Grants

NINDS - National Institute of Neurological Disorders and Stroke

ABSTRACT. Fetal development remains one of the final frontiers in medical science. It is an exceptionally brief period during which rapid, precise biological processes must unfold to ensure a successful transition to life outside the womb and normal function after birth. In the fetal period, human neural precursors generate a vast number of neurons and glia in a highly regulated manner to form the intricate, gyrencephalic brain providing the extraordinary computational power. The pre- and perinatal periods are recognized as critical windows for our neurological and behavioral development, representing both a significant risk and an opportunity for intervention. Unraveling the developmental mechanisms of the fetal brain thus has far-reaching implications, extending beyond prenatal and neurodevelopmental disorders to conditions related to aging. Despite recent advances in understanding the diversity of neural precursors and their genetic regulation, most research has been conducted in the lissencephalic mouse model. Emerging evidence from gyrencephalic species suggests that neural precursor types and their developmental mechanisms are differently tuned in species with larger, more complex brains. Notably, cortical gyrification appears to result from the coordinated actions of multiple factors interacting at different levels. Studies in mouse, ferret, macaque, and human brains have shown that key events underlying this process include region-specific neurogenesis in the ventricular and subventricular zones (VZ/SVZ) and the tangential dispersion of radial glial cells. We thus hypothesize that the spatiotemporal modulation of specific neural precursors in the VZ/SVZ plays critical role in the formation of a convoluted cortical structure. While single- cell transcriptomic data from species with complex brains, such as ferret and non-human primates, have provided insights into gene expression patterns, prenatal in vivo confirmation of these findings is challenging due to limitations in existing models. To address these challenges, we will establish a new fetal model, the Göttingen minipig, to study the prenatal mechanisms of gyrencephalic neocortical development - one of the key unresolved questions in neuroscience. Pigs provide a powerful model for studying complex brain development. The cytoarchitecture of the porcine VZ/SVZ closely mirrors that of humans, and our recent single-cell sequencing has identified unique cell populations in the piglet SVZ that are also present in humans but absent in rodents. Notably, for the first time, we have successfully established an in utero electroporation technique in fetal minipigs, allowing us to genetically label VZ/SVZ precursors with specific plasmid probes. By leveraging this unique model in combination with modern genetic and cellular imaging techniques, we will characterize germinal regions and identify and test key cellular/molecular events that contribute to the construction of a gyrencephalic neocortex. This study will provide the first direct evidence linking the modulation of specific neural precursors to structural changes in the fetal gyrencephalic neocortex. Such insights will be transformative not only for understanding cortical formation but also for improving outcomes in a wide range of neurodevelopmental disorders.

Up to $647K

2031-05-31

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Decoding Neuron Nuclear Condensation in Differentiation: Imaging & Molecular Insights

NINDS - National Institute of Neurological Disorders and Stroke

Project Summary This project addresses the critical role of neuronal differentiation in brain development, focusing on the interplay between chromatin remodeling, gene expression, and nuclear organization. Errors in these processes can lead to severe neurological disorders, underscoring the importance of our research. Despite advances, the dynamic understanding of chromatin states in living cells remains limited, partly due to the static nature of current molecular biology methods and challenges in studying rare neuron types. We focus on how cerebellar granule neurons (CGNs) integrate nuclear changes during differentiation, highlighted by our discovery that CGNs condense their nuclei within four hours of differentiation. This project employs a tripartite strategy: innovative cMAP epigenetic imaging probes for observing chromatin in living CGNs, unbiased proteomics for identifying chromatin-modifying complexes in early differentiation stages, and cutting-edge microscopy to study CGN nuclear organization with unprecedented temporal and spatial resolution. Aim 1 utilizes cMAP probes to visualize and manipulate chromatin reorganization in GNP differentiation, overcoming the limitations of reductionist methods. This approach will provide a dynamic model of chromatin dynamics in neuronal differentiation, enhancing our understanding of nuclear condensation. Aim 2 defines the molecular pathways promoting CGN nuclear condensation and chromatin compaction. By investigating Histone H1 and the ISWI complex's roles, we aim to uncover the regulatory mechanisms behind chromatin reorganization during CGN differentiation. This research promises to revolutionize our understanding of nuclear organization in neuronal differentiation, with implications for neurological disorder therapeutics. By integrating innovative technologies and methodologies, this project aims to provide new insights into the causes of neuronal lamination disorders and pediatric cancer mechanisms, potentially leading to novel therapeutic strategies.

Up to $690K

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Decoding of inter-organelle phospholipid transport by fluxome profiling

NIGMS - National Institute of General Medical Sciences

Project Summary/Abstract Cells continuously synthesize, degrade, and redistribute phospholipids. While vesicular trafficking was once considered the mechanism of this redistribution, recent studies have highlighted the critical roles of lipid transfer proteins (LTPs) in various contexts. For example, large quantities of phospholipids must be supplied to repair damaged lysosomal membranes or to form autophagosomes during starvation. However, it remains unclear why cells expend substantial energy to transport phospholipids even under normal physiological conditions. A major barrier to addressing this question has been the lack of methods to directly and comprehensively measure phospholipid transport in vivo without introducing bulky tags that perturb native lipid behavior. To circumvent this challenge, Aim 1 will establish a method to comprehensively profile inter-organelle phospholipid transport, referred to here as a “fluxome profile,” starting with phosphatidylcholine (PC). Using phospholipase D (PLD), I will perform organelle-specific pulse labeling by converting PC into deuterated PC (d- PC). After a chase period, d-PC distribution will be measured by stimulated Raman scattering (SRS) imaging, which detects vibrational modes of subcellular chemical bonds as well as the carbon–deuterium bond. This minimally perturbative label enables the observation of natural PC transport under physiological conditions. In parallel, I will create a “lipoprint map” by reclassifying organelles based on lipid-derived SRS spectral fingerprints. By projecting d-PC pulse-chase data from various organelles onto this map, I will obtain the fluxome profile, a comprehensive landscape of inter-organelle relationships defined by lipid composition and transport dynamics. In Aim 2, I will extend this strategy to other phospholipid classes by engineering PLD to alter its substrate specificity. This will involve three approaches: (i) an in vivo strategy that converts cellular PLD activities toward two different substrates into spectrally separated fluorescent signals for high-throughput screening; (ii) an in vitro method to pulldown PLD by phospholipids to enrich PLD sequences with desired substrate specificity; and (iii) an in silico deep learning model that predicts PLD activity for virtual screening. These approaches will enable selective deuterium labeling of major phospholipid classes and allow construction of fluxome profiles beyond PC. In Aim 3, I will first establish a method for the absolute quantification of organelle phospholipids. These data will enable quantitative comparison of phospholipid transport when different organelles serve as the pulse- labeling origin, providing the basis for a quantitative network model of inter-organelle phospholipid transport. I will then assess the structural robustness of this network model and experimentally validate it through LTP overexpression or knockout and engineered PLD-based perturbations. These analyses will test the hypothesis that the lipid transport network alone is a sufficient and efficient mechanism for maintaining organelle phospholipid compositions, uncovering fundamental design principles by which cells preserve membrane homeostasis under normal physiological conditions.

