Biology subjects

Goda, Y.

Publications and source records attributed to Goda, Y..

10 recordsLinked to original sources

bioRxiv2026

A chromatin relay from AIRE to ETS transcription factors sustains peripheral antigen expression in the thymic mimetic cells to ensure central tolerance.

Medullary thymic epithelial cells (mTECs) establish central tolerance by expressing a diverse repertoire of peripheral tissue-specific antigens (TSAs). This diversity is regulated not only by the transcriptional regulator AIRE, but also by lineage-defining factors in tissue-mimetic, AIRE-negative descendants of Aire mTECs (post-Aire mimetic TECs). However, whether and how prior AIRE activity contributes to TSA expression in post-AIRE mimetic TECs remains unclear. Here, we identify the ETS transcription factors, EHF and ELF3, as key regulators that sustain AIRE-primed gene expression in these cells. EHF and ELF3 preferentially bind distal genomic regions which are rendered accessible in advance by AIRE. Combined loss of EHF and ELF3 disrupts expression of AIRE-regulated genes expressed in mimetic TECs, leading to tissue-selective autoimmunity. Our findings reveal a relay mechanism in which AIRE primes chromatin for ETS factors to maintain TSA expression in post-AIRE mimetic TECs, thereby safeguarding self-tolerance.

immunology↗

bioRxiv2026

Hierarchical processing and polarization encoding in the cephalopod visual system

Coleoid cephalopods (octopus, cuttlefish and squid, hereafter cephalopods) have evolved a range of complex visually-guided behaviours, from dexterous hunting to skin-pattern based camouflage and communication1. They have also evolved sensitivity to the polarization of light2, an adaptation thought to help detect camouflaged or semitransparent predators and prey in low visibility underwater environments3-10. How visual information is processed by the cephalopod brain to support their behaviours remains unclear. Here, studying the bigfin reef squid Sepioteuthis lessoniana, we performed calcium imaging and electrophysiological recordings from populations of neurons in the large visual center of the cephalopod brain, the optic lobe (OL). We revealed that the retina-recipient superficial OL contains a diversity of functionally distinct cell types, spatially organized into sub-layers, processing spatio-temporal features of light intensity and possessing polarization angle specificity. More complex features, e.g. direction selectivity, are seen in deeper regions of the OL cortex, which also exhibits spontaneous waves of neural activity in the absence of visual input. Neurons in the downstream OL medulla exhibit visual receptive field sizes and spontaneous activity levels which increase with brain depth, consistent with the hierarchical processing of visual information through the medullas tree-like anatomical organization. Medulla neurons exhibit sensitivity to local decreases in the degree of linear polarization (DoLP), which they integrate additively with light intensity information. Underwater imaging in the squids habitat off the coast of Okinawa, Japan, demonstrate that polarization sensitivity confers a robust short-range boost in object-background contrast over a range of objects and environmental conditions. These findings reveal convergent principles of hierarchical visual processing shared between cephalopods and vertebrates, and highlight how cephalopods utilise their distinct adaptation of polarization sensitivity to solve universal visual challenges underwater.

neuroscience↗

bioRxiv2024

SpyDen: Automating molecular and structural analysis across spines and dendrites

Investigating the molecular composition across neural compartments such as axons, dendrites, or synapses is critical for our understanding of learning and memory. State-of-the-art microscopy techniques can now resolve individual molecules and pinpoint their position with micrometre or even nanometre resolution across tens or hundreds of micrometres, allowing the labelling of multiple structures of interest simultaneously. Algorithmically, tracking individual molecules across hundreds of micrometres and determining whether they are inside any cellular compartment of interest can be challenging. Historically, microscopy images are annotated manually, often using multiple software packages to detect fluorescence puncta (e.g. labelled mRNAs) and then trace and quantify cellular compartments of interest. Advanced ANN-based automated tools, while powerful, are often able to help only with selected parts of the data analysis pipeline, may be optimised for specific spatial resolutions or cell preparations or may not be fully open source and open access to be sufficiently customisable. To address these challenges, we developed SpyDen. SpyDen is a Python package based upon three principles: i) ease of use for multi-task scenarios, ii) open-source accessibility and data export to a common, open data format, iii) the ability to edit any software-generated annotation and generalise across spatial resolutions. Equipped with a graphical user interface and accompanied by video tutorials, SpyDen provides a collection of powerful algorithms that can be used for neurite and synapse detection as well as fluorescent puncta and intensity analysis. We validated SpyDen using expert annotation across numerous use cases to prove a powerful, integrated platform for efficient and reproducible molecular imaging analysis.

