Trustees Of Indiana University

NIH Research Projects · FY 2026 · 2017-08

PROJECT SUMMARY The fundamental view of bacterial cells is that they are not organized because they generally lack membrane-bound organelles. Despite the textbook perception that bacteria are disorganized, a growing array of non-membrane-bound organelles called “biomolecular condensates” have been identified. These condensates are formed through the physical process of liquid-liquid phase separation and have the capacity to selectively organize enzymes and substrates into distinct subcellular locations, suggesting bacterial cells may be highly organized. The Schrader lab identified the first bacterial condensate in the bacterium C. crescentus, termed the BR-body, which was found to organize the bacterial RNA decay machinery, facilitating its complex multi-step biochemical pathway. Bioinformatic signatures of BR-bodies have been identified across bacteria including many pathogens, suggesting they are broadly conserved. In addition, several bacterial biomolecular condensates have subsequently been identified that are involved in diverse biochemical pathways, suggesting that bacterial cells are generally organized by non-membrane-bound organelles, yet the number and diversity of such structures remains poorly characterized. By combining in vivo imaging experiments and in vitro biochemistry we seek to define the important aspects of biomolecular condensate function and diversity in bacteria. We believe that many of the characteristics of C. crescentus BR- bodies will be shared in pathogenic organisms, potentially leading to the identification of new antibiotic targets.

NIH Research Projects · FY 2026 · 2017-08

Inward-rectifier K+ (Kir) channels and G protein-coupled receptors (GPCRs) are membrane proteins that are regulated by cholesterol and anionic lipids found in their native membranes. We will use solid-state NMR (SSNMR) to study proteins with functional lipids in bilayer environments ranging from proteoliposomes to biological membranes. These measurements will compliment functional assays, fluorescence techniques, and molecular dynamics (MD) simulations under identical conditions. Kir channels are involved in long-QT syndrome, hypoglycemia, Bartter’s syndrome, epilepsy, substance abuse, and periodic paralysis. Kir Channels are ligand gated, but details of the structure and dynamics of gated channels are largely unknown. The Kir2 channel family is gated by the anionic lipid phosphatidylinositol 4,5-bisphosphate (PIP2) but inactivated by cholesterol which competes with PIP2 to access the protein. G protein-activated Kir channels (GIRK, Kir3) are gated by the coaction of PIP2 and Gbγ protein heterodimers. In the Kir3 family, cholesterol increases rather than suppresses activity. Here we will explore the differing roles of functional lipids and quantify the structure and dynamics of the observed active and inactivated states. We will continue our studies of the Kir channel, KirBac1.1. We assigned 90% of the 15N and 13C chemical shifts in this protein (over 1600 unique heavy atoms) and used these assignments to identify allostery, the activation mechanism, the inactivated structure bound to a cholesterol dimer, refined the structure of the closed state, and solved the structure of the open state of the channel. Now we will measure the channel dynamics and identify the multiple gated states of the channel reflected in our data. We will study structural changes in the channel under voltage and identify discrete channel states and lipid contacts using freeze-trapped Dynamic Nuclear Polarization. In tandem, we will also study the Kir3.1-KirBac1.3 channel chimera. Preliminary data identifies PIP2 binding residues and membrane-water interfacial residues key for channel function. The eventual goal will be the mammalian Kir3.2 (GIRK2) channel and its full complement of functional activators. In a second project we will study the CC motif chemokine receptor CCR3 with the CCL11 chemokine in lipid bilayers. No drug trial targeting CCR3 has succeeded, which is unfortunate as it is involved in cancer metastasis, HIV entry, and the COVID19 cytokine storm. To date, we identified both CCL11 docking, and signal transduction are dose dependent upon bilayer cholesterol. Preliminary SSNMR studies found cholesterol conformationally selects for optimal ligand binding configurations of the receptor. We plan to fully assign the 15N and 13C chemical shifts of CCR3 in cholesterol and anionic lipid enriched membranes. The structures of this protein with CCLL11 in different functional states will be solved, and regional dynamics measured following a similar workflow established for KirBac1.1. NMR will also be used to solve the structures of CCL11 in solution and in complex with CCR3. We will pursue cholesterol oligomerization, CCR3 dimerization, and the relationship between these events. Throughout we will examine lipid oligomerization, dynamics, and protein affinity.

