Biology subjects

Yamaguchi, S.

Publications and source records attributed to Yamaguchi, S..

31 records · Page 2Linked to original sources

bioRxiv2024

Augmentation of DNA exonuclease TREX1 in macrophages as a therapy for cardiac ischemic injury

Noncoding RNAs (ncRNAs) are increasingly recognized as bioactive. Here we report the development of TY1, a synthetic ncRNA bioinspired by a naturally-occurring human small Y RNA with immunomodulatory properties. TY1 upregulates TREX1, an exonuclease that rapidly degrades cytosolic DNA. In preclinical models of myocardial infarction (MI) induced by ischemia/reperfusion, TY1 reduced scar size. The cardioprotective effect of TY1 was abrogated by prior depletion of macrophages and mimicked by adoptive transfer of macrophages exposed either to TY1 or TREX1. Inhibition of TREX1 in macrophages blocked TY1 cardioprotection. Consistent with a central role for TREX1, TY1 attenuated DNA damage in the post-MI heart. This novel mechanism--pharmacologic upregulation of TREX1 in macrophages--establishes TY1 as the prototype for a new class of ncRNA drugs with disease-modifying bioactivity. One Sentence SummaryUpregulation of three prime exonuclease, TREX1, in macrophages enhances tissue repair post myocardial infarction.

molecular biology↗

bioRxiv2023

Lymphatic vessel development in human embryos

Lymphatic vessel development has been a subject of research for about 120 years. Studies employing mice and zebrafish models have elucidated that lymphatic endothelial cells (LECs) predominantly differentiate from venous endothelial cells via the expression of transcription factor Prospero homeobox protein 1 (Prox1), a master regulator of lymphatic vessel development. On the other hand, it has been found that LECs can also be generated from undifferentiated mesodermal or hemogenic endothelial cells, suggesting potential diversity in their origins depending on the organ or anatomical location. However, knowledge of human lymphatic vessel development remains limited. Here, we examined early lymphatic development in humans by analyzing 31 embryos and three 9-week old fetuses. We found that human embryos produce Prox1-expressing LECs in and around the cardinal veins, which converged to form initial lymph sacs. Furthermore, we also examined lymphatic vessel development in the heart, lungs, lower jaw, mesentery, intestines and kidneys. Lymphatic vessels appeared to develop at different rates in each organ and to display temporal differences in marker expression. These observation showed the possibility that there could exist different patterns of lymphatic vessel development across organs, which may reflect different cellular origins or developmental signaling in each organ. Our research clarifies the early development of human lymphatic vessels, contributing to a better understanding of the evolution and phylogenetic relationships of lymphatic systems, and enriching our knowledge of the role of lymphatics in various human diseases. Significance StatementLymphatic vessel development has been a focus of research for over a century. Recent studies across a variety of species have demonstrated that lymphatic endothelial cells originate from embryonic veins, and undifferentiated mesodermal cells. However, whether these findings are applicable to human has yet to be determined. In this study, we explored lymphatic vessel development in humans. Our analysis demonstrated that lymphatic endothelial cells in human embryos initially derived from embryonic veins. Notably, we found that lymphatic vessels in different organs displayed distinct developmental and marker expression patterns, suggesting a diversity in lymphatic vessel development across organs. Our research revealed the human lymphatic vessel development, contributing to the understanding of phylogenetics of lymphatic vessels and lymph-related diseases.

developmental biology↗

bioRxiv2023

Biosynthesis of gibberellin-related compounds modulates far-red light responses in the liverwort Marchantia polymorpha

The phytohormone gibberellins (GAs) are key regulators of growth, development and environmental responses in angiosperms. From an evolutionary perspective, all major steps of GA biosynthesis are conserved among vascular plants, while GA biosynthetic intermediates such as ent-kaurenoic acid (KA) are also produced by bryophytes. Here we show that in the liverwort Marchantia polymorpha, KA and GA12 are synthesized by evolutionarily conserved enzymes, which are required for developmental responses to far-red light (FR). Under FR-enriched conditions, mutants of various biosynthesis enzymes consistently altered thallus growth allometry, delayed the initiation of gametogenesis, and affected the morphology of gamete-bearing structures (gametangiophores). By chemical treatments and LC-MS/MS analyses, we confirmed these phenotypes were caused by deficiency of some GA-related compounds derived from KA, but not bioactive GAs from vascular plants. Transcriptome analysis showed that FR enrichment induced the up-regulation of genes related to stress responses and secondary metabolism in M. polymorpha, which was largely dependent on the biosynthesis of GA-related compounds. Due to the lack of the canonical GA receptors in bryophytes, we hypothesize that GA-related compounds are commonly synthesized in land plants but co-opted independently to regulate responses to light quality change in different lineages during the past 450 million years of evolution.