neuroscience↗

bioRxiv2023

A role for APP in the development of astrocyte morphological complexity

The amyloid precursor protein (APP), whose proteolytic cleavage gives rise to amyloid-{beta} peptide, has been extensively studied for its role in Alzheimers disease, but its physiological function remains less understood. In neurons, APP and its two homologs, the amyloid precursor-like protein 1 (APLP1) and 2 (APLP2), are present in the synaptic compartment and promote synaptogenesis. Over recent years, astrocytes, an abundant glial cell in the brain, have attracted much attention for their role in regulating synapse formation and function. Although APP is also found in astrocytes, its role in these cells remains largely unexplored. Here we have sought to investigate the expression and function of APP in rodent astrocytes in vitro and in vivo. We find that APP along with its family members, APLP1 and APLP2, are expressed in astrocytes in vitro and in vivo. In primary hippocampal cultures, shRNA-mediated knockdown of astrocytic APP, APLP1 or APLP2 compromises astrocyte morphological elaboration to varying degrees. We have then focused on APP to characterize its role in astrocyte development in the intact brain. We show that astrocytic APP shapes the morphological complexity of astrocyte processes in vivo and may also modulate postsynaptic assembly. Our results highlight a role of astrocytic APP and possibly of APLPs that could potentially impact neuronal functions.

neuroscience↗

bioRxiv2023

Linking spontaneous and stimulated spine dynamics

Our brains continuously acquire and store memories through synaptic plasticity. However, spontaneous synaptic changes can also occur and pose a challenge for maintaining stable memories. Despite fluctuations in synapse size, recent studies have shown that key population-level synaptic properties remain stable over time. This raises the question of how local synaptic plasticity affects the global population-level synaptic size distribution and whether individual synapses undergoing plasticity escape the stable distribution to encode specific memories. To address this question, we (i) studied spontaneously evolving spines and (ii) induced synaptic potentiation at selected sites while observing the spine distribution pre- and post-stimulation. We designed a stochastic model to describe how the current size of a synapse affects its future size under baseline and stimulation conditions and how these local effects give rise to population-level synaptic shifts. Our study offers a new understanding of how seemingly spontaneous synaptic fluctuations and local plasticity both contribute to population-level synaptic dynamics.

neuroscience↗

bioRxiv2023

High-throughput 3D imaging flow cytometry of adherent 3D cell cultures

Three-dimensional (3D) cell cultures are indispensable in recapitulating in vivo environments. Among many 3D culture methods, the strategy to culture adherent cells on hydrogel beads to form spheroid-like structures is powerful for maintaining high cell viability and functions through an efficient supply of nutrients and oxygen. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high-throughput, scalable 3D imaging flow cytometry (3D-iFCM) platform for analyzing spheroid models on hydrogel beads. This platform is realized by integrating a single objective lens-based fluorescence light-sheet microscopy with a microfluidic device employing a combination of hydrodynamic and acoustofluidic focusing techniques. This integration enabled an unprecedentedly high-throughput, robust optofluidic 3D imaging, processing 513 cells s-1 and a total of more than 104 cells within a minute. The large dataset obtained allows us to quantify and compare the nuclear morphology of adhering and suspended cells, revealing adhering cells have smaller nuclei with non-round surfaces. This platforms high throughput, robustness, and precision for analyzing the morphology of subcellular compartments in 3D culture models holds promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.

