Biology subjects

Padmanabhan, K.

Publications and source records attributed to Padmanabhan, K..

17 recordsLinked to original sources

bioRxiv2026

Nutrition mediates extreme growth variation through deep changes in gene expression in the water strider Microvelia longipes

Exaggerated sexually selected traits are known to be highly variable and their degree of expression is dependent on nutritional input. Yet the molecular mechanisms linking nutritional variation to phenotypic variation remain poorly understood. Here, we investigate how nutritional input shapes the development of male rear leg length, an exaggerated and highly variable trait in the water strider Microvelia longipes, using comparative transcriptomics and RNA interference gene knockdown experiments. We demonstrate that nutrition is the primary driver of gene expression variation, with male exaggerated rear legs exhibiting the highest number of nutrition-responsive genes. Moreover, the increase in morphological divergence between leg types or sex, which is systematically exacerbated by rich nutrition, is associated with increased number of leg-biased genes. These comparative analyses allowed us to identify BMP11 as specifically enriched in female and male rear legs. Knockdown of BMP11 abolishes nutritional plasticity in leg length only in males, positioning it as a key integrator of environmental, sex and developmental signals. Our findings reveal that transcriptional modulation provides a molecular interface between nutrition and trait exaggeration. This work advances our understanding of how environmental cues are translated into complex phenotypes and highlights the role of developmental plasticity as a substrate for evolutionary change.

evolutionary biology↗

bioRxiv2026

Divergent molecular and circuit mechanisms underlie light entrainment of retinal and suprachiasmatic nucleus circadian clocks

The circadian system aligns behavior and physiology with the 24-hour environmental cycle through a distributed network of clocks including the master pacemaker in the suprachiasmatic nucleus (SCN) and an autonomous retinal clock critical for local retinal physiology and function. Although both clocks are entrained by light, they differ in their photoreceptor inputs and light sensitivity. The specific contributions and mechanisms by which distinct photoreceptor pathways drive their photoentrainment, however, remain incompletely understood. In this study, we conducted a comprehensive transcriptomic and integrative comparative analysis of retinal and SCN circadian light responses using mouse models lacking specific photoreceptors or key components of signaling pathways. Under photopic conditions, we found that each tissue displays distinct light-responsive transcriptional signatures across genotypes, yet both shared a conserved cluster of rod-driven immediate early-genes. Strikingly, the light-evoked transcriptional response was not sufficient to shift the phase of the SCN clock, in contrast to its robust phase-shifting effect on the retinal clock. Furthermore, by genetically disrupting rod/cone electrical coupling and pharmacologically isolating rod pathways, we identified the OFF-cone bipolar cell circuit as both necessary and sufficient to mediate light-induced phase resetting of the retinal clock. Together, these findings delineate the specialized retinal circuitry that underlies circadian entrainment and reveal a fundamental divergence between retinal and SCN mechanisms of photic timekeeping.

neuroscience↗

bioRxiv2026

In utero transduction resolves gut cell lineages and enables conditional gene perturbation in the developing enteric nervous system

