Biology subjects

Maeda, M.

Publications and source records attributed to Maeda, M..

18 recordsLinked to original sources

bioRxiv2026

Fluorescence in situ hybridization reveals endophytic and epiphytic root colonization of the novel plant growth-promoting bacterium Citrobacter sedlakii CESi7

Plant growth-promoting bacteria are gaining significant attention as promising biofertilizers. However, the inconsistency between in vitro plant growth-promoting traits and actual field performance remains a challenge, driven partly by a limited understanding of in situ colonization. This study characterized the colonization patterns of Citrobacter sedlakii CESi7, a novel plant growth-promoting bacterium, isolated from oil palm waste compost, during Brassica rapa cultivation. The in situ behavior of CESi7 was observed in both sterilized medium and non-sterilized soil using fluorescence in situ hybridization with a strain-targeting probe. The results revealed that CESi7 can establish both epiphytic and endophytic populations that transiently colonize roots. In a sterilized medium, CESi7 was widely distributed throughout the root tissues. Conversely, in non-sterilized soil, the bacterium formed dense aggregates specifically at the root tips. This study provides direct microscopic evidence of the colonization strategy of CESi7, offering crucial insights for its development as an effective biofertilizer.

microbiology↗

bioRxiv2026

Dorsal fins are not universal stabilizers in cetaceans: limited yaw effects and flipper-coupled roll stability

Cetacean dorsal fins are traditionally regarded as vertical stabilizers for yaw and roll, yet marked variation in fin area and position suggests that this function is not universal. We combined computational fluid dynamics simulations of five cetacean species with comparative analyses of dorsal fin and flipper morphology across 81 species to test whether variation in dorsal fin morphology reflects the evolution of hydrodynamic stabilization. Yaw-destabilizing moments were dominated by the trunk regardless of flipper posture, whereas dorsal fins were generally too small and too close to the center of rotation to provide substantial static yaw restoration. In contrast, dorsal fins influenced roll stability in concert with extended anhedral flippers. Although dorsal fins were likely present in the common ancestor of extant cetaceans, strong dorsal fin-mediated roll stabilization was largely restricted to oceanic bite-feeding delphinids, in which rapid evolutionary enlargement of the dorsal fin and persistently extended anhedral flippers likely enhanced roll stability. In most other lineages, roll stability could be maintained by flipper posture alone despite small dorsal fins. These results recast the cetacean dorsal fin not as a universal stabilizer, but as a lineage-specific roll stabilizing structure whose function emerges through mechanical coupling with the flippers.

evolutionary biology↗

bioRxiv2025

Phosphorylation-Coupled Autoregulation Maintains Functional ER Exit Sites

Secretory proteins are synthesized in the endoplasmic reticulum (ER) and begin their transport from specialized domains on the ER called ER exit sites (ERES). We previously demonstrated that the interaction between TANGO1 and Sec16 is critical for ERES formation. In this study, we reveal that the phosphorylation of TANGO1 and Sec16 is regulated by a FAM83A/CK1-mediated negative feedback loop. Conversely, their dephosphorylation is regulated in a spatially distinct manner by different phosphatase complexes: PPP6R3/PPP6C for Sec16 and PPP1R15B/PPP1C for TANGO1. Excessive phosphorylation of either TANGO1 or Sec16 leads to ERES disassembly, while excessive dephosphorylation impairs secretion. Our findings demonstrate that maintaining a balanced phosphorylation state of TANGO1 and Sec16 through autoregulation by FAM83A/CK1 and the phosphatases PP1 and PP6 is essential for sustaining proper secretory activity at the ERES.

cell biology↗

bioRxiv2024

High-throughput robotic isolation of human iPS cell clones reveals frequent homozygous induction of identical genetic manipulations by CRISPR-Cas9

Genome editing in human iPS cells is a powerful approach in regenerative medicine. CRISPR-Cas9 is the most common genome editing tool, but it often induces byproduct insertions and deletions in addition to the desired edits. Therefore, genome editing of iPS cells produces diverse genotypes. Existing assays mostly analyze genome editing results in cell populations, but not in single cells. However, systematic profiling of genome editing outcomes in single iPS cells was lacking. In this study, we developed a method for high-throughput iPS cell clone isolation based on the precise robotic picking of cell clumps derived from single cells grown in extracellular matrices. We analyzed over 1,000 genome-edited iPS cell clones and found that homozygous editing was much more frequent than heterozygous editing. We also observed frequent homozygous induction of identical genetic manipulations, including insertions and deletions. Our new cloning method and findings will facilitate the application of genome editing to human iPS cells.

