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Sakurai, K.

Publications and source records attributed to Sakurai, K..

At least 19 recordsLinked to original sources

Nup153 regulates neuronal responsiveness through HDAC1-mediated epigenetic modulation

Neural activity-dependent gene regulation is central to the development of neural networks and neuronal plasticity. Induction of activity-dependent gene programs is equally important as repression of these programs, and both need to be balanced carefully. However, little is known about how repressive mechanisms modulate neuronal responsiveness across the genome before stimulation. Here, we identify nucleoporin-dependent regulation of neuronal responsiveness, in which Nup153 represses neuronal genes including activity-regulated genes (ARGs), in the basal state. By characterizing the genome-wide landscape of chromatin accessibility, histone modifications and Nup153 chromatin binding, we show that Nup153 bidirectionally regulates chromatin states through both basal activity-dependent and -independent mechanisms and influences associated genes. Mechanistically, Nup153 associates with HDAC1 to modulate histone acetylation and chromatin accessibility at target regulatory regions. Our data suggests Nup153 organizes chromatin states that regulate neuronal gene programs involved in maintaining neuronal responsiveness. TeaserNup153 primes neuronal responsiveness through multi-layered epigenetic regulation.

neuroscience↗

Cross Potential Selection for Multiple Traits Considering the Progeny Distribution of Future Inbred Lines in Plant Breeding Programs

In plant breeding, it is often necessary to improve a target trait while maintaining other essential traits within desirable ranges. When genetic relationships exist among these traits, improvements in the target trait may lead to undesirable changes in essential traits, complicating cross selections. In such cases, it is critical to select cross-pairs that are expected to produce progeny that satisfy the requirements for all traits. The progeny distribution of each crossing pair can be predicted using the estimated genotypic values and genetic (co)variances of the target and essential traits. By utilizing this distribution, the probability of generating progeny that satisfy predefined trait requirements can be evaluated, allowing a direct comparison of alternative crosses. In this study, we developed Cross Potential Selection for Multiple Traits (CPS-MT), a breeding strategy designed to improve a target trait while maintaining one or more essential traits within desirable ranges. CPS-MT extends the original Cross Potential Selection (CPS) framework to explicitly handle trade-offs between traits under genetic correlations. We evaluated the performance of CPS-MT through simulations involving four types of genetic relationships and two genetic causal factors between traits, resulting in seven scenarios. Across all scenarios, CPS-MT consistently improved the likelihood of obtaining desirable progeny, indicating that CPS-MT provides a practical and effective framework for cross selection under multi-trait constraints in breeding programs. Article SummaryThis study developed Cross Potential Selection for Multiple Traits (CPS-MT), a new breeding strategy designed to improve a target trait while maintaining one or more essential traits within desirable ranges. CPS-MT evaluates crossing pairs by predicting progeny distributions based on estimated genotypic values and genetic covariances, enabling direct comparison of alternative crosses under multi-trait constraints. Through simulations incorporating four types of genetic relationships and two causal factors (seven scenarios), CPS-MT consistently increased the likelihood of obtaining progeny that satisfied the predefined trait requirement. These results indicate that CPS-MT provides a practical, robust framework for target trait improvement under trait constraints.

genetics↗

Tau interactions with inner nuclear envelope proteins modulates chromatin

Abstract/SummaryThe intracellular re-distribution of the neuronal microtubule-associated protein Tau, from the axon into the somatodendritic compartment, is a physiological stress-related event and occurs early in Alzheimers disease (AD). Nuclear envelope distortions have been linked to the presence and aggregation of pathological Tau near the nucleus in these diseases. How physiologically increased soma Tau levels, enabling Tau interactions with the nucleus, impact nuclear integrity and neuronal physiology is unclear. Combining proximity biotinylation interactomics with chromatin imaging and molecular assays, we show that soluble Tau interacts with proteins coordinating chromatin at the inner nuclear membrane, including lamin B receptor and SUN1. This interaction promotes nuclear envelope invaginations and damage and changes the coordination of DNA at the nuclear lamina. Increasing somatodendritic Tau is sufficient to upregulate the expression of multiple transcription factors implicated in AD pathogenesis and to reduce expression of genes involved in cholesterol biosynthesis, which seem coordinated at lamin associated domains. These nuclear envelope-related mechanisms suggest that physiological, neuronal stress-related somatodendritic Tau missorting can initiate chromatin-related cascades important for early changes in AD and tauopathies.