NIH Research Projects · FY 2026 · 2017-02

SUMMARY: The discovery and refinement of brain-based signatures of autism spectrum disorder (ASD) has for many years been a highly desired, but as yet elusive, goal. One key challenge identified has been that numerous levels and sources of variability — between sites, between participants, and within participants — obscure the search for these reproducible neural signatures, complicating the search for biomarkers and undermining the elucidation of cognitive and neural mechanisms. In this renewal application we propose a sequence of studies to dissociate and quantify these sources of variability. We will acquire a new fMRI dataset that is partly continuous with data accrued during the prior funding period and has 3 key features. First, we will scan participants with ASD and matched controls while they watch complex videos with rich narrative content. Evoked responses to videos constrain variability within and across participants and data collection sites, as borne out by strong pilot data, and naturalistic videos better approximate the demands of processing complex real-world social situations. Second, we will use densely-sampled, longitudinally-acquired, high- quality neuroimaging data that will permit precise, stable, and reliable measurements of an individual's brain function. Third, we will collect primary data at two sites (Indiana University and Caltech) in order to ensure broader generalizability. Using machine learning techniques, Aim 1 will learn where in the brain and when, in response to the video, individuals with ASD diverge most from control participants. Extending beyond group- level averages, we will also take a dimensional approach to link brain differences to phenotypic variation, and a clustering approach to identify variation consistent with the presence of ASD subgroups. In Aim 2, we will leverage these results together with state-of-the-art computer vision and speech algorithms to quantify the stimulus features of the videos that evoke these neural differences, both at the level of the group and of the individual, and examine their relationship to phenotypic differences. Our comprehensive feature decomposition of the videos will query high-level semantic features, object-level features like faces, and low- level perceptual features. Finally Aim 3 will share the all the products of this work — e.g., raw and processed data, acquisition tools, annotations, analysis scripts — on OpenNeuro, NDA, and Github in modern formats (e.g., using BIDS format, and with fMRIprep and MRIQC as processing and quality assurance tools) to make them maximally accessible to others. Uniquely, this data release will be validated and refined at yet a third site, the University of Iowa, on a smaller sample of control participants. This renewal application will thus build upon tools, data, and progress from the current funding period, and capitalize on state-of-the-art computer vision and neuroimaging analysis methods to identify audiovisual stimulus features that evoke atypical neural activity in individuals with ASD. This project will provide new insight into neural and cognitive differences in ASD, and help guide future investigations toward neuroimaging-based markers.

NIH Research Projects · FY 2025 · 2016-08

Project Summary The Tennessen Lab uses the fruit fly, Drosophila melanogaster, as a model to understand how carbohydrate metabolism supports the biosynthetic and energetic demands of animal growth and development. Our ongoing studies focus on a metabolic program known as the Warburg effect (aerobic glycolysis). This metabolic program allows growing and proliferating cells to metabolize large quantities of glucose in order to generate biomass and synthesize pro-growth signaling molecules. While aerobic glycolysis is most commonly associated with tumors, where it promotes the growth and survival of cancer cells, healthy animal cells, such as stem cells and activated T cells, also use this metabolic program to drive biosynthesis and regulate cell fate decisions. Therefore, basic studies of aerobic glycolysis have the potential to not only identify metabolic mechanisms that could be targeted to inhibit tumor growth but also to reveal how healthy cells manipulate glycolytic metabolism as a means of supporting normal developmental growth. I have discovered that the fruit fly Drosophila melanogaster also uses aerobic glycolysis to promote growth and have established the fly as a model system for studying the genetic mechanisms that regulate this metabolic program. My initial efforts using this model have proven successful, as I have determined that the Drosophila Estrogen-Related Receptor (dERR) is a master regulator of aerobic glycolysis. My lab will now expand upon these initial observations to identify the molecular mechanisms that both activate and repress aerobic glycolysis in vivo. Furthermore, we have determined that Drosophila larvae use aerobic glycolysis to synthesize the oncometabolite L-2-hydroxyglutarate (L-2HG). This compound is almost exclusively studied in the context of cancer metabolism and endogenous L-2HG function remains largely unexplored. We will determine how L-2HG synthesis is controlled in vivo and explore how this oncometabolite controls normal animal growth. Finally, we will use a combination of genetics, genomics, and metabolomics to determine how the disruption of key reactions in aerobic glycolysis affects growth and physiology. Many of these enzymes represent potential therapuetic targets and our innovative approach provides a rare opportunity to systematically evaluate the effects of inhibiting individual glycolytic enzymes in a whole animal system. Moreover, our studies also explore the compensatory metabolic pathways that are activated in response to decreased glycolytic flux, which in a clinical setting, could render tumors insenstive to drug treatments. Finally, we have uncovered an unexpected correlation between the repression of aerobic glycolysis, increased levels of fatty acid oxidation, and pyrimidine metabolism. My lab will use this unexpected discovery as a foundation to explore the poorly understood role of fatty acid beta-oxidation in nucleotide production. Our studies will allow, for the first time, a genetic dissection of the mechanisms regulating aerobic glycolysis within the context of normal animal development and will potentially uncover novel approaches to control cellular growth at a metabolic level.

