Biology subjects

Jayaraman, V.

Publications and source records attributed to Jayaraman, V..

At least 19 recordsLinked to original sources

bioRxiv2026

Hidden symmetries in network connectivity support ring attractor dynamics in the fly's neural compass

Theoretical models can explain how network structure shapes neural computation, but they typically assume idealized connectivity that is inconsistent with the heterogeneous wiring of biological circuits. We address this issue in the Drosophila head-direction system, a recurrent network with ring-attractor dynamics that enable angular velocity integration. The networks symmetric wiring motifs are reminiscent of classical models, but with additional heterogeneity that should, in principle, destabilize attractor dynamics. Inspired by novel architectures discovered through machine-learning-based optimization, we develop an algorithm that transforms attractor models with symmetric connectivity into functionally equivalent models with heterogeneous connectivity. By replacing each unit with multiple clones that preserve its output, the algorithm embeds hidden symmetries in heterogeneous connectivity, maintaining ring-attractor dynamics and accurate integration. Analysis of multiple fly connectomes provides evidence for duplicated units whose connectivity reflects hidden symmetries, consistent with our theory. Our framework helps reconcile idealized models of neural computation with heterogeneous biological circuits.

neuroscience↗

bioRxiv2026

GluDs are ionotropic dopamine receptors tuned by G-proteins

Dopamine is a neurotransmitter essential for cognition, and its dysregulation is associated with neurological diseases1,2. Historically, dopamine has been understood to signal exclusively through metabotropic receptors3. Delta-type ionotropic glutamate receptors (GluDs), which have recently been established as ligand-gated ion channels4,5, are fundamental for synaptic maintenance, are implicated in neurological disorders, and co-localize with dopaminergic machinery. Here, we report that dopamine is a direct agonist of GluDs, eliciting ionotropic activity, as visualized by cryo-electron microscopy (cryo-EM), bilayer recordings, mutagenesis, and patch clamp recordings. Dopamine binds to the GluD ligand binding domain, inducing clamshell closure and channel activation through a distinct molecular interface. GluD channel activity is tightly regulated by G-proteins, which act as molecular switches to tune GluD activity: free G{beta}{gamma} inhibits ligand-gating, while G or inactive G-protein heterotrimers enable dopamine-induced GluD currents. This tuning of GluD activity by G-proteins is uncoupled in a point mutation associated with neurodegeneration. These findings expand mechanisms of neuronal dopaminergic signaling, uncover how G-proteins tune GluD channel activity, and provide a framework for targeting GluDs in neurological diseases.

biophysics↗

bioRxiv2026

Rheb membrane orientation dynamics and functional consequences elucidated by molecular simulations, single-molecule-FRET and signaling assays

Membrane binding and dynamics of prenylated Ras family small GTPases are being increasingly recognized as key regulators of their cellular signaling. However, previous studies have focused primarily on the plasma membrane-associated Ras proteins. The Ras homolog enriched in brain (Rheb) is predominantly found in endo-membranes, such as the endoplasmic reticulum and lysosomes where it directly activates mTORC1 to control cell growth and proliferation. Little is known about the molecular details and functional consequences of Rheb membrane engagement, interaction with lipids, and orientational dynamics. In this work, we combined molecular dynamics simulations, hidden Markov modeling and single-molecule FRET measurements to map the modes of membrane binding and orientation landscape of Rheb. We also assessed the functional consequence of these processes on mTORC1 activation through simulation-guided mutagenesis and cell signaling assays. We found that Rheb interconverts between two dominant orientation states through two intermediates, and that mutationally destabilizing some of these orientation states modulates mTORC1 activity. Together, these results establish membrane orientation dynamics as a functionally relevant phenomenon in the endo-membrane localized Rheb and suggest a broader role of orientational dynamics for the regulation of functional in lipid-modified small GTPases.

