: Specific Aim 1. Determine how peroxisomal import function declines with age. Specific Aim 2. Determine the role of peroxisome-derived ether phospholipids in age-related alterations of mitochondrial dynamics. Specific Aim 3. Determine the role of ATF4 in transcriptional regulation of Gnpat and peroxisomal ether phospholipid biosynthesis during aging.

NIH Research Projects · FY 2024 · 2023-08

Abstract. The objective of this research is to identify carbohydrate-compatible photolabile protecting groups and light sources to facilitate the parallel on-surface synthesis of high-density glycan microarrays—e.g. glycan chips—in a manner similar to the synthesis of gene chips. Instead of using monochromatic light and a single photolabile protecting group to spatially control the extension of a linear polymer (DNA) on the microchip, as in gene chip manufacture, irradiation with different wavelengths of light combined with wavelength-selective tem- porary protecting groups will allow for constructing complex, branched glycans on a microchip surface. I aim to: (1) identify carbohydrate-compatible photolabile protecting groups and optimal light sources to pair with each; and (2) identify a pair of wavelength-selective (`chromatically orthogonal') protecting groups and demonstrate their use in branched glycan synthesis, paving the way towards the parallel on-chip synthesis of high-density glycan microarrays. Wavelength-selective photochemistry will be achieved by separating the absorptions of pho- tolabile protecting groups to allow for selective excitation. Such high-density combinatorially-synthesized glycan chips are expected to permit rapid epitope mapping and screening of the selectivity of glycan binding partners. For example, exposing a dye-labeled lectin, antibody, or virus/bacteria/pathogen binding protein to the chip will allow its binding specificity for numerous glycan structures to be determined from a single experiment. The ability to synthesize high-density combinatorial libraries of carbohydrates will aid in resolving the structure-function relationships of carbohydrates, help to understand the target epitopes of glycan binding partners, and accelerate efforts to uncover the structure and function of the glycome.

NIH Research Projects · FY 2025 · 2023-07

Project Summary Malaria disease remains a serious public health problem. Progress in Malaria control has slowed in recent years while resistance to frontline antimalarials is emerging in the most afflicted regions, underscoring a pressing need for deciphering fundamental parasite biology to provide novel therapeutic strategies. This obligate intracellular parasite exports a battery of effector proteins out of a vacuolar niche to drastically remodel its host cell, a process that depends on the Plasmodium Translocon of EXported proteins (PTEX). PTEX is built on a vacuole nutrient pore formed by EXP2 which is further functionalized by the adaptor PTEX150 and AAA+ chaperone HSP101 to form the effector translocon. PTEX has emerged as a novel drug target owing to its essential role in blood stage parasite survival and disease pathogenesis but it is unknown how translocon cargo is identified or how the complex is assembled and regulated to perform its function. Recent results suggest HSP101 identifies export-destine cargo in the parasite ER and then brings it to the vacuole where assembly into the PTEX complex stimulates HSP101’s unfolding activity to drive membrane translocation into the erythrocyte. Importantly, while a similar export process is expected to occur in the initial liver infection that establishes the blood stage, only EXP2 and PTEX150 are present in the intrahepatic vacuole but not HSP101. This implies that PTEX components mediate protein export into both erythrocytes and hepatocytes but that mechanistic distinctions have evolved to meet the demands of subverting these remarkably different host cells. In support of this, we recently determined that EXP2 is critical to intrahepatic parasite development, clearly showing for the first time that PTEX components are also functional in the liver stage vacuole. We hypothesize that EXP2/PTEX150 constitutes a minimal effector translocon for vertebrate host cell subversion that is further adapted by HSP101 to meet the unique demands on protein export to remodel the erythrocyte. This proposal will answer key questions about the PTEX export mechanism to determine the basis for host cell subversion and provide new targets to combat this devastating pathogen. Aim 1 will determine the basis for PTEX cargo selection in the blood stage by dissecting the ER-localized function of HSP101 along with the role of a newly discovered HSP101-interacting ER protein. Aim 2 will define features required to form PTEX and identify the interaction that stimulates HSP101 unfolding activity in the assembled translocon complex using a photoreactive unnatural amino acid crosslinking system. Finally, Aim 3 will uncover the HSP101-independent function of EXP2/PTEX150 in the liver and identify novel exported effectors that enable hepatocyte subversion to establish the blood stage.