NIH Research Projects · FY 2025 · 2016-06

ABSTRACT Bacterial infectious disease is a global threat to human health and there is an urgent need to develop new antimicrobials that limit the impact of life-threatening pathogens. These pathogens include the major causative agents of nosocomial infections, e.g., Acinetobacter baumannii and Staphylococcus aureus, and a major respiratory pathogen, Streptococcus pneumoniae. In this renewal application, we seek continuation of our innovative, strongly integrated and topical research program positioned at an intersection of inorganic chemistry and microbial physiology, designed to tackle significant gaps in our knowledge in bacterial transition metal homeostasis (metallostasis) and hydrogen sulfide homeostasis. My group has long-standing interests in the transcriptional repressor proteins (metallosensors) and metallochaperones that allow a bacterium to respond to host efforts to restrict transition metal availability or induce metal toxicity. Our subsequent discovery of transcriptional regulators that “sense” downstream more oxidized forms of hydrogen sulfide, collectively termed reactive sulfur species (RSS), is foundational to our understanding of hydrogen sulfide signaling via protein persulfidation (S-sulfuration). Indeed, an emerging consensus holds that the biogenesis of hydrogen sulfide and RSS provides protection against host weapons reactive oxygen and reactive nitrogen species, and antibiotics, where they function as antioxidants and signaling molecules. Future research will be carried out in four general areas: 1) Investigating allostery in transcriptional regulation, where we extend our comprehensive physical description of metallosensors as dynamically-anchored “allosteric inorganic switches” to RSS sensors, using state-of-the-art methyl-specific NMR relaxation experiments and a novel mass spectrometry-based kinetic profiling method used to elucidate the broad principles of RSS specificity in diverse structural classes of regulators; 2) critically evaluate the RSS signaling hypothesis in A. baumannii, which posits that persulfidation is a regulatory modification, completely unexplored in bacteria; 3) deduce the global impact of host transition metal (zinc, iron) starvation (nutritional immunity) using complementary proteomics and metalloproteomics workflows to define changes in the metalloproteome while identifying metallochaperone targets, in A. baumannii; and 4) elucidate a poorly understood, infection-relevant iron-catecholate acquisition and detoxification pathway in S. pneumoniae. Our multidisciplinary approach, which seamlessly spans biophysical, bioinorganic and analytical chemistries to microbial physiology, will transform our understanding of foundational principles of pathogen metallostasis and hydrogen sulfide/RSS biogenesis in an effort to discover and characterize new players and biological processes that can be targeted by novel antibacterial strategies.

NIH Research Projects · FY 2025 · 2016-03

Summary The capsid of the Hepatitis B Virus (HBV) is a 120-homodimer T=4 icosahedron. In vivo, it self-assembles, packages viral RNA, serves as a metabolic compartment for DNA synthesis, and trafficks within the cell. Its assembly and disassembly have become targets for potent antivirals. In the previous funding period, we characterized assembly and disassembly with purified protein using structural, single molecule, and bulk studies of assembly products and reactions. We characterized the allosteric transitions that activated assembly, demonstrated the importance of reversibility during self-association for fidelity, and identified roles of nucleation for directing the assembly path. In this proposal, we develop hypotheses to take advantage of these results to engineer virus-like particles with programmable assembly, cargo packaging, delivery, and release. In preliminary studies, we developed a method for targeting cargo to a capsid by linking the cargo to a small molecule that binds capsid with high affinity, essentially using an antiviral as a targeting device. This method can be applied to any cargo. In some cases, it is desirable to display cargo on the capsid exterior, in other cases it is desirable to package it within the capsid. In preliminary data, we demonstrate an approach to making “holey” capsids that expose the particle interior and can be re-sealed to enclose the contents. Using this same technology, we can make patches on the capsid surface; this can be used for displaying patches of receptor-binding ligands or cell-penetrating peptides. Cargo, packaged within a capsid, is not deliverable unless it can be released. In preliminary data, we developed techniques for triggering capsid disassembly in response to redox potential, taking advantage of chemically-induced metastability. This same approach can be applied to other triggering signals. The ultimate goal of these studies is to combine the approaches to a practical end: we propose to build two model biotech reagents, one to measure antibody levels and the other to deliver packaged cargo to specific cells. These approaches are each built on an understanding of the biochemistry and biophysics of HBV capsid assembly. HBV is one the smallest human pathogens. It is remarkably efficient at packaging its genome and delivering it to target cells. Based on our understanding of capsid assembly and capsid biophysics, we will develop approaches to specifically packaging cargo molecules and delivering these reagents intracellularly. The tools arising from this research will provide a means for man to take advantage of HBV.