How diverse cell lineages emerge and are genetically regulated during organogenesis are central questions in understanding the developmental origins of disease. However, the mouse gut, including its intrinsic enteric nervous system (ENS) derived from migratory neural crest, has remained difficult to experimentally target. Here, we introduce an in utero lentiviral nano-injection strategy that enables early and efficient access to progenitor cells of all major cell types within the developing gut as well as gut-innervating ganglia. Leveraging this approach in combination with DNA barcoding and single cell transcriptomics, we resolve clonal relationships in all gut lineages, including epithelial, neural, immune, and mesenchymal cell types. Clonal coupling between distinct subsets of fibroblasts and either pericytes, mesothelial cells, or interstitial cells of Cajal, suggested a developmental logic whereby the mesenchymal compartment arises from a set of fate-biased progenitors. Yet, mesenchymal regionalization along the anterior-posterior axis establishes early, whereas the ENS displays broad clonal dispersion across gut regions and acquires subsequent regional identities. We further adapted the platform for temporally controlled cell-type specific gene manipulation and, as a proof-of-principle, show that induced expression of the proneural factor Ascl1 biases ENS progenitor cells toward neuronal differentiation. Together, this work provides insights into refined spatiotemporal lineage relationships within a multigerm-layer organ and establishes a broadly applicable in vivo framework for probing gene function during gastrointestinal and neural crest development. SIGNIFICANCEThe gastrointestinal tract comprises diverse cell types originating from all three germ layers and includes the neural crest-derived enteric nervous system (ENS). Progress in defining these lineages and their gene regulation is challenged by the limited experimental access to the developing gut. Here, we establish in utero lentiviral transduction as an efficient approach to resolve clonal lineages and address gene functions in defined gut cell types. We show that mesenchyme assumes positional allocation early and differentiates through fate-restricted progenitors, linking specialized mesenchymal cell types to different fibroblasts. In contrast, the ENS differentiates stochastically and acquires late regional identities. Our study reveals fundamental principles of multi-lineage organogenesis and provides a framework to dissect the contribution of developmental programs to visceral dysfunction.

developmental biology↗

bioRxiv2025

Projection-Specific Intersectional Optogenetics for Precise Excitation and Inhibition in the Marmoset Brain

The primate cerebral cortex relies on long-range connections to integrate information across spatially distributed and functionally specialized areas, yet tools for selectively modulating these pathways remain limited. Here, we present an optimized intersectional viral and optogenetic strategy for precisely exciting and inhibiting projection-specific neurons in the common marmoset. Building on a mouse-to-marmoset pipeline, we first validated that optogenetic activation of inhibitory neurons (via AAV9-Dlx-ChR2) enables robust local cortical inhibition. We then combined retrograde delivery of Cre-recombinase (AAVretro-Cre) with locally injected Cre-dependent vectors encoding excitatory or inhibitory opsins (AAV8-FLEx-ChR2 or Jaws) to achieve directionally selective expression in callosal and frontoparietal pathways. Dual-opsin co-expression enabled precise stimulation or suppression of projection neurons in vivo with minimal off-target labeling. These results establish a scalable framework for projection-specific optogenetic interrogation of distributed circuits in primates, expanding the experimental toolkit for causal studies of higher-order brain function with enhanced anatomical precision and functional specificity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/660378v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1b88c22org.highwire.dtl.DTLVardef@f831fdorg.highwire.dtl.DTLVardef@9a1403org.highwire.dtl.DTLVardef@197d351_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Circadian PERIOD proteins sculpt themammalian alternative splicing landscape

Mammalian circadian oscillators are driven by a transcription-translation feedback loop where CLOCK:BMAL1 activity is repressed by the PER:CRY complex. While transcriptional regulation by PER is well established, the role of circadian feedback in co- and post- transcriptional processes remains unclear. Here, we used Nanopore long-read direct RNA sequencing (dRNAseq) and quantitative mass spectrometry (qMS) to uncover a critical function of PERs in alternative splicing (AS) regulation in the liver. Our expanded long-read transcriptome revealed significant changes in rhythmic expression of annotated transcripts, novel isoforms of known genes, and previously unannotated genes, with widespread perturbations in Per1-/-;Per2-/- (PerKO) livers. Rhythmic AS events were restricted to a distinct subset of transcripts, and splicing entropy - a metric of AS complexity - displayed oscillations in only a limited number of pathways, primarily those associated with glucose homeostasis and cellular responses to insulin. In PerKO livers, however, we detected increased isoform complexity and altered splicing entropy across a broad range of pathways linked to cell growth, morphogenesis, ER-associated degradation (ERAD), insulin response and histone methylation. Biochemical analyses and qMS data indicate that these changes are not due to mis-expression of splicing factors, but rather stem from altered nuclear abundance and chromatin retention of a few Serine-Arginine-rich splicing factors (SRSFs). In particular, SRSF3 acts proximal to the core-clock by defining both the period and amplitude of cellular rhythms. Our findings highlight a critical role for PER proteins in shaping the circadian liver proteome by integrating rhythmic transcription with the regulation of a complex and dynamic splicing landscape.