biophysics↗

bioRxiv2025

Octopamine instructs head direction plasticity

Many plasticity rules rely on adjusting the strength of synapses between pairs of cells based on their coincident activity. We uncovered a new mechanism for coincidence detection in the Drosophila head direction network. To maintain an accurate sense of direction, head direction neurons that signal orientation during navigation must learn to anchor to relevant external sensory cues in novel environments. Yet the synaptic mechanism for this form of unsupervised learning is unknown in any organism. In Drosophila, GABAergic visual inputs converge onto head direction neurons, and these inhibitory synapses change strength with experience to learn the relationship between visual landmarks and head direction. However, how coincident pre- and postsynaptic activity is detected across this inhibitory synapse is not understood. We discovered that neurons which release the monoamine octopamine close a feedback loop that conveys postsynaptic head direction activity onto presynaptic terminals of visual inputs. This octopamine pathway is required for anchoring the head direction network to visual cues. Furthermore, pairing structured activation of octopamine neurons with a visual cue is sufficient to drive rapid plasticity, even without postsynaptic head direction cell activity. Previous work has extensively characterized coincidence detection mechanisms at excitatory synapses; our work defines a novel mechanism for coincidence detection at an inhibitory synapse, in which postsynaptic activity is relayed via a neuromodulatory neuron onto presynaptic terminals.

neuroscience↗

bioRxiv2025

JNJ-55511118 Stabilizes a Desensitized-like Conformation of γ8-Containing AMPA Receptors through Long-Range Allosteric Modulation

AMPA receptors (AMPARs), glutamate-gated ion channels, are dynamically regulated by auxiliary proteins such as TARP {gamma}8. JNJ-55511118 (JNJ-118) is a selective inhibitor of {gamma}8-containing AMPARs. The resting-state structure shows JNJ-118 binding near the transmembrane entrance at the AMPAR-{gamma}8 interface, producing only localized structural effects. However, the mechanism by which JNJ-118 inhibits agonist-bound receptors remains unclear, as no activated-state structures are available. Using single-molecule fluorescence resonance energy transfer, fluorescence lifetime imaging, and electrophysiology, we examined how JNJ-118 reshapes AMPAR conformations in the presence and absence of glutamate. JNJ-118 shifts the glutamate-bound {gamma}8-containing receptor toward a desensitized-like conformation by destabilizing the ligand-binding domain dimer interface, and this effect is supported by functional evidence showing allosteric competition between cyclothiazide and JNJ-118. Although the dimer interface adopts a configuration similar to that of AMPARs lacking TARPs, fluorescence lifetime measurements confirm that {gamma}8 remains associated with the receptor. These findings demonstrate that under agonist-bound conditions, JNJ-118 acts as a long-range allosteric modulator that stabilizes a desensitized-like inhibited state without disrupting AMPAR-{gamma}8 complex integrity.

biochemistry↗

bioRxiv2025

RubyACRs Enable Red-Shifted Optogenetic Inhibition in Freely Behaving Drosophila

Optogenetic activators with red-shifted excitation spectra, such as Chrimson, have significantly advanced Drosophila neuroscience. However, until recently, available optogenetic inhibitors required shorter activation wavelengths, which dont penetrate tissue as effectively and are stronger visual stimuli to the animal, potentially confounding behavioral results. Here, we assess the efficacy of two newly identified anion-conducting channelrhodopsins with spectral sensitivities similar to Chrimson: A1ACR and HfACR (RubyACRs). Electrophysiology and functional imaging confirmed that RubyACRs effectively hyperpolarize neurons, with stronger and faster effects than the widely used inhibitor GtACR1. Activation of RubyACRs led to circuit-specific behavioral changes in three different neuronal groups. In glutamatergic motor neurons, activating RubyACRs suppressed adult locomotor activity. In PPL1-{gamma}1pedc dopaminergic neurons, pairing odors with RubyACR activation during learning produced odor responses consistent with synaptic silencing. Finally, activation of RubyACRs in the pIP10 neuron suppressed pulse song during courtship. Together, these results demonstrate that RubyACRs are effective and reliable tools for neuronal inhibition in Drosophila, expanding the optogenetic toolkit for circuit dissection in freely behaving animals.

neuroscience↗

bioRxiv2025

The Role of SARS-CoV-2 Nucleocapsid Protein Persistence in Inducing Chronic Type I Interferon and Mitochondrial Dysfunction.

