Massachusetts Institute Of Technology

NIH Research Projects · FY 2025 · 2017-07

Biomolecules, such as nucleic acids, lipids, and proteins, are nanoscale in size, and often localized with nanoscale precision with respect to each other, and to cellular structures. Analyzing the nanoscale configurations of biomolecules in cells and tissues is critical for understanding how they work, as well as how they go wrong in disease states. Not surprisingly, much effort has been devoted to inventing methods (e.g., super-resolution microscopy, cryo-electron microscopy) for nanoimaging biological specimens, primarily in their preserved state. However, all of these technologies require expensive equipment, and specialized skillsets. Given that all biological systems involve nanoscale building blocks and their interactions, a major question is whether nanoimaging can be democratized, so that anyone could do it, without expensive equipment or extensive training. This grant is a first competitive renewal of our group’s primary grant that supports the development of a technology that we think could potentially meet this goal. We recently announced that in contrast to all previous methods for imaging preserved biological specimens, which magnify their images, specimens could themselves be physically magnified. This technology, which we call expansion microscopy (ExM), involves equipping key biomolecules or labels within a specimen with anchoring molecules, then densely and evenly permeating the biological specimen with a mesh of swellable polymer (that binds to the anchors, thus anchoring key biomolecules or labels to the polymer), softening the specimen to disrupt endogenous molecular interactions, and adding water to swell the polymer, which in turn pulls the biomolecules or labels apart from each other. The process is even down to the nanoscale, and thus enables nanoimaging of cells and tissues on ordinary microscopes. In addition, several recent papers point to an additional advantage of ExM – by pulling biomolecules apart from each other, you decrowd them for better labeling by fluorescent probes, sometimes turning invisible biomolecules into visible ones. ExM is already in use by many hundreds of research groups, with over 250 experimental preprints and papers appearing to date. Here we propose to make ExM simpler, more powerful, faster, more applicable to human samples, and more precise in resolution. Specifically, we will (Aim 1) create a unified, simple, high-speed ExM protocol; (Aim 2) create a unified, simple, high-speed, single-step 20x expansion protocol; (Aim 3) optimize the new unified, simple, and high-speed ExM protocols for human tissues. We propose a fast-paced, 4 year, technology development grant, with the goal of delivering, to the entire biology and medical community, a truly democratized toolbox that enables anyone to do nanoimaging. We will share all protocols as freely as possible both on the web and through protocol papers, as well as through hosting people at hands-on workshops.

NIH Research Projects · FY 2025 · 2017-07

ABSTRACT Our research is focused on fundamental questions related to cell polarity. Cell polarity describes the ability of cells to spatially organize their internal constituents along a specific axis. It is critical for cell migration (where cells need to generate a front and a back), and also for developing specialized cell shapes that are needed for many cells to function. In addition, derangements of the polarity machinery can contribute to several diseases, for example by enabling cancer metastases. Thus, an understanding of the mechanisms, regulation, and consequences of cell polarity is of both fundamental and medical interest. Studies on cell polarity have identified an evolutionarily ancient and conserved core machinery centered on a primary regulator of polarity called Cdc42. However, many of the most interesting questions remain unsolved. How is it that most cells only make a single “front” enriched in Cdc42, but some cells with more complex shapes can specify several sites to act as fronts? How do cells read their environment to determine the direction in which they should orient the polarity axis? Once polarity is established, how is the precise downstream set of events orchestrated to give each cell type the right shape? And then, how do cells know what shape they are? We use the uniquely tractable yeast model system to investigate these questions, and apply a combination of cutting-edge microscopy, genetics, and computational modeling. Our previous work identified a positive feedback mechanism that explains how Cdc42 becomes concentrated at polarity sites to establish a polarity axis. Our recent work on polarization during yeast mating, when yeast cells orient in response to spatial gradients of pheromones, suggests a new paradigm, called Exploratory Polarization, for tracking chemical gradients. And new findings on marine fungi reveal novel lifestyles whose cell biology has yet to be characterized. For the next 5-year grant cycle, our major goals are to (i) address how cell polarity is regulated by cell cycle and pheromone signaling; (ii) address remaining open questions about the new exploratory polarization mechanism that enables mating cells to find each other, and (iii) to understand how marine fungi that make several buds in each cell cycle can partition their nuclei and organelles among the different buds. We are poised to make significant advances on the questions posed above, and to exploit the answers to those questions to provide insights that extend well beyond the yeast system.

NIH Research Projects · FY 2026 · 2017-06

Project Summary/Abstract: The ability to systematically construct highly functionalized molecules in a general and reliable manner is central to synthetic organic chemistry and key for drug discovery, development, and scale-up in both academia and, in particular, the pharmaceutical industry. Our proposed work includes palladium- catalyzed cross coupling methods for the formation of aromatic and heterocyclic carbon-nitrogen bonds, carbon-oxygen bonds and carbon-fluorine bonds. One aspect of the chemistry that we are proposing involves the design of improved ligands and methods for aromatic carbon-heteroatom bond formation. Our work in this area is used throughout academia and industry for the preparation of complex molecules and has become mainstay processes for synthetic chemists. As part of this, we have developed numerous new ligands and catalysts that are now commercially available and widely employed. The invention of new, more general, and more user-friendly techniques will not only allow access to important compounds but also the means to be able to efficiently and selectively modify them. This allows chemists to rationally make new derivatives, with decreased side effects and better properties. We are also working on copper-catalyzed methods for the highly regio-, diastereo-, and enantioselective synthesis of aliphatic amines, copper-catalyzed methods for the asymmetric formation of carbon-carbon bonds and dual copper- and palladium-catalyzed processes. A portion of this work aims to design new more economically, environmentally, and generally applicable methods for the formation of carbon-carbon bonds by using alkenes as pronucleophiles. We wish to develop chemistry that will allow us to replace standard, highly reactive reactants with more benign and useful ones. We will also carry out mechanistic studies to help understand the fundamental features of these transformations and to help guide us in advancing the efficiency and utility of this work. The substrates we are targeting are representative of common structural components found in pharmaceuticals, natural products, agrochemicals, and sensory materials. The availability of these new technologies will allow others to prepare a variety of highly- functionalized and structurally diverse compounds, many of which have previously been inaccessible, which will have a great impact in a range of areas that are directly important to human health.