bioengineering↗

bioRxiv2024

Mechanosensory representation of wing deformations

Locomotor control is facilitated by mechanosensory inputs that report how the body interacts with a physical medium. Effective representation of compliant wing deformations is particularly challenging due to the many degrees of freedom. Structural configurations can constrain the stimulus space, and strategic placement of sensors can simplify computation. Here, we measured and modelled wing displacement fields and characterized spatiotemporal encoding of the wing mechanosensors. Our data show how dragonfly wing architecture prescribes deformation modes consistent across models and measurements. We found that the wings state under normal flapping conditions is detected by the spike timing of few sensors, with additional sensors recruited under perturbation. The functional integration of wing biomechanics and sensor placement enables a straightforward solution for information transfer. Significance StatementMany systems in nature precisely control highly deformable structures, yet monitoring structural deformations has posed a significant challenge for biologists and engineers. By measuring and modelling the intricate structure of compliant dragonfly wings, we demonstrate an elegant solution for mechanosensory representation. We show that the functional integration of natural wing biomechanics and sensor placement provides a straightforward solution for information transfer. Wing morphology passively constrains the range of natural deformations, producing strain patterns that align with sensor locations, allowing them to monitor the wing using a simple timing-dependent encoding strategy. The way insects monitor aerodynamic and inertial forces via wing deformations during flight could apply to many sensory systems in nature and inspire artificial neural networks for controlling diverse dynamic systems.

neuroscience↗

bioRxiv2024

A Novel Method to Visualize Active Small GTPases Unveils Distinct Sites of Sar1 Activation During Collagen Secretion.

Small GTPases are essential in various cellular signaling pathways, and detecting their activation within living cells is crucial for understanding cellular processes. Fluorescence resonance energy transfer is widely used to study the interaction between activated small GTPases and their effectors, but it is limited to those with well-defined effectors, excluding Sar1. Here, we present a novel method, SAIYAN (Small GTPase ActIvitY ANalyzing), for detecting the activation of endogenous small GTPases via fluorescent signals utilizing a split mNeonGreen system. We demonstrated Sar1 activation at the endoplasmic reticulum (ER) exit site and successfully detected its activation state in various cellular conditions. Utilizing the SAIYAN system in collagen-secreting cells, we discovered activated Sar1 localized both at ER exit sites and ER-Golgi intermediate compartment (ERGIC) regions. Additionally, impaired collagen secretion led to the confinement of activated Sar1 at the ER exit sites, underscoring the significance of Sar1 activation through the ERGIC in collagen secretion.

cell biology↗

bioRxiv2023

Biallelic variants in LARS1 induce steatosis in developing zebrafish liver via enhanced autophagy

Acute liver failure is a life-threatening condition during infancy. Biallelic pathogenic variants in LARS1 cause infantile liver failure syndrome type 1 (ILFS1), which is characterized by acute hepatic failure in infants. LARS functions as a protein associated with mTORC1 and plays a crucial role in amino acid-triggered mTORC1 activation and autophagy regulation. A previous study demonstrated that larsb-knockout zebrafish show a condition resembling ILFS. However, a comprehensive analysis of larsb-knockout zebrafish has not yet been performed because of early mortality. We herein generated a long-term viable zebrafish model carrying a LARS1 variant identified in an ILFS1 patient (larsb-I451F zebrafish) and analyzed the pathogenesis of the affected liver of ILFS1. Hepatic dysfunction is most prominent in ILFS1 patients during infancy; correspondingly, the larsb-I451F zebrafish manifested hepatic anomalies during the developmental stages. The larsb-I451F zebrafish demonstrates augmented lipid accumulation within the liver under autophagy activation. Inhibition of DGAT1, which converts fatty acids to triacylglycerols, improved lipid droplets in the liver of larsb-I451F zebrafish. Notably, treatment with an autophagy inhibitor ameliorated hepatic lipid accumulation in this model. Our findings suggested that enhanced autophagy caused by biallelic LARS1 variants contributes to ILFS1-associated hepatic dysfunction. Furthermore, the larsb-I451F zebrafish model, which has a prolonged survival rate compared to the larsb-knockout model, highlights its potential utility as a tool for investigating the pathophysiology of ILFS1-associated liver dysfunction. Author SummaryInfantile liver failure (ALF) is a rare but life-threatening condition primarily caused by various genetic and infectious factors during infancy. Comprehensive research into its causes is crucial for treatment decisions, including liver transplantation and supportive interventions. While specific therapies exist for some conditions, a significant proportion of infant ALF cases remains unresolved. Recent advances in genetic sequencing have identified congenital disorders, particularly involving the LARS1 gene, as contributors to ALF. LARS1 is essential for regulating processes related to amino acids and autophagy. To better understand this condition, we created a zebrafish model carrying specific LARS1 gene variants seen in ALF patients. These zebrafish displayed liver abnormalities similar to those observed in infants with ALF. Our study revealed that enhanced autophagy, triggered by biallelic LARS1 variants, plays a significant role in liver dysfunction associated with ALF. Notably, inhibiting specific enzymes involved in fat metabolism and autophagy showed promising results in reducing hepatic lipid accumulation in our zebrafish model. This research provides insights that may lead to improved understanding and potential treatments for this devastating condition.

