Biology subjects

Sakai, Y.

Publications and source records attributed to Sakai, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

AI-Driven System for Large-Scale Automated Collection of Mouse Profile Images

As with human communication, recent studies have revealed that animals convey a substantial amount of information through their facial expressions. In these studies, artificial intelligence (AI) technologies have been increasingly employed to analyze animal facial image data. However, collecting large amounts of facial image data for such studies has been labor-intensive. In this study, we developed a system that automatically recognizes and saves the faces of freely moving mice using AI-based object detection and image classification technologies. Through validation experiments, we confirmed that the system can detect, classify, and save a variety of mouse profiles with high accuracy. To further expand the versatility of the system for diverse research applications, the technology has been improved to include a feature for determining mouse sex based on their profiles, leveraging AI algorithms for this purpose. A small dataset was used to evaluate the performance of the sex determination system, yielding 100% accuracy for both male and female classifications. This application enables researchers to efficiently collect facial image data, providing high-quality datasets suitable for AI training. Consequently, the efficiency of facial expression analysis in mice is significantly improved. Importantly, this technology is not limited to mice and has the potential to be applied to other animal species and a wide range of research fields, offering promising potential for diverse applications.

animal behavior and cognition↗

bioRxiv2025

Continuous Neural Correlates of Imbalanced Reinforcement Learning in Obsessive-Compulsive Disorder and Healthy Individuals

AimObsessive-compulsive disorder (OCD) is characterized by imbalanced reinforcement learning. This study investigated neural correlates of this imbalance by examining resting-state functional connectivity (rs-fMRI) in non-medicated OCD patients and healthy controls (HCs) exhibiting varying degrees of memory trace imbalance. MethodsWe employed network-based statistics (NBS), suitable for identifying network-level alterations of rs-fMRI data from 49 OCD patients and 53 HCs (Core Discovery Dataset: Core-DS) to identify a significant network. We validated this network in an independent dataset of 10 OCD patients and 18 HCs (Independent Validation Dataset: IndV-DS). Additionally, we compared functional connectivity in the identified network between subgroups of HCs with imbalanced (OCD-like) and balanced learning profiles (Extension Dataset: Ext-DS; n=10 each). ResultsNBS identified an OCD network with increased connectivity in OCD patients (padjusted = 0.022), comprising regions in the dorsolateral prefrontal cortex (DLPFC), parietal cortex, retrosplenial cortex, and hippocampal formation. This networks increased connectivity in OCD patients was replicated in IndV-DS (p = 0.0027). Importantly, imbalanced HCs showed a significant increase in functional connectivity, particularly between the DLPFC and presubiculum, in the identified OCD network, compared to balanced HCs (p = 0.0051, padjusted = 0.066). ConclusionIncreased functional connectivity in the OCD network, especially between the DLPFC and presubiculum, is present in both OCD patients and a subgroup of HCs with learning imbalances. These findings provide evidence for a continuous neural basis of imbalanced reinforcement learning, suggesting a continuum of traits associated with OCD between patients and "healthy" individuals.

neuroscience↗

bioRxiv2024

Hippocampal sharp-wave ripples decrease during physical actions including consummatory behavior in immobile rodents