neuroscience↗

Progeny-based genomic selection reveals untapped genetic potential in an underutilized medicinal plant, Perilla frutescens

O_LIDespite their substantial therapeutic value, medicinal plants have undergone limited genetic improvement through breeding because of the scarcity of expert breeders. Moreover, quantifying bioactive compounds is expensive. Genomic selection (GS), which leverages genome-wide markers to predict breeding values and assemble favorable alleles, offers a practical way to unlock latent genetic potential. As a model case, we evaluated GS in red perilla (Perilla frutescens). C_LIO_LIBuilding on previous work, we implemented a cross-selection strategy that prioritized segregation variance by selecting crosses based on predicted additive genotypic values of the progeny, and evaluated its effectiveness through actual crossing experiments targeting three key medicinal compounds. C_LIO_LIProgeny from GS-based crosses (Crs1-Crs7) outperformed those from phenotypic selection (Crs8) in the G2 generation, demonstrating a higher mean, greater variance, and superior top individuals. The best G2 individual exhibited nearly twofold higher levels of two target compounds relative to the existing cultivar Sekiho. C_LIO_LIThis study provides the first empirical demonstration that GS can improve multiple medicinal compounds in red perilla and highlights the effectiveness of cross-selection based on predicted progeny performance. In addition, the evidence presented here supports the broader application of GS in underutilized medicinal plants. C_LI

genetics↗

Mesenchymal Stem Cell Membrane Coating of Gelatin Nanospheres with Drug Release Ability for Inflammatory Tissue Targeting

Improvements in drug delivery have been achieved using nanospheres to prolong drug efficacy, accelerate absorption, and target tissues with ongoing inflammation. Although nanospheres have numerous pharmacokinetic advantages their tissue-targeting ability is poor. In contrast, mesenchymal stem cells (MSC) accumulate in high numbers in inflammatory tissues via the interaction between CXC-chemokine receptor 4 (CXCR4) expressed on MSC and stromal cell-derived factor 1 (SDF-1) secreted during inflammation. Therefore, this study investigated coating gelatin nanospheres (GNS) with MSC membranes (MSC-GNS) by extrusion and ultrasonication methods to enhance their inflammatory tissue tropism. {zeta}-potential measurements, western blotting and single-particle analysis of MSC-GNS by flow cytometry demonstrated the GNS surface was successfully coated with MSC membranes. Dot blotting demonstrated the binding ability of CXCR4 for SDF-1 was retained by MSC-GNS but absent for MSC-membrane-free GNS. The blood clearance of MSC-GNS was examined by their intravenous injection into mice. Although MSC-GNS and GNS were retained during the early distribution phase, MSC-GNS had a higher retention than GNS during the later elimination phase. Finally, we investigated the tissue distribution of MSC-GNS by intravenous injection into a mouse model of liver fibrosis and their potential therapeutic effect on liver fibrosis. We found a higher accumulation of MSC-GNS in inflamed livers and higher blood retention compared with MSC-membrane-free GNS. Furthermore, MSC-GNS loaded with an anti-fibrotic agent (LSKL, a 4-amino acid peptide that inhibits fibrosis progression) had an enhanced therapeutic effect on liver fibrosis than uncoated nanoparticles. Therefore, MSC-GNS might be a drug carrier with inflammatory tissue targeting and controlled drug release abilities. Synopsis Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/657318v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@12331d8org.highwire.dtl.DTLVardef@19d7b43org.highwire.dtl.DTLVardef@79591org.highwire.dtl.DTLVardef@1ec805a_HPS_FORMAT_FIGEXP M_FIG C_FIG Mesenchymal stem cell membrane coated gelatin nanosphere as DDS nanocarrier