NIH Research Projects · FY 2025 · 2023-06

Project Summary The proposed work is for a cooperative agreement between the Iowa State University Veterinary Diagnostic Laboratory (ISU-VDL) and the FDA Center for Veterinary Medicine Vet- LIRN program to provide support in the following areas: 1) To participate in FDA/Vet-LIRN sanctioned sample analysis for chemical contaminants. 2) To provide analytical data to support potential regulatory use. 3) To participate in additional projects such as small scale methods development, method validation, and matrix extension for analysis of chemical contaminants. 4) To participate in the Vet-LIRN AMR Monitoring Program as a source laboratory. These activities are designed to support the FDA in strengthening coordination of veterinary diagnostic laboratory efforts in enhancing the national food safety system. The ISU-VDL is a full-service laboratory, fully accredited by the AAVLD, which provides cutting- edge diagnostic services to the State of Iowa and beyond. The case load at the ISU-VDL is unique in the nation because it is predominantly food-animal related. Iowa is a major food animal producing state. The laboratory is not only the first line of defense in the area of food safety to food animal producers across the country, but is also heavily engaged in protection of companion animal health. This project will specifically address issues related to chemical contamination leading to animal illnesses or death. A significant amount of our food animal products from Iowa are exported overseas to the EU and Asia markets which are sensitive to food safety. Participation in this cooperative agreement program will not only benefit the FDA, but the lab and the State of Iowa as well because all aspects of this project add value to our product, namely, accurate and timely analysis of test results to protect animal and human health from chemical contaminants. The ISU-VDL is well-equipped and staffed to positively impact the needs of the FDA as outlined in the FOA. Specifically, we have the necessary infrastructure to support training, participate in quality assurance processes and proficiency tests, and share data to support national capacity development. We will quickly and accurately test diagnostic samples to assist the FDA in case investigations. As members and long-term participants in the Food Emergency Response Network (FERN) and also as founding members of Vet-LIRN, we have demonstrated that we have the infrastructure to report out results accurately and efficiently. The quality of our work product is overseen by an independent Quality Assurance Unit. In summary, we have the resources and infrastructure to deliver our work product in a timely manner. We are ready to collaborate with the FDA on this grant if the application is successful.

NIH Research Projects · FY 2026 · 2023-05

There is a critical need to develop a new device to noninvasively treat mesh infections without removing the mesh. In the absence of such a device, the treatment of many mesh infections will remain highly invasive and costly. This study's objective is to develop cavitation-based histotripsy to treat surgical mesh infections. Histotripsy generates/excites a cloud of micron sized bubbles in the tissue which mechanically shred the targeted cells. The physics of microbubble collapse promotes lysis of bacteria attached to the implant enhancing the destruction of the bacteria biofilm causing the infection. Specific Aim #1: Improve pulsing scheme to reduce the impact of cavitation memory. We hypothesize that adding lower amplitude pulses will reduce cavitation memory in our application as well drastically reducing treatment times. The impact of the exposures on mesh properties will also be determined for the different exposure conditions. Specific Aim #2: Improve mesh Contrast. We hypothesize that it will be easier to visualize the mesh if we combine shear-wave and pulse echo imaging and/or increase mesh contrast by adding glass microspheres to the polypropylene fibers. Increasing the contrast may also increase the effectiveness of our therapy by providing a stronger reflection off the mesh increasing the pressure fields in the immediate vicinity of the mesh. Specific Aim #3: Test therapies safety and effectiveness in an animal model. We hypothesize that our therapy will be able to treat bacteria biofilms on hernia mesh safely and effectively in an animal model. This hypothesis will be evaluated by implanting infected mesh samples in a swine model at varying implant locations and depths while also carefully assessing the tissue for any unintended damage. This project is significant because once developed thousands of patients each year would have an alternative to invasive surgery for treating mesh infections. In addition, improving mesh contrast could improve patient care even when no infection develops. Once feasibility has been shown for mesh infections, numerous other implanted devices may be candidates for our same histotripsy-based treatment.

