Biology subjects

Okamoto, H.

Publications and source records attributed to Okamoto, H..

15 recordsLinked to original sources

bioRxiv2025

Structural basis and physiological significance of non-canonical Gs coupling to the prototypical Gi-coupled melatonin MT1 receptor

G protein-coupled receptors (GPCRs) transduce extracellular stimuli into intracellular signals by coupling to various heterotrimeric G proteins. However, the rules governing G protein preference remain largely elusive. MT1 and MT2 are prototypical Gi/o-coupled GPCRs responding to melatonin, a hormone secreted in a circadian manner. We show here that MT1, but not MT2, couples also to Gs proteins in vitro and activates the Gs/cAMP pathway upon long-term melatonin exposure in vivo, mimicking physiological dawn conditions. We solved the cryo-electron microscopy structure of the melatonin-MT1-Gs complex at 3.0[A] resolution, which revealed a strikingly distinct binding mode compared to the MT1-Gi complex. The third intracellular loop of MT1 emerges as a key stabilizer for Gs coupling, a feature previously unrecognized. This is the first solved receptor-Gs complex of a primary Gi-coupled GPCRs, providing new structural and functional insights into G protein selectivity and circadian switch of G protein coupling.

molecular biology↗

bioRxiv2025

Predicting individual learning trajectories in zebrafish via the free-energy principle

The free-energy principle has been proposed as a unified theory of brain function, and recent evidence from in vitro experiments supports its validity. However, its empirical application to in vivo neuronal dynamics during active decision-making remains limited. This work reverse-engineered generative models--cast as canonical neural networks--from large-scale calcium imaging data of zebrafish performing a visually guided go/no-go task in a virtual-reality environment. Leveraging the formal equivalence between neural network dynamics and variational Bayesian inference, we constructed biologically plausible synthetic agents capable of active inference. These agents recapitulated individual variability in zebrafish neuronal dynamics and behaviour by identifying subject-specific prior and posterior beliefs. Additionally, they enabled quantitative predictions of long-term changes in neural activity, effective synaptic connectivity, and behavioural performance, including task accuracy after training. Our results demonstrate a powerful framework of active inference for modelling in vivo neuronal self-organisation and highlight the predictive validity of the free-energy principle in behaving animals.

neuroscience↗

bioRxiv2025

Image-based leaf SPAD value and chlorophyll measurement using a mobile phone: enabling accessible and sustainable crop management

AO_SCPLOWBSTRACTC_SCPLOWThis study evaluates a practical, low-cost solution for image-based leaf SPAD (Soil and Plant Analysis Development) value and chlorophyll content monitoring using a mobile phone. We compare laboratory assay and SPAD-502+ measurements with image-based estimates from a mobile phone app (PhotoFolia). Performance is tested for four commercial rice varieties grown in Thailand. Results show that the image-based method can predict SPAD values within {+/-} 1.2 units Mean Absolute Error (MAE) and- chlorophyll concentrations within 7.2% Mean Absolute Percentage Error (MAPE) of laboratory results. Achieving a SPAD value error close to the industry standard of {+/-}1 unit and a relative error of less than 10% in chlorophyll concentration estimation (compared to a laboratory method) demonstrates that an image-based approach using standard mobile phones can serve as an accessible, low-cost tool for on-farm chlorophyll monitoring, without the need for specialised equipment. Key Points / HighlightsNovel low-cost approach for chlorophyll assay and SPAD-value measurement using standard mobile phone. Achieves accuracy comparable to commercial tools. Eliminates need for specialised sensors or laboratory equipment. ImpactThis study demonstrates that mobile phone-based image analysis can accurately estimate leaf SPAD and chlorophyll levels in rice under ambient lighting conditions, offering a low-cost, accessible tool for monitoring plant health.

plant biology↗

bioRxiv2023

Brain enlargement with a rostral bias in larvae from a spontaneously variant Xenopus female line: implications for vertebrate evolution