cell biology↗

bioRxiv2022

Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range

Magnetic resonance imaging (MRI) is a noninvasive neuroimaging method beneficial for the identification of normal developmental and aging processes and data sharing. Marmosets have a relatively shorter life expectancy (approximately 10 years) than other primates, including, humans because they grow and age faster. Hence, the common marmoset model is effective in aging research. The current study investigated the aging process of the marmoset brain and provided an open MRI database on marmosets with a wide age range. The Brain/MINDS Marmoset Brain MRI Dataset contains brain MRI information on 216 marmosets aged between 1 and 10 years. During its release date, it is the largest public dataset worldwide. Further, it comprises multi contrast MRI images. In addition, 91 of 216 animals have corresponding ex vivo high-resolution MRI datasets. Our MRI database, which is available at the Brain/MINDS Data portal might help understand the effects of different factors, such as age, sex, body size, and fixation, on the brain. Moreover, it can contribute to and accelerate brain science studies worldwide.

neuroscience↗

bioRxiv2022

Genome Editing Is Induced in a Binary Manner in Single Human Cells

Even when precise nucleotide manipulations are intended, the outcomes of genome editing can be diverse, often including random insertions and deletions. The combinations and frequencies of these different outcomes in single cells are critical not only in the generation of genetically modified cell lines but also in the evaluation of the clinical effects of genome editing therapies. However, current methods only analyze cell populations, not single cells. Here, we utilized the Single Particle isolation System (SPiS) for the efficient isolation of single cells to systematically analyze genome editing results in individual human cultured cells. As a result, we discovered that genome editing induction has a binary nature, that is, the target alleles of cells tend to be all edited or not edited at all. This study enhances our understanding of the induction mechanism of genome editing and provides a new strategy to analyze genome editing outcomes in single cells.

bioengineering↗

bioRxiv2021

Hydrodynamics of gliding penguin flipper suggests the adjustment of sweepback with swimming speeds

Hydrodynamic performance of a gliding penguin flipper (wing) considering the backward sweep was estimated with computational fluid dynamics (CFD) simulation. A flipper of a gentoo penguin (Pygoscelis papua) was 3D scanned, smoothed, and a numerical fluid mesh was generated. For accurate yet resource-saving computation, an embedded large-eddy simulation (ELES) methods was employed, where the flow near the flipper was solved with large-eddy simulation (LES) and flow far away from the flipper was solved with Reynolds-averaged Navier-Stokes (RANS). The relative flow speed was fixed at 2 m s-1, close to the typical foraging speed for the penguin species. The sweep angle was set to be 0{degrees}, 30{degrees}, and 60{degrees}, while the angle of attack was varied between -40{degrees} and 40{degrees}, both are within the realistic ranges in the wing kinematics measurement of penguins in an aquarium. It was revealed that a higher sweep angle reduces the lift slope, but the lift coefficient is unchanged at a high angle of attack. Drag coefficient was reduced across the angles of attack with increasing the sweep angles. The drag polars suggest the sweep angle may be adjusted with the change in swimming speed and anhedral (negative dihedral) angle to minimise drag while maintaining the vertical force balance to counteract the positive buoyancy. This will effectively expand the swimming envelope of the gliding penguin, similar to a flying counterpart such as swift.

zoology↗

bioRxiv2021

Complete neuroanatomy and sensor maps of Odonata wings for fly-by-feel flight control