NIH Research Projects · FY 2024 · 2022-08

1. PROJECT SUMMARY Oral drug delivery via the gut mucosa is considered more patient-friendly than an intravenous infusion or subcutaneous injection regarding induction of treatment. The practical advantages include reduced need for trained medical personnel, cost efficiency, and increased safety. While progress has been made increasing stability and innate activation of potential orally delivered mucosal drugs, significant knowledge gaps exist at the intercellular and intracellular levels, which leaves poor understanding of the specific and non-specific factors determining recognition and transport of drug candidates across the intestinal epithelia. Furthermore, understanding how nanoparticles-based oral drug delivery systems transport through intestinal epithelium and how the transport behavior can be manipulated through surface modification to create guided transport pathways through intestinal epithelium will provide fundamental and essential knowledge on future design and development of effective drug delivery systems for oral administration. Thus, there is an urgent need to fill these gaps in learning because the intercellular and organ level interactions and resultant biological influences are critical for precise control of nanoparticles-based oral drug delivery systems targeting intestinal mucosa and mucosal-associated lymphoid tissue (MALT). My long-term goal is to study and rationally design nanoparticles- based oral drug delivery systems to treat inflammatory and infectious diseases. My overall objective in this project is to determine how artificial virus-like nanoparticles (AVNs) based drug delivery systems target and transport within a gut mucosal immunological model. My central hypothesis is that the mammalian orthoreovirus cell attachment protein σ1 (MRV σ1) functionalized polymeric AVNs will target delivery through induced M-cells to MALT cells in the intestinal epithelium ex vivo and in vivo. The rationale for the proposed research is that in- depth knowledge of the parameters determining recognition and transport of nanoparticles across the intestinal epithelia and guided vehicle of oral drug delivery in vivo will be gleaned. The harvested knowledge will further equip us to understand genetic changes of intestinal stem cells (ISCs) and MALT cells during reprogramming progression and offer new insights to develop orally available drug delivery strategies to treat inflammatory and infectious diseases. If it is successful, my strategy would be instrumental in developing precise and efficient methods and formulas for producing rationally designed oral drugs for clinical applications, thereby fundamentally advancing the fields of oral drug delivery.

NIH Research Projects · FY 2026 · 2022-07

The constant search for new chemical entities to address unmet medical needs compels the continued invention of new molecular editing approaches to derivatize complex small molecules. Single atom changes in a molecule alter the electronic properties of the molecule without extensive accompanying structural changes and are known to dramatically alter its biological activity. However, methods that enable substitutions of atoms embedded in the carbon framework of a molecule remain sparse. Substitution of a single atom – “atom swapping” – in the core structure of a molecule, rather than on the periphery, is challenging to execute because it involves multiple bond- breaking and bond-forming events. The conventional approach for introducing single atom changes in a molecule is thus to re-design synthesis routes to access atom-swapped derivatives. We challenge this long-standing practice by presenting a general strategy for atom swapping that proceeds in two stages – oxidation and transition metal-catalyzed carbon-extrusion reactions. The proposed research encompasses carbon-to-oxygen and carbon-to-nitrogen substitutions, and the conversion of lactones to lactams or cycloalkenes. The key step in all the proposed transformations is a transition metal-catalyzed decarbonylation or decarboxylation reaction. We will focus our efforts on the discovery and development of catalysts that promote decarbonylation and decarboxylation reactions on core motifs native to natural products and pharmaceuticals. These proposed reactions require that the catalyst be able to: 1) activate inert amide or ester bonds yet promote challenging carbon-heteroatom reductive eliminations; and 2) undergo site-selective oxidative addition. To identify catalysts that fulfil both criteria, we will examine ligand effects in each step of the catalytic cycle to enable rational ligand design and optimization. We will then interface the newly developed catalytic systems with well-documented C- H oxidation and rearrangement reactions to directly modify the carbon framework of cyclic natural products and pharmaceuticals. Realization of the goals of this proposal will circumvent tedious de novo synthesis for a single atom change and bring to fruition a highly desired transformation in the pharmaceutical industry.