NIH Research Projects · FY 2026 · 2017-02

Project Summary/Abstract Section The rise of resistant strains of Mycobacterium tuberculosis (Mtb) demands new approaches to combating this infectious agent. The survival of Mtb depends on the cell envelope, which is both durable and dynamic. Mycobacteria modulate their cell envelope composition to subsist in the harsh environments they encounter in the host. The proposed aims focus on developing new tools to probe, perturb, and observe changes in the mycobacterial cell envelope. The focus of Aim 1 is on visualizing arabinofuranose and mannose residues within the cell wall and the immunomodulatory lipoarabinomannan (LAM). In Aim 2, we shall develop a complementary probe that identifies methylthioxylofuranose (MTX)-capped LAM, a glycan that has been detected in pathogenic mycobacteria. The probes generated in Aims 1 and 2 can reveal how cell envelope composition varies under different conditions and between strains. In Aim 3, we shall deploy a fluorogenic probe to visualize the changing mycobacterial cell envelope in real time. This probe provides a means to explore phenotypic changes in the mycobacterial cell envelope upon antibiotic treatment or uptake into macrophages. By pursuing the three aims, we expect to uncover vulnerabilities in mycobacterial defenses that will lead to new antibiotic strategies. Significance: The overall objective of this application is to develop new chemical probes to understand how the mycobacteria modify and maintain their cell envelope to survive under the extreme and varied conditions they encounter in human hosts. We anticipate that this knowledge will ultimately lead to the identification of new strategies to treat tuberculosis (TB).

NIH Research Projects · FY 2026 · 2015-03

PROJECT SUMMARY/ABSTRACT Advances in catalytic science and technology enable the preparation of pharmaceutical agents used to treat human disease. This project has the long-term goal of developing a broad class of inexpensive nonmetal catalysts that promote catalytic transformations via formal oxidation state cycling in qualitative analogy to transition metal catalysis. Within this overarching goal, the primary focus of this proposal is the design and application of phosphorus-based catalysts that function in the P(III)⇌P(V) redox couple. While phosphines are well-established in catalysis as spectator ligands for transition metal catalysis and as nucleophilic catalysts, this research describes innovative phosphorus-based catalysts of novel com- position and structure that explore the structural and electronic conditions required to enable new catalyt- ically-relevant reactivity via reversible P(III)⇌P(V) oxidation state cycling. The first major effort is the de- velopment of new methods for activation of amides and stable oxoanions for direct functionalization via P(III)⇌P(V) redox reactivity. The second major effort is the development of phosphine-catalyzed O-atom transfer methods that result in reductive transformations of nitroarene compounds to furnish functional- ized anilines through the formation of new carbon-nitrogen bonds. The third major effort involves the de- velopment of P(III)⇌P(V)-catalyzed O-atom transfer methods that result in reductive N-functionalization of nitroalkanes, including new phosphacyclic structures that express biphilic P(III)⇌P(V) redox reactivity. The proposed research is expected to yield new practical catalytic methods for the construction of phar- macologically-relevant small molecules that meet the challenges of sustainable synthesis, and an im- proved fundamental understanding the interplay between structure and reactivity in the p-block that will underpin future development of nonmetals for atom transfer, bond activation, and catalysis. Taken to- gether, these outcomes will advance nonmetal-based redox catalysis as a powerful modality in pharma- ceutical synthesis.

NIH Research Projects · FY 2026 · 2014-06

In the current application, we propose to characterize molecular mechanisms that generate and control presynaptic output strength across several neuronal subtypes using Drosophila as a model system. Synaptic vesicle fusion occurs through a highly probabilistic process, often with only a small percent of action potentials triggering release from individual active zones (AZs). Although AZs largely share the same complement of proteins, release probability (Pr) is highly variable across different neurons and between AZs of the same neuron. Indeed, some AZ-specific proteins are non-uniformly distributed, and the molecular composition of AZs can undergo rapid changes. To date, Ca2+ channel abundance and Ca2+ influx have been most strongly linked to Pr heterogeneity, though other factors are likely to contribute as well. The Drosophila neuromuscular junction (NMJ) has emerged as a robust model system to characterize determinants of Pr. We have developed tools for birth dating and serial in vivo imaging of the same AZ population over a multi-day period beginning shortly after synapse formation. In addition to intravital imaging of AZ development and associated protein content, we developed biosensors that allow quantal imaging of all SV fusion events occurring through both spontaneous and evoked release at single AZs. We also defined the transcriptomes of Drosophila tonic and phasic glutamatergic motoneuron subtypes that display distinct AZ structure, Ca2+ influx and synaptic output. Using these toolkits, we propose to characterize how Ca2+ channels traffic to and accumulate at AZs to regulate presynaptic output. In addition, we will determine the molecular underpinnings that generate distinct synaptic structure and function associated with two closely related glutamatergic cell types. Finally, we will determine how alterations in neuronal activity regulate AZ development and structure. Together, these studies will provide new insights into presynaptic mechanisms that control synaptic communication across several neuronal subtypes.

NIH Research Projects · FY 2025 · 2013-08

Detection of novel stimuli that may predict reward or punishment requires long-term memory for, and recognition of, stimuli that are familiar. Novelty detection and familiarity recognition are often impaired in neuropsychiatric disease, so understanding the neurobiological underpinnings is an important goal. We recently discovered that memory of visual stimulus familiarity is stored via synaptic modifications in primary visual cortex of mice. The primary aims of our research are now to (a) identify how information is stored by the collective activity of neurons in primary visual cortex and the reciprocally connected thalamus, (b) pinpoint the key sites in the cortical microcircuit where the essential synaptic modifications occur, and (c) determine how these modifications are expressed at the level of circuits and behavior. Beyond the relevance of our proposed research to identifying the mechanisms underlying visual recognition memory, they will broaden our understanding of how primary sensory areas are modified by sensory experience in order to modify behavior, which remains one of the great challenges in basic neuroscience.

NIH Research Projects · FY 2025 · 2011-02

Project Summary The World Health Organization estimates that globally nearly 13 million children are visually impaired, with over a million of them being blind. Over 80% of these children reside in third-world countries, with bleak prospects for medical care, even though in many cases, the conditions are treatable or preventable. The lives such children lead are difficult and deprived ones. Project Prakash (Sanskrit for `light') was born out of the realization that the humanitarian mission of bringing sight to blind children offers a valuable opportunity to address important scientific questions related to visual learning and brain plasticity. With support from NIH and philanthropic foundations, Project Prakash is operationalized as a three-part effort, comprising rural outreach, medical treatment and scientific research. The highly regarded Dr. Shroff's Charity Eye Hospital in Delhi serves as our medical partner. Pursuing its dual mission of service and science, the initiative has provided ophthalmic screening to over 62,000 children, sight restoring surgeries to over 520 blind children, and non- surgical care to over 2000 others. Several of the children treated for long-standing congenital blindness have gone on to participate in scientific studies designed to probe the development of visual proficiencies and cortical changes after sight onset. Following their visual progress has demonstrated both the possibility of, as well as constraints on, functional gains after several years of severely compromised pattern vision. Even as Prakash children are found to exhibit persistent impairments in basic aspects of visual function, such as acuity and contrast sensitivity, they are able to acquire complex object perception skills in the months following surgery. Building on these results, our goal now is to elucidate the mechanisms that underlie the observed limitations and proficiencies in post-surgical development. Using psychophysical, electrophysiological, and neuroimaging techniques, we will attempt to determine, on the one hand, the neural bottlenecks that limit recovery and, on the other, the mechanisms, both neural and functional, that act as enablers of functional gains in object perception.