plant biology↗

bioRxiv2022

Expected Costs of Mental Efforts are Updated When People Exert Effort, not by Prospective Information

To understand why people avoid mental effort, it is crucial to reveal the mechanisms by which we learn and decide about mental effort costs. This study investigated whether mental effort cost learning aligns with temporal-difference (TD) learning or alternative mechanisms. Model-based fMRI analyses showed no correlation between cost prediction errors (CPEs) and activity in the dorsomedial frontal cortex/dorsal anterior cingulate cortex (dmFC/dACC) or striatum at the time of a fully informative effort cue about upcoming effort demands, contradicting the TD hypothesis. Instead, CPEs correlate with dmFC/dACC (positively) and caudate (negatively) activity at effort completion. Furthermore, only activity patterns at effort completion predict subsequent choices. These results show that decision policies are updated retrospectively at effort completion, updating expected costs with prediction error between experienced effort and prior expectations, demonstrating mental effort cost learning is retrospective, and imply that adaptive learning of mental effort cost does not follow canonical TD learning. Significance StatementUnderstanding how people learn about mental effort costs is essential for advancing theories of motivation and cognitive control. However, the algorithms supporting such learning remain unclear. This study addressed this gap and found that temporal-difference learning, commonly used to explain reward learning, could not account for how people learn about effort. Instead, decision policies were updated retrospectively at effort completion, based on a prediction error between experienced effort and prior expectations. These findings reveal that mental effort cost learning is fundamentally retrospective and imply that it relies on mechanisms distinct from canonical temporal-difference learning.

neuroscience↗

bioRxiv2022

Comparing Deep Learning Models for Age Prediction Based on the Resting State fMRI Dataset from the "Brain Dock" Service in Japan

In Japan, many hospitals provide the unequaled service of medical check-up called the "Brain Dock"; however, there is a paucity of studies aimed at leveraging functional magnetic resonance imaging (fMRI) in hospitals. We obtained the resting-state fMRI (rs-fMRI) scans of about 695 patients who accessed this service for preventive medicine against Alzheimers Disease. In this study, we created deep learning models for age prediction with the ultimate aim of arriving at standard protocols for introducing rs-fMRI into clinical settings, particularly in Brain Docks. With that view, an assemblage of modeling conditions was attempted, changing multiple parameter values, features based on data extraction methods (region of interest-wise mean blood-oxygen-level-dependent lump-sum time series models or dynamic functional connectivity models), deep learning algorithms (Transformer, Multi-task Transformer, and unidirectional or bidirectional long short-term memory models), and different atlas-dependent brain region segmentation methods (including the Automated Anatomical Labeling and Harvard-Oxford atlases). As a result, a robust and highly significant correlation was obtained between actual and predicted ages from all types of methodologies. In addition, we determined that some conditions had a relatively large impact on prediction performance based on extended comparisons. The accuracy decreased, particularly according to the choice of atlases but with the same modeling conditions. Notwithstanding, we found that atlases based on intrinsic functional connectivity provided significant prediction accuracy even with a small number of regions to a similar extent as networks lowered spatial granularity. Moreover, we found that multi-task learning with other phenotype data (related to gender differences) was possible, but did not improve the prediction accuracy as much as expected. Despite these limitations, our results could provide a hopeful prospect of introducing fMRI into the field of neuro-clinical practice. HighlightsO_LIAge prediction modeling was performed using the rs-fMRI data of a Japanese "Brain Dock" service targeting mainly elderly people, which made prediction more challenging. C_LIO_LIA robust and highly significant correlation was obtained from all types of methodologies changing data extraction methods, deep learning algorithms, and brain atlases. C_LIO_LIAge prediction was successful even with a very small number of regions exclusively based on intrinsic functional connectivity networks, although there was a difference in the achievement of modeling. C_LI

neuroscience↗

bioRxiv2022

Chemoenzymatic fluorescence labeling of intercellularly contacting cells using lipidated sortase A

Methods to label intercellular contact attract particular attention due to their potential in cell biological and medical applications through analysis of intercellular communications. In this study, a simple and versatile method for chemoenzymatically labeling the intercellularly contacting cell was developed by using a cell-surface anchoring reagent of poly(ethylene glycol)(PEG)-lipid conjugate. The surfaces of each cell in cell pairs of interest were efficiently decorated with sortase A (SrtA) and triglycine peptide that were lipidated with PEG-lipid, respectively. In the mixture of the two cell populations, the triglycine-modified cells were enzymatically labeled with a fluorescent labeling reagent by contacting with the SrtA-modified cells both on the substrate and in cell suspensions. Such selective labeling of the contacting cells was confirmed by confocal microscopy and flow cytometry. The results show a proof of principle that the present method is a promising tool for selective visualization and quantification of the intercellularly contacting cells among cell mixtures in cell-cell communication analysis.