Hippocampal sharp-wave ripples (SWRs) are intermittent, fast synchronous oscillations that play a pivotal role in memory formation. It has been well-established that SWRs occur during "consummatory behaviors", e.g., eating or drinking a reward for correct action. However, most of typical behavioral experiments using freely moving rodents have not rigorously distinguished between the act of eating/drinking (regardless of consummation or consumption) from stopping locomotion (immobility). Therefore, in this study, we investigated the occurrence of SWRs during a reward-seeking action and subsequent consummatory reward licking in constantly immobile rats maintained under head fixation and body covering. Immobile rats performed a pedal hold-release action that was rewarded with water every other time (false and true consummation). Unexpectedly, the SWRs remarkably decreased during reward licking as well as pedal release action. Unlearned rats also showed a similar SWR decrease during water licking. Conversely, SWRs gradually increased during the pedal hold period, which was enhanced by reward expectation. A cluster of hippocampal neurons responded to cue/pedal release and reward, as previously shown. Some other clusters exhibited spike activity changes similar to the SWR occurrence, i.e., decreasing during the pedal release action and reward licking, and enhanced by reward expectation during pedal hold period. These task event-responsive neurons and SWR-like neurons displayed stronger spiking synchrony with SWRs than task-unrelated neurons. These findings suggest that the hippocampus generates SWRs, which may associate action with outcome, in "relative immobility" (action pauses) rather than specific consummation or consumption. Significance StatementTo clarify the characteristics of hippocampal sharp-wave ripples (SWRs), we analyzed the SWRs occurring during operant task performance in immobile rats under both head fixation and body covering. First, we found that SWRs decreased when they licked and drank water, conflicting with the theory that SWRs occur in consummatory behavior. Second, hippocampal neurons showed different task-related activities, particularly those that resembled SWR occurrences or conveyed specific signals on task events. Third, these task-related neurons displayed strong synchronous discharges during SWRs in task-engaged periods. These findings may explain the neuronal mechanisms underlying the association between an action and its outcome.

neuroscience↗

bioRxiv2024

Coral anthozoan-specific opsins employ a novel chloride counterion for spectral tuning

Animal opsins are G protein coupled receptors that have evolved to sense light by covalently binding a retinal chromophore via a protonated (positively charged) Schiff base. A negatively charged amino acid in the opsin, acting as a counterion, stabilizes the proton on the Schiff base, which is essential for sensitivity to visible light. In this study, we investigate the spectroscopic properties of a unique class of opsins from a reef-building coral belonging to the anthozoan-specific opsin II group (ASO-II opsins), which intriguingly lack a counterion residue at any of established sites. Our findings reveal that, unlike other known animal opsins, the protonated state of the Schiff base in visible light-sensitive ASO-II opsins is highly dependent on exogenously supplied chloride ions (Cl-). By using structural modelling and QM/MM calculations to interpret spectroscopy data, we conclude that, in the dark state, ASO-II opsins employ environmental Cl- as their native counterion, while a nearby polar residue, Glu292 in its protonated neutral form, facilitates Cl- binding. In contrast, Glu292 plays a crucial role in maintaining the protonation state of the Schiff base in the light-activated protein, serving as the counterion in the photoproduct. Furthermore, Glu292 is involved in G protein activation of the ASO-II opsin, suggesting that this novel counterion system coordinates multiple functional properties.

biophysics↗

bioRxiv2024

PATROL1-mediated H+-ATPase translocation boosts plant growth under drought by optimizing root and leaf functions

Optimizing leaf photosynthesis and root water and mineral uptake in crops during drought is crucial for enhancing agricultural productivity under climate change. Although plasma membrane H+-ATPase plays a key role in plant physiological processes, its overexpression alone does not consistently improve growth. While PROTON ATPASE TRANSLOCATION CONTROL 1 (PATROL1) regulates H+-ATPase translocation in response to various environmental stimuli in leaves, its function in roots remains largely unknown. Here we show that H+-ATPase was coimmunoprecipitated with PATROL1 in roots of Arabidopsis thaliana. Micrografting between wild type and PATROL1 knockout or overexpression lines showed that PATROL1 are indispensable in both shoots and roots, indicating that root uptake and leaf photosynthesis are simultaneous limiting factors for plant growth under drought conditions. PATROL1 overexpression in whole plants resulted in a 41% increase above wild type in shoot dry weight under drought conditions. These findings highlight the potential of H+-ATPase regulation in roots as a new strategy to improve plant productivity, particularly under drought conditions.

plant biology↗

bioRxiv2024

Sequence determinants of intron-mediated enhancement learned from thousands of random introns