The potential mechanisms that link SARS-CoV-2 infection to post-acute sequelae of SARS-CoV-2 symptoms and ultimately transition to new onset of autoimmune disease remain poorly understood. Here, we report the consequences of SARS-CoV-2 nucleocapsid (N) protein persistence in the absence of detectable SARS-CoV-2 replication in otherwise healthy individuals, a set of systemic lupus erythematosus (SLE) patients, and a case of a 60-year-old man who developed a new onset of lupus nephritis seven months following mild COVID-19 disease. We have identified that N protein persistence in peripheral blood mononuclear cells (PBMC) did not correlate with detectable SARS-CoV-2 RNA in blood but is associated with significantly increased secretion of type I interferons (IFN) and presence of tubuloreticular structures in peripheral leukocytes. We further demonstrate that the N protein colocalizes in the mitochondrial fraction of PBMCs from individuals positive for N protein alongside mitochondrial antiviral signaling protein (MAVS). In vitro expression of the N protein in a monocytic cell line showed that the N protein itself was directly capable of interacting with MAVS in the absence of viral RNA, and this interaction was enhanced if the cell was exposed to oxidative stress. We show that the type I IFN signature in the presence of N protein expression was MAVS, but not STING signaling pathway-dependent. Our findings suggest a mechanism for the onset and promotion of type I IFN signature after COVID-19; in our model, the SARS-CoV-2 N protein can independently trigger sustained type I IFN production via direct activation of MAVS and its spontaneous oligomerization. This long-lasting type I IFN generation may create a chronic inflammatory milieu, favoring autoimmunity with SLE-like symptoms in susceptible individuals. One Sentence SummaryThe persistence of SARS-CoV-2 nucleocapsid in the absence of viral replication is associated with an induction of mitochondria-mediated inflammatory milieu, which can favor autoimmunity in susceptible individuals.

immunology↗

bioRxiv2024

Temperature Sensitive Glutamate Gating of AMPA-subtype iGluRs

Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that mediate the majority of excitatory neurotransmission1. iGluRs are gated by glutamate, where upon glutamate binding, they open their ion channels to enable cation influx into post-synaptic neurons, initiating signal transduction2. The structural mechanism of iGluR gating by glutamate has been extensively studied in the context of positive allosteric modulators (PAMs)3-15. A fundamental question has remained - are the PAM activated states of iGluRs representative of glutamate gating in the absence of PAMs? Here, using the -amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype iGluR (AMPAR) we show that glutamate gating is unique from gating in the presence of PAMs. We demonstrate that glutamate gating is temperature sensitive, and through temperature-resolved cryo-electron microscopy (cryo-EM), capture all major glutamate gating states. Physiological temperatures augment channel activation and conductance. Activation by glutamate initiates ion channel opening that involves all ion channel helices hinging away from the pores axis in a motif that is conserved across all iGluRs. Desensitization occurs when the local dimer pairs decouple and enables closure of the ion channel below through restoring the channel hinges and refolding the channel gate. Our findings define how glutamate gates iGluRs, provide foundations for therapeutic design, and point to iGluR gating being temperature sensitive.

biophysics↗

bioRxiv2024

Memantine Inhibits Calcium-Permeable AMPA Receptors

Memantine is an US Food and Drug Administration (FDA) approved drug that selectively inhibits NMDA-subtype ionotropic glutamate receptors (NMDARs) for treatment of dementia and Alzheimers. NMDARs enable calcium influx into neurons and are critical for normal brain function. However, increasing evidence shows that calcium influx in neurological diseases is augmented by calcium-permeable AMPA-subtype ionotropic glutamate receptors (AMPARs). Here, we demonstrate that these calcium-permeable AMPARs (CP-AMPARs) are inhibited by memantine. Electrophysiology unveils that memantine inhibition of CP-AMPARs is dependent on their calcium permeability and the presence of their neuronal auxiliary subunit transmembrane AMPAR regulatory proteins (TARPs). Through cryo-electron microscopy we elucidate that memantine blocks CP-AMPAR ion channels in a unique mechanism of action from NMDARs. Furthermore, we demonstrate that memantine reverses a gain of function AMPAR mutation found in a patient with a neurodevelopmental disorder and inhibits CP-AMPARs in nerve injury. Our findings alter the paradigm for the memantine mechanism of action and provide a blueprint for therapeutic approaches targeting CP-AMPARs.