NIH Research Projects · FY 2025 · 2009-12

Rett syndrome (RTT) is a severe neurodevelopmental disorder primarily affecting girls. In its classical form, RTT is predominantly caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2). MeCP2 is a multifunctional regulator of gene expression which regulates transcription through diverse mechanisms such as DNA-binding, interaction with transcription factor complexes, modulation of chromatin structure and regulation of miRNAs – mechanisms that are engaged pleiotropically through different developmental stages. MeCP2 was considered to act predominantly through late development into adulthood, but recent clinical studies of RTT children point to very early signs of the disorder. The early developmental mechanisms of MeCP2 are poorly understood. We previously used RTT patient iPSCs to show that reduction of MeCP2 leads to overexpression of miRNA-199 and miRNA-214, an increase in neural progenitors, and reduction in neurogenesis and neuronal migration in cortical organoids. We now propose to analyze the migration deficits in detail, and examine the mechanisms underlying the deficits. The objective of this proposal is to develop a novel live-cell imaging platform merging 3D stem cell technologies, microfluidics and multiphoton microscopy, and combine it with state-of-the- art molecular approaches, including mass spectrometry proteomics and single cell RNA sequencing, to examine mechanisms of neuronal migration deficits associated with RTT-causing mutations in MECP2. In Aim 1, we propose to develop label-free third-harmonic generation three-photon microscopy and use it to characterize neuronal migration deficits in RTT organoids compared to isogenic controls. We will additionally develop a microfluidics-based live imaging platform where organoids can be stably imaged and neurons tracked for days. In Aim 2, we will examine the consequence of MECP2 mutations on downstream molecular pathways involved in neuronal differentiation and migration. We will examine mechanisms of anomalous overexpression of AKT in RTT organoids and neural progenitors, and use a proteomic and phospho-proteomic screen to define new proteins and pathways of neuronal migration dysregulated in RTT. We will exploit the transcriptomic profile of single cells to reveal cell types, populations and transcriptomic differences between RTT and control organoids. In Aim 3, we will use the technologies of Aim 1, and results of Aim 2, to examine the role of implicated signaling pathways in neuronal migration. We will interrogate the function of AKT and downstream signaling molecules, and that of new proteins, including modulators of cell adhesion and cytoskeleton organization identified from our screens, that are predicted as involved in migration. We will validate in vivo in mice the ability of specific pathways and focal adhesion proteins to rescue RTT neuronal migration deficits. Together, we expect that these results will advance our understanding of mechanisms involved in deficits of early cortical development in RTT, and suggest potential novel therapeutics targeting these stages.

NIH Research Projects · FY 2024 · 2009-09

Project Summary This proposal aims to elucidate the structure and mechanism of action of three ion channels and transporters of viruses and bacteria. Pathogenic organisms use their membrane-bound ion channels and transporters for survival. Molecular structural information about these membrane proteins forms the basis for rational design of antiviral and antibiotic compounds to fight and prevent viral and bacterial infections. We propose to 1) determine the structure of the SARS-CoV-2 envelope (E) protein, which assembles into a cation-selective channel that stimulates the host inflammasome; 2) investigate the structural mechanism of the influenza M2 protein, which forms an acid-activated tetrameric proton channel for influenza virus uncoating; 3) determine the structure of a multidrug-resistant bacterial transporter, EmrE, to elucidate the mechanisms of proton-coupled substrate transport. These membrane proteins – E, M2, and EmrE – are drug targets to curb the COVID-19 pandemic, influenza infections, and antibiotic resistance. In Aim 1 we will investigate the structural basis of the proton conduction direction in M2 proteins by examining an influenza B M2 (BM2) mutant. Wild-type (WT) AM2 conducts protons only inward, like a transporter, while WT BM2 conducts protons bidirectionally, like a canonical channel. This difference is correlated with recent data that AM2 undergoes alternating-access motions to activate while BM2 undergoes a scissor-like motion to activate. To understand these differences, we will study a BM2 mutant that recapitulates the AM2 inward-rectifying phenotype. We will measure its structure and dynamics using multidimensional solid-state NMR spectroscopy and correlate the structural information with channel activities. In Aim 2 we will determine the SARS-CoV-2 E protein’s transmembrane (TM) structure in lipid bilayers. We will investigate the E structures under different cation concentrations, pH and with a bound inhibitor, to understand how E conducts cations and how the conductance can be blocked. 2D and 3D correlation solid-state NMR experiments will be carried out in conjunction with channel activity measurement. In Aim 3 we will investigate the conformation and membrane interaction of the cytoplasmic region of E by 31P and 13C NMR, to address the mechanism of action of the second function of the E protein, which is mediating virus budding and release. In Aim 4, we will investigate EmrE, which effluxes cationic drugs in a proton-coupled manner to cause antibiotic resistance in E. coli. We will employ multidimensional 19F NMR techniques to measure protein-drug distances to constrain the structure of the substrate-binding pocket. These studies should provide detailed structural insights into the mechanism of membrane transport in some of the most devastating viruses and bacteria, and should establish the basis for drug design to improve human health.

