Biology subjects

Smith, S. L.

Publications and source records attributed to Smith, S. L..

At least 19 recordsLinked to original sources

bioRxiv2026

Arousal-informed neuronal avalanches operate near criticality

Cortical networks are thought to operate near a "critical point" that optimizes information processing, but this has been difficult to test at single-cell resolution across large brain areas, as narrow fields of view miss overlapping neural avalanches, causing subcritical estimates, Using mesoscopic two-photon calcium imaging in awake mouse visual cortex, we recorded thousands of neurons and applied convolutional non-negative matrix factorization to decompose population activity into distinct, overlapping spatiotemporal avalanches. Rather than occupying a single dynamical state, we find that the cortex hosts multiple overlapping subnetworks distributed across a phase diagram at varying distances from the critical point. Arousal-linked avalanches propagate widely and operate nearest the critical point, showing optimized dynamic range, minimized algorithmic complexity, and maximized temporal entropy. Our results reveal how the awake brain tunes parallel near-critical subnetworks to support robust sensory computation.

neuroscience↗

bioRxiv2026

Disrupted O-GalNAc glycosylation as a mechanism and biomarker of SLC35A2-associated epilepsy

Rare germline and somatic variants in SLC35A2 cause a spectrum of severe glycosylation disorders that commonly present with epilepsy. SLC35A2 encodes the Golgi transporter for UDP-galactose, but how its deficiency leads to severe neurodevelopmental disorders is unknown. Using a mouse model deficient for Slc35a2 in the forebrain, we identified a specific defect in O-GalNAc glycan synthesis, while other galactose-containing glycoconjugates remained intact. O-GalNAc glycans were absent from their normal location within neuronal tracts of the corpus callosum, and truncated precursors accumulated in the cortex on critical extracellular matrix molecules. Cultured primary neurons lacking Slc35a2 showed impaired development, hyperexcitability, and impaired O-GalNAc glycosylation. Finally, human brain tissue from cases of SLC35A2-associated intractable epilepsy displayed a strong correlation between variant burden and truncated O-GalNAc glycans. These findings provide a mechanistic link between genetic causes of SLC35A2-associated epilepsy and protein O-glycosylation that can be targeted for biomarker and therapeutic development.

neuroscience↗

bioRxiv2025

Class-I myosin responds to change in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells

Clathrin-mediated endocytosis (CME) is an essential cellular process that needs to operate efficiently across a wide range of conditions. Internalization of the endocytic site involves forces generated by membrane-bound proteins and Arp2/3-mediated branched actin filament assembly to bend the plasma membrane (PM) from flat to omega-shaped. In mammalian CME, the requirement for a branched actin filament network varies depending on cell type and differences in membrane tension. However, how the actin network adapts to changes in load in order to ensure robustness of this process over a range of membrane tensions is not understood. Here, we combine live-cell imaging and super-resolution microscopy of genome-edited human induced pluripotent stem cells (hiPSCs) to investigate the role of the mammalian class-I myosin, Myosin1E (Myo1E), in load adaptation. Under normal conditions, sites that recruit Myo1E are rare and exhibit slow CME dynamics. However, as membrane tension increases and CME dynamics are slowed globally, Myo1E is recruited to more sites, likely to assemble more branched actin, resulting in increased force generation to rescue stalled sites and promote internalization. Loss of Myo1E results in increased Arp2/3 complex lifetime at CME sites under normal conditions, and at high membrane tension, these sites fail to recruit as many Arp2/3 molecules. We propose that Myo1E is recruited to CME sites that have stalled due to increased membrane tension, where it helps build a more effective branched actin network by generating force through motor activity and recruiting additional Arp2/3 complexes to rescue stalled sites. SignificanceFor mammalian cells to internalize extracellular cargo via clathrin-mediated endocytosis (CME), specific regions of the plasma membrane (PM) must bend from flat to inwardly curved, a process that requires force-generating proteins. One key component in generating this force during CME is the branched actin network, in which actin filaments polymerize against the plasma membrane. When PM tension increases, more force is required to generate curvature, prompting the assembly of actin and actin associated proteins to aid the process. We demonstrate that the class-I myosin motor, Myosin1E (Myo1E), becomes increasingly crucial as membrane tension rises, presumably to build a more effective branched actin network to facilitate internalization of slowed sites.