physiology↗

bioRxiv2024

Adult-neurogenesis allows for representational stability and flexibility in early olfactory system

In the olfactory system, adult-neurogenesis results in the continuous reorganization of synaptic connections and network architecture throughout the animals life. This poses a critical challenge: How does the olfactory system maintain stable representations of odors amidst this ongoing circuit instability? Utilizing a detailed spiking network model of early olfactory circuits, we uncovered dual roles for adult-neurogenesis: one that both supports representational stability to faithfully encode odor information and also one that facilitates plasticity to allow for learning and adaptation. In the main olfactory bulb, adult-neurogenesis affects neural codes in individual mitral and tufted cells but preserves odor representations at the neuronal population level. By contrast, in the olfactory piriform cortex, both individual cell responses and overall population dynamics undergo progressive changes due to adult-neurogenesis. This leads to representational drift, a gradual alteration in stimulus-evoked activity patterns. Both processes are dynamic and depend on experience such that repeated exposure to specific odors reduces the drift due to adult-neurogenesis; thus, when the odor environment is stable over the course of adult-neurogenesis, it is spike-timing-dependent plasticity that leads representations to remain stable in piriform cortex; when those olfactory environments change, adult-neurogenesis allows cortical representations to track environmental change. Whereas perceptual stability and plasticity due to learning are often thought of as two distinct, often contradictory processes in neuronal coding, we find that adult-neurogenesis serves as a shared mechanism for both. In this regard, the quixotic presence of adult-neurogenesis in the mammalian olfactory bulb that has been the focus of considerable investigation in chemosensory neuroscience may be the mechanistic underpinning behind an array of complex computations.

neuroscience↗

bioRxiv2023

Network size affects the complexity of activity in human iPSC-derived neuronal populations

Multi-electrode recording of neural activity in cultures offer opportunities for understanding how the structure of a network gives rise to function. Although it is hypothesized that network size is critical for determining the dynamics of activity, this relationship in human neural cultures remains largely unexplored. By applying new methods for analyzing neural activity to human iPSC derived cultures at either low-densities or high-densities, we uncovered the significant impacts that neuron number has on the individual neurophysiological properties of cells (such as firing rates), the collective behavior of the networks these cultures formed (as measured by entropy), and the relationship between the two. As a result, simply changing the densities of neurons generated dynamics and network behavior that differed not just in degree, but in kind. Beyond revealing the relationship between network structure and function, our findings provide a novel analytical framework to study diseases where network level activity is affected.

neuroscience↗

bioRxiv2023

Decoding Nucleosome-Depleted Regions: Insights from Epigenetic Marks, Nucleosome Size, and Thermodynamic Modelling

Elucidating the global and local rules that govern genome-wide nucleosome organisation and chromatin architecture remains a critical challenge. Thermodynamic modelling based on DNA elastic properties predicts the presence of sequence-encoded nucleosome-inhibiting energy barriers (NIEBs) along vertebrate genomes. They delineate in vivo nucleosome-depleted regions (NDRs) flanked by 2-3 well positioned nucleosomes. Here, we compared mouse NIEBs to NDRs observed at CTCF binding sites and active TSSs to reveal specific chromatin organizations. We uncover in MNase-seq chromatin profiles the presence of particles of subnucleosomal length specifically positioned at the border of NIEBs with an enrichment of H3.3 and its modification H3.3 S31Ph, whereas the positioning of nucleosomes bearing H3K27ac appears insensitive to NIEBs. Surprisingly, post-translational modifications affect the size distribution of nucleosomes as seen by MNase digestion and so likely their breathing capability. We implemented an extension of our thermodynamic model allowing for variable particle size and suggest that subnucleomes at NIEB borders would result from the recruitment of chromatin remodellers at NIEBs. Our findings provide new insights into the mechanisms by which the DNA sequence and epigenetic marks shape the nucleosome positioning and breathing.