NIH Research Projects · FY 2025 · 2015-08

Project Summary/Abstract This unique program leverages two developments in medicine and clinical science to enhance the predoctoral training of psychological and brain scientists to make breakthroughs in understanding, preventing, and treating psychopathology. One development, the NIH initiative to foster clinical translational science (CTS), is motivated by the unmet critical need to move clinically relevant scientific discoveries along the translational pipeline—from basic science to controlled research with clinical populations to dissemination and implementation—to make a substantive public mental-health impact. A second development, the NIMH Research Domain Criteria (RDoC) initiative, is motivated by the critical need to develop multi-dimensional, multi-unit-of-analysis approaches to understanding psychopathology. Advances in clinical psychological science will come from a new generation of investigators with expertise at the intersection of these two NIH-driven developments. The goal of this training program is to maximize the likelihood of producing independent clinical research scientists and leaders with expertise in cutting-edge translational research designs, frameworks, and methodologies that will usher in breakthroughs in the identification of mental-illness mechanisms, prevention, and treatment. To our knowledge, this program is one-of-a-kind in the nation and the success of our prior trainees supports its core values and impact. Following continued success in the previous training period (years 5–9), federal funds are requested to continue supporting six predoctoral trainees per year, complemented by two institutionally supported trainees, for up to two years. Training opportunities focus on four basic aims for each trainee: (1) to gain exposure to foundational concepts, theories, and methodologies, as well as exemplars of both CTS and multiple units of analysis informed by the RDoC; (2) to apply this integrated framework to research addressing a public-health issue; (3) to learn to foster collaborative opportunities that stretch the boundaries of research both along the CTS continuum and across multiple units of analysis; and (4) to develop professionally to continue this line of research as an independent clinical scientist. Trainees begin their intensive training by identifying a public-health issue on which to focus their research efforts. These aims are then realized through (a) structured research activities under the dual mentorship of a primary and a “stretch” mentor (designed to extend the research either along the CTS continuum or across units of analysis); (b) dual research mentoring of the trainee leading to submission of a research proposal (e.g., an F31 NRSA application); (c) peer, advanced trainee, and expert guidance and feedback on their research through a year-long seminar; (d) tailored doctoral qualifying examinations; (e) coursework and advanced seminars focused on addressing mental-health issues within the CTS and RDoC frameworks; (f) workshops in professional development, responsible conduct of research, and grant writing; and (g) colloquia and conferences to offer networking and collaborative opportunities. Trainees work with their dual mentors to design an individualized program of study in combination with the activities listed above.

NIH Research Projects · FY 2025 · 2014-09

PROJECT SUMMARY / ABSTRACT The high and increasing prevalence as well as the staggering social and financial costs of Alzheimer’s Disease (AD) and AD-related dementia (ADRD) emphasize the importance of finding strategies to prevent or slow their progression. Here we aim to elucidate the basic biology of neuronal maintenance and energy homeostasis to enable us to design new therapeutic strategies independent of tau or beta-amyloid theories. Almost all neurons are born early in life and require an active neuroprotection program for their survival in response to the myriad of internal and external challenges they face throughout life. NMNAT2 is a bifunctional protein that we and others have identified as an important neuronal maintenance factor. NMNAT2 synthesizes nicotinamide mononucleotide (NAD+) and serves as a molecular chaperone for day-to-day axonal function and to protect neurons from proteinopathies such as hyperphosphorylated tau. In AD patients, NMNAT2 abundance is greatly reduced to less than 50% of normal level and its level correlates with cognitive function. We found that deleting NMNAT2 from mouse cortical glutamatergic neurons results in AD/ADRD-like phenotypes, such as glucose hypometabolism, axonopathy and neuroinflammation. The current mouse and human results strongly support a causal relationship between NMNAT2 hypofunction and neurodegeneration. Axonal degeneration is a key step in AD/ADRD and many neurodegenerative diseases. Axonal transport plays critical roles in neuronal function and survival and is extremely energy demanding. Abnormal axonal transport is an early defect in axons destined to degenerate. Increasing evidence reveals dysregulated glucose metabolism in AD. Our preliminary studies suggest that NMNAT2 plays a critical role in fast axonal transport by maintaining axonal energy homeostasis. Deleting NMNAT2 in glutamatergic neurons reduces glycolysis while at the same time augmenting the pentose phosphate. These findings raise the following questions: Does NMNAT2 in glutamatergic neurons play essential roles in maintaining energy homeostasis for normal axonal function? Does glucose hypometabolism caused by loss of NMNAT2 cause axonopathy? Will supplement strategies bypassing NMNAT2 support neurons and attenuate axonopathy? To answer these questions, we propose the following aims: 1. Test the hypothesis that NMNAT2 is required in cortical neurons for axonal transport. 2. Test the hypothesis that NMNAT2 contributes to axonal energy homeostasis. 3. Test the hypothesis that NMNAT2 in cortical neurons is essential for glucose metabolism The knowledge gained from our proposed studies will help us gain mechanistic understanding into how NMNAT2 contributes to active neuronal maintenance and will provide necessary insights to assist in drug discovery using NMNAT2 as a therapeutic target for neurodegeneration.