bioengineering↗

Spatiotemporal dynamics of CD73 in mouse retina under physiological conditions

Adenosine is essential to energy metabolism and neuromodulation in the central nervous system. The retina is a highly energy-demanding neural tissue, and dysregulation of adenosine signaling causes retinal diseases. However, the dynamics of ecto-5-nucleotidase (CD73), a key enzyme for extracellular adenosine generation, remain elusive. Here, we investigate its spatiotemporal profile from development to adulthood using two transgenic mouse lines. We found that CD73 is transiently expressed in the early astrocyte lineage (Embryonic day 16.5 to Postnatal day [P] 3), becomes prominent in the rod-photoreceptor lineage by P3, and appears in the inner nuclear layer from P7 onward. CD73 deletion delays rod-response recovery and shortens the implicit time in scotopic ERG under dim light. These findings indicate that light and other physiological cues influence CD73 expression, which has significant consequences for retinal function, thereby providing a foundation for exploring disease-related alterations in CD73 and designing therapies that restore adenosine homeostasis.

developmental biology↗

Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations

In the breeding programs of self-pollinated plants, achieving genetic improvement in multiple traits can be challenging when relying solely on a single biparental population. Interpopulation crosses are employed to integrate favorable alleles from multiple biparental populations to overcome this limitation. In this context, it is crucial to consider the distinct genetic effects in different populations. In this study, we utilized a selection method based on the usefulness criterion (UC) to identify cross pairs suitable for interpopulation crosses. We expanded this approach to enhance breeding programs accounting for varying genetic backgrounds within the genomic selection framework. Using the medicinal plant red perilla as the study material, we conducted simulations to compare the efficacy of selection based on estimated genomic breeding values with that based on UC. Our findings demonstrate that the proposed method is effective in facilitating the simultaneous improvement of multiple traits, particularly by considerably increasing genetic gains among the top-performing individuals in the population. Furthermore, we provide guidelines for implementing interpopulation crosses, including recommendations for the optimal generation for crossing and the appropriate reference generation for calculating the UC. The results obtained in this study offer valuable insights for small-scale breeding programs aimed at simultaneously enhancing multiple traits through inter-population crosses and are applicable to a wide range of crops, including neglected and underutilized species. Key MessageHerein, a method has been proposed for selecting optimal cross pairs based on the genetic potential of progeny in inter-population crosses, considering different genetic effects among populations.

bioinformatics↗

Sex-dependant differences in the ability of nicotine to modulate discrimination learning and cognitive flexibility in mice.

1Nicotine, an addictive compound found in tobacco, functions as an agonist of nicotinic acetylcholine receptors (nAChRs) in the brain. Interestingly, nicotine has been reported to act as a cognitive enhancer in both human subjects and experimental animals. However, its effects in animal studies have not always been consistent, and sex differences have been identified in the effects of nicotine on several behaviors. Specifically, the role that sex plays in modulating the effects of nicotine on discrimination learning and cognitive flexibility in rodents is still unclear. Here, we evaluated sex-dependent differences in the effect of daily nicotine administration at various doses (0.125, 0.25, and 0.5 mg/kg) on visual discrimination (VD) learning and reversal (VDR) learning in mice. In male mice, nicotine significantly improved performance in VDR, but not VD, task, while, in female mice, nicotine significantly worsened performance in the VD, but not VDR, task. Next, to investigate the cellular mechanisms that underlie the sex differences in the effects of nicotine on cognition, transcriptomic analyses were performed on prefrontal cortex tissue samples from male and female mice that had undergone VD and VDR tasks. Pathway enrichment analysis and Protein-protein interaction (P-PI) analysis using gene sets with altered gene expression found three types of effects of nicotine: those common to both sexes, those in males only, and those in females only. Decreased expression of postsynaptic-related genes in males and increased expression of innate immunity-related genes in females were identified as possible molecular mechanisms related to sex differences in the effects of nicotine on cognition in discrimination learning and cognitive flexibility.

animal behavior and cognition↗

Importin α4 deficiency induces psychiatric disorder-related behavioral deficits and neuroinflammation in mice.