NIH Research Projects · FY 2025 · 2009-09

Project Summary: Structures and Dynamics of Proton- and Cation-Conducting Viroporins We seek to elucidate the structure, assembly, and mechanism of ion channels in two classes of pandemic-causing viruses, influenza and coronaviruses. These viruses encode viroporins, small membrane proteins that form pores to cause pathogenicity to cells. Elucidating the structures and mechanism of these viroporins is essential for expanding the arsenal of antiviral drugs to treat deadly viral infections and for advancing basic knowledge about the principle of ion conduction by membrane proteins. We will use solid-state NMR (ssNMR) spectroscopy to investigate three viroporins: the influenza B virus M2 (BM2) protein, the SARS-CoV-2 envelope (E) protein, and the human coronavirus OC43 E protein. In Aim 1, we will investigate the structures and mechanisms of polar and aromatic residues that are key to the functions of BM2 and SARS-CoV-2 E. Using ssNMR, we will measure the sidechain conformation and dynamics of the proton-selective histidine and the gating tryptophan in wild-type and mutant BM2 channels. These experiments will reveal how these residues interact to regulate the proton conduction direction in this archetypal proton channel. We will also investigate the ion conduction mechanism of SARS-CoV-2 E by studying two mutants, T9I and N15A. We hypothesize that these mutants disrupt an N-terminal polar network that mediates proton and cation permeation. In Aim 2, we will investigate the oligomeric structure of full-length E of SARS-CoV-2. Biochemical and ssNMR data suggest that E’s oligomerization may be plastic, and this plasticity may allow this multi-functional protein to perform the right function at the right place and time. We will develop a dynamic nuclear polarization sensitivity-enhanced 19F spin diffusion NMR technique to determine oligomer structure distributions of membrane proteins in lipid bilayers and will apply this technique to full-length E. Our recent NMR data showed that E’s transmembrane domain form pentamers that cluster in membranes that contain phosphatidylinositol, an essential lipid for a myriad of cellular functions. In Aim 3, we will investigate the structure of the phosphatidylinositol-E complex by 13C-labeling the lipid using yeast and measuring protein-lipid contacts by ssNMR. These experiments will not only illuminate the structural basis of phosphatidylinositol interaction with E but also pave the way for general studies of protein- lipid interactions. To determine the molecular features of coronavirus E proteins that correlate with pathogenicity, in Aim 4 we will investigate the E protein of OC43, one of the coronaviruses that cause the common cold. Using 2D and 3D ssNMR and nanometer-distance measurement techniques, we will determine the structure of OC43 E’s transmembrane domain. Together, these studies will transform our understanding of the principles of ion conduction by pathogenic virus proteins and establish a basis for designing viroporin inhibitors as antiviral drugs.

NIH Research Projects · FY 2025 · 2009-04

Heterogeneity in Damages from A Pandemic∗ Amy Finkelstein, MIT and NBER Geoffrey Kocks, MIT Maria Polyakova, Stanford University and NBER Victoria Udalova, U.S. Census Bureau June 10, 2024 Abstract We use linked survey and administrative data to document differences across multi- ple socio-economic and demographic groups in the extent of adverse economic and health impacts of the first two years of the COVID-19 pandemic in the United States. Across a wide set of characteristics—including race/ethnicity, education, industry, and occupation—the impacts of the pandemic on all-cause mortality and on employment were disproportionately concentrated in the same groups in the population. As the pan- demic progressed, disparities in the pandemic’s mortality impacts narrowed substan- tially between Black and White Americans and between Hispanic and White Ameri- cans, but persisted along the educational divide. For economic damages, only Hispanic- White disparities narrowed; Black-White and educational disparities persisted for the first two years of the pandemic. We also document greater mortality impacts for lower income individuals, with this negative income-excess mortality gradient becom- ing steeper in the pandemic’s second year. Together our findings—using a consistent set of methods and measures on nationally representative data with a wide set of mea- sures of socio-economic status—paint a detailed picture of the heterogeneous impacts of the first two years of the COVID-19 pandemic on health and economic well-being. ∗ This manuscript is intended to inform interested parties of ongoing research and to encourage discussion. Any views expressed are those of the authors and not those of the U.S. Census Bureau. We acknowledge funding from the National Institute on Aging under grant R01-AG032449 (Finkelstein), grant T32-AG000186 (Kocks), grant U01-AG076557 (Polyakova), National Science Foundation Graduate Research Fellowship under grant 2141064 (Kocks) and National Institute for Health Care Management Foundation (Polyakova). We are grateful to Miray Omurtak for excellent research assistance, to the NBER Racial and Ethnic Health Disparities Conference and the NBER Longer-Term Health and Economic Effects of COVID-19 Conference, and to Ben Handel (the editor) and six anonymous referees for helpful comments. The U.S. Census Bureau reviewed this data product for unauthorized disclosure of confidential information and approved the disclosure avoidance practices applied to this release under authorization numbers CBDRB-FY22-POP001-0104, CBDRB-FY22-POP001-0117, CBDRB-FY23-POP001- 0001. This research project was conducted as part of the Census Bureau’s Enhancing Health Data (EHealth) program under DMS project 7515435 (Social Determinants of Health). 1 1 Introduction The United States has long exhibited striking variation in health and economic well-being across demographic groups, including education, income, race, and ethnicity.1 The COVID- 19 pandemic – which was both a health and an economic crisis – was no exception. To characterize its heterogeneous impacts, we assemble rich, nation-wide, representative data on both economic and health damages from the pandemic. We document how the economic and health impacts of the pandemic varied across a wide set of pre-pandemic socio-economic characteristics, as well as how these disparities evolved over the course of the first two full years of the pandemic in the U.S. – from March 2020 through February 2022. We define the pandemic’s health damages by the increase in all-cause annual mortality relative to what was expected based on the historical linear trend. We define the pandemic’s economic damages by the average monthly decline in the employment-to-population ratio, again relative to the historical linear trend. We present estimates of average impacts over the first two years of the pandemic, and also show how these impacts evolved during this time period. We leverage linked administrative and survey data for the mortality analysis. Specifically, we use the U.S. Census Bureau’s version of the Social Security Administration’s Numerical Identification database (Census Numident), which provides individual-level data on the date of death (if applicable) for the near universe of the U.S. population. We link these admin- istrative all-cause mortality records to a record of race/ethnicity from the 2010 Decennial Census, and to a rich set of additional, pre-pandemic socio-economic covariates—including 1There is a vast literature documenting these disparities and investigating causal origins. Examples of the literature on health variation include Fuchs (1974), Case et al. (2002), Deaton (2002), Williams and Jackson (2005), Meara et al. (2008), Currie (2009), 2011, Boustan and Margo (2015), Case and Deaton (2015), Chetty et al. (2016), Weinstein et al. (2017), Lleras-Muney (2022), Polyakova and Hua (2019), Chetty et al. (2020), Bailey et al. (2021), Finkelstein et al. (2021), Schwandt et al. (2021), and Novosad et al. (2022). Examples of the literature on variation in economic well-being include Hoynes et al. (2012), Bayer and Charles (2018), and Derenoncourt et al. (2022). 2