Spliceosomal introns are a ubiquitous feature of eukaryotic genes, whose presence often boosts the expression of their host gene, a phenomenon known as intron-mediated enhancement (IME). IME has been noted across diverse genes and organisms, but remains mysterious in many respects. For example, how does intron sequence affect the magnitude of IME? In this study, we performed a massively parallel reporter assay (MPRA) to assess the effect of varying intron sequence on gene expression in a high-throughput manner, in human cells, using tens of thousands of synthetic introns with natural splice sites and randomized internal sequence. We observe that most random introns splice efficiently and enhance gene expression as well as or better than fully natural introns. Nearly all introns stimulate gene expression [~]eight-fold above an intronless control, at both mRNA and protein levels, suggesting that the primary mechanism acts to increase mRNA levels. IME strength is positively associated with splicing efficiency and with the intronic content of poly-uridine stretches, which we confirm using reporter experiments. Together, this work elucidates sequence determinants of IME from tens of thousands of random introns, and confirms that enhancement of gene expression is a general property of splicing.

molecular biology↗

bioRxiv2024

Single-step in vitro ribosome reconstitution mediated by two GTPase factors, EngA and ObgE

When bacterial ribosomes are assembled in vitro, manipulation of incubation temperature and magnesium ion concentration have been an essential procedure, which is a crucial step for the assembly of active large subunits. The present study tackles with this issue to develop a single-step procedure, which can be performed in a near-physiological condition, where cell-free protein synthesis is active. We found that GTPase factors EngA and ObgE can complement the changes in temperature and magnesium ion concentrations. In the presence of these factors, both the ribosome assembly and translation processes were successfully integrated in the reconstituted cell-free protein synthesis system. Furthermore, we found that these GTPase factors can reassemble the ribosomes to an active state, whose structure was disrupted by EDTA chelation of magnesium ions, indicating that these two factors can reversibly induce the ribosome structure to an intact state. The findings are essential for the bottom-up construction of synthetic cells.

biochemistry↗

bioRxiv2024

Evolutionary acquisition of a primitive light-dependent nuclear relocation in Marchantia polymorpha

The terrestrialization of plants was accompanied by exposure to several environmental stresses. Adaptation to these stresses required numerous changes at the cellular and molecular level. One such adaptation in the leaves of Arabidopsis thaliana is the movement of cell nuclei to avoid UV damage. In the dark, the nuclei locate to the bottom walls of leaf cells to distance genetic material from external stresses, but in response to intense blue light (an indication of the presence of UV), they move to the side walls to escape UV-induced DNA damage1. The movement is driven by the photoreceptor phototropin and the actin cytoskeleton2. However, how this protective mechanism evolved in land plants remains unclear. Here, we show that in the liverwort Marchantia polymorpha, nuclei show a similar, but less stable movement in response to intense blue light. In the dark, M. polymorpha positioned nuclei on the upper walls of epidermal cells in young thalli, but in response to intense blue light, the nuclei immediately moved to the side walls, similar to A. thaliana. However, the movement was transient and the nuclei returned to the upper walls through both the actin and microtubule cytoskeletons. Unlike A. thaliana, M. polymorpha responded to prolonged (> 1 day) exposure to low light by moving nuclei from the upper to the side walls through both the actin and microtubule cytoskeletons and two photoreceptors (phototropin and phytochrome). However, no light-dependent nuclear relocation was observed in charophyte algae, suggesting that light-dependent nuclear relocation was initially established in the common ancestor of land plants as a result of terrestrialization and then diverged during land plant evolution.

plant biology↗

bioRxiv2024

Evolutionary conserved RLF, a plant cytochrome b5-like heme-binding protein, is essential for organ development in Marchantia polymorpha

In Arabidopsis thaliana, REDUCED LATERAL ROOT FORMATION (RLF), a cytochrome b5-like heme-binding domain (Cytb5-HBD) protein, is necessary for proper lateral root formation. Whereas the other Cytb5-HBD proteins in A. thaliana regulate different metabolic reactions, RLF is unique as it specifically regulates organ development. However, it remains unknown whether heme binding to RLF is necessary for its function, and whether RLF orthologs in different plant species also regulate organ development. We demonstrate that RLF binds to heme in vitro and that the two histidine residues, which are conserved among Cytb5-HBD, are crucial for both heme binding and its biological function in A. thaliana. In addition, MpRLF, a RLF ortholog in Marchantia polymorpha, rescues the lateral root formation phenotype of the A. thaliana rlf mutant. Mprlfge, the loss-of-function mutation in the MpRLF, resulted in delayed thallus growth and inhibited both gemma cup and antheridiophore formation. Transcriptome analysis using Mprlfge revealed that MpRLF affects several metabolic pathways. Our findings indicate that MpRLF is essential for vegetative and reproductive development in M. polymorpha, suggesting that the RLF-dependent redox reaction systems are evolutionarily conserved as crucial mechanisms for organ development across diverse plant species.