biochemistry↗

bioRxiv2021

An ancestral function of strigolactones as symbiotic rhizosphere signals

In flowering plants, carotenoid-derived strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), a previously unidentified SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating that it is ancestral in land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone.

plant biology↗

bioRxiv2020

Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge

Even after total resection of glioblastoma core lesions by surgery and aggressive post-surgical treatments, life-threatening tumors inevitably recur. A characteristic obstacle in effective treatment is high intratumoral heterogeneity, both longitudinally and spatially. Recurrence occurs predominantly at the brain parenchyma-tumor core interface, a region termed tumor edge. Given the difficulty of accessing it surgically, the composition of the tumor edge, harboring both cancerous and non-cancerous cells, remains largely unknown. Here, to identify phenotypic diversity among heterogeneous glioblastoma core and edge lesions, we uncovered the existence of three phenotypically-distinct clonal subpopulations within individual tumors from glioblastoma patients. Clones from the tumor core shared the same phenotype, exclusively generating tumor-core cells. In contrast, two distinct clonal subtypes were identified at the tumor edge: one generated only edge-lesion cells and the other expanded more broadly to establish both edge- and core-lesions. Using multiple xenograft experimental models in mouse brains, tumor edge development was found to require that both somatic and tumor cells express the NADase CD38, combinedly elevating glioblastoma malignancy. In vitro data suggested that intracellular NADase activity at the edge was provoked through intercellular communication between edge clones and normal astrocytes. Systemic treatment of tumor-bearing mice with 78c, a small-molecule CD38 inhibitor, attenuated the formation of glioblastoma edge lesions, suggesting its clinical potential to pharmacologically eliminate tumor-edge lesions. Collectively, these findings provide novel phenotypic and mechanistic insights into clonal heterogeneity within glioblastoma, particularly in the surgically unresectable, currently understudied tumor edge.

cancer biology↗

bioRxiv2020

Brain aging-dependent glioma traits reversible by NAD+/BDNF-mediated neuronal reactivation

The rise in aging population worldwide is increasing death from cancer, including glioblastoma. Here, we explore the impact of brain aging on glioma tumorigenesis. We find that glioblastoma in older patients and older mice displayed reduced neuronal signaling, including a decline of NTRK-like family member 6 (SLITRK6), a receptor for neurotrophic factor BDNF. This reduction was linked to the systemic decline of nicotinamide adenine dinucleotide (NAD+) with aging, as old mice exposed to young blood via parabiosis or supplemented with the NAD+ precursor NMN (nicotinamide mononucleotide) reverted phenotypically to young-brain responses to glioma, with reactivated neuronal signaling and reduced death from tumor burden. Interestingly, the phenotypic reversal by NMN was largely absent in old mice undergoing parabiosis with BDNF+/- young mice and in BDNF+/- mice undergoing tumor challenge, supporting the notion that the lower NAD+-BDNF signaling in the aging brain aggravated glioma tumorigenesis. We propose that the aging-associated decline in brain NAD+ worsens glioma outcomes at least in part by decreasing neuronal/synaptic activity and increasing neuroinflammation.

cancer biology↗

bioRxiv2020

Thermostable mutants of glycoside hydrolase family 6 cellobiohydrolase from the basidiomycete Phanerochaete chrysosporium

Thermal inactivation of saccharifying enzymes is a crucial issue for the efficient utilization of cellulosic biomass as a renewable resource. Cellobiohydrolases (CBHs) is a kind of cellulase. In general, CBHs belonging to glycoside hydrolase (GH) family 6 (Cel6) act synergistically with CBHs of GH family 7 (Cel7) and other carbohydrate-active enzymes during the degradation of cellulosic biomass. However, while the catalytic rate of enzymes generally becomes faster at higher temperatures, Cel6 CBHs are inactivated at lower temperatures than Cel7 CBHs, and this represents a limiting factor for industrial utilization. In this study, we produced a series of mutants of the glycoside hydrolase family 6 cellobiohydrolase PcCel6A from the fungus Phanerochaete chrysosporium, and compared their thermal stability. Eight mutants from a random mutagenesis library and one rationally designed mutant were selected as candidate thermostable mutants and produced by heterologous expression in the yeast Pichia pastoris. Comparison of the hydrolytic activities at 50 and 60 {degrees}C indicated that the thermal stability of PcCel6A is influenced by the number and position of cysteine residues that are not involved in disulfide bonds.

biochemistry↗

bioRxiv2019

Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and conversion of 18-hydroxylcarlactonoates to canonical and non-canonical strigolactones in Lotus japonicus