cell biology↗

bioRxiv2025

Synergy mediates Long-Range Correlations in the Visual Cortex Near Criticality

Long-range correlations are a key signature of systems operating near criticality, indicating spatially-extended interactions across large distances. These extended dependencies underlie other emergent properties of critical dynamics, such as high susceptibility and multi-scale coordination. In the brain, along with other signatures of criticality, long-range correlations have been observed across various spatial scales, suggesting that the brain may operate near a critical point to optimise information processing and adaptability. However, the mechanisms underlying these long-range correlations remain poorly understood. Here, we investigate the role of synergistic interactions in mediating long-range correlations in the visual cortex of awake mice. We leverage recent advances in mesoscale two-photon calcium imaging to analyse the activity of thousands of neurons across a wide field of view, allowing us to confirm the presence of long-range correlations at the level of neuronal populations. By applying the Partial Information Decomposition (PID) framework, we decompose the correlations into synergistic and redundant information interactions. Our results reveal that the increase in long-range correlations during visual stimulation is accompanied by a significant increase in synergistic rather than redundant interactions among neurons. Furthermore, we analyse a combined network formed by the union of synergistic and redundant interaction networks, and find that both types of interactions complement each other to facilitate efficient information processing across long distances. This complementarity is further enhanced during the visual stimulation. These findings provide new insights into the computational mechanisms that give rise to long-range correlations in neural systems and highlight the importance of considering different types of information interactions in understanding correlations in the brain.

neuroscience↗

bioRxiv2025

Open-source modular FPGA system for two-photon mesoscope enabling multi-layer, multi-depth neural activity recording and lifetime imaging

Large field-of-view (FOV) two-photon microscopy makes it possible to record a large number of neural activities from multiple brain regions simultaneously. However, the larger the field of view, the longer it takes to scan the entire FOV. To increase imaging speed, we have developed open-source software to digitize analogue signals from a photomultiplier tube using a field-programmable gate array (FPGA) at a rate of 3.2 GS/s. By combining this with a newly developed a circular delay-path module for a custom two-photon mesoscope (Diesel2p), we succeeded in simultaneous recording of >10,000 neurons from the entire bilateral dorsal cortex at up to four depths. We also demonstrated large FOV lifetime imaging using the same system. Our modular, open-source FPGA system can be readily integrated into any type of two-photon microscope and will accelerate the biomedical application of multi-scale two-photon imaging in a wide range of pathophysiological investigations.

neuroscience↗

bioRxiv2025

Harnessing fusion of genome-edited human stem cells to rapidly screen for novel protein functions in vivo

Genome editing has enabled the integration of fluorescent protein coding sequences into genomes, resulting in expression of in-frame fusion proteins under the control of their natural gene regulatory sequences. While this technique overcomes the well-documented artifacts associated with gene overexpression, editing genomes of metazoan cells incurs a significant time cost compared to simpler organisms, such as yeast. Editing two or more genes to express multiple fluorescent fusion proteins in a single cell line has proven to be a powerful strategy for uncovering spatio-dynamic, and therefore functional, relationships among different proteins, but it can take many months to edit each gene within the same cell line. Here, by utilizing cell fusions, we quickly generated cells expressing pairwise permutations of fluorescent fusion proteins in genome-edited human cells to reveal previously undetected protein-organelle interactions. We fused human induced pluripotent stem cells (hiPSCs) that express in-frame fusions of clathrin-mediated endocytosis (CME) and actin cytoskeleton proteins with hiPSCs that express fluorescently tagged organelle markers, uncovering novel interactions between CME proteins, branched actin filament networks, and lysosomes. Significance StatementO_LICell fusion can be used to generate new multi-colored genome-edited cell lines, which can be clonally expanded. C_LIO_LIIn combination with genome-edited fluorescent cell line libraries such as the collection from the Allen Institute for Cell Science, cell fusion can be used as a screening tool to look for novel protein localization on a variety of intracellular structures. C_LIO_LIMultiple endocytic proteins localize to the surface of lysosomes in healthy, non-stressed cells, and these proteins exhibit a broad range of behaviors on the lysosome surface. C_LI

cell biology↗

bioRxiv2025

Non-inertial scan angle multiplier for expanded fields-of-view

In many laser scan engines, mechanical inertia imposes a tradeoff between mirror diameter (mass) and scan speed (cycle time) and/or scan angle amplitude. Ultimately, this limits the field-of-view and/or scan speed in multiphoton and confocal imaging, laser-based manufacturing, and other applications. To push parameters past this inertia limit, we present a non-inertial (stationary) add-on unit that doubles the scan angle amplitude while preserving both the beam size and cycle time, thus doubling the etendue (optical invariant) and overall system throughput. We demonstrate its use in two-photon calcium imaging of neural activity in living mice. We also adapt the approach to present a phase doubling unit that doubles the maximum range of phase modulators. Finally, we describe further variants including generalizing the approach to Nx scan angle multiplication (N = 2, 3, 4, ...) with diffraction limited performance across a wide scan angle range and over a broad wavelength bandwidth. These non-inertial scan angle multipliers (called Nisam2x, 3x, ...) can expand the capabilities of a range of technologies including imaging, adaptive optics, sensing, marking, and manufacturing.