Can mechanosensors in animal wings allow reconstruction of the wing aeroelastic states? Little is known about how flying animals utilize wing mechanosensation to monitor the dynamic state of their highly deformable wings. Odonata, dragonflies and damselflies, are a basal lineage of flying insects with excellent flight performance, and their wing mechanics have been studied extensively. Here, we present a comprehensive map of the wing sensory system for two Odonata species, including both the external sensor morphologies and internal neuroanatomy. We identified eight morphological classes of sensors; most were mechanosensors innervated by a single neuron. Their innervation patterns and morphologies minimize axon length and allow morphological latency compensation. We further mapped the major veins of another 13 Odonata species across 10 families and identified consistent sensor distribution patterns, with sensor count scaling with wing length. Finally, we constructed a high-fidelity finite element model of a dragonfly wing for structural analysis. Our dynamic loading simulations revealed features of the strain fields that wing sensor arrays could detect to encode different wing deformation states. Taken together, this work marks the first step toward an integrated understanding of fly-by-feel control in animal flight.

neuroscience↗

bioRxiv2020

From wing shape to fluid dynamics in the barn owl (Tyto alba)

Birds morph their wings and tail in order to glide under a wide range of aerodynamic conditions. Gross wing morphing has been described in a multitude of studies, but the finer details of wing morphing are still unknown. Here, we measured the changes in wing shape and pose in a barn owl, Tyto alba, when gliding across a range of fifteen self-selected speeds. We found that T. alba does not use fine-wing shape control to glide at slow speeds in steady conditions, with the measured wing shapes being highly consistent across all flights. Instead, T. alba relied upon wing postural control (gross pitch) and changes in both tail shape and pose to modulate aerodynamic force. A consistent wing shape provides an exceptional aerodynamic tool for understanding gliding flight in birds through postural change and tail morphing. This geometry was used as the basis for computational fluid dynamics simulations which gave very similar wake measurements and weight support to those measured in flight. This geometry is provided here to assist other researchers interested in exploring the fluid dynamics behind gliding flight in birds.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2019

Targeted brain tumor radiotherapy using an Auger emitter

Glioblastoma multiforme is a highly aggressive form of brain cancer whose location, tendency to infiltrate healthy surrounding tissue, and heterogeneity significantly limit survival, with scant progress having been made in recent decades. 123I-MAPi (Iodine-123 Meitner-Auger PARP1 inhibitor) is a precise therapeutic tool composed of a PARP1 inhibitor radiolabeled with an Auger- and gamma-emitting iodine isotope. Here, the PARP inhibitor, which binds to the DNA repair enzyme PARP1, specifically targets cancer cells, sparing healthy tissue, and carries a radioactive payload within reach of the cancer cells DNA. The high relative biological efficacy of Auger electrons within their short range of action is leveraged to inflict DNA damage and cell death with high precision. The gamma ray emission of 123I-MAPi allows for the imaging of tumor progression and therapy response, and for patient dosimetry calculation. Here we demonstrated the efficacy and specificity of this small molecule radiotheranostic in a complex preclinical model. In vitro and in vivo studies demonstrate high tumor uptake and a prolonged survival in mice treated with 123I-MAPi when compared to vehicle controls. Different methods of drug delivery were investigated to develop this technology for clinical applications, including convection enhanced delivery (CED) and intrathecal injection. Taken together, these results represent the first full characterization of an Auger-emitting PARP inhibitor, demonstrate a survival benefit in mouse models of GBM, and confirm the high potential of 123I-MAPi for clinical translation.\n\nOne Sentence SummaryA novel PARP1-targeted Auger radiotherapeutic shows translational potential as a theranostic tool for imaging and killing cancer cells, resulting in tumor delineation and prolonged survival in a glioblastoma model.

cancer biology↗

bioRxiv2019

Mitotic ER exit site dissociation is mediated by TANGO1 phosphorylation with CK1.

Golgi fragmentation and ER exit site dissociation are considered as the leading causes of mitotic block of secretion from the ER. Although the mechanisms of Golgi fragmentation have been extensively characterized, ER exit block early in mitosis is not well-understood. We previously found that TANGO1 organizes ER exit sites by directly interacting with Sec16. Here, we showed that TANGO1 is phosphorylated by casein kinase 1 (CK1) during mitosis. Interestingly, the interaction with Sec16 was abrogated by phosphorylation of TANGO1, leading to dissociation of the ER exit sites. Moreover, a TANGO1 mutant deficient in phosphorylation inhibited the mitotic dissociation of ER exit sites. In contrast, a TANGO1 mutant mimicking CK1-mediated phosphorylation dissociated ER exit sites in interphase cells. Although CK1 activity remains constant throughout the cell cycle, PP1, a phosphatase for which activity decreases during mitosis, participates in the regulation of TANGO1 phosphorylation. This is the first report demonstrating the mechanisms of ER exit site dissociation during mitosis.