genomics↗

bioRxiv2022

Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology

Alzheimers Disease (AD) is a progressive neurodegenerative disorder characterized by a range of behavioral alterations including memory loss as well as cognitive and psychiatric symptoms. While there is growing evidence that cellular and molecular pathologies, such as the accumulation of amyloid beta (A{beta}) plaques may contribute to AD, it remains unclear how this histopathology can give rise to such disparate behavioral deficits. One hypothesis for these diverse behavioral presentations is that A{beta} accumulation has differential effects on neuronal circuits across brain regions, depending on the diverse neurophysiological properties and connections within and between the neurons in these different areas. To test this, we recorded from large neuronal populations in the dorsal and ventral CA1 regions of the hippocampus, areas that are known to be structurally and functionally diverse, in both APP/PS1 animals, a mouse model of A{beta} pathology, and age-matched C57BL/6 controls. Although we found similar levels of A{beta} pathology in the two subregions, populations of neurons in dorsal and ventral CA1 in APP/PS1 mice showed distinct signatures of disrupted neuronal activity as animals navigated a virtual reality environment. In dorsal CA1, pairwise correlations and entropy, a measure of the diversity of activity patterns, were decreased in the APP/PS1 mice. However, in ventral CA1, the opposite findings were observed; pair-wise correlations and entropy was increased in APP/PS1 mice relative to C57BL/6 controls. When we attempted to connect the microscopic features of population activity (the correlations) with the macroscopic features of the population code (the entropy) using a pairwise Ising model, we found that the models performance decreased in predicting dorsal CA1 activity but increased in predicting vCA1 activity in APP/PS1 mice, as compared to the C57BL/6 animals. Taken together, these findings suggest that A{beta} pathology exerts distinct effects across different hippocampal regions. Our results suggest that the diverse behavioral deficits associated with AD and the cellular pathology that arises from A{beta} accumulation may be mechanistically linked by studying the dynamics of neural activity within these diverse hippocampal circuits.

neuroscience↗

bioRxiv2021

Top-down feedback enables flexible coding strategies in olfactory cortex

In chemical sensation, multiple models have been proposed to explain how odors are represented by patterns of neuronal activity in the olfactory cortex. One hypothesis is that the identity of combinations of active neurons within specific sniff-related time windows are critical for encoding information about odors. Another model is that patterns of neural activity evolve across time and it is this temporal structure that is essential for encoding odor information. Interestingly, we found that top-down feedback to the olfactory bulb dictates what information is transmitted to the olfactory cortex by switching between these two strategies. Using a detailed model of the early olfactory system, we demonstrate that feedback control of inhibitory granule cells in the main olfactory bulb influences the balance between excitatory and inhibitory synaptic currents in mitral cells, thereby restructuring the firing patterns of piriform cortical cells across time. This resulted in performance gains in both the accuracy and reaction time of odor discrimination tasks. These findings lead us to propose a new framework for early olfactory computation, one in which top-down feedback to the bulb flexibly controls the temporal structure of neural activity in olfactory cortex, allowing the early olfactory system to dynamically switch between two distinct models of coding. HighlightsO_LICentrifugal feedback shapes the temporal structure of neuronal firing in piriform cortical cells C_LIO_LIFeedback controls information to piriform cortex by restructuring the ratio of excitatory and inhibitory synaptic inputs in the bulb C_LIO_LICentrifugal feedback restructures how identity and timing of glomerular activity is represented in temporal patterns of activity in piriform cortex C_LIO_LITemporal information improves behavioral performance in accuracy and reaction time of odor discrimination C_LI