Up to $125K

2028-04-30

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the epigenetic networks that orchestrate endometrial function

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

PROJECT SUMMARY Infertility and subfertility are pervasive problems in women worldwide, with approximately half of conceptions ending in early pregnancy loss. Recurrent implantation failure (RIF) remains a major clinical barrier in women undergoing assisted reproductive technologies, even in women of reproductive age with high quality embryos. Among those who achieve pregnancy, recurrent pregnancy loss (RPL) poses an additional challenge. These failures underscore the critical importance of the uterine environment, particularly the endometrium, in mediating successful implantation and pregnancy maintenance. However, the molecular mechanisms underlying uterine dysfunction in RIF, RPL, and related disorders remain poorly understood. Emerging evidences suggest that epigenetic mechanisms—including DNA methylation, histone modification, and non-coding RNAs—play essential roles in orchestrating transcriptional networks that regulate uterine function during pregnancy (e.g., implantation and decidualization) and disease (e.g., endometriosis and endometrial cancer). This proposal focuses on Ten-Eleven Translocation (TET) family proteins—TET1, TET2, and TET3—which mediate active DNA demethylation by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Beyond their catalytic activity, TET proteins also interact with transcription factors (e.g., WT1) and epigenetic modifiers (e.g., SIN3A), suggesting additional regulatory roles. TET expression in both human and mouse endometrial cells peaks during the window of receptivity and is reduced in endometriosis. Using Pgr-Cre, we have generated uterine-specific conditional knockout models for Tet1, Tet2, and Tet3. While all three lines of female mice show subfertility, Tet2d/d and Tet3d/d females display pronounced reductions in fertility. Strikingly, Tet2-Tet3 double knockout females are completely infertile due to implantation failure. The goal of this proposal is to define the in vivo roles of TET2 and TET3 in uterine receptivity to implantation of blastocyst and stromal decidual transformation using multi-omics approaches in genetically engineered mouse models (Aim 1), and to translate these findings to human biology using primary human endometrial stromal cells and epithelial organoids (Aim 2). Deciphering the TET2/TET3-dependent regulatory networks will identify novel molecular targets for improving implantation outcomes and treating RIF, RPL, endometriosis, and endometrial cancer.

Up to $673K

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Decoding the gene regulatory network of mammalian cardiac maturation

NHLBI - National Heart Lung and Blood Institute

PROJECT SUMMARY/ABSTRACT The mammalian heart undergoes profound transcriptional and phenotypical remodeling during postnatal development, a process known as cardiac maturation. However, the molecular mechanisms driving this transition is not fully understood, posing a major challenge in cardiac regenerative medicine, where induced cardiomyocytes from pluripotent stem cell differentiation or non-myocyte reprogramming exhibit an overall immature phenotype that severely limits their application in cell therapy and in vitro disease modeling. In this K99/R00 application, I propose to integrate cutting-edge single cell multiomics with state-of-the-art computational methods to unravel the cell-type-specific gene regulatory networks governing cardiac maturation, and develop a novel dual-reporter system to model and enhance cardiac maturation in vitro and in vivo. During the K99 phase, I will characterize the epigenomic changes of the mouse heart during postnatal development at a single cell resolution using various single cell multiomic technologies (Aim 1), and construct cell-type-resolved gene regulatory networks underlying cardiac maturation using bioinformatic approaches coupled with deep learning (Aim 2). I will also establish cell culture and mouse models with CRISPR-mediated knock-in of dual-fluorescent reporters to track and assess cardiomyocyte maturation (Aim 3a). During the R00 phase, I will experimentally characterize key regulatory elements and novel transcriptional regulators using functional genomic approaches (Aim 3b). I will also leverage these findings to enhance the maturation of in vitro-derived cardiomyocytes for improved therapeutic potential (Aim 3c). The expected outcomes of my proposed research will deepen our understanding of postnatal cardiac development and uncover new therapeutic strategies to improve cardiac function after injury. My career goal is to lead an independent research group that develops and employs innovative technologies to study the regulatory mechanisms underlying cardiac development, regeneration, and disease. In my K99 phase, I will acquire crucial knowledge and skills in advanced single cell genomics and computational biology to complement my previous expertise in developmental biology and cardiac research. My career development will be supported by an exceptional mentoring and advisory committee from UCSD/Salk/HHMI, along with world-class resources, training opportunities, and institutional support at UC San Diego. These elements will provide a strong foundation for my successful transition to an independent tenure- track faculty position.

Up to $125K

2028-03-31

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the glycan forms of glycoRNA-L and glycoRNA-S from leukocytes

NIAID - National Institute of Allergy and Infectious Diseases

Project Summary In mammalian cells, RNAs are predominantly located within cytoplasm and nucleus. A recent study, however, has reported that RNAs can be glycosylated, and such glycosylated RNAs (called glycoRNAs) are localized on out cell surface. The glycoRNAs are glycan-modified small non-coding RNAs. These RNAs are transcribed and maturated in nucleus and transported to cytoplasm for processing and then conjugated with glycan chains in endoplasmic reticulum. The conjugated molecules are then transported to cell membrane and anchored on cell membrane by binding to transmembrane RNA binding proteins. The cell surface glycoRNAs can serve as ligands or receptors to mediate cell-cell interaction, communication and infiltration and may also trigger cell signal transductions. Our recent works suggest that there were two forms of glycoRNAs, named glycoRNA-L and glycoRNA-S, robustly expressed in leukocytes, but not non-immune cells. GlycoRNA-L was migrated with ~11 kb RNA, whereas glycoRNA-S was migrated with ~0.6 kb RNAs. Using RNase removed the RNA frag- ments, the migration of both glycoRNA-L and glycoRNA-S was slightly faster, suggesting that the migration of glycoRNA-L and glycoRNA-S was determined by the glycan chains, but not RNA fragments. Further studies suggest that the glycan structures and functions of glycoRNA-L and glycoRNA-S may be distinguished. How- ever, the compositions and structures of glycan forms of glycoRNA-L and glycoRNA-S remain unknown. We hypothesize that the glycoforms of glycoRNA-L and glycoRNA-S from leukocytes are determinants of their functional significance. The goal of this proposal is to decode the compositions and structures of glycan forms of glycoRNA-L and glycoRNA-S from leukocytes. We will reach this goal by two approaches: 1) metabolic labeling combined with enzymatic digestion; 2) glycoRNA-L and glycoRNA-S purification and LC/MS analysis. Completion of the project will significantly advance our understanding of the role and mechanisms of glycoRNA- L and glycoRNA-S in the regulation of immune response and immune-related human diseases. The study will also provide a method for mapping the glycan structures of glycoRNAs from other cells such as cancer cells, which may provide insights for generating innovative diagnostic and therapeutic strategies.