Importin 4, which is encoded by the Kpna4 gene, is a well characterized nuclear-cytoplasmic transport factor known to mediate transport of transcription factors including NF-{kappa}B. Here, we report that Kpna4 knock-out (KO) mice exhibit psychiatric disorder-related behavioral abnormalities such as anxiety-related behaviors, deceased social interaction and sensorimotor gating deficits. Contrary to a previous study predicting attenuated NF-{kappa}B activity as a result of Kpna4 deficiency, we observed a significant increase in expression levels of NF-{kappa}B genes and pro-inflammatory cytokines such as TNF, Il1{beta} or Il-6 in the Prefrontal Cortex or Basolateral Amygdala of the KO mice. Moreover, examination of inflammatory responses in primary cells revealed that Kpna4 deficient cells have an increased inflammatory response, which was rescued by addition of not only full-length, but also a nuclear transport deficient truncation mutant of importin 4, suggesting contribution of its non-transport functions. Furthermore, RNAseq of sorted adult Microglia and Astrocytes and subsequent transcription factor analysis suggested increases in Polycomb repressor complex 2 (PRC2) activity in Kpna4 KO cells. Taken together, importin 4 deficiency induces psychiatric disorder-related behavioral deficits in mice, along with an increased inflammatory response and possible alteration of PRC2 activity in glial cells.

neuroscience↗

Cross Potential Selection: A Proposal for Optimizing Crossing Combinations in Recurrent Selection Based on the Ability of Future Inbred Lines

In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior individuals may not always be superior parents. The choice of the crossing pair significantly influences the genotypic value of the resulting progeny. This study introduced a new strategy for selecting crossing pairs, termed Cross Potential Selection (CPS), designed to expedite the production of novel varieties. The CPS assesses the potential of each crossing pair to generate a novel variety. It considers the segregation of each crossing pair and computes the expected genotypic values of the topperforming individuals, assuming that the progeny distribution of genotypic values follows a normal distribution. We simulated a 10-year breeding program to compare CPS with three other selection strategies. CPS consistently demonstrated the highest genetic improvements among the four strategies in early cycles. In particular, during the middle cycles of the breeding program, CPS exhibited the highest genetic improvement of 73% of the 300 independent breeding simulations. In a long-term breeding scheme, some progeny distributions of genotypic values may deviate from normal distribution, affecting the efficiency of CPS. Nevertheless, compared with the other three strategies, CPS achieved significant short-term genetic improvements. In conclusion, CPS holds substantial promise for enhancing the efficiency of plant breeding programs. Article SummaryThis study introduces a novel plant breeding strategy termed Cross Potential Selection (CPS), which was designed to expedite the production of novel varieties. The CPS evaluates the potential of each crossing pair for the target generation. Through comparative breeding simulations, CPS demonstrated superior performance over the three alternative breeding strategies, particularly in the early cycles. These findings suggest that CPS holds significant promise for enhancing plant breeding efficiency.

genetics↗

Sequential Transitions of Male Sexual Behaviours Driven by Dual Acetylcholine-Dopamine Dynamics

The neural mechanisms regulating sequential transitions of male sexual behaviors, such as mounting, intromission, and ejaculation, in the brain remain unclear. Here, we report that dopamine (DA) and acetylcholine (ACh) dynamics in the ventral shell of the nucleus accumbens (vsNAc) closely aligns with serial transitions of sexual behaviors in male mice. During intromission, the vsNAc exhibits dual ACh-DA rhythms generated by reciprocal regulation between ACh and DA signaling via nicotinic acetylcholine (nAChR) and dopamine D2 (D2R) receptors. Knockdown of choline acetyl transferase (ChAT) or D2R in the vsNAc diminished the likelihood of intromission and ejaculation. Optogenetic manipulations reveal that DA signaling sustains male sexual behaviors by suppressing activities of D2RvsNAc neurons. Moreover, ACh signaling promotes the initiation of mounting and intromission, but also induces the intromission-to-ejaculation transition by triggering a slowdown of DA rhythm. Therefore, dual ACh-DA dynamics harmonize in the vsNAc to drive sequential transitions of male mating behaviors.