NIH Research Projects · FY 2024 · 2022-06

PROJECT SUMMARY Antimicrobial resistance (AMR) is recognized as a significant threat to the health of animals, humans and plants, leading to calls to improve antimicrobial stewardship in all sectors. In order to assure the best utilization of limited resources, there is a critical need to identify the diseases and associated alternative strategies that, if implemented, would lead to the greatest impact on improving antimicrobial stewardship. This proposal seeks to address this critical gap with an approach that integrates evidence-based and decision-making methods such as scoping reviews, structured expert elicitations (informed in some cases by proprietary large- scale data and experience), and multi-criteria decision analysis (MCDA) across four livestock groups. This approach provides a comprehensive, systematic, and transparent framework to identify and prioritize the most important disease, and then the most promising alternative approaches to reduce the use of medically important antimicrobials in food animals, while maintaining animal health and wellbeing. The proposed project is significant in that, in contrast to the present situation, successful completion of the project will generate comprehensive and nuanced assessments of the disease drivers and recommendations on how to mitigate antimicrobial use in chickens, beef cattle, dairy cattle and swine. This integrated methodology, combined with application to four major food producing species, allows for a consistent and innovative approach to addressing the specific needs outlined by FDA in this PAR. This effort will be led by the National Institute of Antimicrobial Resistance Research and Education (NIAMRRE), a member organization that fosters cross-sector engagement to combat the challenges presented by AMR, in collaboration with RTI International, a nonprofit research institute with expertise in scoping reviews, expert elicitation, and multi-criteria decision analysis. NIAMRRE expertise includes investigators and subject matter experts from four major agricultural research universities with deep expertise in animal health and livestock production: University of California Davis (dairy cattle lead), The Ohio State University (beef cattle lead), the University of Georgia (broiler chicken lead), and Iowa State University (swine lead). Collectively, this team provides an outstanding environment for successful completion of the project. The outcome of this framework is that a consistent approach will be applied across four major livestock species, resulting in consistent communications of recommendations for strategies to reduce reliance on medically important antimicrobials.

NIH Research Projects · FY 2026 · 2022-02

Project Summary Due to the unique property of hematopoietic stem cells (HSCs) to reconstitute the entire blood system of the organism, these stem cells are utilized clinically to treat blood disorders. The possibility of culturing and expanding HSCs in vitro would make hematopoietic stem cell transplantation (HSCT)-based therapies more feasible. However, this has eluded the field for more than three decades, necessitating a closer examination of the native developmental mechanisms that govern the emergence of HSCs. Many years of investigation have revealed that HSCs require multiple molecular inputs for proper specification, including activity of the Notch, nitric oxide (NO), Wnt, FGF, and BMP signaling pathways. In addition, inflammatory signaling (Tnfa, NF-kB, Tlr4, interferons, Il1b and inflammasome) have been recently reported as a novel group of HSC fate modulators, yet the underlying molecular mechanisms are unclear. Addressing this knowledge gap will be critical to help develop in vitro protocols for the generation of patient-specific HSCs. The goal of this proposal is to reveal in vivo the inflammatory network that unlocks HSC specification from the hemogenic endothelium (HE), and its relationship with the Notch and nitric oxide pathways. To attain this goal, the following three specific aims will be pursued: (1) Identify the role of Nod1 signaling during HSC development; (2) determine the mechanism of NF-kB-directed HSC specification; and (3) analyze the impact of the NOD1/RIPK2/NF-kB inflammatory axis on human pluripotent stem cell-derived definitive hematopoietic progenitor cells. Since hematopoietic development is highly conserved between vertebrate species, the zebrafish model provides a unique opportunity to circumvent the challenges of in utero experimentation, permitting non-invasive experiments that avoid the artifactual inflammation caused by cellular stress. To achieve this application's goals, a combination of novel zebrafish reporter and mutant lines, new methods to perform epigenomic and transcriptomic profiling of the HE by CUT&RUN-sequencing and RNA-sequencing, live imaging of HSC development by confocal and light-sheet microscopy, qPCR, FACS-sorting, and lineage tracing using Cre- mediated reporter systems will be utilized. In addition, to translate these in vivo findings to human health, this proposal will be complemented with a model of hematopoietic differentiation from human pluripotent stem cells (hPSCs). Upon successful completion of the proposed research, a previously undescribed inflammatory pathway affecting HSC specification will be identified, in addition to the central molecular mechanism by which inflammatory signaling drives HSC fate and crosstalk to other main HSC inductors. These new findings could provide key insights needed to instruct HSC fate, informing in vitro approaches to generate HSCs from pluripotent precursors for the treatment of blood disorders.