Up to $158K

2028-03-31

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the interplay between QKI and m7G methylation on 3'UTR

NIGMS - National Institute of General Medical Sciences

PROJECT SUMMARY Post-transcriptional regulation is a critical mechanism controlling cellular differentiation and development, driven by coordinated interactions between RNA-binding proteins (RBPs) and RNA modifications. This proposal investigates the interplay between Quaking (QKI) isoforms and N7-methylguanosine (m7G) RNA modifications. QKI isoforms exhibit distinct subcellular localizations and functions, yet their roles in binding m7G-modified transcripts at 3′ untranslated regions (UTRs) during differentiation remain poorly understood. The central hypothesis is that QKI isoforms regulate differentiation by binding m7G-modified mRNAs at 3′ UTRs, with cytoplasmic QKI6 stabilizing transcripts essential for myeloid differentiation. Furthermore, m7G modifications may independently regulate gene expression in ways yet to be defined. Our preliminary evidence demonstrates that cytoplasmic QKI isoforms mediate myeloid differentiation, highlighting a critical gap in understanding m7G’s functional roles in steady-state cellular processes. Current methods for detecting m7G methylation at single- nucleotide resolution face technical limitations. This project addresses these challenges by employing direct RNA long-read sequencing and orthogonal methods to map m7G modifications with precision and identify QKI isoform-specific mRNA targets. Integrating these approaches will elucidate how QKI-m7G interactions influence myeloid differentiation, with broader implications for RNA modifications in stem cell biology, neurodevelopment, and cancer. Over the next five years, the laboratory’s mission is to (1) develop novel methods for base-resolution m7G detection, (2) define mRNA targets regulated by distinct QKI isoforms, and (3) determine the functional impact of QKI-m7G interactions on myeloid differentiation. These studies will advance understanding of RNA modification-driven gene regulation and may inform therapeutic strategies for diseases such as leukemia. By resolving the interplay between QKI and m7G at 3′UTRs, this work will reveal how their coordination regulates cellular functions across human cell types, directly addressing NIGMS’s mission to support foundational discovery science. The proposed research will provide mechanistic insights into RNA modifications dysregulated in cancer, potentially uncovering new targets for therapeutic intervention in malignancies and developmental disorders.

Up to $506K

2030-12-31

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Decoding the Mechanisms and Regulatory Networks of Plant U-Box/RING Ubiquitin Ligase Complexes under biotic stress

NIGMS - National Institute of General Medical Sciences

PROJECT SUMMARY/ABSTRACT The ubiquitin-proteasome system is a cornerstone of eukaryotic cellular regulation, orchestrating critical processes such as protein homeostasis, signal transduction, cell cycle progression, and stress responses. Central to this system are E3 ubiquitin ligases, which determine substrate specificity and mediate the transfer of ubiquitin from E2 enzymes to target proteins. This research focuses on unraveling the molecular mechanisms, structural dynamics, and regulatory networks of two highly conserved and essential classes of E3 ligases: Plant U-box (PUB) ligases and a specific family of RING ligases, with a particular emphasis on their roles under biotic stress conditions. U-box and RING ligases are conserved across eukaryotes, including humans, where their dysregulation is associated with various diseases. In plants and human U-box and specific RING ligases are integral to immunity, development, and stress adaptation, yet their precise biochemical mechanisms, including substrate recognition and regulation, remain poorly understood. Our preliminary studies have provided significant insights into these ligases. We determined the crystal structure of the U-box domain of a PUB E3 ligase in complex with E2 enzyme that represents a large and highly conserved class of E2s in eukaryotes, revealing a novel dimeric interface. We discovered a redox- sensitive disulfide bond switch in the E2 enzyme that dynamically modulates ubiquitin transfer and chain formation, both in vitro and particularly under biotic oxidative stress conditions. Using proximity labeling coupled with mass spectrometry, we performed distinct experiments including mapping the interactome of a PUB E3 ligase, and investigating the RING complex module under both normal and pathogen-exposed conditions. The experiment informed dynamic proteome changes in response to pathogen exposure, uncovering new relationships and previously unknown target substrates. Additionally, our CryoEM studies of the RING complex module provided critical insights into its dynamic substrate recognition mechanisms, proposing how structural adaptations can drive ubiquitination activity. Together, these findings provide a strong foundation to scale up and expand our studies, enabling deeper exploration of structure-function relationships as well as interactome networks to reveal novel regulatory pathways and mechanisms. This project seeks to decode how U-box and RING ligases integrate into and regulate broader cellular processes. It aims to uncover the molecular mechanisms of substrate specificity, ubiquitin transfer dynamics, and regulatory networks of these ligases. Leveraging structural and functional approaches in vitro and in planta, this research will elucidate plant stress responses and reveal conserved ubiquitination pathways with broad implications for eukaryotic biology and therapeutic innovation.

Up to $391K

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Decoding the Molecular Logic of Visual Map Formation in Drosophila

NEI - National Eye Institute

Project Summary: Precise mapping of sensory neural circuits is fundamental to perception and behavior. In the visual system, retinotopy—an orderly mapping of retinal inputs onto target brain regions—preserves spatial relationships and enables computation of motion, depth, and object localization. While the overall topology of visual maps is well understood, the molecular and developmental mechanisms by which such precise spatial wiring is established and propagated across higher-order brain regions remain unclear. This project aims to uncover how spatial codes in developing photoreceptors guide topographic connectivity in downstream neural circuits and ultimately shape visually guided behavior. Using the Drosophila visual system as a model, this research relies on its well-characterized anatomy, powerful genetic toolkit, and high-resolution imaging potential to address these questions in vivo. Aim 1 examines how the temporal order of photoreceptor neurogenesis contributes to precise spatial targeting in early visual circuits. Aim 2 investigates how dorsal-ventral positional cues and planar cell polarity (PCP) signaling define region-specific connectivity. Aim 3 proposes to explore how retinotopic organization is interpreted by higher-order visual neurons, and how disruptions in this logic alter visually guided behavior. This K99/R00 proposal integrates training in advanced single-cell transcriptomics, microscopy, circuit mapping tools (e.g., trans-Tango, GRASP), and behavioral analysis, along with structured career development in scientific writing, mentorship, and leadership. The research will provide mechanistic insights into how spatial information is encoded and transmitted during circuit assembly, a fundamental problem in neurodevelopment with relevance to disorders of neural connectivity such as amblyopia, autism, and schizophrenia.