neuroscience↗

Assessing the potential for genome-assisted breeding in red perilla using quantitative trait locus analysis and genomic prediction

Red perilla is an important medicinal plant used in Kampo medicine, and the development of elite varieties of this species is urgently necessary. Medicinal compounds are generally considered target traits in medicinal plant breeding; however, selection based on the phenotypes of the compounds (i.e., conventional selection) is expensive and time-consuming. Here, we proposed genomic selection (GS) and marker-assisted selection (MAS) as suitable selection methods for medicinal plants, and evaluated the effectiveness of GS and MAS in red perilla breeding. Three breeding populations generated from crosses between one red and three green perilla genotypes were used to elucidate the genetic mechanisms underlying the production of major medicinal compounds using quantitative trait locus analysis and to evaluate the accuracy of genomic prediction (GP). We found that GP had sufficiently high accuracy for all traits, confirming that GS was an effective method for perilla breeding. Moreover, the three populations showed varying degrees of segregation, suggesting that use of these populations in breeding may yield simultaneous enhancements of different target traits. This study can contribute to research on the genetic mechanisms of the major medicinal compounds of red perilla as well as the breeding efficiency of this medicinal plant.

genomics↗

An integrative framework of stochastic variational variable selection for joint analysis of multi-omics microbiome data

High-dimensional multi-omics microbiome data plays an important role in elucidating microbial communities interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of soybean dataset, including 377 samples with 16,943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.

bioinformatics↗

The cholesterol pathway of the Golgi stress response induces cell death and transcription of Golgi-related genes through metabolic dysregulation of phosphatidylinositol-4-phosphate

The Golgi stress response is an important cytoprotective system that enhances Golgi function in response to cellular demand, while cells damaged by prolonged Golgi stress undergo cell death to ensure the survival of organisms. OSW-1, a natural compound with anticancer activity, acts as a potent inhibitor of OSBP that transports cholesterol and phosphatidylinositol-4-phosphate (PI4P) at contact sites between the endoplasmic reticulum and the Golgi apparatus. Previously, we reported that OSW-1 induces the Golgi stress response, resulting in Golgi stress-induced transcription and cell death. However, the underlying molecular mechanism has been unknown. To reveal the mechanism of a novel pathway of the Golgi stress response regulating transcriptional induction and cell death (the cholesterol pathway), we performed a genome-wide knockout screen and found that transcriptional induction as well as cell death induced by OSW-1 was repressed in HeLa cells deficient in factors involved in the PI4P metabolism, such as PITPNB and PI4KB genes. Our data indicate that OSW-1 induces Golgi stress-dependent transcriptional induction and cell death through dysregulation of the PI4P metabolism in the Golgi apparatus.

cell biology↗

Evaluating drought tolerance stability in soybean by theresponse of irrigation change captured from time-seriesmultispectral data

