Biology subjects

Maeda, T.

Publications and source records attributed to Maeda, T..

At least 19 recordsLinked to original sources

bioRxiv2026

A genomic and proteomic characterization of mannan-degradable Bacillus sp. TTS1, isolated from Tomakomai Forest in Hokkaido

A challenge in using plant biomass is its highly recalcitrant nature, which makes it economically infeasible to utilize. In natural environments, various microbes, including bacteria and fungi, are reported to decompose plant cell wall materials such as cellulose and hemicellulose, and there may be undescribed microbes that contribute to the degradation of plant biomass. We focused on isolating novel plant biomass-degrading bacteria and screened more than 100 isolates from the Tomakomai experimental forest in Hokkaido, Japan. Among them, one novel Bacillus species was chosen for whole-genome sequencing. Comparative genomics and a carbon source utilization assay indicated that the isolate belongs to a subspecies of Bacillus subtilis, which we named B. sp. TTS1. Glucose, cellobiose, xylose, xylan, mannose, or mannan was used as the sole carbon source in the minimum medium, and the growth of this bacterium was determined. Furthermore, a proteomic analysis of B. sp. TTS1 was performed using culture supernatants from various polysaccharide-containing media. In the present study, several key enzymes involved in plant biomass degradation were identified, namely {beta}-1,4-mannanase and xylanase, and they were highly enriched in all tested polysaccharides.

microbiology↗

bioRxiv2026

Regulation of sphingolipid synthesis by the C2H2 zinc finger transcription factor Com2 through ubiquitin-proteasome mediated degradation pathway

Membrane lipid synthesis is globally coordinated by a limited set of master transcription factors that regulate broad gene networks encoding lipid-metabolic enzymes and their regulators. Here, we identify the C2H2 zinc-finger transcription factor Com2 as a regulator of sphingolipid homeostasis in Saccharomyces cerevisiae that promotes transcription of downstream targets, including the protein kinase Ypk1, a key activator of sphingolipid synthesis. Com2 protein abundance increased upon treatment with myriocin, an inhibitor of sphingolipid synthesis, but rapidly decreased after addition of phytosphingosine (PHS), a precursor of complex sphingolipids; this decrease was blocked by proteasome inhibitors. These results suggest that Com2 is regulated in a sphingolipid-dependent manner through proteasome-mediated degradation. Moreover, a Com2 mutant in which lysine residues putatively involved in ubiquitination were replaced with arginine exhibited attenuated PHS-dependent degradation and elevated phosphorylation. Likewise, a mutant in which putative phosphorylation sites were replaced with alanine showed reduced PHS-dependent degradation. Together, these findings indicate that Com2 undergoes phosphorylation-dependent degradation via the ubiquitin-proteasome system in response to sphingolipid levels.

cell biology↗

bioRxiv2026

Direct observation of feeding behavior in the kleptoplastic sea slug Plakobranchus ocellatus type black (Gastropoda, Sacoglossa)

The feeding ecology of sacoglossans, an exceptionally stenophagous group among marine animals, has been extensively studied because these organisms exhibit kleptoplasty--a phenomenon in which chloroplasts derived from ingested algae are sequestered and functionally maintained within animal cells. The genus Plakobranchus is notable for its exceptional capacity to retain photosynthetically active chloroplasts for prolonged periods. Nevertheless, direct observations of its feeding behavior have remained limited, largely due to subsequent taxonomic revisions and its cryptic, benthic lifestyle. In the present study, we focus on Plakobranchus ocellatus type black (PoB). Using high-resolution macro videography, we obtained, for the first time, video recordings that directly document the feeding behavior of this lineage. Under illuminated conditions, we demonstrate active feeding on the fan-shaped fronds of udoteacean algae, clarify which algal life-history stages serve as food, and identify Ventalia sp. 4 as a previously unrecognized dietary component. We further describe a characteristic inverted "headstand" posture adopted during feeding and discuss this behavior in relation to the species benthic and semi-burrowing lifestyle, proposing that it may partly explain the historical rarity of feeding observations in the field. The confirmation of feeding behavior represents a critical step toward establishing a stable laboratory culture system essential for experimental studies of kleptoplasty.

animal behavior and cognition↗

bioRxiv2025

ADGRG1 blockade drives astrocyte positioning into the extracellular matrix to reduce scar size

After the central nervous system (CNS) injury, inflammatory cells enter the lesion core and a fibrotic extracellular matrix accumulates. Astrocytes subsequently cluster around this matrix, forming a glial scar, but the role of the extracellular matrix in scar formation remains poorly understood. Here, we identify type III collagen, a major fibrotic extracellular matrix component after spinal cord injury, as a key regulator of astrocyte behavior. Using single-nucleus transcriptomics, spatial transcriptomics, and time-lapse cell imaging, we show that type III collagen positions astrocytes at the boundary of the fibrotic matrix by activating the adhesion G protein-coupled receptor G1 (ADGRG1) and its downstream effector RhoA. Blocking ADGRG1 genetically or pharmacologically allows astrocytes to enter the fibrotic matrix, resulting in a smaller scar, improved neuronal regeneration, and better motor recovery. The migration of human-induced pluripotent stem cell-derived astrocytes was inhibited by type III collagen via the ADGRG1-RhoA pathway, supporting their therapeutic potential. Our findings reveal the importance of controlling glial scar positioning via the type III collagen-ADGRG1 axis, providing a novel therapeutic target for CNS injury.