plant biology↗

bioRxiv2024

Methanol chemoreceptor MtpA- and flagellin protein FliC-dependent methylotaxis determines the spaciotemporal colonization of PPFM in the phyllosphere

Pink-pigmented facultative methylotrophs (PPFMs) capable of growth on methanol are dominant and versatile phyllosphere bacteria that provide positive effects on plant growth through symbiosis. However, the spatiotemporal behavior of PPFMs on plant surfaces and its molecular basis are unknown. Here we show that Methylobacterium sp. strain OR01 inoculated onto red perilla seeds colonized across the entire plant surface in the phyllosphere concomitant with the plant growth. FliC flagellin proteins required for motility were necessary for distributed colonization on plant leaves, but not for colonization at the leaf periphery. Methanol-sensing chemoreceptor MtpA-dependent chemotaxis (methylotaxis; chemotaxis toward methanol) facilitated the bacterial movement from the peripheral to the inner part of leaves and further entry into the stomatal cavity, indicating that methanol functions as a volatile messenger attracting PPFMs to particular leaf locations possibly to support with photosynthesis and to afford protection from pathogenic invasion.

microbiology↗

bioRxiv2024

Modeling of vascular interactions in endochondral ossification using human embryonic stem cells-derived organoid on a microfluidic chip

Vascular interactions play a crucial role in embryogenesis, including skeletal development. During endochondral ossification, vascular networks are formed as mesenchymal cells condense and later invade skeletal elements to form the bone marrow. We and other groups developed a model of endochondral ossification by implanting human embryonic stem cell (hESC)-derived sclerotome into immunodeficient mice. However, in vitro models of endochondral ossification, particularly vascular interaction with mesenchymal cells at its initial stage, are yet to be established. Therefore, we developed a method to model the initial stage of endochondral ossification using a microfluidic chip-based platform, with a particular focus on the vascular interaction. On the chip, we found that the fibrin gel helped align mCherry-expressing human umbilical vein endothelial cells (HUVECs) better than the collagen-I gel, suggesting that the fibrin gel is more suitable for the formation of a vascular-like network. The perfusability of the vascular-like networks was partially confirmed using fluorescein isothiocyanate (FITC)-dextran and fluorescent microbeads. We then mixed hESC-derived sclerotome with enhanced green fluorescent protein (EGFP)-expressing HUVECs and applied this mixture on the chip. We named this mixture of cells SH organoids. The SH organoids showed superior abilities to maintain the vascular-like network, which was formed by the mCherry-expressing HUVECs, compared with the sclerotome spheroids on the chip. The EGFP-expressing HUVECs migrated from the SH organoid, formed a vascular-like networks, and partially interacted with the mCherry-expressing vascular-like networks on the chip. Histological analysis showed that SRY-box transcription factor 9 (SOX9) and type I collagen were expressed mutually exclusively in the condensed mesenchymal cells and perichondrial-like cells, respectively. This study demonstrates that our SH organoid-on-a-chip method reproduces vascular networks that are formed at the initial stage of endochondral ossification. This model may provide insights into human endochondral ossification and has potential applications in bone disease modeling and drug screening.

bioengineering↗

bioRxiv2024

Prediction of antidepressant treatment response with thalamo-somatomotor functional connectivity revealed by generalizable stratification of depressed patients