Up to $140K

2028-06-30

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Decoding the Molecular Mechanisms of a Kappa Opioid Receptor Selective Negative Allosteric Modulator

NIDA - National Institute on Drug Abuse

Project Summary The widespread prescription and illicit use of opioids over the past several decades has created a public health epidemic known as the "opioid crisis." Synthetic opioids acting as Mu Opioid receptor (µOR) agonists have demonstrated effectiveness as pain management therapeutics yet have high addiction and overdose potential in addition to fatal side effects which have driven this ongoing crisis. Towards mitigating this crisis, naloxone is the primary therapeutic used to reverse opioid overdose, yet its use can precipitate withdrawal symptoms. Kappa Opioid receptor (κOR) has emerged as a promising target within the opioid receptor family, as selective antagonists have shown to counter emotional states and behaviors associated with withdrawal in preclinical studies. However, the utilization of κOR-targeted therapeutics has been limited by gaps in our understanding of receptor signaling and inhibition, resulting in unintended effects and unsuccessful clinical trials. As such allosteric modulators have gained attention due to their potential to provide a more fine-tuned way to modulate κOR signaling. As allosteric modulators occupy binding pockets that are distinct from the highly conserved orthosteric site, negative allosteric modulators (NAMs) can be drastically more selective than conventional antagonists. Furthermore, NAMs, by definition, enable residual endogenous signaling, which significantly broadens their therapeutic window. Until recently, no κOR-selective NAMs have been characterized. This proposal seeks to address these gaps by investigating the molecular mechanisms of a recently discovered NAM at κOR. By elucidating the structural and functional basis of κOR modulation via negative allosteric modulation, this research will contribute to the framework towards enhancing the clinical utility of κOR antagonists. To explore this fundamental aspect of κOR inhibition, we will delve into the molecular aspects of negative allosteric modulators (NAMs) in the context of our recent findings. Our first ever cryoEM structures of a novel conformational state of an inhibitor bound receptor κOR: G protein complex with inverse agonists JDTic, GB18 and norBNI highlight that inhibition is driven by highly complex mechanisms including the allosteric modulation of receptor-G protein affinities or even G protein nucleotide exchange which can result from stabilizing different states along the receptor activation pathway. Similar to orthosteric antagonists, NAMs may also stabilize distinct receptor states along the receptor activation pathway, promoting the inhibitory effects of orthosteric ligands. Taken together, this highlights the importance of investigating novel conformational states to provide a more complete picture of opioid receptor signaling and pharmacology. Using cryo-electron microscopy (cryoEM), in vitro, and ex vivo techniques to investigate inhibition via a κOR-selective NAM we will test the hypothesis that signaling inhibition arises from structural alterations that modulate G-protein dynamics. Through an extensive 1) Pharmacological Characterization of a κOR-selective NAM and 2) Structural Analysis of NAM-Induced Conformational States and Their Impact on Downstream Signaling we will link NAM-induced conformational changes at the atomic level to distinct pharmacological profiles. The results of this study will support the development of more effective therapeutic strategies at κOR and across the opioid receptor family.

Up to $108K

2028-01-31

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the molecular mediators and consequences of host-microbe interactions in inflammatory bowel diseases

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

PROJECT SUMMARY Microbes and their hosts have co-evolved an extensive interaction interface, and these interactions can be used as a tool to help illuminate fundamental biology of both the microbe and the host. The microbiome has been extensively described in both health and disease, and there are many strains that are associated with particular disease states. Ruminococcus gnavus is a commensal bacteria in the human microbiota, which has consistently been found to be associated with inflammatory bowel disease. The interplay between microbiota and host via small molecule metabolites has been extensively studied, however, in homeostasis, members of the microbiota are restricted to the lumen of the gut, meaning they are physically excluded from making direct contact with host cells. Inflammatory bowel diseases represent a particularly interesting lens through which to investigate direct interaction between bacteria and the host, as breakdown of the barrier can allow direct access to host tissues. Recently, R. gnavus was identified to have several specific interactions with host proteins, including immunoglobulins, the co-stimulatory molecule CD7, and the mucus components trefoil tactors (TFFs). This confluence of a gut commensal associated with IBD that possesses several surface features that directly target host proteins makes it an ideal example to investigate the direct interaction interface between host and microbiota member. These studies will interrogate strain-level differences of a commensal bacteria and illuminate how particular features allow it to occupy host niches and influence the immune environment. This will also provide a framework for interrogating protein-protein interactions at the host-commensal interface. These studies will provide a fundamental understanding of how microbes may influence human immune states in the gut and mechanisms of how the microbiota may drive inflammation in patients with inflammatory bowel disease. The principal investigator is a postdoctoral fellow in the Dept. of Immunobiology at Yale School of Medicine with a background in structural biology and biochemistry. The K99 phase of this award will provide training in mucosal immunology in gnotobiotic mouse models, which will enable the R00 phase of this award and launch an independent research program using interdisciplinary approaches to mechanistically study host-microbe interactions.

Up to $92K

2028-06-30

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Decoding the Muscle Epitranscriptome: Deep Learning Detection of RNA Modifications in Aging Muscle

NIA - National Institute on Aging

ABSTRACT RNA modifications represent a critical but poorly understood mechanism regulating protein production in aging muscle tissue. This proposal develops innovative computational and experimental approaches to map and understand how chemical modifications of RNA molecules change during muscle aging. Using a combination of cutting-edge nanopore sequencing technology and artificial intelligence, we will create new methods to precisely detect RNA modifications, particularly 5-methylcytosine (m5C), in muscle tissue. We will then apply these methods to examine how modification patterns differ between fast- and slow-twitch muscle fibers across age and sex, while determining their impact on protein synthesis. The project introduces novel synthetic RNA training strategies for improved modification detection while integrating chemical biology, machine learning, and muscle physiology. This work will establish new paradigms for studying RNA modifications in aging tissues while revealing fundamental mechanisms of muscle aging. The findings will identify potential RNA-based therapeutic targets for age-related muscle loss while providing valuable resources for the broader aging research community.