biophysics↗

bioRxiv2024

Exploration and exploitation are flexibly balanced during local search in flies

After finding food, a foraging animal must decide whether to continue feeding, or to explore the environment for potentially better options. One strategy to negotiate this tradeoff is to perform local searches around the food but repeatedly return to feed. We studied this behavior in flies and used genetic tools to uncover the underlying mechanisms. Over time, flies gradually expand their search, shifting from primarily exploiting food sources to exploring the environment, a change that is likely driven by increases in satiety. We found that flies search patterns preserve these dynamics even as the overall scale of the search is modulated by starvation-induced changes in metabolic state. In contrast, search induced by optogenetic activation of sugar sensing neurons does not show these dynamics. We asked what navigational strategies underlie local search. Using a generative model, we found that a change in locomotor pattern after food consumption could account for repeated returns to the food, but failed to capture relatively direct, long return trajectories. Alternative strategies, such as path integration or sensory taxis could allow flies to return from larger distances. We tested this by individually silencing the flys head direction system, olfaction and hygrosensation, and found that the only substantial effect was from perturbing hygrosensation, which reduced the number of long exploratory trips. Our study illustrates that local search is composed of multiple behavioral features that evolve over time based on both internal and external factors, providing a path towards uncovering the underlying neural mechanisms.

neuroscience↗

bioRxiv2024

Bi-directional allosteric pathway in NMDA receptor activation and modulation

N-methyl-D-aspartate (NMDA) receptors are ionotropic glutamate receptors involved in learning and memory. NMDA receptors primarily comprise two GluN1 and two GluN2 subunits. The GluN2 subunit dictates biophysical receptor properties, including the extent of receptor activation and desensitization. GluN2A- and GluN2D-containing receptors represent two functional extremes. To uncover the conformational basis of their functional divergence, we utilized single-molecule fluorescence resonance energy transfer to probe the extracellular domains of these receptor subtypes under resting and ligand-bound conditions. We find that the conformational profile of the GluN2 amino-terminal domain correlates with the disparate functions of GluN2A- and GluN2D-containing receptors. Changes at the pre-transmembrane segments inversely correlate with those observed at the amino-terminal domain, confirming direct allosteric communication between these domains. Additionally, binding of a positive allosteric modulator at the transmembrane domain shifts the conformational profile of the amino-terminal domain towards the active state, revealing a bidirectional allosteric pathway between extracellular and transmembrane domains.

biophysics↗

bioRxiv2023

Allosteric Competition and Inhibition in AMPA Receptors

Excitatory neurotransmission is principally mediated by AMPA-subtype ionotropic glutamate receptors (AMPARs). Dysregulation of AMPARs is the cause of many neurological disorders and how therapeutic candidates such as negative allosteric modulators inhibit AMPARs is unclear. Here, we show that non-competitive inhibition desensitizes AMPARs to activation and prevents positive allosteric modulation. We dissected the noncompetitive inhibition mechanism of action by capturing AMPARs bound to glutamate and the prototypical negative allosteric modulator, GYKI-52466, with cryo-electron microscopy. Noncompetitive inhibition by GYKI-52466, which binds in the transmembrane collar region surrounding the ion channel, negatively modulates AMPARs by decoupling glutamate binding in the ligand binding domain from the ion channel. Furthermore, during allosteric competition between negative and positive modulators, negative allosteric modulation by GKYI-52466 outcompetes positive allosteric modulators to control AMPAR function. Our data provide a new framework for understanding allostery of AMPARs and foundations for rational design of therapeutics targeting AMPARs in neurological diseases.

biophysics↗

bioRxiv2023

A rotational velocity estimate constructed through visuomotor competition updates the fly's neural compass