NIH Research Projects · FY 2025 · 2008-08

Summary Alternative splicing is nearly universal in human genes, producing multiple distinct mRNAs and proteins from each individual gene locus. This process is regulated by over one hundred splicing factors that bind to specific RNA motifs in the primary transcript and modulate splicing by interaction with core splicing machinery or with other splicing factors. This proposal seeks to understand the rules that govern the activities of splicing factors. Each splicing factor's activity can be summarized by an RNA map that describes how its activity depends on location of binding relative to the regulated exon or splice sites. It is organized around the following aims. SA1. To develop and test second-generation (2G) “RNA Maps” describing splicing factor activity SA2. To understand the protein sequence determinants of splicing regulatory activity and improve RNA maps using engineered splicing factors SA3. To improve RNA maps by incorporating indirect and interaction effects In Aim 1, we will develop models that distinguish notions of “affinity”, “binding”, “location”, and “regulatory activity”, and will develop software to generate 2G RNA maps from different combinations of data types, including in vitro and/or in vivo binding data and RNA sequencing data, and will extend these maps to several types of RNA processing events. In Aim 2 we will identify protein sequence features that confer different types of splicing regulation, and will engineer “hyperactive” splicing factors to produce larger splicing changes and improve functional inference. Finally, we will dissect direct regulation by a factor from indirect regulation – where one splicing factor regulates another that directly regulates the splicing of other genes – and will also consider how splicing factors may cooperate or antagonize one another's regulatory activity. Together, these studies will improve our understanding of how RNA splicing factors work, enabling improved understanding of disease states where splicing factors are mutated (including many blood cancers), and improved prediction of the effects of sequence variants in the human genome that cause disease by altering splicing factor binding sites in exons and introns.

NIH Research Projects · FY 2025 · 2003-05

Project Summary/Abstract Productivity in basic and clinical neuroscience research is accelerating due to technological advances in the area of biomedical imaging. These new technologies have the potential to advance knowledge about the underlying etiology of brain-based disorders, mechanisms of treatment, and predictors of response. This competing renewal grant proposal describes a Neuroimaging Training Program (NTP) established in 2003 within the framework of the longstanding and highly successful doctoral degree program offered by the Harvard-MIT Program in Health Sciences and Technology (HST). HST is an ideal home for the NTP. The sponsoring institutions, MIT and Harvard, and the affiliated teaching hospitals, have been and continue to be at the forefront of the development and application of biomedical imaging technologies. The faculty has consistently mentored leaders in the fields of biomedical imaging and clinical translational imaging neuroscience. The goal of the NTP is to increase the number of exceptional, interdisciplinary research scientists and engineers who are trained at the interface of biomedical imaging technology, neuroscience, and clinical application to fill the needs of academia, industry, and government. In the past four funding cycles, the NTP developed a comprehensive core curriculum and became established as an exceptional program for those wishing to pursue advanced training in neuroimaging. The unique strengths of the NTP include in-depth, direct clinical training, a comprehensive didactic curriculum specifically geared to this cadre of students, and vast faculty and technology resources. Our outstanding faculty exemplify the highest standards in teaching, advising, and mentoring. Each member of the faculty prioritizes their students' needs to explore, identify, and achieve their career aspirations. Not focused on any particular niche of neuropsychiatric disease (e.g., alcoholism or brain injury), or specific imaging modality or approach, the NTP also prides itself on its multimodal approach to training and demonstrated record of training students in a diverse array of technologies and their basic and clinical applications. Funding is requested to support 6 pre-doctoral students each year, providing 2 years of funding per student.

NIH Research Projects · FY 2025 · 2003-04

Abstract: The human immune system can combat various antigens—from natural to unnatural entities. This plasticity is the immune system's strength. Still, some target antigens fail to produce a desired immune response, either because they do not elicit the desired T cell response (e.g., Th1, Th2, or Th17) or because they fail to elicit robust immune signaling. This project aims to generate and investigate antigens that can deliver combinatorial signals. Our strategy is to use chemical probes to supply the tailored signals. Aim 1 draws on our previous results showing that antigens that can bind the dendritic cell (DC) lectin DC-SIGN and the toll-like receptor 7 (TLR7) elicit a potent Th1 response. This outcome is distinct from that of an untargeted antigen equipped with a TLR7 agonist or an antigen lacking the TLR agonist but targeted to DC-SIGN. Harnessing this response in a mouse tumor model provides robust antitumor activity. We now propose to compare the signaling and immune responses of other TLR-lectin combinations by fashioning antigens that can combinatorially engage target receptors (Aim 1). Effective combinations will be assessed in vivo and compared to signals from our previous conjugate (Aim 3). In Aim 2, we shall evaluate an alternative strategy to augment immunity, which involves exploiting the flexibility of the T cell receptor. Studies of allergic reactions to covalent drugs (e.g., penicillins) indicate that peptides bearing residues beyond those found in the canonical 20 amino acids can be presented on major histocompatibility complexes (MHCs) and recognized by the T cell receptor. We postulate that antigens that can elicit responses from the B cell and T cell receptors will lead to robust immune responses. To this end, we propose to develop a synthetic platform to explore and harness T cell receptor plasticity to augment immune responses to poorly immunogenic species, such as glycans. We anticipate that the results from these studies will yield new strategies to recruit the immune system to treat human disease.

NIH Research Projects · FY 2026 · 2000-08

The striatum is critically important to health and well-being, and to our ability to adapt behaviorally to our environment. As the great input-output center of the basal ganglia, the striatum receives projections from all parts of the neocortex including mood-related areas connecting to specialized striatal zones called striosomes, and sensorimotor areas projecting to action control circuits, involving mainly the other compartment, the matrix. Crucially, the striatum is the main target of the tract input carrying dopamine (DA) from the substantia nigra pars compacta (SNc), which degenerates in Parkinson’s disease. Striosomes project back to the SNc, so as to form the nigro-striato-nigral loop famed in the clinic. The DA SNc cells not only modulate movement initiation, but also mood, vigor, learning and decision-making. The ‘return’ striatonigral tract mainly arises in striosomes. Thus striosomes are strategically wired to directly influence these DA neurons. Due to formidable technical hurdles, the functions of this critical part of the nigro-striato-nigral loop remain unclear. Yet, there are clues about the functions. Previous studies suggest that striosomes could process mood-related cortical information and send the resultant neural signals to DA neurons in SNc. Models suggest, among others, that striosomes could serve as critics in actor-critic reinforcement learning models. However, critically lacking is the understanding of the relationship between the striosome-matrix axis—striosomes (S) receiving limbic, and the surrounding matrix (M) receiving sensorimotor/associative cortical inputs—and the D1-D2 axis of the striatum—composed of direct (D1) movement-promoting striatal projection neurons (dSPNs) and indirect (D2) movement-suppressing iSPNs, due to the lack of experimental tools to dissociate the two axes. We have overcome some of the technical hurdles and propose to address these issues guided by our overarching hypotheses, that the cortico-striosomal circuit gates the state transitions of brain networks underlying mood, motivation, or vigor of action; that this circuit modulates learning processes through its powerful connections with DA-containing SNc neurons; and that striosome-dopamine circuits can adjust functional balance across distinct SPN subtypes with identities multiplexed across S-M compartments and D1-D2 pathways. We will use intersect methods in mice to dissect individual SPN subtypes according to their D1-D2 and S-M identities, DA sensors to measure DA release under the control of the striatonigral path, and chemogenetics to manipulate each component of the nigro-striato-nigral circuit so as to assess its causal role in behavior. Thus, we are fully equipped, standing on our groundworks that found that cost-benefit, approach-avoidance conflict recruit the cortico-striosomal circuit, that identified by snRNA-seq differential gene-expression patterns of individual SPN subtypes, and that have developed strategies for simultaneously recording and individually manipulating the SPN subtypes. This work is directly in line with the goals of the NIMH to advance human health and well-beings by directly addressing profoundly important gaps in knowledge about key functional circuits affected in a range of mental health disorders.