neuroscience↗

bioRxiv2025

Biologically-informed machine learning identifies a new clinically-actionable bladder cancer subgroup characterised by NRF2 overactivity

Muscle-invasive bladder cancer is a diverse disease where subtyping is ambiguous. Gene expression profiling followed by unsupervised machine learning (ML) has broadened our understanding of tumour biology, but has failed to provide high-confidence clinically-actionable subgroups. To focus on tissue-specific urothelial biology, we generated co-expression networks from histologically normal bladder, including multiple differentiation states and prioritising transcription factors (TFs). This strategy revealed an emergent set of 98 TFs which we used to stratify The Cancer Genome Atlas bladder cancer cohort, revealing a subdivision of basal tumours characterised by the detoxification and glutaminolysis activity of NRF2, rendering them resistant to standard bladder cancer interventions. These 20 tumours (4.9%) expressed squamous markers, were highly aggressive (15% 2-year survival), and had signatures of active PI3K, MTOR and retinoic acid signalling. Intriguingly, only half of the subgroup had activating mutations in the NRF2/KEAP1 pathway, whilst half of putative driver NFE2L2 mutations were excluded. This highlighted the importance of expression-based classification, particularly as re-analysis of NFE2L2-mutated lung cancer trial data showed only mutations consistent with our classification strategy responded to NRF2 inhibition. Our approach provides the first direct evidence that unsupervised ML can be biologically-informative in identifying clinically-actionable subgroups.

cancer biology↗

bioRxiv2024

Standardised Measurements for Monitoring and Comparing Multiphoton Microscope Systems

The goal of this protocol is to enable better characterisation of multiphoton microscopy hardware across a large user base. The scope of this protocol is purposefully limited to focus on hardware, touching on software and data analysis routines only where relevant. The intended audiences are scientists using and building multiphoton microscopes in their laboratories. The goal is that any scientist, not only those with optical expertise, can test whether their multiphoton microscope is performing well and producing consistent data over the lifetime of their system.

neuroscience↗

bioRxiv2023

Visual information is broadcast among cortical areas in discrete channels

Withdrawal StatementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2018/469114. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: 10.1101/469114

neuroscience↗

bioRxiv2023

Mesoscale functional architecture in medial posterior parietal cortex

The posterior parietal cortex (PPC) in mice has various functions including multisensory integration1-3, vision-guided behaviors4-6, working memory7-13, and posture control14,15. However, an integrated understanding of these functions and their cortical localizations in and around the PPC and higher visual areas (HVAs) has not been completely elucidated. Here we simultaneously imaged the activity of thousands of neurons within a 3 x 3 mm2 field-of-view, including eight cortical areas around the PPC, during behavior with a two-photon mesoscope16. Mice performed both a vision-guided task and a choice history-dependent task, and the imaging results revealed distinct, localized, behavior-related functions of two medial PPC areas. Neurons in the anteromedial (AM) HVA responded to both vision and choice information, and thus AM is a locus of association between these channels. By contrast, the anterior (A) HVA stores choice history with sequential dynamics and represents posture. Mesoscale correlation analysis on the intertrial variability of neuronal activity demonstrated that neurons in AM exhibited diverse, area-dependent interactions, while neurons in area A shared fluctuations with the primary somatosensory area. Pairwise interareal interactions among neurons were precisely predicted by the anatomical input correlations, with the exception of some global interactions. Thus, the medial PPC has two distinct modules, areas AM and A, with each having distinctive modes of cortical communication. These medial PPC modules can serve separate higher-order functions: area AM for multisensory and cognitive integration with locally processed signals and area A for transmission of information including posture, movement, and working memory.

neuroscience↗

bioRxiv2022

The Cousa objective: a long working distance air objective for multiphoton imaging in vivo

Multiphoton microscopy can resolve fluorescent structures and dynamics deep in scattering tissue, but applying this technique in vivo can be limited by short working distance water-immersion objectives. Here we present an ultra long working distance (20 mm) air objective called the Cousa objective. It is optimized for performance across multiphoton imaging wavelengths, offers a > 4 mm2 field-of-view with submicron lateral resolution, and is compatible with commonly used multiphoton imaging systems. We share the full optical prescription, and report performance including in vivo 2-photon and 3-photon imaging in a range of species and preparations.