NIH Research Projects · FY 2025 · 2014-08

The Bloomington Drosophila Stock Center (BDSC) supports a large, worldwide community of scientists using the insect Drosophila melanogaster as a model organism for biomedical experimentation. The goals of the BDSC are to provide a collection of documented living stocks of broad value to current research, to preserve documented strains with clear future value, and to provide information and support services that promote maximal exploitation of these materials. These goals facilitate research by providing universal and rapid access to the most generally useful stocks by preserving specialty genotypes with exceptional characteristics, and by providing information that helps researchers identify stocks appropriate to their needs. The genetic technologies available to Drosophila researchers are among the most sophisticated in any multicellular organism; consequently, Drosophila is used extensively in studies of biological processes relevant to human health and investigations of molecular mechanisms underlying disease. As the most comprehensive source of stocks for genetic experimentation with Drosophila, the BDSC is central to the success of thousands of research projects and hundreds of NIH grants yearly. The first specific aim of this proposal is to continue acquiring, maintaining and distributing Drosophila strains while simultaneously eliminating obsolete stocks. The work will preserve federal investments in genetic resource development by maintaining stocks securely using regimented practices. It aims to maximize the rigor and reproducibility of genetic studies by encouraging stock reuse. The second specific aim is to continue developing robust and transparent information resources to meet the operational needs of the facility and the research needs of Drosophila scientists while maintaining and promoting excellent user support. The third specific aim is to undertake research to increase the utility of one of the largest subsets of BDSC stocks, the split-GAL stocks, which were developed to characterize neurons in the brain. Split-GAL4 transgenes are used to force expression of other transgenes in cell-specific patterns, allowing investigators to manipulate cell characteristics experimentally in otherwise normal individuals. The research proposed here aims to characterize the expression of split-GAL4 transgenes outside the brain to benefit the analysis of diverse cell types and to help distinguish the physiological effects of gene expression in the brain versus other tissues in split-GAL4 studies. Key to all three aims is the administration and advancement of the existing, highly successful cost recovery program that finances most operational expenses from user fees. Consequently, the proposal focuses on support and development of the core management team as the most effective way to leverage the investment of federal funds.

NIH Research Projects · FY 2026 · 2014-08

Mammalian orthoreovirus (MRV) genomic RNA is detected by host cells to induce an innate immune response. Detection of MRV RNA also contributes to the induction of cell death. Because viral genomic RNA remains contained within particles throughout infection, how the RNA becomes exposed and accumulates to the level that induces a host response remains unknown. In this proposal, we will uncover how viral RNA becomes detectable by the host cell. In Aim 1 of this proposal, we will build on the data that specific endosomal uptake pathways, endosomal protease activity, and endosomal maturation are required for exposure of viral genomic RNA from incoming particles. We will identify how these endosomal properties influence genomic RNA exposure. We will also determine how viral determinants control exposure and transport of viral genomic dsRNA for detection by cytoplasmic sensors. In Aim 2, we will determine how the assembly of the viral µ1 capsid protein on progeny cores blocks excessive accumulation of viral RNA. We will perform biochemical and virological experiments to identify structure-function relationships in µ1 that mediate these effects. We will also define the structural basis of µ1-mediated shut down of viral RNA transcription by solving the structure of a MRV assembly intermediates. In Aim 3 of the proposal, we will follow up on our preliminary data indicating that cellular RNA transporter SIDT2 controls MRV RNA levels. We will define whether the RNautophagy function of SIDT2 governs its antiviral effect and determine whether viral RNA turnover is influenced by RNautophagy. Finally, we will define how RNAs are specifically recognized by the RNautophagy machinery. Completion of this work will reveal viral and cellular factors that control the detection of MRV and other related dsRNA viruses by host cells.

NIH Research Projects · FY 2025 · 2012-12

Abstract Circadian clocks orchestrate endogenous daily rhythms in physiology, metabolism, and behavior that must be adjusted (i.e., entrained) to environmental cycles to maintain properly timed outputs. Post- industrial environments have significantly reduced the reliability of the time cues that the circadian system relies upon for entrainment and this has had widespread and negative consequences for human health. Understanding the network properties of circadian timekeeping in the brain and the ways in which time cues impinge upon it is required if we are to address the adverse effects of circadian misalignment and dysfunction. The complexity of the brain’s clock center is a significant barrier to our understanding of the daily adjustment of the circadian system. Work in relatively “simple” clock neuron networks can therefore enrich and inform our understanding of circadian timekeeping and entrainment in the mammalian brain. The goal of this competing renewal application is to continue a productive and impactful research program on the network properties of circadian timekeeping and entrainment in Drosophila melanogaster, which, despite its relative simplicity, shares molecular, anatomical, and physiological features that are remarkably similar to those of mammalian clock networks. Within the fly’s clock neuron network, we will determine how endogenous circadian timekeeping is supported by the network structure of the of the brain’s clock center and how specific neural pathways and neurotransmitters mediate entrainment to environmental cycles. The goals of our three specific aims are to elucidate: 1) the nature and timekeeping functions of the synaptic and modulatory connections of the circadian clock neuron network, 2.) how the CCNN integrates light input to entrain circadian rhythms, and 3) how neurons that do not themselves express molecular clocks participate in the clock neuron network to support endogenous timekeeping. The unifying goal of this research program is to advance our understanding of circadian timekeeping and entrainment in the brain. The results of this work will inform future interventions for the alleviation of the adverse health effects of circadian dysfunction in post-industrial environments.