neuroscience↗

bioRxiv2021

Divergence in Population Coding for Space between Dorsal and Ventral CA1

Molecular, anatomic, and behavioral studies show that the hippocampus is structurally and functionally heterogeneous, with dorsal hippocampus implicated in mnemonic processes and spatial navigation and ventral hippocampus involved in affective processes. By performing electrophysiological recordings of large neuronal populations in dorsal and ventral CA1 in head-fixed mice navigating a virtual environment, we found that this diversity resulted in different strategies for population coding of space. We found that the populations of neurons in dorsal CA1 had a higher dimensionality and showed more complex patterns of activity, translating to more information being encoded, as compared ensembles in vCA1. Furthermore, a pairwise maximum entropy model was better at predicting the structure of global patterns of activity in ventral CA1 as compared to dorsal CA1. Taken together, we uncovered different coding strategies that likely emerge from anatomical and physiological differences along the longitudinal axis of hippocampus and that may, in turn, underpin the divergent ethological roles of dorsal and ventral CA1. HighlightsO_LINo differences in dCA1 and vCA1 place field size in recordings of neuronal populations in mice navigating a virtual environment C_LIO_LIdCA1 has higher single-neuron and population-level spatial information compared to vCA1 due to differences in the sparsity of firing. C_LIO_LIPopulation activity of dCA1 has higher entropy and is higher dimensional than vCA1 C_LIO_LIPairwise maximum entropy models are better at predicting population activity in vCA1 compared to dCA1 C_LI

neuroscience↗

bioRxiv2020

Transient cell-in-cell formation underlies tumor resistance to immunotherapy

Despite the remarkable success of immunotherapy in cancer, most patients will develop resistant tumors. While the main conceptual paradigm suggests that relapsed clones emerge through a process of clonal selection and immunoediting, currently little evidence directly demonstrates this process in epithelial cancers. To study this process, we established several mouse models in which tumors drastically regress following immunotherapy, yet resistant tumors relapse within a few weeks of treatment cessation. Whole exome analyses indicated that relapsed tumors share hundreds of neo-antigens with the primary tumors and are comparably killed by reactive T cells. Examination of tumor cells that survive immunotherapies revealed that they structure a transient cell-in-cell formation, which is impenetrable to immune-derived cytotoxic compounds and to chemotherapies. This formation is mediated predominantly by a cell-membrane protein on activated T cells, which subsequently induces epidermal growth factor receptors and STAT3 phosphorylation in tumors cells. In contrast to previous reports on cell-in-cell formations, here both cells remain alive and can disseminate into single tumor cells once T cells are no longer present. Overall, this work highlights a powerful resistance mechanism which enable tumor cells to survive immune pressure and provides a new theoretical framework for combining chemotherapies and immunotherapies.

immunology↗

bioRxiv2020

Changes in weak pair-wise correlations during running reshapes network state in the main olfactory bulb

Neural codes for sensory representations are thought to reside in a broader space defined by the patterns of spontaneous activity that occur when stimuli are not being presented. To understand the structure of this spontaneous activity in the olfactory system, we performed high-density recordings of population activity in the main olfactory bulb of awake mice. We found that spontaneous activity patterns of ensembles of mitral and tufted (M/T) cells in the main olfactory bulb changed dramatically during locomotion, including decreases in pairwise correlations between neurons and increases in the entropy of the population. Maximum entropy models of the ensemble activity revealed that pair-wise interactions were better at predicting patterns of activity when the animal was stationary than while running, suggesting that higher order (3rd, 4th order) interactions between neurons shape activity during locomotion. Taken together, we found that locomotion influenced the structure of spontaneous population activity at the earliest stages of olfactory processing, 1 synapse away from the sensory receptors in the nasal epithelium. New and NoteworthyThe organization and structure of spontaneous population activity in the olfactory system places constraints of how odor information is represented. Using high-density electrophysiological recordings of mitral and tufted cells, we found that running increases the dimensionality of spontaneous activity, implicating higher-order interactions among neurons during locomotion. Behavior thus flexibly alters neuronal activity at the earliest stages of sensory processing.

neuroscience↗

bioRxiv2020

Top-down Control of Inhibition Reshapes Neural Dynamics Giving Rise to a Diversity of Computations