NIH Research Projects · FY 2025 · 1998-07

Project Summary/Abstract Human cancer genomes show a complex pattern of mutations that, upon computational deconvolution, resolves into a systematic series of over 80 “Mutational Signatures” (the pattern of mutations across all possible trinucleotide sequence contexts). Some signatures are common to many cancers (e.g., CGàTA in CpG sites) whereas others appear in single tumor types (e.g., signatures involving GCàTA mutations that are presumably associated with aflatoxin B1 (AFB1) exposure in hepatocellular carcinoma (HCC)). Current sequencing efforts sometimes provide hints, via examination of the details of mutational signatures, as to cancer mechanistic etiology. The first two Aims of the present proposal are a bottom up approach to determine which specific chemical insults to DNA cause mutational patterns that match mutational signatures in tumors. We have formulated a model that describes three variables that contribute to the complexity of mutational spectra: The likelihood that a DNA lesion will form in a particular context, the likelihood that it will evade repair, and the likelihood that it will miscode when traversed by a polymerase. Aim 1 uses a combination of synthetic and analytical chemistry to generate the adduct-formation spectrum of a host of DNA damaging agents (AFB1, sterigmatocystin, N-methyl-N-nitrosourea, streptozotocin, temozolomide, chloroacetaldehyde and the oxidant SIN-1). A strategy involving the use of heavy isotope containing defined-sequence oligonucleotides will be used along with mass spectrometry to map the binding specificities of electrophiles derived from these agents. Aim 2 takes a two-pronged approach to define the biological effects of DNA damage from the studied agents. Since the DNA adducts of the compounds evaluated are known, we shall insert those adducts one at a time into defined-sequence oligonucleotides in all 16 possible 3-base contexts (i.e., 5’-NXN-3’, where X is the adduct and N is A, G, C or T). The oligonucleotides will be inserted into viral genomes, replicated in cells of defined repair or replication status, and the areas of the genome that contained the lesion will be characterized to define the type, amount, genetic requirements for - and sequence context dependency of - mutagenesis. The second part of Aim 2 is to use a newly developed mouse embryo fibroblast (MEF) line to define, using Duplex Consensus Sequencing (DCS), the high-resolution mutational spectra (HRMS) of the agents under study. These data are compared via informatics techniques (e.g., cosine similarity) to human cancer mutational signatures and to the DNA binding (Aim 1) and mutagenic properties of individual adducts. Lastly, a damaged nucleotide pool is an often-overlooked source of mutations. Aim 3 uses the MEF line of Aim 2 to probe the opportunity of a pool damaged with products of oxidative stress (e.g., 8-oxoG and 5-chlorocytosine) to impact the HRMS of the MEF line. Further, we have custom-designed a pool mutagen (fKP1212), which we believe might be useful to diversify the neoantigen arrays of cancer cells in advance of cancer immunotherapy. We plan to apply our HRMS tools to investigate the pre-clinical potential of a novel adjuvant therapy for cancer. 1

NIH Research Projects · FY 2024 · 1997-07

PROJECT DESCRIPTION Human pancreatic ribonuclease (RNase 1) is a secretory enzyme that can block the flow of biochemical information by catalyzing the cleavage of cellular RNA. Our intent is to use ideas and methods from biological chemistry, molecular biology, and cell biology to reveal key mechanistic aspects of the cytotoxicity of human RNase 1 in physiological and (potentially) clinical settings. During the next grant period, this intent will be achieved in four Specific Aims. Specific Aims. In Aim 1, we will determine whether the complex of RNase 1 with the cytosolic ribonuclease inhibitor protein (which has femtomolar affinity for RNase 1) acts as a “sensor” for oxidative damage within a human cell. In Aim 2, we will determine the structural and physiological roles of the N-linked glycans that are installed on RNase 1. In Aim 3, we will develop an RNase 1 zymogen as a “prodrug” that is activated by matrix metalloproteases. In Aim 4, we will evaluate RNase 1 as an endogenous antimicrobial agent. Significance. The results of the research proposed herein will provide a detailed biochemical understanding of the cytotoxic activity of RNase 1, and could ultimately lead to new chemotherapeutic agents based on an endogenous human enzyme.

NIH Research Projects · FY 2026 · 1997-06

Over the past four decades, MIT has had a focused effort in cancer research, first in the form of the MIT Center for Cancer Research (CCR) and, since 2007, as the Koch Institute for Integrative Cancer Research at MIT. This effort has been continuously supported by a Cancer Center Support Grant (CCSG) from the National Cancer Institute (NCI), providing the designation as an NCI-designated Cancer Center at MIT. By supplying infrastructural support for Core Facilities and other organizational components of the Koch Institute as well as funds for faculty recruitment and pilot projects, this CCSG is a critical resource for cancer research at MIT. From the establishment of the CCR in 1974 to the transition to the Koch Institute and continuing to the present, the NCI Cancer Center designation has had a strong influence on the MIT administration, leading to significant institutional support over this entire period. The investment in construction of the Koch Institute building (opened in late 2010) is a recent indication of this support. The building brings together 27 cancer scientists and cancer-oriented engineers to form a highly inter-disciplinary and collaborative research environment. The building is also the hub of cancer research on the MIT campus, with a nearly equal number of Members of the Center having their laboratories in other research buildings nearby. The 56 Center Members are drawn from eight academic departments at the School of Science or School of Engineering at MIT. Beyond the discovery research and technology development being pursued by the Members of this Center, significant emphasis is placed on translational research in the form of collaborations with clinical centers and industry partners. Research in the Koch Institute is organized into three Programs. Each of these Programs has made significant advances over the current grant period. Program 1: Genetic & Cellular Programs in Cancer is co-led by Ors. Phillip Sharp, J Christopher Love, and Eliezer Calo. Program 2: Cancer Biology & Immunology is co-led by Ors. Richard Hynes, Dane Wittrup, and Stefani Spranger. Program 3: Systems and Engineering Approaches to Cancer is co-led by Ors. Michael Yaffe, Scott Manalis, and Angela Koehler. These Programs function to stimulate new research initiatives by their Members as well as to foster intra- and inter-programmatic collaborations. In aggregate the 56 Members of this Center have published 1006 cancer-related articles over the past grant period. Of those, nearly 18% have involved multiple Members. The Center has a cancer-related funding base of $58,596,507 TDC (see Data Tables 2A/2B).