NIH Research Projects · FY 2025 · 2011-07

The American Society for Virology (ASV) seeks renewal of a multi-year block grant to provide partial support for predoctoral students, postdoctoral fellows, and U.S. teachers of undergraduate virology to travel to and participate in the annual ASV scientific meetings in 2021-2025. The ASV 2021 meeting will be held July 17-21 at the Palais des Congrès de Montréal, Quebec, Canada, in conjunction with local hosts from McGill University; the subsequent 4 meetings will be held at US venues. Travel awards are awarded with emphasis on participation by women and underrepresented minority virologists, with the goal of benefiting future virology research. Pre- and postdoctoral awards will be $500 each, and teacher awards $1,000 each, for a total of $14,000 per year. Members of the ASV Travel Award Committee will evaluate the applications. Pre- and postdoctoral awardees are selected based on an abstract of their work for presentation in workshops or poster sessions. Teachers are selected based on an essay explaining the benefit of ASV meeting attendance to their teaching (and research, if applicable). In addition to announcing the travel award program to its members, ASV promotes it to ~100 U.S. undergraduate institutions serving primarily underrepresented populations. Post- meeting evaluations are required of awardees and obtained anonymously, focusing on how they benefited from participation. The ASV meeting provides an opportunity for U.S. junior scientists to meet and interact directly with senior virologists in symposia, workshops, poster sessions, and special satellite symposia covering the most recent developments in virus research. These include studies of viruses of humans, animals, plants, invertebrates and prokaryotes, and the scope spans topics such as virus genetics, replication, structure, pathogenesis, ecology, evolution and emergence, disease control, virus-host interactions, and new technologies. The ASV is the largest general virology meeting in North America, enhancing opportunities for cross-fertilization of ideas and technologies across the entirety of the virus world. In addition to scientific sessions, over the last 10 years the meeting has included opportunities for trainees and teachers of undergraduate students to network with and receive mentoring from virologists with experience in academia in both research and primarily undergraduate institutions, industry, government research, publishing, clinical virology, and other scientific careers through career, education, and communication workshops and lunch discussion tables with senior scientists. The ASV annual meeting positively impacts U.S. efforts in public health and research needed to effectively combat viral diseases. The ASV has actively and successfully increased the diversity of speakers and participants, and it has a strong ethos of promoting the development of the next generation of virologists through ample opportunities to actively present their research and participate in ASV. Travel awards to trainees and teachers of undergraduate students are the foundation of this mission of ASV. .

NIH Research Projects · FY 2025 · 2011-03

Flaviviruses, including dengue, West Nile and Zika viruses, pose significant threats as emerging diseases and potential bioterror agents. Despite the considerable impact of flavivirus infection on world-wide health, no antiviral therapies are available and existing flavivirus vaccines are of limited utility. Our long-term goal is to obtain detailed structural and biochemical information regarding the flavivirus replication process and to use this information for the development of antiviral therapeutics and vaccines. The flavivirus replication complex, consisting of virally-encoded non-structural proteins (NS), unidentified cellular proteins, and the viral RNA genome, is responsible for copying the viral genome. Viral replication begins with negative-strand synthesis from the positive-strand RNA genome, leading to dsRNA formation, which in turn is transcribed into positive- strand RNA. Because the positive-sense RNA genome is used for both viral translation and replication, flavivirus must be able to regulate whether the genome is used either as a transcript for viral protein synthesis or as a template for RNA synthesis. This decision tree depends on a reorganization of the genome from a linear to a circular form, which promotes RNA synthesis. Viral polymerase NS5 then recognizes an RNA promoter at the 5’-end of the circularized genome, called stem-loop A (SLA), and translocates to the 3’ terminus to initiate RNA synthesis. However, the mechanism by which NS5 selectively recognizes the circular genome for negative- strand RNA synthesis is not well understood. In particular, the viral genome has differently predicted 3’ terminal stem-loop (3’SL) structures in the linear and circular genome, yet how these differences relate to negative strand synthesis is not known. The goal of this project is thus to understand the molecular mechanism of negative- strand RNA synthesis. In aim 1, we will determine how the structural changes of 3’SL in the linear and circular forms of the viral genome modulate NS5 interaction and polymerase activity, and whether NS5 recognizes both 5’ SLA and 3’SL structures simultaneously. In aim 2, we will determine the structures of 3’SL in the linear and circular genomes using a tRNA-scaffold approach, and also characterize the NS5 initiation complex assembled on dengue virus mini-genome. The change from linear to circular genome is conserved in all flaviviruses. Thus, the combined structural, biochemical, and virological studies will help elucidate the mechanism for negative- strand RNA synthesis in flavivirus.