Up to $616K

2029-01-31

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Decoding the neuroimmune control of cutaneous gamma/delta cell function in allergic immunity

NIAID - National Institute of Allergy and Infectious Diseases

Project Abstract Allergic diseases result from dysregulated Type-2 immune responses to environmental allergens, with sensory neurons playing a key role in both allergen detection and immune activation. Sensory neurons, specifically TRPV1+ peptidergic (PEP) neurons, detect protease allergens, triggering itch and releasing Substance P, which activates dendritic cells to initiate Type-2 immunity. Recent findings reveal a bidirectional neuroimmune circuit involving sensory neurons and a subset of epidermal  T cells, termed GD3s, which produce IL-3. GD3s reside near free nerve endings, where their IL-3 primes Il3ra-expressing PEP1 neurons to enhance allergen detection and promote allergic immunity. Our long-term goal is to elucidate the mechanisms that regulate GD3 maintenance and function in both model organisms and humans. Type-2 immunity depends on feedback loops between sensory and immune cells that amplify allergic inflammation. Our central hypothesis is that sensory neurons not only respond to IL-3, but also sustain murine GD3s and their human counterparts – epidermal  T cells – through ligand-receptor interactions. Supporting this, we find that PEP1 neurons express Ccl8 and Bdnf, while GD3s express the corresponding receptors Ccr8 and Ntrk2, respectively. GD3s depend on Ccr8 for localization and proliferate in response to BDNF, suggesting that neurons actively regulate GD3 positioning and function. Furthermore, we find that human epidermal  T cells share common transcriptional signatures with murine GD3s, suggesting that epidermal  T cells may serve as the human correlate of GD3s. To test our central hypothesis, we will integrate cellular immunology, neurobiology, and molecular biology approaches across three specific aims: (1) Evaluate the chemokine-mediated pathways driving cutaneous GD3 localization, (2) Determine the neuronal factors driving GD3 function, and (3) Identify the human equivalent of GD3 cells. These studies will establish a fundamental understanding of the neuroimmune interactions that drive allergic immune activation, laying the foundation for therapeutic strategies to prevent allergic sensitization, treat chronic itch, and target chronic allergic inflammatory disorders.

Up to $776K

2031-01-31

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Decoding the principles of gamma-delta T cell selection and functional maturation through IL17RA, a novel superantigen-like gamma-delta TCR ligand.

NIAID - National Institute of Allergy and Infectious Diseases

PROJECT SUMMARY/ABSTRACT Three types of antigen receptors – BCR, αβTCR, and γδTCR – define the three types of lymphocytes that constitute the adaptive immune system of jawed vertebrates. Understanding the rules of antigen recognition by these receptors is the key to understanding the biological functions of these cell types. While the antigen receptor specificities and therefore the functions of B cells and αβT cells are well-understood, the principles of antigen recognition by γδT cells remain unclear and the nature of these antigens is largely elusive. Multiple lines of evidence indicate that the TCR repertoire, functional properties, and tissue localization of γδT cells can be shaped by interactions with endogenous γδTCR ligands. However, the nature of such endogenous γδTCR ligands remains largely unknown. Recent findings showed that superantigen-like interactions of butyrophilin family members with germline-encoded sequences of Vγ chains regulate several epithelial γδT cell subsets. However, it remains unclear whether similar interactions could control γδT cells in other tissues. To assess how prevalent the recognition of endogenous ligands by γδTCRs is and to what extent it can be explained by known γδTCR ligands, we established a pipeline for screening of γδTCR reactivities. Assessment of the reactivities of a panel of murine γδTCRs indicated that a large fraction of these TCRs recognize a diverse set of unknown self-molecules. To start revealing the molecular nature of these ligands, we performed a cDNA library screen that identified IL17 receptor A (IL17RA), a proinflammatory cytokine receptor chain not previously implicated in γδTCR signaling, as an unexpected γδTCR ligand candidate. Further analysis demonstrated that IL17RA is responsible for the accumulation and induction of an effector program in up to 20% of γδT cells found in secondary lymphoid organs. Repertoire analysis and mutagenesis experiments demonstrated that germline- encoded sequences in Vδ7 chain were the principal determinants of IL17RA reactivity, indicating that IL17RA is acting in superantigen-like fashion. In this project, we will utilize this novel ligand to explore the molecular and cellular mechanisms that regulate development and homeostasis of γδ lineage cells. In Aim 1 of this project, we will use mutagenesis and structural approaches to define the molecular basis of this unique interaction between a class of TCRs utilized by up to 20% of peripheral γδT cells and a cytokine receptor. In Aim 2 we will utilize this novel ligand to uncover the fundamental mechanisms governing the selection, functional maturation and maintenance of γδ lineage cells. Taken together, these experiments will allow us to uncover the molecular mechanisms and functional implications of the superantigen-like interaction between IL17RA and Vδ7 γδTCRs, thereby clarifying the fundamental principles of γδT cell lineage regulation by their endogenous TCR ligands. They will also reveal for the first time how the endogenous superantigen-like γδTCR ligands shape the γδT cell compartment of non-epithelial tissues.

Up to $668K

2031-06-30

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Decoding the repair and immunomodulatory functions of lymphatic vessels in wound healing

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

PROJECT SUMMARY Proper skin restoration after the damage is vital for organismal survival. The lymphatic vascular system is spread throughout the human body and has a critical function in mammalian physiology. In physiological conditions, its main function is the regulation of tissue drainage, immunosurveillance, and regeneration. Lymphatic dysfunction causes lymphedema a medical condition that manifests as tissue swelling and fibrosis. This serious condition results in profound severe delays in wound repair and the formation of chronic non-healing wounds. The mechanism by which lymphatic vessels regulate skin repair is unexplored. Additionally, while the role of lymphatic vessels in immune cell egress from tissues is well-established, how lymphatic vessels may directly modulate immune function in damaged tissues is poorly-defined. Recently, I discovered that lymphatic vessels are actively remodeled during wound healing to form small capillaries which are present in close localization to the wound front and hair follicles. This remodeling is critical for optimal repair as skin-specific loss of lymphatic vessels results in a significant delay in wound closure accompanied by a massive infiltration of immune cells. This proposal aims to leverage these observations by 1) delineating the mechanisms and consequences of lymphatic vessel remodeling during skin repair, and 2) determining the role of lymphatic vessels and fluid pressure in macrophage behavior during skin repair. This research stands to have a significant clinical impact because it can serve as a basis for developing new therapeutic avenues for lymphedema ulcers and chronic wound management. In addition, career-oriented guidance from my mentor and advisors, along with career development activated during the K99 phase that includes formal coursework on grant writing and project management, will further facilitate my transition to the R00 phase and my long-term productivity as an independent academic investigator. Collectively, the proposed research and career development plans are expected to generate data with a significant impact on understanding the repair and immunomodulatory functions of lymphatic vessels in skin repair and setting the basis of my future research as an independent researcher.