NIH Research Projects · FY 2025 · 1988-02

Metabolons are non-covalent complexes of enzymes that play crucial roles in primary and secondary metabolism. Such supramolecular complexes carry out a series of reactions in a pathway while protecting intermediates from diffusion into the bulk phase and promoting product channeling. This mechanism increases reaction efficiency and fidelity and protects labile intermediates. Although there has been tremendous progress in understanding the structures and functions of soluble metabolons, the study of membrane-associated metabolons is complicated by the extra dimensions added by membrane and lipidic substrates. A membrane- associated metabolon of significance is the eukaryotic dolichol pathway in which the dolichol diphosphate-linked glycan for asparagine (N)-linked of glycosylation is assembled. Bacterial glycoproteins in the epsilon proteobacteria including Campylobacter, are also generated through stepwise, membrane-associated pathways and culminate in the biosynthesis of important virulence-associated glycoproteins. Study of the bacterial pathway and extensive genomic information from Campylobacter, providing data on the enzymes and substrates in vivo across >50 discrete genera, adds a important dimension to our studies as operon order is highly conserved but, glycan output varies and there is considerable sequence divergence. Development of systematic approaches for investigating the pgl pathways will provide a valuable template for future studies on important multistep biological processes occurring at the membrane. Despite the importance of such pathways, our understanding of how the enzymes function, and whether as a metabolon or in a distributed fashion with diffusion of substrates/products between enzymes is limited. It is also unknown how the GT-B fold, common to most pgl glycosyltransferases (GTs) leads to function and substrate selectivity, as the similarity of active-site residues does not lead to a clear structure/function view, or account for the impact of the interaction of enzymes or substrates with the membrane. The research has three aims. In Aim 1, PglA, J, H1 and H2 from the C. concisus glycan assembly metabolon will be investigated via X-ray structure determination of complexes with UDP-sugar and PrenPP-sugar substrates, ligand binding and kinetic analysis, MD simulations and membrane association determination in model membrane (styrene maleic acid lipoparticles). In Aim 2, we will predict and validate protein-protein and protein-membrane interactions, determine the effect of protein-protein interactions on pathway flux and test for product channeling. Aim 3 will generate sequence similarity networks and genome neighborhood diagrams to identify orthologs in divergent species to identify structural elements governing membrane and membrane-bound substrate interactions. We will also investigate why a GT-A fold (GT) is recruited to perform the ultimate biosynthetic step. If successful, the research will provide a newly proposed paradigm for specificity established by membrane interactions and the approaches to enable study of other membrane-resident biosynthesis pathways.

NIH Research Projects · FY 2025 · 1987-04

Project Summary – GM132997 This proposal is focused on the development of high frequency dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) to enhance sensitivity in NMR based structural biology experiments. 1 CW DNP at 527 GHz/800 MHz: The 800/89 magnet with a sweep coil and console is operating. We plan to use the 800 MHz/527 GHz system to examine amyloid proteins and other interesting systems and to develop the methodology to perform DNP experiments at high fields. This is the sole 527 GHz/800 MHz DNP instrument available for biophysics experiments in North America. 2. Applications to Peptides and Proteins: The familial mutants of A which lead to early onset AD, are sparsely available. Thus, and structural studies require methods with high sensitivity and we intend to determine the structure of the Arctic mutant, E22G-A1-42, and other familial mutants, such as D23N. 2 High Resolution 17O NMR: With new isotope labeling procedures, high fields, and high spinning frequencies which improve sensitivity, it is finally possible to record high resolution spectra of 17O. We plan to incorporate DNP in 17O experiments to increase sensitivity and to examine model systems GGVVIA to develop the methodology and to 17O label proteins for structural studies. 3 Time Domain DNP Experiments: To translate pulsed DNP to 250 GHz we have developed a series of new swept frequency and pulsed DNP experiments. Using a fast AWG, and a TWT amplifier operating at 250 GHz, we will investigate off resonance NOVEL, the frequency sweep integrated solid effect (FS-ISE) and the stretched solid effect (SSE) and new versions of time optimized DNP (TOP DNP) as approaches for time domain polarization transfer. These should eventually replace standard CW techniques like the solid effect and cross effect. 6 1H Detected DNP: We propose to develop methods for 1H detected DNP of 13C, 15N and 17O resonances using recently developed diamond rotors and a helium recirculation system that will permit r/2>100 kHz at 90 K. The system will initially use 1.3 and 0.7 mm ZrO2 rotors and we will convert to laser machined diamond rotors which we have successfully produced that will spin at >100 kHz. The recirculation system will also be useful for spinning at ambient temperatures at >200 kHz and will permit design of a variety of new pulse experiments for structural studies.