Increased brain size and its rostral bias are hallmarks of vertebrate evolution, but the underlying developmental and genetic basis remains poorly understood. To provide clues to understanding vertebrate brain evolution, we investigated the developmental mechanisms of brain enlargement observed in the offspring of a previously unrecognized, spontaneously occurring female variant line of Xenopus that appears to reflect a genetic variation. Brain enlargement in larvae from this line showed a pronounced rostral bias that could be traced back to the neural plate, the primordium of the brain. At the gastrula stage, the Spemann organizer, which is known to induce the neural plate from the adjacent dorsal ectoderm and give it the initial rostrocaudal patterning, was expanded from dorsal to ventral in a large proportion of the offspring of variant females. Consistently, siamois expression, which is required for Spemann organizer formation, was expanded laterally from dorsal to ventral at the blastula stage in variant offspring. This implies that the active region of the Wnt/{beta}-catenin signaling pathway was similarly expanded in advance on the dorsal side, as siamois is a target gene of this pathway. Notably, the earliest detectable change in variant offspring was in fertilized eggs, in which maternal wnt11b mRNA, a candidate dorsalizing factor that activates Wnt/{beta}-catenin signaling, had a wider distribution in the vegetal cortical cytoplasm. Since lateral spreading of wnt11b mRNA, and possibly that of other potential maternal dorsalizing factors in these eggs, is expected to facilitate lateral expansion of the active region of the Wnt/{beta}-catenin pathway during subsequent embryonic stages, we concluded that aberrant Wnt/{beta}-catenin signaling could cause rostral-biased brain enlargement via expansion of siamois expression and consequent expansion of the Spemann organizer in Xenopus. Our studies of spontaneously occurring variations in brain development in Xenopus would help uncover genetic mutations that drive analogous morphogenetic variations during vertebrate brain evolution.

developmental biology↗

bioRxiv2023

Transgenic tools targeting striatal and pallidal subpopulations revealed evolutionary conservation and specialization of the cortico-basal ganglia circuit in zebrafish

The cortico-basal ganglia circuit mediates decision-making. Here, we generated transgenic tools for adult zebrafish targeting specific subpopulations of the components of this circuit and utilized them to identify evolutionary homologs of the mammalian direct- and indirect-pathway striatal neurons which respectively project to the homologs of the internal and external segment of the globus pallidus (dEN and Vl) as in mammals. Unlike in mammals, the Vl mainly projected to the dEN directly, not by way of the subthalamic nucleus. Further single-cell RNA sequencing analysis revealed two pallidal output pathways: a major shortcut pathway directly connecting the dEN with the pallium and the evolutionarily conserved closed loop by way of the thalamus. Our resources and circuit map provide the common basis for the functional study of the basal ganglia in a small and optically tractable zebrafish brain for the comprehensive mechanistic understanding of the cortico-basal ganglia circuit.

neuroscience↗

bioRxiv2021

Astroglial CD38 regulates social memory and synapse formation through SPARCL1 in the medial prefrontal cortex

Social behavior is essential for the health, survival and reproduction of animals, yet the role of astrocytes in social behavior is largely unknown. CD38 is critical for social behaviors by regulating oxytocin release from hypothalamic neurons. On the other hand, CD38 is most abundantly expressed in astrocytes especially in the postnatal cortex, and is important for astroglial development. Here, we demonstrate that astroglial CD38 plays a pivotal role in the social behavior. Selective deletion of CD38 in postnatal astrocytes, but not in adult astrocytes, specifically impaired social memory without any other behavioral abnormalities. Morphological analysis revealed reductions in spine numbers, mature spines and excitatory synapse numbers in the pyramidal neurons of the medial prefrontal cortex (mPFC) due to deletion of astroglial CD38 in the postnatal brain. Astrocyte-conditioned medium (ACM) of CD38 KO astrocytes reduced synaptogenesis of cortical neurons by reducing extracellular SPARCL1, a synaptogenic protein. Finally, the release of SPARCL1 from astrocytes is regulated by CD38/cADPR/calcium signaling. Our data indicate that astroglial CD38 developmentally regulates social memory and neural circuit formation in the developing brain by promoting synaptogenesis through SPARCL1.