Up to $249K

2029-01-31

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the role of adipocyte-derived extracellular vesicle cargo in modulating distal inflammation

NHLBI - National Heart Lung and Blood Institute

PROJECT SUMMARY/ABSTRACT Obesity is on the rise, with over half the United States population predicted to be obese within the next decade. Cardiovascular disease (CVD), the leading cause of death worldwide, is influenced by obesity and is an independent risk factor for CVD. While obesity leads to metabolic complications, such as metabolic syndrome that affects CVD, patients with obesity who are metabolically healthy are still at risk of developing CVD. Adipose tissue (AT) inflammation occurs in obesity, with evidence suggesting its role in CVD; however, the mechanism by which adipocytes influence vascular inflammation remains unclear. Therefore, this multidisciplinary proposal integrates advanced mouse models, bioengineering, and artificial intelligence (AI) to investigate how inflamed AT modulates vascular inflammation through adipocyte-derived extracellular vesicles (AdEVs). Preliminary data demonstrate that AdEVs constitute a significant interorgan signaling mechanism that accelerates atherosclerosis in recipient mice, particularly when harvested from obese but not lean donors. The central hypothesis is that AT inflammation alters the bioactive cargo of AdEVs delivered to the arterial wall, promoting vascular inflammation in tissue-resident cells while serving as a biomolecular predictor of CVD. To address this hypothesis, the proposal is divided into three aims. Aim 1 will compare the role of AdEVs harvested from inflamed and non-inflamed AT on inflammation and the progression of atherosclerosis. Aim 2 will utilize an integrated AI model to identify bioactive cargo in AdEVs from inflamed AT, engineer AdEVs to overexpress candidate cargo, and evaluate their effects on inflammation and atherosclerosis. Lastly, in Aim 3, disease-inducing cargo in AdEVs, in conjunction with machine learning (ML), will be utilized as a prognostic assay for CVD. The proposal will be conducted under the primary mentorship of Dr. Willa A. Hsueh, a leading physician-scientist in the field of immunometabolism. During the K99 mentored phase, the candidate will receive formal training in metabolic phenotyping, flow cytometry, vascular biology, immunology, AdEV bioengineering, AI/ML, and clinical translation for obesity and CVD. To achieve these goals, the candidate assembled a multidisciplinary mentorship team comprising experts in extracellular vesicle (EV) cargo loading, AI/ML, CVD clinical translation, and EV characterization. The multidisciplinary mentorship team and comprehensive training plan, along with the collaborative research environment and cutting-edge resources provided by The Ohio State University, position the candidate for a successful transition to an independent career during the R00 phase, with the long-term goal of establishing a research program on adipocyte interorgan signaling at the interface of bioengineering and medicine. This proposal has the potential to advance mechanistic understanding of CVD, enabling AdEV- based early-detection prognostic assays in the short term and informing novel therapeutics in the long term.

Up to $122K

2028-05-31

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the role of Aire-expressing Thetis cells in peripheral self-tolerance

NIAID - National Institute of Allergy and Infectious Diseases

PROJECT SUMMARY Establishing and maintaining immune tolerance to self-antigens is vital to prevent destructive autoimmune inflammation. Within the thymus, Aire plays a critical role in establishing self-tolerance, acting within medullary thymic epithelial cells (mTECs) to promote ectopic expression of tissue-restricted antigens which in turn leads to deletion of self-reactive T cells and generation of regulatory T (Treg) cells. However, a significant proportion of self-reactive T cells escape deletion in the thymus. A central unresolved question is how these self-reactive T cells are restrained within the periphery. To this end, we recently uncovered a novel lineage of antigen- presenting cells, named Thetis cells (TC), comprising four distinct subsets (TC I-IV). Our work thus far has demonstrated an essential role for TCs in extra-thymic Treg generation and tolerance to commensal and dietary antigens within the intestine. These studies established the tolerogenic potential of TCs. Whether and how TCs also regulate peripheral tolerance to self-antigens remain open questions. In a remarkable parallel, we found that TC I and Aire+ mTECs share a core transcriptional program that includes Aire and are critically dependent on the same transcription factors. These findings raise the tantalizing possibility that Aire+ TCs and Aire+ mTECs have shared immune regulatory functions. We hypothesize that Aire+ TCs restrain self-reactive T cells within the periphery through the expression of tissue-restricted self-antigens and immune-regulatory molecules. In the proposed project, we will determine i) the role of Aire+ TCs and extra-thymic Aire in peripheral immune tolerance, and ii) the molecular mechanisms by which Aire+ TCs mediate immune tolerance. Our preliminary data has established symmetry between Aire+ mTECs and Aire+ TCs and demonstrated the power of parallel analyses of these two cell types. In each aim, we will use novel genetic models and advanced computational approaches to address the Aire-dependent and independent functions of mTECs and TCs. In Aim 1 we will determine the role of Aire+ TC I in peripheral self-tolerance during steady- state and upon inflammation. In aims 2 and 3, we will address the mechanisms by which Aire+ TC I and mTECs regulate T cell tolerance, testing two non-mutually exclusive scenarios: expression of a ‘tolerogenic’ program that endows both Aire+ mTECs and TC I with the ability to induce T cell tolerance upon antigen presentation (Aim 2), and Aire-dependent regulation of tissue-restricted self-antigen expression (Aim 3). We anticipate that these studies will reveal fundamental mechanisms of immune tolerance and establish a new framework for self-tolerance. Elucidation of the role of TCs in peripheral immune tolerance will pave the way towards therapeutic manipulation of TCs with relevance to a broad range of autoimmune and inflammatory diseases.

Up to $616K

2031-01-31

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the role of chromatin architecture in alveolar epithelial cell identity and disease

GeneticsInduced Pluripotent Stem Cell ResearchLung+2

NHLBI - National Heart Lung and Blood Institute

Project Abstract The alveolar epithelium is composed of two distinct cell types—alveolar epithelial type I (AT1) cells, which facilitate gas exchange, and alveolar epithelial type II (AT2) cells, which act as progenitors for AT1 cells. Successful lung repair following alveolar injuries requires AT2 cell proliferation and differentiation into AT1 cells, a process that involves the restructuring of gene regulatory networks and cell-type specific chromatin landscapes that underly these two cell fates. A dysfunctional regenerative response has been observed in a variety of severe lung diseases, involving AT2 cells acquiring a pathologic, alveolar-basal intermediate (ABI) cell state at the expense of an AT1 fate. The mechanisms that facilitate the cell fate decisions involved in AT2 cell maintenance and differentiation are not well understood, which has resulted in a lack of effective treatments to promote alveolar regeneration. This project aims to identify and characterize regulatory, 3-dimensional “hubs” of chromatin interaction that instruct distinct alveolar epithelial cell fates, and to determine how these hubs and their associated transcription factors regulate the acquisition of healthy and disease-associated states. Using human induced pluripotent stem cell (iPSC) models of AT1- and AT2-like cells (iAT1s and iAT2s), we will apply advanced chromatin mapping techniques to identify cell-type specific enhancer-promoter interactions and to characterize chromatin hubs that potentially regulate normal AT1 and AT2 cell identity. In Aim 1, we will map these interactions in healthy iAT1 and iAT2 cells, comparing their chromatin landscapes to pinpoint regulatory hubs that we hypothesize are responsible for cell-type specific gene expression. In Aim 2, we will explore the effects of haploinsufficiency of the lung lineage transcription factor, NKX2-1, on chromatin topology of iAT2 cells, hypothesizing that reduced NKX2-1 expression disrupts normal AT2 cell identity and favors a pathological ABI state. The findings from this research will enhance our understanding of the chromatin-based mechanisms that control lung cell fate decisions and provide insights into how disruptions of chromatin organization contribute to pulmonary disease.