cell biology↗

bioRxiv2019

Comparison of prokaryotic communities between the fields showing different disinfestation effects by anaerobic soil disinfestation

Anaerobic soil disinfestation (ASD) is a chemical-independent fumigation method used for reducing the abundance of pathogens at soil depths of <40 cm. However, its disinfestation efficiency is unstable under field conditions. The microbial community reflects the soil environment and is a good indicator of soil health. Therefore, soil with a good disinfestation efficiency may have a unique microbial community. The aim of the present study was to compare the prokaryotic communities among soils obtained from 17 geographically different greenhouses that experienced tomato bacterial wilt but exhibited different disinfestation efficiencies after ASD treatment with the same substrate. In the present study, soil prokaryotic communities in the field, which indicate difference in disinfestation effects after ASD treatment among several fields, were compared using next-generation sequencing. The prokaryotic communities in the fields showing different disinfestation effects were roughly separated into sampling fields. The relative abundances of Betaproteobacteria and Clostridia were significantly increased in well-disinfested fields. Overall, 25 operational taxonomic units (OTUs) were specifically increased in various well-disinfested soils and 18 OTUs belonged to phylogenetically diversified Clostridia. Other OTUs belonged to aerobic bacteria and were not previously detected in sample collected from ASD-treated fields. The results showed that the changes to the prokaryotic communities did not affect ASD efficiency, whereas changes in the abundance of specific microbes in the community were related to disinfestation.

microbiology↗

bioRxiv2018

cTAGE5 acts as a Sar1 GTPase regulator for collagen export

Secretory proteins synthesized within the endoplasmic reticulum (ER) are exported via coat protein complex II (COPII)-coated vesicles. The formation of the COPII-coated vesicles is initiated by activation of the small GTPase, Sar1. cTAGE5 directly interacts with a guanine-nucleotide exchange factor (GEF), Sec12, and a GTPase-activating protein (GAP) of Sar1, Sec23. We have previously shown that cTAGE5 recruits Sec12 to the ER exit sites for efficient production of activated Sar1 for collagen secretion. However, the functional significance of the interaction between cTAGE5 and Sec23 has not been fully elucidated. In this study, we showed that cTAGE5 enhances the GAP activity of Sec23 toward Sar1. In addition, the interaction of cTAGE5 with Sec23 is necessary for collagen exit from the ER. Our data suggests that cTAGE5 acts as a Sar1 GTPase regulator for collagen secretion.

cell biology↗

bioRxiv2017

The Brain/MINDS 3D digital marmoset brain atlas

We present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file format (NIfTI). The atlas can be registered to new data, is useful for connectomics, functional studies, simulation and as a reference.\n\nThe atlas was based on previously published work but we provide several critical improvements to make this release valuable for researchers. Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres. The data is in the NIfTI format making it easy to integrate into neuroscience pipelines, whereas the previous atlas was in an inaccessible file format. We also provide cortical, mid-cortical and white matter boundary segmentations useful for visualization and analysis.

neuroscience↗

bioRxiv2017

Remodeling of ER-exit sites initiates a membrane supply pathway forautophagosome biogenesis

Autophagosomes are double-membrane vesicles generated during autophagy. Biogenesis of the autophagosome requires membrane acquisition from intracellular compartments, the mechanisms of which are unclear. We previously found that a relocation of COPII machinery to the ER-Golgi intermediate compartment (ERGIC) generates ERGIC-derived COPII vesicles which serve as a membrane precursor for the lipidation of LC3, a key membrane component of the autophagosome. Here we employed super-resolution microscopy to show that starvation induces the enlargement of ER-exit sites (ERES) positive for the COPII activator, SEC12, and the remodeled ERES patches along the ERGIC. A SEC12 binding protein, CTAGE5, is required for the enlargement of ERES, SEC12 relocation to the ERGIC, and modulates autophagosome biogenesis. Moreover, FIP200, a subunit of the ULK protein kinase complex, facilitates the starvation-induced enlargement of ERES independent of the other subunits of this complex and associates via its C-terminal domain with SEC12. Our data indicate a pathway wherein FIP200 and CTAGE5 facilitate starvation-induced remodeling of the ERES, a prerequisite for the production of COPII vesicles budded from the ERGIC that contribute to autophagosome formation.

cell biology↗