neuroscience↗

bioRxiv2021

A generalized distribution interpolated between the exponential and power law distributions and applied to the walking data of the pill bug (Armadillidium vulgare)

The Levy walk, a type of random walk in which the frequency of linear step-lengths follows a power-law distribution, can be observed in the migratory behavior of organisms at various levels, from bacteria and T cells to humans. Compared to the Brownian walk, which is also a type of random walk (characterized by an exponential distribution of the frequency of occurrence of step-length), the Levy walk is characterized by the occasional appearance of linear movements over very long distances. In this paper, we propose a general distribution that includes the power-law and exponential distributions as special cases. This distribution has two parameters: the first parameter represents the exponent, similar to the power-law and exponential distributions and the second is a shape parameter representing the shape of the distribution. By introducing this distribution, an intermediate distribution model can be interpolated between the power-law and exponential distributions. The shape parameter measures whether a distribution assimilates a power-law or exponential distribution. In this study, the proposed distribution was fitted to the frequency distribution of the step-length calculated from the walking data of pill bugs. The autocorrelation coefficients were also calculated from the time-series data of the step-length, and the relationship between the shape parameter and time dependency was investigated. The results showed a significant negative correlation between the two (r=-0.61, n=30, t=4.04, and p=0.00037). This means that pill bugs with gait patterns closer to Levy than Brownian walks have a stronger time dependence with respect to step-length changes.

animal behavior and cognition↗

bioRxiv2021

Simulation of foraging behavior using a decision-making agent with Bayesian and inverse Bayesian inference: Levy and Brownian walk-like search patterns derived from differences in prey distributions

It has been stated that in human migratory behavior, the step length series may have temporal correlation and that there is some relationship between this time dependency and the fact that the frequency distribution of step length follows a power-law distribution. Furthermore, the frequency of occurrence of the step length in some large marine organisms has been found to switch between power-law and exponential distributions, depending on the difficulty of prey acquisition. However, to date it has not been clarified how the aforementioned three phenomena arise: the positive correlation created in the step length series, the relation between the positive correlation of the step length series and the form of an individuals step length distribution, and the switching between power-law and exponential distributions depending on the abundance of prey. This study simulated foraging behavior using the Bayesian decision-making agent simultaneously performing both knowledge learning and knowledge-based inference to analyze how the aforementioned three phenomena arise. In the agent with learning and inference, past experiences were stored as hypotheses (knowledge) and they were used in current foraging behavior; at the same time, the hypothesis continued to be updated based on new experiences. The simulation results show that the agent with both learning and inference has a mechanism that simultaneously causes all the phenomena.

animal behavior and cognition↗

bioRxiv2021

Bimanual digit training improves right-hand dexterity in older adults by reactivating declined ipsilateral motor-cortical inhibition

Improving deteriorated sensorimotor functions in older individuals is a social necessity in a super-aging society. Previous studies suggested that the declined interhemispheric sensorimotor inhibition observed in older adults is associated with their deteriorated hand/finger dexterity. Here, we examined whether bimanual digit exercises, which can train the interhemispheric inhibitory system, improve deteriorated hand/finger dexterity in older adults. Forty-eight healthy, right-handed, older adults (65-78 years old) were divided into two groups, i.e., the bimanual (BM) digit training and right-hand (RH) training groups, and intensive daily training was performed for 2 months. Before and after the training, we evaluated individual right hand/finger dexterity using a peg task, and the individual state of interhemispheric sensorimotor inhibition by analyzing ipsilateral sensorimotor deactivation via functional magnetic resonance imaging when participants experienced a kinesthetic illusory movement of the right-hand without performing any motor tasks. Before training, the degree of reduction/loss of ipsilateral motor-cortical deactivation was associated with dexterity deterioration. After training, the dexterity improved only in the BM group, and the dexterity improvement was correlated with reduction in ipsilateral motor-cortical activity. The capability of the brain to inhibit ipsilateral motor-cortical activity during a simple right-hand sensory-motor task is tightly related to right-hand dexterity in older adults.

