Biology subjects

Gautam, M.

Publications and source records attributed to Gautam, M..

7 recordsLinked to original sources

bioRxiv2026

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

Many fundamental mammalian brain functions emerge from the coordinated activity of cells distributed across large, brain-wide networks. To understand these processes in healthy and diseased states, ideally one would simultaneously measure and analyze single-cell activity at the brain-wide scale, an enduring challenge for live-measurement approaches that often face an inherent tradeoff between spatial resolution and scale. Here, we present GLOBE (sinGle-cell spatiotemporaL recOrding Brain-widE), a technology for brain-wide single-cell recording of cellular activity in vivo with spatiotemporal resolution, physiological sensitivity, and parallelization-accelerated readout. GLOBE leverages genetically encoded intracellular protein tape recorders and a high-throughput computational platform for integrated image and signal analysis. GLOBE records analog signal amplitudes across a continuous time axis, requires only standard light microscopy for in situ readout, and is compatible with expansion microscopy and RNA readouts. We applied GLOBE to simultaneously record transcriptional activity of the immediate early gene Fos in up to 219,703 neurons simultaneously across a single mouse brain over 5.5 continuous days, with a timestamp precision of 3.1-6.7 hours (median absolute error), a local recording density of 69-90% of neurons per imaging field of view, and a post-mortem imaging readout speed of 2.9 seconds per neuron on average. GLOBE resolves the brain-wide spatiotemporal structure of single-cell activity, revealing that Fos transcriptional dynamics associated with fear learning and memory retrieval are distributed across the brain with region-specific temporal heterogeneity, and that the variance of this structure scales down as the number of sampled cells increases. We envision GLOBE to have broad applications for dissecting and decoding physiological and pathological processes at the brain-wide scale.

neuroscience↗

bioRxiv2025

Segmentation Matters: Recognizing the Cell Segmentation Challenge in Spatial Transcriptomics

Probe-based in situ hybridization spatial transcriptomics has emerged as a state-of-the-art for neuroscience research. Accurate segmentation of neurons and non-neuronal cells, a critical step for downstream analysis, remains a big challenge. Using human sensory ganglia neurons as an example, we systematically explore this problem. We evaluated multiple automatic segmentation approaches using quantitative performance metrics and downstream results. We show that careful parameter tuning is essential for achieving accurate segmentation; however, even with optimized parameters, different models still yield distinct classes of errors. To mitigate these errors, we propose a manual quality check, which can validate and refine automated segmentation results. As a future direction, integrating multi-modal imaging data with tailored neural networks may further improve segmentation accuracy. In summary, our results argue that each automated segmentation method has distinct strengths, weaknesses, and characteristic error patterns; and that a manual review is necessary.

neuroscience↗

bioRxiv2025

3D confinement physically regulates cell cycle progression in budding yeast

Our understanding of cell division control traditionally comes via using liquid broths or 2D flat-plate cultures -- which cannot recapitulate the complex visco-elasto-plastic properties of natural habitats such as tissues, mucus, and soil. Consequently, how such regimes of physical confinement influence proliferative growth remains unknown. Here, using engineered, mechanically tunable and transparent growth matrices, we directly visualize yeast budding and division across 3D viscoelastic regimes. We discover that elevated physical confinement drastically prolongs budding intervals without any physiological defects or activating global regulatory programs. Remarkably, extended cell division times are not associated with transcriptional or proteomic signatures of mechanosensation or cell cycle regulation. Rather, 3D confinement physically constrains the volumetric growth of incipient buds -- manifesting as delayed cell cycle progression. Hence, our findings establish that physical constrainment regulates eukaryotic cell division.

biophysics↗

bioRxiv2025

Zebra finch introductory notes do not influence female response to song and juvenile song learning accuracy

Many songbirds begin their song bouts with introductory notes (INs). In some songbird species like rufous-sided towhees and white-crowned sparrows, INs are believed to function in communication, to alert conspecifics about song onset or as a signal for species identification, but it is unclear whether this function is conserved in other species. Here, we addressed this question using the zebra finch, a well-studied songbird. Male zebra finches begin their song bouts with several INs and the number of INs increases when males sing to females or juveniles, suggesting a possible role of INs in female song preference and/or juvenile song learning. To test these hypotheses, we first recorded and analyzed call responses of female zebra finches to playbacks of different song stimuli. Female zebra finches responded equally to songs with and without INs, even when songs were degraded or when background noise was present. Second, we examined song learning accuracy of juveniles and found that juveniles copied songs accurately from their fathers independent of the fathers number of INs. Overall, these results show that zebra finch INs do not influence female response to song or juvenile song learning and suggest that INs might have different functions in different songbird species.

animal behavior and cognition↗

bioRxiv2024

Synthesis of ionizable lipopolymers using split-Ugi reaction for pulmonary delivery of various size RNAs and gene editing

