Biology subjects

Smith, I. T.

Publications and source records attributed to Smith, I. T..

8 recordsLinked to original sources

bioRxiv2026

Disrupted Brain Organoid Circuitry, Structural Organization, and Spine Morphology in 7q11.23 Copy Number Variant Syndromes

The 7q11.23 chromosomal region represents a model of gene dosage-dependence, where a hemizygous deletion causes Williams Syndrome (WS) and a duplication leads to 7q11.23 Duplication Syndrome (Dup7). It is not understood how these copy number variations (CNVs) disrupt development and functional cortical circuit assembly. Utilizing iPSC-derived cerebral organoids and longitudinal imaging from post-differentiation day 30 to 150, we characterized the aberrant neural rosette morphogenesis in WS and Dup7 during early stages, establishing an early structural divergence from control lines. We observed accelerated early cortical rosette morphogenesis in WS, characterized by a premature increase in both rosette number and layer thickness compared to controls. In contrast, Dup7 organoids consistently exhibit a significantly lower number and reduced thickness of rosettes from early stages onward. This early structural disruption progressively impacted synaptic-level architecture as the organoids matured. Dendritic spine characterization at later stages revealed Dup7 organoids exhibited a significantly higher dendritic spine density compared to WS. Pharmacological antagonism of CCR5 (C-C chemokine receptor type 5) with Maraviroc significantly enhanced dendritic spine density in control and WS organoids; however, this effect was absent in Dup7. To determine how these structural anomalies translate into circuit-level behavior, we performed longitudinal calcium imaging using GCaMP. Control organoids sustained synchronized activity and high spike correlations at all time points. This synchronization was delayed and highly transient in WS organoids, and completely abolished in Dup7 organoids, which exhibit significantly low spike correlations at all stages. Developmentally, GABA changes from acting as an excitatory signal in the immature brain to an inhibitory signal as the brain matures. As control lines matured gabazine-induced desynchronization progressively diminished, but persisted in WS organoids. Dup7 organoids failed to establish synchronization at any developmental time point, but displayed a negligible increased synchrony following gabazine treatment. These functional aberrations were paralleled by genotype-specific defects in structural organization, specifically in rosette morphogenesis and dendritic spine density. Collectively, our findings demonstrate that 7q11.23 CNVs trigger pathogenic neurodevelopmental defects by derailing the trajectories of structural organization, circuit assembly, and functional synchronization during cortical maturation.

neuroscience↗

bioRxiv2026

Functional and structural characterization of dendritic spine pathology in a mouse model of tauopathy

Abnormal deposition of the microtubule-associated protein tau has long been associated with neurodegenerative diseases. While spine loss and neuronal death are hallmarks of tauopathy, how pathological tau affects synaptic activity in vivo and whether functional properties of individual synapses dictate the survival fate of dendritic spines remain elusive. Here we examined the visual response properties of dendrites and spines of layer 2/3 primary visual cortical neurons, using longitudinal two-photon calcium imaging in P301S mouse model of tauopathy. We found that neuronal outputs in tau mutant mice were hyperactive and poorly tuned whereas dendritic spine responses were also poorly tuned but hypoactive. Moreover, we found that spines that were stably retained across two imaging sessions were larger in size and more sharply tuned but less active compared to those that turned over in controls. Such structure-to-function relationship was not observed in mutants. Our findings illustrate how the preferential maintenance of well-tuned inputs in healthy neural circuitry may be affected by tauopathy, resulting in neurons with poorly tuned visual responses.

neuroscience↗

bioRxiv2025

daf-16/FOXO promotes the activity of ligand-bound DAF-12/NHR to coordinate dauer recovery and post-dauer seam cell fate

Animal development occurs in the context of varying environmental conditions. Many animal species can withstand adverse conditions by entering a stress-resistant and developmentally arrested diapause stage. If conditions improve, animals can recover and complete development. In Caenorhabditis elegans larvae that encounter adverse environments, dauer diapause can interrupt developmental progression after the second larval molt. During continuous (non-dauer) development, a heterochronic molecular timer comprised primarily of microRNAs and their targets controls the progression of stage-specific cell fates in lateral hypodermal seam cells. In unfavorable conditions, the DAF-16/FOXO transcription factor promotes dauer formation in part through opposing production of the ligand for the DAF-12 nuclear hormone receptor. Ligand-free DAF-12 promotes dauer formation and represses expression of heterochronic microRNAs in the let-7 family. Here, we show that daf-16 acts before dauer formation in anticipation of growth after dauer by promoting both dauer exit and developmental progression. We found that daf-16(0) post-dauer adults showed delayed dauer exit, reiterative heterochronic defects, and reduced expression of let-7-family microRNAs. These phenotypes were suppressed by addition of the DAF-12 ligand, dafachronic acid. Dafachronic acid is synthesized from cholesterol, and dauer larvae sequester cholesterol in the intestinal lumen until dauer exit. We found that a fluorescent cholesterol analog was not retained in daf-16 mutant larvae during dauer recovery. Timed auxin-mediated depletion of DAF-16 indicated that daf-16 is required before dauer formation to prevent reiterative seam cell fates in post-dauer animals. We propose a model whereby daf-16 acts prior to dauer formation to enable dafachronic acid synthesis by retaining cholesterol during dauer recovery. Ligand-bound DAF-12 then promotes dauer exit and expression of let-7-family microRNAs, thereby promoting developmental progression. Thus, daf-16 coordinates dauer entry with anticipation of recovery and post-dauer development.