neuroscience↗

bioRxiv2020

Fgf/Ets signalling in Xenopus ectoderm initiates neural induction and patterning in an autonomous and paracrine manners

Fibroblast growth factor (Fgf) and anti-bone morphogenetic protein (Bmp) signals are derived from the organiser of mesoderm origin and cooperate to promote Xenopus neural development from the gastrula ectoderm. Using antisense oligos to Fgf2 and Fgf8 and dominant-negative Ets transcription factors, we showed that the expression of Fgf2, Fgf8, and Ets in ectoderm cells is essential to initiate neural induction both in vivo and in vitro. Our findings show that neural induction is initiated primarily by autonomous signalling in ectoderm cells, rather than by paracrine signalling from organiser cells. The signalling in ectoderm cells is transduced via the Fgf/Ras/Mapk/Ets pathway, independent of Bmp signal inhibition via the Fgf/Ras/Mapk/Smad1 route, as indicated by earlier studies. Through the same pathway, Fgfs activated position-specific neural genes dose-dependently along the anteroposterior axis in cultured ectoderm cells. The expression of these genes coincides with the establishment of the activated Ets gradient within the gastrula ectoderm. Organiser cells, being located posteriorly to the ectoderm, secrete Fgfs as gastrulation proceeds, which among several candidate molecules initially promote neural patterning of the induced neuroectoderm as morphogens. Summary statementFgf/Ets signalling in ectodermal cells is required to initiate the expression of both anterior and posterior neural genes from the late blastula to gastrula stages, independent of anti-Bmp signalling.

developmental biology↗

bioRxiv2019

A role of causal inference in non-stationary environments

Bayesian inference is the process of narrowing down the hypotheses (causes) to the one that best explains the observational data (effects). To accurately estimate a cause, a considerable amount of data is required to be observed for as long as possible. However, the object of inference is not always constant. In this case, a method such as exponential moving average (EMA) with a discounting rate is used to improve the ability to respond to a sudden change; it is also necessary to increase the discounting rate. That is, a trade-off is established in which the followability is improved by increasing the discounting rate, but the accuracy is reduced. Here, we propose an extended Bayesian inference (EBI), wherein human-like causal inference is incorporated. We show that both the learning and forgetting effects are introduced into Bayesian inference by incorporating the causal inference. We evaluate the estimation performance of the EBI through the learning task of a dynamically changing Gaussian mixture model. In the evaluation, the EBI performance is compared with those of the EMA and a sequential discounting expectation-maximization algorithm. The EBI was shown to modify the trade-off observed in the EMA.

animal behavior and cognition↗

bioRxiv2019

Future state prediction errors guide active avoidance behavior by adult zebrafish.

Human predicts future. To ask if fish also has this capacity, we established the virtual reality training system with live imaging of the telencephalic neurons of adult zebrafish in the active avoidance and found that, at the onset of the trial, learned fish conceives two future conditions as the favorable status on its way to the safe goal, i.e. one with the backwardly moving landscape and the other with the color of the safe goal. And the two different neural ensembles monitor the discrepancy between these predictions and the perceived real external status. Once fish reaches the goal, another ensemble is set to work to monitor whether fish keeps staying in the safe goal. The manipulation to artificially enhance these prediction errors elevated the activities of these ensembles and induced fish to behave to correct errors, revealing that fish sets behavioral strategy to actively realize these predictions.