We present an efficient approach for synthesizing cationic poly(ethylene imine) derivatives using the multicomponent split-Ugi reaction to rapidly create a library of complex functional ionizable lipopolymers. We synthesized a diverse library of 155 polymers, formulated them into polyplexes to establish structure-activity relationships crucial for endosomal escape and efficient transfection. After discovering a lead structure, lipopolymer-lipid hybrid nanoparticles are introduced to preferentially deliver to and elicit effective mRNA transfection in lung endothelium and immune cells, including T cells with low in vivo toxicity. The lipopolymer-lipid hybrid nanoparticles showed 300-fold improvement in systemic mRNA delivery to the lung compared to in vivo-JetPEI(R). Lipopolymer-lipid hybrid nanoparticles demonstrated efficient delivery of mRNA-based therapeutics for treatment of two different disease models. Lewis Lung cancer progression was significantly delayed after treatment with loaded IL-12 mRNA in U155@lipids after repeated i.v. administration. Systemic delivery of human CFTR (hCFTR) mRNA resulted in production of functional form of CFTR protein in the lungs. The functionality of hCFTR protein was confirmed by restoration of CFTR- mediated chloride secretion in conductive airway epithelia in CFTR knockout mice after nasal instillation of hCFTR mRNA loaded U155@lipids. We further showed that, U155@lipids nanoparticles can deliver complex CRISPR-Cas9 based RNA cargo to the lung, achieving 5.6 {+/-} 2.4 % gene editing in lung tissue. Moreover, we demonstrated successful PD-1 gene knockout of T cells in vivo. Our results highlight a versatile delivery platform for systemic delivering of mRNA of various sizes for gene therapy for a variety of therapeutics.

bioengineering↗

bioRxiv2023

Distinct Local and Global Functions of Aβ Low-Threshold Mechanoreceptors in Mechanical Pain Transmission

The roles of A{beta} low-threshold mechanoreceptors (LTMRs) in transmitting mechanical hyperalgesia and in alleviating chronic pain have been of great interest but remain contentious. Here we utilized intersectional genetic tools, optogenetics, and high-speed imaging to specifically examine functions of SplitCre labeled A{beta}-LTMRs in this regard. Genetic ablation of SplitCre-A{beta}-LTMRs increased mechanical pain but not thermosensation in both acute and chronic inflammatory pain conditions, indicating their modality-specific role in gating mechanical pain transmission. Local optogenetic activation of SplitCre-A{beta}-LTMRs triggered nociception after tissue inflammation, whereas their broad activation at the dorsal column still alleviated mechanical hypersensitivity of chronic inflammation. Taking all data into consideration, we propose a new model, in which A{beta}-LTMRs play distinctive local and global roles in transmitting and alleviating mechanical hyperalgesia of chronic pain, respectively. Our model suggests a new strategy of global activation plus local inhibition of A{beta}-LTMRs for treating mechanical hyperalgesia.

neuroscience↗

bioRxiv2022

SBT-272 improves TDP-43 pathology in the ALS motor cortex by modulating mitochondrial integrity, motility, and function

Mitochondrial defects are one of the common underlying causes of neuronal vulnerability in motor neuron diseases, such as amyotrophic lateral sclerosis (ALS), and TDP-43 pathology is the most common proteinopathy in ALS. Disrupted inner mitochondrial membrane (IMM) reported in the upper motor neurons (UMNs) of ALS patients with TDP-43 pathology is recapitulated in the UMNs of well-characterized mutant hTDP-43 mouse models of ALS. The construct validity, such as common cellular pathology in mice and human, offers a unique opportunity to test treatment strategies that may translate. SBT-272 is a well-tolerated brain-penetrant small molecule that stabilizes cardiolipin, a phospholipid found in IMM, thereby restoring mitochondrial structure and respiratory function. We investigated whether SBT-272 can improve IMM structure and health in UMNs diseased with TDP-43 pathology in our well-characterized UMN reporter line for ALS. We found that SBT-272 significantly improved mitochondrial structural integrity and restored mitochondrial motility and function. This led to improved health of diseased UMNs in vitro. In comparison to edaravone and AMX0035, SBT-272 appeared more effective in restoring health of diseased UMNs. Chronic treatment of SBT-272 for sixty days starting at an early symptomatic stage of the disease in vivo led to a reduction in astrogliosis, microgliosis, and retention of UMN degeneration in the ALS motor cortex. Our results underscore the therapeutic potential of SBT-272, especially within the context of TDP-43 pathology and mitochondrial dysfunction. HighlightsO_LIEarly and progressive upper motor neuron (UMN) degeneration defines ALS pathology C_LIO_LIMitochondrial defects are prominent and common in UMNs with TDP-43 pathology C_LIO_LISBT-272 treatment improves mitochondrial stability, mobility and function C_LIO_LISBT-272 treatment reduces astrogliosis, microgliosis and improves UMN health C_LI

neuroscience↗