Up to $50K

2029-02-28

Free to search & build · $99 one-time to unlock the application pack · No subscription

Decoding the sequence basis of genome regulation

NIGMS - National Institute of General Medical Sciences

Project Summary Deciphering how DNA sequences encode regulatory activities provides a new lens for dissecting the underlying molecular mechanisms of genome regulation. However, although deep learning approaches have significantly advanced our ability to predict chromatin accessibility, transcription factor binding, 3D genome architecture, and transcription from DNA sequence, current models remain limited in their ability to deliver mechanistic insights, cannot effectively capture long-range sequence dependencies, and do not reflect the heterogeneous and dynamic nature of molecular-level genome regulation. Motivated by our observation that simple explainable models can simultaneously contribute to improved biological understanding and predictive power— indicating that we are still in a data-limited regime—this proposal aims to address these challenges by developing a new generation of sequence-based AI frameworks focusing on biology-informed simplicity, explainability, and mechanistic insights without compromising on performance. Our approach is built on three key pillars: (i) We will develop explainable sequence models that discover simple rules for diverse regulatory functions. (ii) We will develop novel architectures to accurately predict long-range regulatory interactions directly from sequence, and generate genome-wide regulatory interaction maps across cell types. (iii) We will pioneer "sequence-to-distribution" generative models to capture the dynamic, single-molecule nature of chromatin regulation, unveiling its inherent heterogeneity and the sequence determinants of molecular cooperativity. Achieving these goals promises both improved predictions and deeper mechanistic insights, ultimately contributing toward making genomic regulation an "open book" where every single base’s contribution can be explained.

Up to $358K

2031-05-31

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Decoding the Structure-Function Relationships of Glycosaminoglycans in the Lung using Heparan Sulfate Libraries

NHLBI - National Heart Lung and Blood Institute

Project Summary Heparan sulfate glycosaminoglycans (HS GAGs) are highly sulfated polysaccharides that regulate many important pulmonary processes, including development, homeostasis, structural support, and inflammation, as well as human diseases such as pulmonary hypertension, chronic obstructive pulmonary disease, pulmonary fibrosis, and asthma. The structural complexity of HS endows it with the ability to regulate these biological processes, but also severely hinders the production of defined HS oligosaccharides. As such, efforts to elucidate the HS sequence `code' have been stymied by a lack of chemical, analytical and computational tools to decipher the biological functions of HS. Thus, the objectives of the proposed research are to: (1) advance synthetic methods and access to comprehensive libraries of structurally-defined HS oligosaccharides; (2) decipher how HS-binding proteins `read' and sulfotransferases `write' the sulfation code; (3) investigate the functional roles of HS structures in pulmonary function and disease, with a focus on targeting HS- binding proteins to modulate pathological processes in the lung. Recently, we developed new, streamlined synthetic strategies that significantly expedite HS synthesis, enabling access to comprehensive, structurally defined libraries of HS tetrasaccharides. Notably, this was achieved in part via the use of automated synthesis, demonstrating the power of our synthetic methods, and proving the feasibility of expanding upon our solution-phase automation platform to accelerate access to large libraries of HS GAGs. Our library enabled systematic investigations that were not previously possible into the HS sequence dependence of several fibroblast growth factor (FGF) and chemokine family members. This work further necessitated the development of new computational, machine learning-based methods to analyze the binding datasets that were produced and visualize the unique sequence preferences or `fingerprints' of each protein. These results combined provided compelling new evidence that the complex structure of HS encodes key biological information that is `read' by interacting proteins. In this grant, we will build on these exciting discoveries, methods, and frameworks. First, we will create expanded libraries of HS oligosaccharides to access new regions of the HS sequence landscape (Aim 1). We will also further develop our promising solution-phase automation platform to significantly enhance access to these libraries (Aim 2). Our HS libraries, both current and proposed, will be used to study the molecular recognition of HS by `readers' (e.g. FGFs and chemokines) and `writers' (e.g. sulfotransferases) and exploit their interactions in pulmonary diseases (Aims 3a, 3b, and 4). Moreover, we will continue developing new computational methods to decipher how the sulfation code is `read' (Aim 3c). Together, these studies will further a fundamental understanding of the structure-function relationships of HS and provide novel strategies for understanding, targeting, and treating diseases in the lung.

Up to $778K

2030-02-28

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Decoding the structure, function and pharmacology of TOK Channels from human-pathogenic fungi

NIAID - National Institute of Allergy and Infectious Diseases

Project Summary/Abstract Fungal pathogens Candida albicans and Aspergillus fumigatus kill millions annually worldwide and are especially dangerous for immunocompromised and aging individuals. The estimated annual economic burden of fungal diseases in the U.S. alone was $11.5 billion in 2019. Despite advances in antifungal therapies, there is a critical need for new molecular targets that bypass evolving resistance mechanisms. This project focuses on TOK channels, a fungal-specific family of potassium channels that control key physiological processes and have not been explored as antifungal targets. Recent breakthroughs in cryo-electron microscopy and electrophysiological assays offer new opportunities to define TOK channel architecture, gating, and ligand engagement at near- atomic resolution. The research in this project will determine high-resolution structures of C. albicans TOK (CaTOK) and A. fumigatus TOK1 (AfTOK1) in various functional states and identify small-molecule modulators that selectively alter channel activity, their mechanism of action at high-resolution, and their effect on fungal growth. Structural insights and comparative analyses will clarify whether these channels share core gating mechanisms while exhibiting distinct binding pockets suited for targeted inhibition. By mapping critical residues through site-directed mutagenesis and linking structural conformations to changes in rectification and ion selectivity, the work will reveal how TOK function underpins fungal fitness under stress, building an unprecedented picture of a highly unexplored potassium channel family and its gating and modulation. The expected translational outcome is a comprehensive framework for developing specialized inhibitors that beneficially modulate either CaTOK or AfTOK1, paving the way for antifungal agents that minimize off-target complications in mammalian cells. These findings will address pressing clinical demands for novel strategies to curb fungal drug resistance.