This study investigated a method to evaluate the drought tolerance stability of a genotype in a single environmental trial by capturing the plant response to irrigation changes. Genotypes that exhibit stable phenotypes under various drought stress conditions are required for stable crop production. However, considerable time and money are required to evaluate the environmental stability of a genotype through multiple environmental trials. As an index of drought tolerance stability, we calculated the coefficient of variation (CV) of shoot fresh weight of 178 soybean (Glycine max (L.) Merr.) accessions in a total of nine types of drought treatments, including changing irrigation treatments (every five or ten days) over 3-year trials. To capture the plant responses to irrigation changes, time-series multispectral (MS) data were collected, including the timings of the irrigation/non-irrigation switch in the changing irrigation treatments. We built a random regression model (RRM) for each of the nine treatments using the time-series MS data. We built a genomic prediction model (MTRRM model) using the genetic random regression coefficients of RRM as secondary traits and evaluated the accuracy of each model for predicting CV. In two out of the three years, the prediction accuracy of MTRRM models built in the changing irrigation treatment was higher than that in the continuous drought treatment in the same year. When the CV was predicted using the MTRRM model across years in the changing irrigation treatment, the prediction accuracy was 61% higher than that of the simple genomic prediction model. These results suggest that drought tolerance stability can be evaluated in a single environmental trial, which may reduce the time and cost of selecting genotypes with high drought tolerance stability.

genetics↗

Dentate neurogenesis mediates cognitive flexibility via modulation of the hippocampal longitudinal-axis network

Adult neurogenesis endows the hippocampus with unparalleled neural plasticity, essential for intricate cognitive functions. However, the manner in which sparse newborn neurons (NBNs) modulate neural activities and subsequently shape behavior remains enigmatic. Utilizing a newly engineered NBN-Tetanus Toxin mouse model, we non-invasively silenced NBNs and confirmed their crucial role in cognitive flexibility, as demonstrated through reversal learning in the Morris water maze and the Go/Nogo task in operant learning. Pairing task-based functional MRI (tb-fMRI) with operant learning revealed a dorsal hippocampal hyperactivation during Nogo task, implying that hippocampal hyperexcitability might underlie the observed behavioral deficits. Notably, resting-state fMRI (rs-fMRI) revealed enhanced functional connectivity between the dorsal and ventral dentate gyrus following NBN silencing. Further exploration of PV+ interneurons and mossy cells activities highlighted NBNs integral part in preserving the excitation/inhibition balance within the hippocampus. Our findings emphasize how the neural plasticity driven by NBNs extensively modulates the hippocampus, sculpting cognitive flexibility.

neuroscience↗

Time-series Multi-spectral Imaging in Soybean for Improving Biomass and Genomic Prediction Accuracy

Multi-spectral (MS) imaging enables the measurement of characteristics important for increasing the prediction accuracy of genotypic and phenotypic values for yield-related traits. In this study, we evaluated the potential application of temporal MS imaging for the prediction of above-ground biomass (AGB) and determined which developmental stages should be used for accurate prediction in soybean. Field experiments with 198 accessions of soybean were conducted with four different irrigation levels. Five vegetation indices (VIs) were calculated using MS images from soybean canopies from early to late growth stages. To predict the genotypic values of AGB, VIs at the different growth stages were used as secondary traits in a multi-trait genomic prediction. The accuracy of the prediction model increased starting at an early stage of growth (31 days after sowing). To predict phenotypic values of AGB, we employed multi-kernel genomic prediction. Consequently, the prediction accuracy of phenotypic values reached a maximum at a relatively early growth stage (38 days after sowing). Hence, the optimal timing for MS imaging may depend on the irrigation levels.

plant biology↗

Integrated Collection of Stem Cell Bank data, a data portal for standardized stem cell information

The last decade has witnessed an extremely rapid increase in the number of newly established stem cell lines. However, due to the lack of a standardized format, data exchange among stem cell line resources has been challenging, and no system can search all stem cell lines across resources worldwide. To solve this problem, we have developed Integrated Collection of Stem Cell Bank data (ICSCB) (http://icscb.stemcellinformatics.org/), the largest database search portal for stem cell line information, based on the standardized data items and terms of the MIACARM framework. Currently, ICSCB can retrieve >16,000 cell lines from four major data resources in Europe, Japan, and the United States. ICSCB is automatically updated to provide the latest cell line information, and its integrative search helps users collect cell line information for over 1,000 diseases including many rare diseases worldwide, which has been a formidable task, thereby distinguishing itself from other database search portals.

bioinformatics↗