developmental biology↗

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

daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71

Many tissue-specific stem cells maintain the ability to produce multiple cell types during long periods of non-division, or quiescence. FOXO transcription factors promote quiescence and stem cell maintenance, but the mechanisms by which FOXO proteins promote multipotency during quiescence are still emerging. The single FOXO ortholog in C. elegans, daf-16, promotes entry into a quiescent and stress-resistant larval stage called dauer in response to adverse environmental cues. During dauer, stem and progenitor cells maintain or re-establish multipotency to allow normal development to resume after dauer. We find that during dauer, daf-16/FOXO prevents epidermal stem cells (seam cells) from prematurely adopting differentiated, adult characteristics. In particular, dauer larvae that lack daf-16 misexpress collagens that are normally adult-enriched. Using col-19p::gfp as an adult cell fate marker, we find that all major daf-16 isoforms contribute to opposing col-19p::gfp expression during dauer. By contrast, daf-16(0) larvae that undergo non-dauer development do not misexpress col-19p::gfp. Adult cell fate and the timing of col-19p::gfp expression are regulated by the heterochronic gene network, including lin-41 and lin-29. lin-41 encodes an RNA-binding protein orthologous to LIN41/TRIM71 in mammals, and lin-29 encodes a conserved zinc finger transcription factor. In non-dauer development lin-41 opposes adult cell fate by inhibiting the translation of lin-29, which directly activates col-19 transcription and promotes adult cell fate. We find that during dauer, lin-41 blocks col-19p::gfp expression, but surprisingly, lin-29 is not required in this context. Additionally, daf-16 promotes the expression of lin-41 in dauer larvae. The col-19p::gfp misexpression phenotype observed in dauer larvae with reduced daf-16 requires the downregulation of lin-41, but does not require lin-29. Taken together, this work demonstrates a novel role for daf-16/FOXO as a heterochronic gene that promotes expression of lin-41/TRIM71 to contribute to multipotent cell fate in a quiescent stem cell model.

genetics↗

bioRxiv2020

The impact of interneurons on nonlinear synaptic integration in the neocortex

Excitatory inputs arriving at the dendrites of a neuron can engage active mechanisms that nonlinearly amplify the depolarizing currents. Interneuron-mediated inhibition can modulate this active process, in a subtype-dependent manner. For example, dendrite-targeting inhibition is hypothesized to increase the amplitude of synaptic input required to activate voltage-dependent nonlinear synaptic integration. To examine how inhibition influences active synaptic integration, we optogenetically manipulated the activity of two different subtypes of interneurons: dendrite-targeting somatostatin-expressing (SOM) and perisomatic-targeting parvalbumin-expressing (PV) interneurons. In acute slices of mouse primary visual cortex, electrical stimulation evoked nonlinear synaptic integration that depended on N-methyl-D-aspartate (NMDA) receptors. Optogenetic activation of SOM neurons in conjunction with electrical stimulation resulted in predominantly divisive inhibitory gain control, reducing the magnitude of the nonlinear response without affecting its threshold. PV activation, on the other hand, had a minimal effect on dendritic nonlinearities, resulting in a small subtractive effect. Furthermore, we found that mutual inhibition among SOM interneurons was strong and more prevalent than previously thought, while mutual inhibition among PV interneurons was minimal. These results challenge previous models of inhibitory modulation of active synaptic integration. The major effect of SOM inhibition is not a shift in threshold for activation of nonlinear integration, but rather a decrease the amplitude of the nonlinear response.

neuroscience↗

bioRxiv2017

Mice use robust and common strategies to discriminate natural scenes

Mice use vision to navigate and avoid predators in natural environments. However, the spatial resolution of mouse vision is poor compared to primates, and mice lack a fovea. Thus, it is unclear how well mice can discriminate ethologically relevant scenes. Here, we examined natural scene discrimination in mice using an automated touch-screen system. We estimated the discrimination difficulty using the computational metric structural similarity (SSIM), and constructed psychometric curves. However, the performance of each mouse was better predicted by the population mean than SSIM. This high inter-mouse agreement indicates that mice use common and robust strategies to discriminate natural scenes. We tested several other image metrics to find an alternative to SSIM for predicting discrimination performance. We found that a simple, primary visual cortex (V1)-inspired model predicted mouse performance with fidelity approaching the inter-mouse agreement. The model involved convolving the images with Gabor filters, and its performance varied with the orientation of the Gabor filter. This orientation dependence was driven by the stimuli, rather than an innate biological feature. Together, these results indicate that mice are adept at discriminating natural scenes, and their performance is well predicted by simple models of V1 processing.

neuroscience↗