Up to $741K

2031-06-30

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Decoding the Sulfation Code: Selectively Sulfated Glycomacromolecules as Tools to Investigate Viral Protein-Carbohydrate Recognition

NIGMS - National Institute of General Medical Sciences

PROJECT SUMMARY Heparan sulfate proteoglycans (HSPGs) are a complex group of glycosylaminoglycans (GAGs) that are involved in several important biological processes including embryonic development, inflammation, angiogenesis, neurodegeneration, cardiovascular disorders, cancer. HSPGs have also been shown to play various roles in the infection of a number of viruses including HSV-1 and HSV-2, Human Papilloma Viruses (HPV), Human Immunodeficiency Virus (HIV), Dengue viruses (DENV), Hepatitis B Viruses (HBV), Hepatitis C Virus (HCV), Hepatitis E Virus, (HEV), Merkel Cell Polyomavirus (MCPyV), Rabies Virus (RABV), Respiratory Syncytial Virus (RSV), coronaviruses such as SARS-CoV-2 and HCoV-NL63, and Human Cytomegalovirus (HCMV). The important role of HSPGs in the viral life cycle has prompted numerous investigations into the use of HS and structural analogues of HS as potential compounds to study HSPG-viral engagement often with the goal of developing a better understanding of sulfation code. In most cases, these structures have been derived from natural sources or prepared synthetically. However, there remain several limitations to their use. First, structures generated from native HSPGs are often heterogeneous, making it difficult to perform the types of structure- function analyses that might unlock the sulfation code. Synthetic and semisynthetic glycans with precise sulfation patterns can be used to overcome this limitation, but they are difficult to prepare. Synthetic sulfated glycomacromolecules (oligomers and polymers) designed to serve as tools to mimic heparan sulfate have helped to overcome some of these limitations, particularly in their relative ease of synthesis. However, it is often difficult to replicate the unique sulfation patterning observed in HS. To address these shortcomings, our team will develop a library of glycomacromolecules (oligomers and polymers) bearing selectively sulfated sugars to more rapidly explore how factors such as carbohydrate content, sulfation patterns, sulfation density, and presentation (flexibility/rigidity) influence viral recognition. We also propose performing an initial assessment of the ability of our library of compounds to engage viral surface proteins of three model respiratory viruses: HPV16, SARS- CoV-2 and IAV. Finally, this proposal will provide exceptional research experiences for multiple undergraduates, fostering the training of the next generation of glycoscientists.

Up to $488K

2029-04-30

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Decoding the temperature and moisture sensory mechanisms in insects

NIGMS - National Institute of General Medical Sciences

SUMMARY – Lina Ni The long-term goal of my lab is to identify how animals detect various environmental stimuli to regulate their behavior. Temperature and moisture are closely interrelated environmental variables that animals continuously encounter; animals must regulate and maintain their temperature and moisture homeostasis to sustain normal physiological functions. Optimal environmental conditions bolster development and reproduction, whereas suboptimal conditions negatively impact these processes, and extreme conditions may lead to rapid mortality and other life-threatening conditions. Temperature and moisture variations are particularly significant for insect population, distribution, and behavior. Both larvae and adults rely on ambient temperatures to set their body temperature and on environmental moisture conditions to maintain their hydration state. These two environmental variables also determine the developmental rate and success of larvae, and unfavorable conditions challenge insects’ immune systems and increase their susceptibility to pathogens. Therefore, temperature and moisture are directly linked to the outbreak of insect disease vectors and agricultural pests. This proposal uses fly larvae as a model system to study how insects detect and integrate temperature and moisture information. Fly larvae possess molecular receptors for these senses that are evolutionarily conserved to those found in other insects. They can detect subtle changes in temperature and moisture and guide robust behaviors toward optimal conditions. Their transparent bodies, short lifespans and generation times, simple nervous systems, and powerful genetic tools enable precise manipulation and visualization of molecular receptors, sensory neurons, and neural circuits. Despite these advantages, the mechanisms of moisture sensing in larvae remain unknown. It is also unclear how animals integrate temperature and moisture information at the molecular, cellular, and circuit levels to guide navigation toward optimal environments. The goal of this proposal is to determine how fly larvae sense and integrate temperature and moisture information in sensory neurons and in the brain. Successful completion of this proposal will identify the larval moisture-sensing mechanisms and uncover how temperature and moisture sensation modulate each other. This work will enhance our understanding of insect sensory biology, evolution, and behavior and support novel strategies to predict outbreaks and control insect disease vectors and agricultural pests.

Up to $432K

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Decoding time-dependent nonlinearities underlying responses to natural stimuli

NEI - National Eye Institute

Summary and expected impact Our understanding of retinal processing, built from decades of work with artificial stimuli, fails to account for responses to natural images and movies. Current mechanistic models fail to generalize across stimuli, while deep learning models with better generalization lack interpretability. This proposal will help close this gap by investigating time-dependent nonlinearities with particular emphasis on bipolar cell synapses—critical sites that exhibit strong synaptic plasticity and serve as convergence points for parallel pathways. We hypothesize that current models fail because they do not capture how diverse time-dependent mechanisms at bipolar synapses and other circuit locations work together during natural viewing. Aim 1: Standard retinal models trained on artificial stimuli fail to engage the time-dependent nonlinearities that dominate responses to natural stimuli. We will develop stimuli that strongly engage time-dependent nonlinearities specifically at bipolar cell output synapses, probing synaptic depression and recovery dynamics. We will then develop dynamic models incorporating time-varying nonlinearities, including our validated biophysical photoreceptor model coupled with synaptic plasticity models, to isolate and quantify bipolar synaptic contributions relative to other adaptive mechanisms. Aim 2: We will determine how time-dependent nonlinearities differ across retinal pathways. First, we will characterize time-dependent nonlinearities in rod versus cone bipolar synaptic outputs at mesopic light levels. Second, we will systematically map time-dependent nonlinearities in commonly encountered RGC types in both primate (midget, parasol) and mouse (alpha) retina, measuring spike outputs, excitatory inputs, and inhibitory inputs to determine where nonlinearities arise and how pathway interactions create emergent properties. This work will advance understanding of retinal computation by creating interpretable models that incorporate the diverse time-dependent nonlinearities at bipolar synapses and other circuit locations. The resulting models will aid in the design of retinal prostheses that must function under natural viewing conditions and provide insights into visual processing deficits.

Up to $428K

2028-05-31