neuroscience↗

bioRxiv2021

Selective representations of texture and motion in mouse higher visual areas

Mice have a constellation of higher visual areas, but their functional specializations are unclear. Here, we used a data-driven approach to examine neuronal representations of complex visual stimuli across mouse higher visual areas, measured using large field-of-view two-photon calcium imaging. Using specialized stimuli, we found higher fidelity representations of texture in area LM, compared to area AL. Complementarily, we found higher fidelity representations of motion in area AL, compared to area LM. We also observed this segregation of information in response to naturalistic videos. Finally, we explored how popular models of visual cortical neurons could produce the segregated representations of texture and motion we observed. These selective representations could aid in behaviors such as visually guided navigation.

neuroscience↗

bioRxiv2021

Long-term Transverse Imaging of the Hippocampus with Glass Microperiscopes

The hippocampus consists of a stereotyped neuronal circuit repeated along the septal-temporal axis. This transverse circuit contains distinct subfields with stereotyped connectivity that support crucial cognitive processes, including episodic and spatial memory. However, comprehensive measurements across the transverse hippocampal circuit in vivo are intractable with existing techniques. Here, we developed an approach for two-photon imaging of the transverse hippocampal plane in awake mice via implanted glass microperiscopes, allowing optical access to the major hippocampal subfields and to the dendritic arbor of pyramidal neurons. Using this approach, we tracked dendritic morphological dynamics on CA1 apical dendrites and characterized spine turnover. We then used calcium imaging to quantify the prevalence of place and speed cells across subfields. Finally, we measured the anatomical distribution of spatial information, finding a non-uniform distribution of spatial selectivity along the DG-to-CA1 axis. This approach extends the existing toolbox for structural and functional measurements of hippocampal circuitry.

neuroscience↗

bioRxiv2021

Flexible Simultaneous Mesoscale Two-Photon Imaging of Neural Activity at High Speeds

Understanding brain function requires monitoring local and global brain dynamics. Two-photon imaging of the brain across mesoscopic scales has presented trade-offs between imaging area and acquisition speed. We describe a flexible cellular resolution two-photon microscope capable of simultaneous video rate acquisition of four independently targetable brain regions spanning an approximate five-millimeter field of view. With this system, we demonstrate the ability to measure calcium activity across mouse sensorimotor cortex at behaviorally relevant timescales.

neuroscience↗

bioRxiv2020

Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry

Imaging the activity of neurons that are widely distributed across brain regions deep in scattering tissue at high speed remains challenging. Here, we introduce an open-source system with Dual Independent Enhanced Scan Engines for Large Field-of-view Two-Photon imaging (Diesel2p). Combining novel optical design, adaptive optics, and temporal multiplexing, the system offers subcellular resolution over a large field-of-view ([~] 25 mm2) with independent scan engines. We demonstrate the flexibility and various use cases of this system for calcium imaging of neurons in the living brain.

neuroscience↗

bioRxiv2020

Locus-specific introgression in young hybrid swarms: drift dominates selection

Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These anthropogenic hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44997 SNPs to identify loci introgressing at excessive rates when compared to the genome wide expectation in an anthropogenic hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centers that were significantly different from the genome wide expectation, and 17.6% had excessive rates of introgression. Based on simulations, we believe that many of these markers have diverged from average due to drift, rather than because of selection. Future work could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are indeed responding to selection in anthropogenic hybrid zones.

evolutionary biology↗

bioRxiv2020

Identifying signal and noise structure in neuralpopulation activity with Gaussian process factormodels

Neural datasets often contain measurements of neural activity across multiple trials of a repeated stimulus or behavior. An important problem in the analysis of such datasets is to characterize systematic aspects of neural activity that carry information about the repeated stimulus or behavior of interest, which can be considered "signal", and to separate them from the trial-to-trial fluctuations in activity that are not time-locked to the stimulus, which for purposes of such analyses can be considered "noise". Gaussian Process factor models provide a powerful tool for identifying shared structure in high-dimensional neural data. However, they have not yet been adapted to the problem of characterizing signal and noise in multi-trial datasets. Here we address this shortcoming by proposing "signal-noise" Poisson-spiking Gaussian Process Factor Analysis (SNP-GPFA), a flexible latent variable model that resolves signal and noise latent structure in neural population spiking activity. To learn the parameters of our model, we introduce a Fourier-domain black box variational inference method that quickly identifies smooth latent structure. The resulting model reliably uncovers latent signal and trial-to-trial noise-related fluctuations in large-scale recordings. We use this model to show that predominantly, noise fluctuations perturb neural activity within a subspace orthogonal to signal activity, suggesting that trial-by-trial noise does not interfere with signal representations. Finally, we extend the model to capture statistical dependencies across brain regions in multi-region data. We show that in mouse visual cortex, models with shared noise across brain regions out-perform models with independent per-region noise.

neuroscience↗