NIH Research Projects · FY 2025 · 2008-07

Abstract This proposal requests support for the third renewal of a highly successful, integrative pre-doctoral training program in the neuroscience of substance use disorder at Indiana University Bloomington. Despite substantial advances in understanding drug addiction within specific levels of analysis (e.g., behavioral, clinical, and molecular), the problem of substance use disorder will not be solved by focusing on a single level of analysis. If the next generation of researchers is to make meaningful progress, they must be well-rounded scientists with an appreciation that addiction is a multi-faceted problem, while possessing the flexibility to respond to and incorporate rapidly evolving technologies that will enable them to understand mechanisms and develop and implement treatments for substance use disorders. To prepare trainees for success in the next decade and beyond, our program emphasizes a team-driven, inter-disciplinary approach based on the translational model. Our program is successful because it brings together 17 core faculty members who are committed to integrative training and have a long history of collaboration on questions integral to substance use disorder research. They include senior and junior investigators, molecular neurobiologists, cognitive neuroscientists, clinical scientists, epidemiologists, and implementation scientists. They come from several departments in the College of Arts and Sciences and the School of Public Health, and most have joint appointments in the campus-wide Program in Neuroscience. Working together in state-of-the-art facilities, this group has access to a pool of highly talented trainees motivated to pursue careers in substance use disorder research. Our training program develops trainees by emphasizing three key components: integrative course work, translational research training, and professional skills development. Course work covers basic neuro- and psychopharmacology, provides an integrative view of biobehavioral processes in substance use disorders, and trains students in principles of dissemination and implementation science, ultimately delivering a translational perspective to theoretical and empirical knowledge. Research is guided by a mentor prioritizing one discipline (e.g., molecular/systems/cognitive/clinical neuroscience, clinical science, public health science), closely integrated with a co-mentor representing a complementary level of analysis. This integrative approach is reinforced through discussion groups, attendance at colloquia, and participation at national meetings. Instruction in ethical scientific behavior includes formal course work and campus workshops as well as specialized training led by a core faculty member who has many years of experience providing instruction in ethical issues unique to substance use research. Trainees also develop skills in grant writing, manuscript preparation, teaching, and community outreach. In short, our program combines and incorporates course work and research training aimed at integrating and translating bench, bedside, and community approaches to produce scientists well prepared for productive and transformative careers in substance use disorder research.

NIH Research Projects · FY 2025 · 2007-09

Project Summary/Abstract Human vision starts when photoreceptors collect and respond to light. Normal photoreceptor function is essential for normal vision, yet techniques to assess these processes in vivo are limited. New optical modalities that are rapid, specific, and non‐invasive promise to greatly expand our capability to monitor more accurately and completely photoreceptors. This study takes advantage of unique adaptive‐optics OCT instrumentation developed in my laboratory in conjunction with custom algorithms for sub‐cellular image registration and phase‐sensitive detection to measure anatomical and physiological properties of individual photoreceptors. We will use this technique to investigate three specific aims that quantify the spectral sensitivity profiles of photoreceptors, the expression of photoreceptor spectral types in color vision deficiencies, and the temporal dynamics of photoreceptor loss in retinitis pigmentosa patients. The long term goal of this research is to establish high resolution, high specificity optical techniques as valid tools for probing structure and physiologic processes of the retina at the cellular scale. The resulting ability to study cells in vivo will improve early detection of and treatment monitoring for diseases that impact the retina.

NIH Research Projects · FY 2026 · 2005-05

Project Summary This proposal requests a third renewal of a highly successful T32 Institutional National Research Service Award to Indiana University, entitled “Common Themes in Reproductive Diversity” (CTRD). The award will support broadly integrative training in the areas of sexual reproduction and development. Training will focus on behavior in both humans and other animals and will address key questions in three related themes: (1) Developmental contributions to reproductive behavior, (2) Origins and expression of differences among the sexes, and (3) Interactions between sex, health, and disease. Indiana University's excellent support for research and its globally recognized strengths in animal behavior, endocrinology, human sexual health, and evolution of development will ensure high quality training. The 21 Training Faculty and 6 Affiliated Resource Faculty are drawn from 3 schools (Medical, Public Health, College of Arts and Sciences, including Ph.D. granting departments in the College (e.g., Anthropology, Biology, Gender Studies, Psychological and Brain Sciences) and 3 additional degree-granting programs (Medical Sciences, Neuroscience, and Cognitive Science). They are also associated with 1 or more of 5 research centers, most importantly the Center for the Integrative Study of Animal Behavior (CISAB), the Kinsey Institute for Research on Sex, Gender and Reproduction, and the Center for Genomics and Bioinformatics. Support is requested for five years to enable training of 4 predoctoral and 2 postdoctoral students each year to be drawn from a deep pool of talented applicants. In addition to course work in the fundamentals and intensive research training, trainees will participate in (1) a research-based course focused on Concepts in Reproductive Diversity, (2) an interdisciplinary, hands-on methods course, Techniques in Reproductive Diversity, a 3) a Research Ethics course, and 4) a Professional development course all co-taught by the training faculty and enhanced by invited distinguished visiting scientists. Active participation in a monthly breakfast research forum and other opportunities will allow trainees to accomplish important professional training including creating individual development plans (IDPs), preparing for more than one career outcome, and enhancing the reproducibility and transparency of their research. Trainees will also organize and present research at a highly successful and broadly attended CISAB conference. Predoctoral trainees will be drawn from the most highly qualified applicants to the degree-granting programs of the Training Faculty. Postdoctoral trainees will be recruited nationally, will be chosen based on their accomplishments and the potential for CTRD training to broaden their skills and perspectives, and will be expected to foster research collaboration among CTRD trainees and laboratories.