neuroscience↗

bioRxiv2019

GUN1 regulates tetrapyrrole biosynthesis

The biogenesis of the photosynthetic apparatus in developing chloroplasts requires the assembly of proteins encoded on both nuclear and chloroplast genomes1. To co-ordinate this process there needs to be communication between these organelles, and while we have a good understanding of how the nucleus controls chloroplast development, how the chloroplast communicates with the nucleus at this time is still essentially unknown2. What we do know comes from pioneering work in which a series of genomes uncoupled (gun) mutants were identified that show elevated nuclear gene expression after chloroplast damage3. Of the six reported gun mutations, five are in tetrapyrrole biosynthesis proteins4-6 and this has led to the development of a model for chloroplast-to-nucleus retrograde signaling in which ferrochelatase 1 (FC1)-dependent heme synthesis generates a positive signal promoting expression of photosynthesis-related genes6. However, the molecular consequences of the strongest of the gun mutants, gun17, is unknown, preventing the development of a unifying hypothesis for chloroplast-to-nucleus signaling. Here, we show that GUN1 directly binds to heme and other metal-porphyrins, affects flux through the tetrapyrrole biosynthesis pathway and can increase the chelatase activity of FC1. These results raise the possibility that the signaling role of GUN1 may be manifested through changes in tetrapyrrole metabolism and supports a role for tetrapyrroles as mediators of a single biogenic chloroplast-to-nucleus retrograde signaling pathway.

plant biology↗

bioRxiv2018

Wide and Deep Imaging of Neuronal Activities by a Wearable NeuroImager Reveals Premotor Activity in the Whole Motor Cortex

Wearable technologies for functional whole brain imaging in freely moving animals would advance our understanding of cognitive processing and adaptive behavior. Fluorescence imaging can visualize the activity of individual neurons in real time, but conventional microscopes have limited sample coverage in both the width and depth of view. Here we developed a novel head-mounted laser camera (HLC) with macro and deep-focus lenses that enable fluorescence imaging at cellular resolution for comprehensive imaging in mice expressing a layer- and cell type-specific calcium probe. We visualized orientation selectivity in individual excitatory neurons across the whole visual cortex of one hemisphere, and cell assembly expressing the premotor activity that precedes voluntary movement across the motor cortex of both hemispheres. Including options for multiplex and wireless interfaces, our wearable, wide- and deep-imaging HLC technology could enable simple and economical mapping of neuronal populations underlying cognition and behavior.

neuroscience↗

bioRxiv2018

Pkd2l1 is required for mechanoception in cerebrospinal fluid-contacting neurons and maintenance of spine curvature

Flow of cerebrospinal fluid (CSF) may contribute to spine morphogenesis, as mutations affecting both cilia motility and CSF flow lead to scoliosis1. However, the mechanisms underlying detection of the CSF flow in the central canal of the spinal cord remain elusive. Here we used full-field optical coherence tomography (FF-OCT) and bead tracking to demonstrate that CSF flows bidirectionally along the antero-posterior axis in the central canal of zebrafish embryos. In the zebrafish mutant cfap298tm304, previously known as kurly, reduction of cilia motility slows transport down the length of central canal. To investigate downstream mechanisms that could transduce CSF flow, we performed calcium imaging in sensory neurons contacting the CSF (CSF-cNs) and found that disruption in cilia motility impaired the activity of CSF-cNs. CSF-cNs across species express the transient receptor potential channel PKD2L1, also known as TRPP3, which contributes to CSF-cN chemosensory properties. Using calcium imaging and whole-cell patch clamp recordings, we found that the loss of the Pkd2l1 channel in pkd2l1 mutant embryos also abolished CSF-cN activity. Whole-cell recordings further demonstrated that opening of a single channel is sufficient to trigger action potentials in wild type CSF-cNs. Recording from isolated cells in vitro, we showed that CSF-cNs are mechanosensory cells that respond to pressure in a Pkd2l1-dependent manner. Interestingly, adult pkd2l1 mutant zebrafish develop an exaggerated spine curvature, reminiscent of kyphosis in humans. Our study indicates that CSF-cNs are mechanosensory cells whose spontaneous activity reflects CSF flow in vivo. Furthermore, Pkd2l1 in CSF-cNs contributes to the maintenance of the natural curvature of the spine.

neuroscience↗