Navigating animals continuously integrate velocity signals to update internal representations of their directional heading and spatial location in the environment. How neural circuits combine sensory and motor information to construct these velocity estimates and how these self-motion signals, in turn, update internal representations that support navigational computations are not well understood. Recent work in Drosophila has identified a neural circuit that performs angular path integration to compute the flys head direction, but the nature of the velocity signal is unknown. Here we identify a pair of neurons necessary for angular path integration that encode the flys rotational velocity with high accuracy using both visual optic flow and motor information. This estimate of rotational velocity does not rely on a moment-to-moment integration of sensory and motor information. Rather, when visual and motor signals are congruent, these neurons prioritize motor information over visual information, and when the two signals are in conflict, reciprocal inhibition selects either the motor or visual signal. Together, our results suggest that flies update their head direction representation by constructing an estimate of rotational velocity that relies primarily on motor information and only incorporates optic flow signals in specific sensorimotor contexts, such as when the motor signal is absent.

neuroscience↗

bioRxiv2023

CD163 and Tim-4 identify resident intestinal macrophages across sub-tissular regions that are spatially regulated by TGF-β

In bodily organs, macrophages are localised in poorly understood tissular and sub-tissular niches associated with defined macrophage ontogeny and activity. In the intestine, a paradigm is emerging that long-lived macrophages are dominantly present in the muscular layer, while highly monocyte-replenished populations are found in the lamina propria beneath the epithelial barrier. Whether longevity is restricted in such a simplified manner has not been well explored. Moreover, the impact of specific gut-associated factors on long-lived macrophage functionality and niche occupancy is unknown. We generated sc-RNA-Seq data from wild-type and Ccr2-/- mice to identify phenotypic features of long-lived macrophage populations in distinct intestinal niches and identified CD163 as a useful marker to distinguish submucosal/muscularis (S/M) from lamina propria (LP) macrophages. Challenging the emerging paradigm, long-lived macrophages, identified by Tim-4 expression, were found in the LP and S/M. Long-lived LP macrophages are restrained in their response to proinflammatory stimulation compared to short-lived populations in the same location, and to the long-lived population within the S/M. Employing a novel Timd4creTgfbr2fl/fl mouse line we demonstrate distinct functions of TGF-{beta} on long-lived macrophages in these two compartments. Importantly, in Timd4creTgfbr2fl/fl mice, zonation of CD163+ macrophages in the S/M was lost, suggesting TGF-{beta} plays an unappreciated role in positioning of macrophages in the tissue. These data highlight the importance of considering ontogeny and niche when assessing the action of key intestinal regulatory signals.

immunology↗

bioRxiv2023

A neuronal substrate for translating nutrient state and resource density estimations into foraging decisions

Foraging animals must balance the costs of exploring their surroundings with the potential benefits of finding nutritional resources. Each time an animal encounters a food source it must decide whether to initiate feeding or continue searching for potentially better options. Experimental evidence and patch foraging models predict that this decision depends on both nutritional state and the density of available resources in the environment. How the brain integrates such internal and external states to adapt the so-called exploration-exploitation trade-off remains poorly understood. We use video-based tracking to show that Drosophila regulates the decision to engage with food patches based on nutritional state and travel time between food patches, the latter being a measure of food patch density in the environment. To uncover the neuronal basis of this decision process, we performed a neurogenetic silencing screen of more than 400 genetic driver lines with sparse expression patterns in the fly brain. We identified a population of neurons in the central complex that acts as a key regulator of the decision to engage with a food patch. We show that manipulating the activity of these neurons alters the probability to engage, that their activity is modulated by the protein state of the animal, and that silencing these neurons perturbs the ability of the animal to adjust foraging decisions to the flys travel time between food patches. Taken together, our results reveal a neuronal substrate that integrates nutritional state and patch density information to control a specific foraging decision, and therefore provide an important step towards a mechanistic explanation of the cognitive computations that resolve complex cost-benefit trade-offs.

neuroscience↗

bioRxiv2023

Enantioselectivity in the Enzymatic Dehydration of Malate and Tartrate: Mirror Image Specificities of Structurally Similar Dehydratases