NIH Research Projects · FY 2026 · 1985-09

Age-related macular degeneration (AMD) is a leading cause of vision loss, affecting one in ten individuals over 40 in the United States. This proposal aims to comprehensively investigate photoreceptors (PR), retinal pigment epithelium (RPE), and choriocapillaris (CC), which collectively undergo progressive alterations in aging and AMD. Detecting disruptions across PR/RPE/CC in a clinical setting is crucial for understanding AMD pathogenesis, differentiating normal aging from AMD, and identifying biomarkers predictive of disease progression. To achieve these goals, we will develop and apply next-generation optical coherence tomography (OCT) and OCT angiography (OCTA) technologies to study subtle structural and vascular alterations in AMD. Aim 1 focuses on developing advanced imaging tools to assess PR/RPE/CC alterations in AMD. We will extend Variable Interscan Time Analysis (VISTA) OCTA to quantify CC blood flow speed, building upon our previous work detecting hemodynamic impairment at the retinal capillary level. Additionally, we will develop high- resolution spectral-domain OCT (SD-OCT) with computational motion-corrected volume fusion and U-net-based segmentation to map features of the outer retina that are below the resolution of commercial OCT. We will also develop 840 nm swept-source OCT technology as a potential one-shot solution for PR/RPE/CC imaging in AMD. Aim 2 will characterize PR/RPE/CC changes in normal aging and early AMD using these novel imaging tools. By quantifying CC blood flow speed in normal aging and AMD, we will establish baseline hemodynamic changes, assess inter-subject variance and examine how the vascular impairment manifests in early AMD. High-resolution structural studies will focus on mapping the basal laminar deposit (BLamD), a marker which was previously only observable in histology. We will conduct the first natural history study of BLamD with longitudinal follow-up. This will also provide insights into how CC impairment and BLamD contribute to drusen formation. Aim 3 will examine CC and PR/RPE alterations in both geographic atrophy (GA) precursors and GA. We will assess CC blood flow impairment and photoreceptor alterations near hypertransmission defects (hyperTDs), a known GA precursor marker, and determine whether co-impairment of CC and PR predicts the future dynamics of the hyperTDs. Additionally, we will examine the correspondence of features between fundus autofluorescence (FAF) and en face OCT RPE imaging. We will investigate whether the banded/diffuse pattern at the GA border, a progression marker in FAF, can be assessed in en face OCT RPE, and whether it predicts faster GA expansion. This study integrates high-resolution OCT and hemodynamic OCTA imaging with quantitative analysis to comprehensively study changes from normative aging to advanced AMD. This research promises to provide a framework for early detection, risk stratification, and development of new therapies, improving the understanding and clinical management of AMD.

NIH Research Projects · FY 2026 · 1984-06

Project Summary Based on its strategic location, the tectorial membrane (TM) has long been thought to play an essential role in hearing, but the important cochlear mechanisms remain unclear. We propose research to improve our understanding of the functional role of the TM in determining (1) the remarkable properties of normal hearing — including its exquisite sensitivity and frequency selectivity — as well as (2) the hearing loss associated with genetic mutations of the TM and other cochlear pathologies. Conventional models of cochlear mechanics represent the TM as a viscoelastic solid, and while the importance of both viscosity and elasticity is well established, these models do not account for the central role of water in this tissue. The TM is a gel: 97% water contained in a macromolecular matrix of proteins and sugar groups. Recent studies show that sound-induced motions of water through this macromolecular matrix plays a critical functional role in determining the timing of mechanical responses – and this timing is central to determining the frequency selectivity that is a hallmark of mammalian hearing. The proposed research will measure and characterize the important consequences of the gelatinous nature of the TM, i.e., its poroelastic properties. This work is organized in two related aims. The first investigates mechanical consequences of poroelasticity. We have developed a technique based on atomic force microscopy to measure mechanical properties of the TM at the level of single hair bundles. We will apply this technique to characterize poroelasticity in TMs from normal-hearing rodents, as well as mice with genetic disorders of hearing. Our second aim focuses on the role of ions (especially calcium) that are dissolved in the liquid phase of the TM. The TM has been shown to concentrate calcium at levels well in excess of those in the surrounding endolymph. Changes in ionic concentrations have been shown to alter the electro-mechanical properties of the TM, and will thereby also affect the closely apposed hair bundles of hair cells. The local concentration of calcium is known to affect not only the sound-induced receptor potentials of hair cells, but also adaptation processes that are necessary to maintain the remarkable sensitivity of hearing. Results from these studies will increase our understanding of the cochlear mechanisms that underlie both normal and impaired hearing. This knowledge has important practical applications for the delineation of inner-ear disorders (and concomitant suggestions for treatment) and for the design of speech-processing devices such as cochlear implants, hearing aids, and speech-recognition systems.

NIH Research Projects · FY 2025 · 1978-01

The long-term objective of this project is to understand how genes specify the functioning of a behavioral system. The anatomically simple neuromuscular system of the nematode Caenorhabditis elegans consists of diverse types of neurons and muscles while being sufficiently small and simple to allow a complete description of its cells, cell lineage, and neural connectivity, facilitating the identification and analysis of anatomical, developmental, and functional abnormalities caused by mutations. Studies of the C. elegans egg-laying system and of the neuromuscular systems that control behaviors often coordinately regulated with egg laying, such as locomotion and feeding, offer opportunities for the analysis of a broad variety of fundamental biological problems of relevance to many human disorders. The major issue that this project will address is the mechanisms used by animals to respond to environmental cues and stresses. More specifically, this project will determine how low oxygen levels and multichromatic light (color) affect C. elegans egg-laying behavior and locomotion, respectively, and will use these C. elegans behaviors as readouts to analyze important evolutionarily conserved pathways that respond to such cues and stresses. The genetic, molecular, cellular, and neural-circuit bases of these responses will be defined. The major focus will be on mechanisms that mediate behavioral responses to oxygen deprivation, which profoundly affects cellular and organismic physiology in humans and is responsible for the cardiac damage in heart attacks as well as for ischemic damage to the kidneys, nervous system and other organs. The evolutionarily conserved EGLN/HIF pathway mediates responses to oxygen deprivation, has been implicated in many human disorders, and has defined major therapeutic targets for cancer. This aim will identify new components of this important pathway and reveal how this pathway acts both broadly and with cell-type specificity to control animal physiology and behavior. The second and more exploratory aim will determine how, despite lacking eyes and opsins (the class of photoreceptor proteins thought to be essential for color discrimination), C. elegans can distinguish different colors. Color detection is used by animals of diverse phyla to sense and respond to colorful natural environments. The proposed studies of the responses of C. elegans to multichromatic light will address a fundamental and intriguing biological question: what mechanisms allow cells that lack opsins to respond to multichromatic light? More specifically, this aim will determine how the evolutionarily conserved Epithelial Sodium Channel (ENaC), which in mammals is crucial for fluid and ion homeostasis, functions in C. elegans to mediate responses to colored light. These studies should both reveal novel aspects of ENaC channel regulation and function and provide novel insights into opsin-independent photobiological responses, which are displayed by a variety of light-sensitive non-visual human cells, including the retinal pigment epithelial (RPE) cells of the mammalian eye.

Other NSERC · FY 2024

Quantum Engineering, Superconducting Qubits, Quantum Amplifiers, RF Engineering, Nanofabrication, Material Science, Quantum Sensing, Radio Astronomy, Particle Phsyics, Axion Searches