Major depressive disorder (MDD) is diagnosed based on symptoms and signs without relying on physical, biological, or cognitive tests. MDD patients exhibit a wide range of complex symptoms, and it is assumed that there are diverse underlying neurobiological backgrounds, possibly composed of several subtypes with relatively homogeneous biological features. Initiatives, including the Research Domain Criteria, emphasize the importance of biologically stratifying MDD patients into homogeneous subtypes using a data-driven approach while utilizing genetic, neuroscience, and cognitive information. If biomarkers can stratify MDD patients into biologically homogeneous subtypes at the first episode of depression, personalized precision medicine may be within our scope. Some pioneering studies have used resting-state functional brain connectivity (rs-FC) for stratification and predicted differential responses to various treatments for different subtypes. However, to our knowledge, little research has demonstrated reproducibility (i.e., generalizability) of stratification markers in independent validation cohorts. This issue may be due to inherent measurement and sampling biases in multi-site fMRI data, or overfitting of machine learning algorithms to discovery cohorts with small sample sizes, i.e., a lack of appropriate machine learning algorithms for generalizable stratification. To address this problem, we have constructed a multi-site, multi-disorder fMRI database with prospectively and retrospectively harmonized data from thousands of samples and proposed a hierarchical supervised/unsupervised learning strategy. In line with this strategy, our previous research first developed generalizable MDD diagnostic biomarkers using this fMRI database of MDD patients via supervised learning. The MDD diagnostic biomarker determines the importance of thousands to tens of thousands of rs-FCs across the whole brain for MDD diagnosis. In this study, we constructed stratification markers for MDD patients using unsupervised learning (Multiple co-clustering) with a subset of top-ranked rs-FCs in the MDD diagnostic biomarker. We developed a method to evaluate the clustering stability between two independent datasets as a generalization metric of stratification biomarkers. To discover stratification biomarkers with high stability across datasets, we utilized two multi-site datasets with substantial differences in data acquisition facilities and fMRI measurement protocols (Dataset-1: a dataset of 138 depressed patients obtained with a unified measurement protocol across three facilities; Dataset-2: a dataset of 181 depressed patients obtained with non-unified measurement protocols across four facilities, distinct from Dataset-1). Starting from several diagnostic biomarkers, we constructed some stratification markers and identified the stratification biomarker with the highest clustering stability between the two datasets. This stratification biomarker was based on several rs-FCs between the thalamus and the postcentral gyrus, and the MDD subgroups stratified by this biomarker showed significantly different treatment responsiveness to a selective serotonin reuptake inhibitor (SSRI). By narrowing down whole-brain rs-FCs using MDD diagnostic biomarkers and further dividing the rs-FCs using multiple co-clustering, the feature dimension was significantly reduced, thereby avoiding overfitting to the training data and successfully constructing stratification biomarkers that are highly stable between independent datasets, i.e., have generalizability. Furthermore, the correlation between MDD subgroups and antidepressant treatment response was demonstrated, suggesting the potential for achieving personalized precision medicine for MDD.

neuroscience↗

bioRxiv2024

Regulation of ROP GTPase cycling between active/inactive states is essential for vegetative organogenesis in Marchantia polymorpha

Rho/Rac of plant (ROP) GTPases are a plant-specific subfamily of Rho small GTP-binding proteins that function as molecular switches by being converted to the active state by guanine nucleotide exchange factors (GEFs) and to the inactive state by GTPase-activating proteins (GAPs). The bryophyte Marchantia polymorpha contains single-copy genes encoding ROP (MpROP), two types of GEFs (ROPGEF and SPIKE (SPK)), and two types of GAPs (ROPGAP and ROP enhancer (REN)). MpROP regulates the development of various organs, including the air chambers, rhizoids, and clonal propagule gemmae. While the sole PRONE-type ROPGEF, KARAPPO (MpKAR), plays an essential role in gemma initiation, little is known about the in-planta functions of other ROP regulatory factors in M. polymorpha. In this study, we focused on the functions of two types of GAPs: MpROPGAP and MpREN. Loss-of-function Mprenge single mutants showed pleiotropic defects in thallus growth, air chamber formation, rhizoid tip growth, and gemma development, whereas MpROPGAP mutants showed no detectable abnormalities. Despite the distinctive domain structures of MpROPGAP and MpREN, MpropgapgeMprenge double mutants showed more severe phenotypes than the Mprenge single mutants, suggesting redundant functions of MpROPGAP and MpREN in gametophyte organogenesis. Interestingly, overexpression of MpROPGAP, MpREN, and dominant-negative MpROP (MpROPDN) resulted in similar air chamber defects, as well as loss-of-function of MpREN and MpROPGAP and overexpression of constitutively active MpROP (MpROPCA), suggesting importance of activation/inactivation cycling (or balancing) of MpROP. Furthermore, we proved the contributions of the sole DOCK family GEF, MpSPK, to MpROP-regulated air chamber formation. In summary, our results demonstrate a significant role of the two GAPs in the development of various organs and that the two GEFs are responsible for organogenesis through the control of the MpROP active/inactive cycle in the vegetative growth of M. polymorpha.