Malate (2-hydroxysuccinic acid) and tartrate (2,3-dihydroxysuccinic acid) are chiral substrates; the former existing in two enantiomeric forms (R and S) while the latter exists as three stereoisomers (R,R; S,S; and R,S). Dehydration by stereospecific hydrogen abstraction and anti- elimination of the hydroxyl group yield the achiral products fumarate and oxaloacetate, respectively. Class-I fumarate hydratase (FH) and L-tartrate dehydratase (L-TTD) are two highly conserved enzymes belonging to the iron-sulfur cluster hydrolyase family of enzymes that catalyze reactions on specific stereoisomers of malate and tartrate. FH from Methanocaldococcus jannaschii accepts only S-malate and S,S-tartrate as substrates while the structurally similar L-TTD from Escherichia coli accepts only R-malate and R,R-tartrate as substrates. Phylogenetic analysis reveals a common evolutionary origin of L-TTDs and two-subunit archaeal FHs suggesting a divergence during evolution that may have led to the switch in substrate stereospecificity preference. Due to the high conservation of their sequences, a molecular basis for switch in stereospecificity is not evident from analysis of crystal structures of FH and predicted structure of L-TTD. The switch in enantiomer preference may be rationalised by invoking conformational plasticity of the amino acids interacting with the substrate, together with substrate reorientation and conformer selection about the C2-C3 bond of the dicarboxylic acid substrates. Although classical models of enzyme-substrate binding are insufficient to explain such a phenomenon, the enantiomer superposition model suggests that a minor reorientation in the active site residues could lead to the switch in substrate stereospecificity.

biochemistry↗

bioRxiv2023

A comparative study of low-pH tolerance and chitinase activity between toxigenic and non-toxigenic strains of Vibrio cholerae

Cholera toxin, encoded by the ctx gene, is a key virulence factor in toxigenic Vibrio cholerae (ctx+) strains. However, some non-toxigenic V. cholerae (ctx-) strains are also pathogenic to humans and the mechanism involved in low-pH tolerance and pathogenicity in these strains remains unclear. To address this, we profiled the growth and chitinase activity in different pH of two clinical isolates of V. cholerae: VC20, a ctx+ strain, and WO5, a ctx- strain. We also compared the expression level of key genes involved in pathogenesis between the strains. WO5, the non-toxigenic strain had robust growth and greater chitinase activity across a wide pH range, in comparison to VC20. Additionally, WO5 expressed higher levels of transcripts from genes implicated in host cell adhesion and virulence, namely ompK and toxT, respectively. Notably, we propose that lower hapR levels in WO5 contrary to VC20 is key to its low-pH tolerance. To systematically identify genes involved in low pH tolerance, we used a sequence-based homology search and found a widespread presence of low-pH adaptation modules, lysine-cadaverine, and ornithine-putrescine in multiple representative species of the Vibrio phylum. Furthermore, our analysis suggests that the loss of a gene encoding nitrite reductase that confers low pH tolerance is specific to V. cholerae and V. mimicus. Together, these findings reveal that the low-pH tolerance enhances the chitinase activity of the non-toxigenic strain that could help V. cholerae to survive the acidic environment of the stomach and readily colonize the intestine.

microbiology↗

bioRxiv2022

Evaluation of Renal Markers in Systemic Autoimmune Diseases

Renal involvement is a common occurrence in subjects with systemic autoimmune diseases. The renal manifestation and its severity depend on the underlying condition and may reversely complicate the clinical course of autoimmune diseases. Renal function markers have been widely used in the assessment of normal functioning of kidneys including glomerular filtration rate and concentrating and diluting capacity of the kidney. An increase or decrease in the values of these markers may indicate kidney dysfunction. In this study, a number of critical renal markers were examined in seropositive autoimmune diseases including systemic lupus erythematosus (SLE), connective tissue disorder (CTD), and rheumatoid arthritis (RA). The data from three cohorts of subjects enrolled in renal markers and autoimmune antibody testing between January 2015 to August 2019 were retrospectively studied. The prevalence of renal markers that were out of the reference range and their average levels in female and male subgroups across SLE, CTD, and RA cohorts were compared and analyzed. The levels of renal markers are significantly affected by the presence of autoantibodies, in particular eGFR, cystatin C, and albumin. Autoantibodies were also more frequent in subjects with severe renal function damage. Close follow-up of both renal markers and autoantibodies may potentially assist in the early diagnosis of kidney diseases and improve the survival and life expectancy of autoimmune patients.

immunology↗