bioengineering↗

bioRxiv2022

A quantitative rule to explain multi-spine plasticity

Neurons receive thousands of inputs onto their dendritic arbour, where individual synapses undergo activitydependent changes in strength. The durable forms of synaptic strength change, long-term potentiation (LTP) and long-term depression (LTD) require calcium entry through N-methyl-D-aspartate receptors (NMDARs) that triggers downstream protein signalling cascades in the dendrite. Notably, changes in postsynaptic strengths associated with LTP and LTD are correlated to changes in spine head volume, referred to as structural LTP (sLTP) and structural LTD (sLTD). Intriguingly, LTP and LTD, including sLTP and sLTD, are not necessarily restricted to the active, targeted synapses (homosynapses), and the changes in synaptic strength can spread and affect the strengths of inactive or non-stimulated synapses (heterosynapses) on the same cell. Moreover, the plasticity outcome at both homo- and heterosynapses can depend on the number of stimulated sites when eliciting multi-spine plasticity. Precisely how neurons allocate resources for implementing the changes in strength at individual synapses depending on their proximity to input activity across space and time remains an open question. In order to gain insights into the elementary processes underlying multi-spine plasticity that engages both homosynaptic and heterosynaptic changes, we have combined experimental and mathematical modelling approaches. On the one hand, we used glutamate uncaging to precisely and systematically stimulate variable numbers of homosynapses sharing the same dendritic branch whilst monitoring tens of other heterosynapses on the same dendrite. Homosynaptic potentiation of clusters of dendritic spines leads to heterosynaptic changes that are dependent on NMDAR, CaMKII and calcineurin. On the other hand, inspired by the Ca2+ levels hypothesis where different amounts of Ca2+ lead to either growth or shrinkage of spines, we have built a model based on a dual-role Ca2+-dependent protein that induces sLTP or sLTD. Comparing our experimental results with model predictions, we find that (i) both collaboration and competition among spines for protein resources are key drivers of heterosynaptic plasticity and (ii) the temporal and spatial distance between simultaneously stimulated spines impact the resulting spine dynamics. Moreover, our model can reconcile disparate experimental reports of sLTP and sLTD at homo- and heterosynaptic spines. Our results provide a quantitative description of the heterosynaptic footprint over minutes and hours post-stimulation across tens of microns of dendritic space. This broadens our knowledge about the operation of non-linear dendritic summation rules and how they impact spiking decisions.

neuroscience↗

bioRxiv2022

Droplet array-based platform for parallel optical analysis of dynamic extracellular vesicle secretion from single cells

Extracellular vesicles (EVs) are essential intercellular communication tools, but the regulatory mechanisms governing heterogeneous EV secretion are still unclear due to the lack of methods for precise analysis. Monitoring the dynamics of secretion from individually isolated cells is crucial because, in bulk analysis, secretion activity can be perturbed by cell-cell interactions, and a cell population rarely performs secretion in a magnitude- or duration-synchronized manner. Although various microfluidic techniques have been adopted to evaluate the abundance of single-cell-derived EVs, none can track their secretion dynamics continually for extended periods. Here, we have developed a droplet array-based method that allowed us to optically quantify the EV secretion dynamics of >300 single cells every 2 hours for 36 hours, which covers the cell doubling time of many cell types. The experimental results clearly show the highly heterogeneous nature of single-cell EV secretion and suggest that cell division facilitates EV secretion, showing the usefulness of this platform for discovering EV regulation machinery.

bioengineering↗

bioRxiv2021

Astrocyte GluN2C NMDA receptors control basal synaptic strengths of hippocampal CA1 pyramidal neurons in the stratum radiatum

Experience-dependent plasticity is a key feature of brain synapses for which neuronal N-Methyl-D-Aspartate receptors (NMDARs) play a major role, from developmental circuit refinement to learning and memory. Astrocytes also express NMDARs although their exact function has remained controversial. Here we identify a circuit function for GluN2C NMDAR, a subtype highly expressed in astrocytes, in layer-specific tuning of synaptic strengths in mouse hippocampal CA1 pyramidal neurons. Interfering with astrocyte NMDAR or GluN2C NMDAR activity reduces the range of presynaptic strength distribution specifically in the stratum radiatum inputs without an appreciable change in the mean presynaptic strength. Mathematical modeling shows that narrowing of the width of presynaptic release probability distribution compromises the expression of long-term synaptic plasticity. Our findings suggest a novel feedback signaling system that uses astrocyte GluN2C NMDARs to adjust basal synaptic weight distribution of Schaffer collateral inputs, which in turn impacts computations performed by the CA1 pyramidal neuron.

neuroscience↗

bioRxiv2020

Heterosynaptic cross-talk of pre- and postsynaptic strengths along segments of dendrites

Dendrites are crucial for integrating incoming synaptic information. Individual dendritic branches are thought to constitute a signal processing unit, yet how neighbouring synapses shape the boundaries of functional dendritic units are not well understood. Here we addressed the cellular basis underlying the organization of the strengths of neighbouring Schaffer collateral-CA1 synapses by optical quantal analysis and spine size measurements. Inducing potentiation at clusters of spines produced NMDA receptor-dependent heterosynaptic plasticity. The direction of postsynaptic strength change showed distance-dependency to the stimulated synapses where proximal synapses predominantly depressed whereas distal synapses potentiated; potentiation and depression were regulated by CaMKII and calcineurin, respectively. By contrast, heterosynaptic presynaptic plasticity was confined to weakening of presynaptic strength of nearby synapses, which required CaMKII and the retrograde messenger nitric oxide. Our findings highlight the parallel engagement of multiple signalling pathways, each with characteristic spatial dynamics in shaping the local pattern of synaptic strengths.

neuroscience↗