plant biology↗

bioRxiv2024

Computational Mechanisms of Neuroimaging Biomarkers Uncovered by Multicenter Resting-State fMRI Connectivity Variation Profile

Resting-state functional connectivity (rsFC) is increasingly used to develop biomarkers for psychiatric disorders. Despite progress, development of the reliable and practical FC biomarker remains an unmet goal, particularly one that is clinically predictive at the individual level with generalizability, robustness, and accuracy. In this study, we propose a new approach to profile each connectivity from diverse perspective, encompassing not only disorder-related differences but also disorder-unrelated variations attributed to individual difference, within-subject across-runs, imaging protocol, and scanner factors. By leveraging over 1500 runs of 10-minute resting-state data from 84 traveling-subjects across 29 sites and 900 participants of the case-control study with three psychiatric disorders, the disorder-related and disorder-unrelated FC variations were estimated for each individual FC. Using the FC profile information, we evaluated the effects of the disorder-related and disorder-unrelated variations on the output of the multi-connectivity biomarker trained with ensemble sparse classifiers and generalizable to the multicenter data. Our analysis revealed hierarchical variations in individual functional connectivity, ranging from within-subject across-run variations, individual differences, disease effects, inter-scanner discrepancies, and protocol differences, which were drastically inverted by the sparse machine-learning algorithm. We found this inversion mainly attributed to suppression of both individual difference and within-subject across-runs variations relative to the disorder-related difference by weighted-averaging of the selected FCs and ensemble computing. This comprehensive approach will provide an analytical tool to delineate future directions for developing reliable individual-level biomarkers.

neuroscience↗

bioRxiv2024

Gluconeogenesis in the YSL-like tissue of cloudy catshark (Scyliorhinus torazame).

Glucose has important roles in the development of hematopoietic stem cells and brain of zebrafish, the vertebrate animal model; however, in most oviparous animals, the amount of maternally provided glucose in the yolk is scarce. For these reasons, developing animals need some ways to supplement glucose. Recently, it was found that developing zebrafish, a teleost fish, undergo gluconeogenesis in the yolk syncytial layer (YSL), an extraembryonic tissue that surrounds the yolk, utilizing yolk nutrients as substrates. However, teleost YSL is evolutionarily unique, and it is not clear how other vertebrates supplement glucose. In this study, we used cloudy catshark, an elasmobranch species which possesses a YSL-like tissue during development, and sought for possible gluconeogenic activities in this tissue. In the catshark yolk sac, an increase in glucose level was found, and our isotope tracking by 13C-labeled substrate combined with LC/MS analysis detected gluconeogenic activities with glycerol most preferred substrate. In addition, expression analysis for gluconeogenic genes showed that many of these were expressed at the YSL-like tissue, suggesting that cloudy catshark engages in gluconeogenesis in this tissue. The gluconeogenesis in teleost YSL and a similar tissue in elasmobranch species implies conservation of the mechanisms of yolk metabolism between these two lineages. Future studies on other vertebrate taxa will be helpful to understand the evolutionary changes in the modes of yolk metabolism that vertebrates have experienced.

physiology↗

bioRxiv2024

An Assumption of The Regulatory Function of Nf2-Amot Complex in Early Mammalian Embryos with A Computational Model