Growing evidence shows that top-down projections from excitatory neurons in higher brain areas selectively synapse onto local inhibitory interneurons in sensory systems. While this connectivity is conserved across sensory modalities, the role of this feedback in shaping the dynamics of local circuits, and the resultant computational benefits it provides remains poorly understood. Using rate models of neuronal firing in a network consisting of excitatory, inhibitory and top-down populations, we found that changes in the weight of feedback to inhibitory neurons generated diverse network dynamics and complex transitions between these dynamics. Additionally, modulation of the weight of top-down feedback supported a number of computations, including both pattern separation and oscillatory synchrony. A bifurcation analysis of the network identified a new mechanism by which gamma oscillations could be generated in a model of neural circuits, which we termed Top-down control of Inhibitory Neuron Gamma (TING). We identified the unique roles that top-down feedback of inhibition plays in shaping network dynamics and computation, and the ways in which these dynamics can be deployed to process sensory inputs. Significance StatementThe functional role of feedback projections, connecting excitatory neurons in higher brain areas to inhibitory neurons in primary sensory regions, remains a fundamental open question in neuroscience. Growing evidence suggests that this architecture is recapitulated across a diverse array of sensory systems, ranging from vision to olfaction. Using a rate model of top-down feedback onto inhibition, we found that changes in the weight of feedback support both pattern separation and oscillatory synchrony, including a mechanism by which top-down inputs could entrain gamma oscillations within local networks. These dual functions were accomplished via a codimension-2 bifurcation in the dynamical system. Our results highlight a key role for this top-down feedback, gating inhibition to facilitate often diametrically different local computations.

neuroscience↗

bioRxiv2019

H2A.Z is dispensable for both basal and activated transcription in post-mitotic mouse muscles

The histone variant H2A.Z is enriched in nucleosomes surrounding the transcription start site of active promoters, suggesting that it might be implicated in transcription. It is also required during mitosis. However, evidences obtained so far mainly rely on correlative evidences obtained in actively dividing cells. We have defined a paradigm in which cell cycle cannot interfere with H2A.Z transcriptional studies by developing an in vivo systems to invalidate H2A.Z in terminally differentiated post-mitotic muscle cells to dissociate its role during transcription from its role during mitosis. ChIP-seq, RNA-seq and ATAC-seq experiments performed on H2A.Z KO post-mitotic muscle cells show that this histone variant is neither required to maintain nor to activate transcription. Altogether, this study provides in vivo evidence that in the absence of mitosis H2A.Z is dispensable for transcription and that the enrichment of H2A.Z on active promoters is rather a marker than an actor of transcriptional activity.

cell biology↗

bioRxiv2019

Altered dorsal CA1 neuronal population coding in the APP/PS1 mouse model of Alzheimer’s disease

While the link between amyloid {beta} (A{beta}) accumulation and synaptic degradation in Alzheimers disease (AD) is known, the consequences of this pathology on coding remain unknown. We found that the entropy across neural ensembles was lower in the CA1 region in the APP/PS1 mouse model of A{beta}, thereby reducing the populations coding capacity. Our results reveal a network level signature of the deficits A{beta} accumulation causes to the computations performed by neural circuits.

neuroscience↗

bioRxiv2019

Sex Differences in Head-fixed Running Behavior

Sex differences in running behaviors between male and female mice occur naturally in the wild. Recent experiments using head restrained mice on a running wheel have exploited locomotion to provide insight in the neural underpinnings of a number of behaviors ranging from spatial navigation to decision making. However, it is largely unknown how males and females behave differently in this experimental paradigm. We found that in head-fixed mice that were initially exposed to a running wheel, all female mice ran forward naturally within the first two days, while almost all male mice scurried backward for up to 4 days. With daily exposure, male mice progressively learned to naturally run forward, with this transition occurring over the course of a 7-day period. Taken together, we have identified a sexually divergent behavior in head-fixed running that should be considered in experiments that use this experimental design. Furthermore, this sex-specific difference could serve as a new way to interrogate the neural underpinnings of a number of behaviors such as anxiety or fear.

neuroscience↗