Strigolactones (SLs) are a group of plant apocarotenoids that act as rhizosphere signaling molecules for both arbuscular mycorrhizal fungi and root parasitic plants. They also regulate plant architecture as phytohormones. The model legume Lotus japonicus produces canonical 5-deoxystrigol (5DS) and non-canonical lotuslactone (LL). The biosynthesis pathways of the two SLs remain elusive. In this study, we characterized the L. japonicus MAX1 homolog, LjMAX1, found in the Lotus japonicus genome assembly build 2.5. The L. japonicus max1 LORE1 insertion mutant was deficient in 5DS and LL production. A recombinant LjMAX1 protein expressed in yeast microsomes converted carlactone (CL) to 18-hydroxycarlactonoic acid (18-HO-CLA) via carlactonoic acid (CLA). Identity of 18-HO-CLA was confirmed by comparison of the methyl ester derivative of the MAX1 product with the chemically synthesized methyl 18-hydroycarlactonoate (18-HO-MeCLA) using LC-MS/MS. (11R)-CL was detected as an endogenous compound in the root of L. japonicus. 13C-labeled CL, CLA, and 18-HO-MeCLA were converted to [13C]-5DS and LL in plant feeding experiments using L. japonicus WT. These results showed that LjMAX1 is the crucial enzyme in the biosynthesis of Lotus SLs and that 18-hydroxylated carlactonoates are precursors for SL biosynthesis in L. japonicus.

plant biology↗

bioRxiv2018

Growth- and stress-related defects associated to wall hypoacetylation are strigolactone-dependent

Mutants affected in the Arabidopsis TBL29/ESK1 xylan O-acetyltransferase display a strong reduction in total wall O-acetylation accompanied by a dwarfed plant stature, collapsed xylem morphology, and enhanced freezing tolerance. A newly identified tbl29/esk1 suppressor mutation affects the biosynthesis of strigolactones (SL) due to the reduced expression of the MAX4 gene. Genetic and biochemical evidence suggests that blocking the biosynthesis of SL is sufficient to recover all developmental and stress-related defects associated with the TBL29/ESK1 loss of function without affecting its direct effect - reduced wall O-acetylation. Altered levels of the MAX4 SL biosynthetic gene, reduced branch number, and higher levels of methyl carlactonoate, an active SL, were also found in tbl29/esk1 plants consistent with a constitutive activation of the SL pathway. These results indicate that the reduction of O-acetyl substituents in xylan is not directly responsible for the observed tbl29/esk1 phenotypes. Alternatively, plants may perceive defects in the structure of wall polymers and/or wall architecture activating the SL hormonal pathway as a compensatory mechanism.

plant biology↗

bioRxiv2017

Identification Of Animal Behavioral Strategy By Inverse Reinforcement Learning ~ Its Application To Thermotaxis In C. elegans ~

Animals are able to reach a desired state in an environment by controlling various behavioral patterns. Identification of the behavioral strategy used for this control is important for understanding animals decision-making and is fundamental to dissect information processing done by the nervous system. However, methods for quantifying such behavioral strategies have not been fully established. In this study, we developed an inverse reinforcement-learning (IRL) framework to identify an animals behavioral strategy from behavioral time-series data. As a particular target, we applied this framework to C. elegans thermotactic behavior; after cultivation at a constant temperature with or without food, the fed and starved worms prefer and avoid from the cultivation temperature on a thermal gradient, respectively. Our IRL approach revealed that the fed worms used both absolute and temporal derivative of temperature and that their strategy comprised mixture of two strategies: directed migration (DM) and isothermal migration (IM). The DM is a strategy that the worms efficiently reach to specific temperature, which explained thermotactic behaviors of the fed worms. The IM is a strategy that the worms track along a constant temperature, which reflects isothermal tracking well observed in previous studies. We also showed the neural basis underlying the strategies, by applying our method to thermosensory neuron-deficient worms. In contrast to fed animals, the strategy of starved animals indicated that they escaped the cultivation temperature using only absolute, but not temporal derivative of temperature. Thus, our IRL-based approach is capable of identifying animal strategies from behavioral time-series data and will be applicable to wide range of behavioral studies, including decision-making of other organisms.\n\nAuthor SummaryUnderstanding animal decision-making has been a fundamental problem in neuroscience and behavioral ecology. Many studies analyze actions that represent decision-making in behavioral tasks, in which rewards are artificially designed with specific objectives. However, it is impossible to extend this artificially designed experiment to a natural environment, because in a natural environment, the rewards for freely-behaving animals cannot be clearly defined. To this end, we must reverse the current paradigm so that rewards are identified from behavioral data. Here, we propose a new reverse-engineering approach (inverse reinforcement learning) that can estimate a behavioral strategy from time-series data of freely-behaving animals. By applying this technique with thermotaxis in C. elegans, we successfully identified the reward-based behavioral strategy.

neuroscience↗