NIH Research Projects · FY 2025 · 2003-07

Project Summary/Abstract: Postnatal development of the human visual system is dependent on visual experience. Abnormal visual experience during infancy and childhood can lead to strabismic misalignment of the eyes and amblyopia. The goal of the proposed research is to understand how the visual system uses its available natural experience to coordinate eye alignment and focus during infancy and early childhood, in the context of prevention of these clinical conditions. There are two interrelated projects: i) To understand how depth information across the visual field can be used to coordinate eye alignment and focus during early postnatal development, and how common clinical disorders during early childhood can disrupt that coordination. ii) To understand which image structure across the visual field is capable of driving a conjugate orienting eye movement during early postnatal development, and how the binocular aspects of that movement can be disrupted by common clinical disorders. These projects will test hypotheses and build models to determine the amounts of conditions such as anisometropia that can disrupt ocular motor control as a function of human postnatal age. Previous studies of the development of focusing accommodation responses and aligning vergence responses have concentrated on 2D stimuli in the central visual field, while the brain needs to function in the full field, dynamic, three-dimensional natural environment in order for a patient to develop typical vision. It is the interaction between this visual environment and the quality of retinal visual experience that motor control can provide that defines a patient’s experience-dependent development. The results will provide i) evidence-based clinical guidelines for the prevention of amblyopia and strabismus ii) constraints for biologically-inspired simulations of the development of vision.

NIH Research Projects · FY 2026 · 2002-04

Project Summary: The Drosophila Genomics Resource Center (DGRC) supports the international community of scientists utilizing Drosophila melanogaster for biomedical research. The mission of the DGRC is to 1) provide broad access to genomics resources by acquiring, authenticating, archiving, curating, and distributing genomics resources including clones, vectors, and cell lines; 2) facilitate effective use of these genomics resources by providing guidance and support; and 3) improve the genomics resources and protocols available for Drosophila research. By preserving vital research materials and distributing them efficiently, the DGRC assures economical access to important research reagents, and enhances scientific rigor and reproducibility. The first aim of this proposal is to continue to strengthen the successful DGRC programs by: A) Continue to acquire, archive, curate, and distribute Drosophila resources including clones, vectors, and cell lines for supporting fundamental research of biological processes and modeling of aspects of human disease. B) Pilot a program with Indiana University Clinical and Translational Science Institute (CTSI) to promote Drosophila genomics reagents for use in non-Drosophila labs; C) Manage the cost recovery program and resource center to maximize the long-term viability of the DGRC and the benefits to its users and the NIH. The second aim is to improve and update our curation process, data management systems and web interface, and incorporate FAIR and TRUST guiding principles into our reagents, metadata and linking data to other repositories. The goal is to maximize the long-term viability of the DGRC and its benefits to users and the NIH. The third aim is to increase the utility of Drosophila as a model system by generating new resources and protocols through four projects: A) Increase the authentication, and reproducibility and quality control of DGRC reagents; B) Generate gut derived cell lines and pilot and expand to generate a neuroblast derived cell line; C) Continue to expand the catalog of recombination mediated cassette exchange compatible stable attP Drosophila cell lines; D) Collaborate to develop metabolic sensors and standards for aerobic glycolysis and other biosynthetic pathways.

NIH Research Projects · FY 2025 · 1995-07

Project Summary (Abstract) This is a basic science training grant focused on an integrative understanding of post-natal human behavioral development. The rationale for the focus on integrative training is that effective translation requires more than merely rapid movement of single-variable basic science findings to efficacy studies, but a different basic science, one that embraces complex causal pathways of development, and considers processes at nested time scales and multiple levels of analysis. The training program focuses on behavioral development (and relations to brain development) because advancing research shows that post-natal behavior and the experiences generated by that behavior modulates both structural and functional connectivity in the brain, tunes specialized neural systems and influences gene expression, with atypical patterns of early behavior and experiences determining the quality and opportunities of whole lifetimes. The trainees are 5 predoctoral candidates in psychology and in two joint PhD programs in psychology and neuroscience and in psychology and cognitive science and 3 post-doctoral fellows from various fields interested in developmental process. The training program for pre- doctoral trainees is 5 years (with 2 years supported by the training grant and 3 years by the department of Psychological and Brain sciences); the training program for post-doctoral trainees is typically 2 years. All trainees are required to submit at least one grant (foundation, F31, F32, or NSF) while affiliated with the program. The training program emphasizes the use of cross- levels methods to study the same problem, basic science that can link to translation, the collection and analysis of large data sets, open data and data sharing, and the ethical conduct of research.