The paper assumed that Nf2-Amot complex regulates the phosphorylation cascade so that each cell in the early mammalian embryo differentiates properly in silico. To confirm the validity of the assumption, it was necessary to verify whether Nf2-Amot complex has an impact on the resulting differentiation. The living embryo is unsuitable for the confirmation since the early mammalian embryo is too small to observe and too ethically sensitive to invade. In such cases, computational models can be used as experimental subjects for operations that cannot be applied to the living embryo. Previous models on the embryo, however, could not verify the assumption because they had not modeled Nf2-Amot complex, and they seldom modeled the Hippo signaling pathway. Therefore, the paper introduced a model of Nf2-Amot complex to the previous study that had modeled the Hippo signaling pathway. Testing the model under diverse conditions revealed that the existence of Nf2-Amot complex reproduces the ideal cell differentiation observed in the living embryo. In this sense, the validity of the model was confirmed. Furthermore, diverse cell-cell contacts that induce various concentrations of Nf2-Amot complex also resulted in ideal cell differentiation. These results suggested the correctness of the assumption in silico.

developmental biology↗

bioRxiv2024

Comprehensive evaluation of pipelines for diagnostic biomarkers of major depressive disorder using multi-site resting-state fMRI datasets

The objective diagnostic and stratification biomarkers developed with resting-state functional magnetic resonance imaging (rs-fMRI) data are expected to contribute to more effective treatment for mental disorders. Unfortunately, there are currently no widely accepted biomarkers, partially due to the large variety of analysis pipelines for developing them. In this study we comprehensively evaluated analysis pipelines using a large-scale, multi-site fMRI dataset for major depressive disorder (MDD) (1162 participants from eight imaging sites). We explored the combinations of options in four subprocesses of analysis pipelines: six types of brain parcellation, four types of estimations of functional connectivity (FC), three types of site difference harmonization, and five types of machine learning methods. 360 different MDD diagnostic biomarkers were constructed using the SRPBS dataset acquired with unified protocols (713 participants from four imaging sites) as a discovery dataset and evaluated with datasets from other projects acquired with heterogeneous protocols (449 participants from four imaging sites) for independent validation. To identify the optimal options regardless of the discovery dataset, we repeated the same procedure after swapping the roles of the two datasets. We found pipelines that included Glassers parcellation, tangent-covariance, no harmonization, and non-sparse machine learning methods tended to result in high classification performance. The diagnosis results of the top 10 biomarkers showed high similarity, and weight similarity was also observed between eight of the biomarkers, except two that used both data-driven parcellation and FC computation. We applied the top 10 pipelines to the datasets of other mental disorders (autism spectral disorder: ASD and schizophrenia: SCZ) and eight of the ten biomarkers showed sufficient classification performances for both disorders, except two pipelines that included Pearson correlation, ComBat harmonization and random forest classifier combination. HighlightsO_LIWe evaluated the analysis pipelines of rsFC biomarker development. C_LIO_LIFour subprocesses in them were investigated with two multi-site datasets. C_LIO_LIGlassers parcellation, tangent covariance, and non-sparse methods were preferred. C_LIO_LIThe weight patterns of eight of the top 10 biomarkers showed high commonality. C_LIO_LIEight of the top 10 pipelines were successful for developing SCZ/ASD biomarkers. C_LI

neuroscience↗

bioRxiv2023

Synaptic tagging and capture underlie neuronal co-allocation and temporal association memory in behaving mice

Episodic memory has the ability to link distinct memories formed at temporal proximity (minutes-hours) into a coherent episodic representation. The neuronal mechanisms supporting such time associations remain however to be understood. The synaptic tagging and capture hypothesis (STC) provides a theoretical framework in which plasticity-related proteins produced for consolidating a memory trace at a synapse can potentially benefit to the consolidation of another trace at another synapse of the same neuron, thereby promoting neuronal co-allocations and temporal associations of memory traces. STC has however never been demonstrated in behaving animals, leaving its existence and functional relevance for memory formation unknown. We therefore investigated STC-like mechanisms in freely-behaving mice by recording hippocampal CA1 neurons during encoding and retrieval of distinct events. We found that reactivation of engram neurons at retrieval and the stability of place cells were strongly impaired by protein synthesis inhibition during encoding, but strikingly, were rescued in neurons that were coactive at another encoding close in time, having potentially benefitted from proteins produced at temporal proximity, as predicted by STC hypothesis. All our results together provide the first evidence of STC-like mechanisms in behaving animals and reveal an instrumental role of STC for time association of memory traces.

neuroscience↗