neuroscience↗

bioRxiv2025

Hidden Markov Models Reveal Behavioral State Dynamics in Depth-Related Locomotion in Mice

Understanding how mice process and respond to visual depth cues is crucial for studying visual perception, yet traditional behavioral analyses often miss key aspects of this process, such as the dynamic transitions between behavioral states, the influence of environmental context, and the integration of multiple spatial cues that shape depth-related behaviors. Here we demonstrate that mouse responses to visual depth cues are more sophisticated than previously recognized, involving both direct avoidance behaviors and complex modulations of exploratory patterns. By combining a modified circular apparatus with Hidden Markov Model analysis, we reveal that mice transition between three distinct behavioral states--resting, exploring, and navigating--in response to visual depth cues. Using this framework, we uncover several fundamental aspects of mouse visual processing: depth perception has an optimal range of spatial frequencies, with strongest responses to patterns between 6-8 cm; visual processing integrates multiple spatial cues rather than triggering simple avoidance; and initial strong cliff-avoidance responses evolve into more nuanced behavioral adaptations over time. Comparisons between wild-type C57BL/6J mice (Mus musculus), retinal degeneration models (rd1-2J, C57BL/6J background, Mus musculus), and control conditions confirm that these behavioral patterns specifically reflect visual processing rather than general exploratory behavior. These findings reveal that mouse depth perception involves sophisticated neural processing that modulates overall exploratory behavior rather than simply triggering avoidance responses. Our approach establishes a new framework for analyzing complex behavioral sequences in neuroscience research, demonstrating how refined behavioral analysis can reveal previously undetectable aspects of sensory processing.

animal behavior and cognition↗

bioRxiv2025

Systematic measurements of dose-dependent responses for combinatorial treatments of SA and JA led to the development of transcriptomic biomarkers

Plants coordinate defence against pathogens and herbivores through the crosstalk between salicylic acid (SA) and jasmonic acid (JA) signalling pathways. However, little is known about how plants integrate the phytohormone concentration profiles to shape defence states in complex field environments. Here we show that systematically varying combinatorial SA and JA concentrations in Arabidopsis thaliana reveals 43 distinct combination-specific transcriptional signatures beyond SA-JA antagonism. Leveraging these data, we developed and validated machine-learning-based transcriptomic biomarkers that enabled independent quantification of SA and JA response states. By applying these biomarkers to field-grown A. thaliana, we revealed that SA/JA response states were dynamically shaped by abundant and co-occurrence of herbivores on individual plants. Our study provides a strategy to decode hormonal responses to biotic environments from field transcriptomes, bridging the gap between molecular signalling and ecological dynamics.

plant biology↗

bioRxiv2025

EASY-CRISPR: a toolbox for high-throughput single-step custom genetic editing in bacteria

Targeted gene editing can be achieved using CRISPR/Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization for each locus to be modified which can be tedious and time-consuming. In this work, we developed a simple, fast and cheap method for the Editing and Assembly of SYnthetic operons using CRISPR/Cas9-assisted recombineering (EASY-CRISPR) in Escherichia coli. Highly efficient editing of the different constitutive elements of the operons can be achieved by using a set of optimized guide RNAs and single- or double-stranded DNA repair templates carrying relatively short homology arms. This facilitates the construction of multiple genetic tools, including mutant libraries or reporter genes. EASY-CRISPR is also highly modular, as we provide alternative and complementary versions of the operon inserted in three loci which can be edited iteratively and easily combined. As a proof of concept, we report the construction of several fusions with reporter genes confirming known post-transcriptional regulation mechanisms and the construction of saturated and unbiased mutant libraries. In summary, the EASY-CRISPR system provides a flexible genomic expression platform that can be used both for the understanding of biological processes and as a tool for bioengineering applications.

microbiology↗

bioRxiv2024

Comprehensive expression data for two honey bee species, Apis mellifera and Apis cerana japonica

Comprehensive expression datasets were constructed for Apis mellifera and Apis cerana japonica. Post-oviposition day 6 to day 58 samples of A. mellifera workers (larva to adult); day 9, 10, 12, and 13 samples of A. mellifera queen (larva to pupa); and day 9 to day 18 samples of A. cerana japonica workers (larva to adult) were prepared, and RNA-Seq data were obtained. For A. cerana japonica, reference transcript sequence data, predicted amino acid sequence data, and functional annotation data were generated based on the genome sequence and RNA-Seq data. Using the transcript sequence and RNA-Seq data, comprehensive expression data for all transcripts of A. mellifera and A. cerana japonica were prepared. Hierarchical clustering analyses and the used sample preparation method ensured that both sets of expression data were reliable for use as comprehensive reference expression datasets. Therefore, these data are applicable for honey bee research or for comparative or evolutionary studies on insect species or social insect species at the genetic and molecular levels.

genetics↗

bioRxiv2024

Simulation study of factors affecting the accuracy of transcriptome models under complex environments

Characterization of molecular responses in real and complex field environments is essential for understanding the environmental response of plants. Field transcriptomics, i.e. modelling large amounts of transcriptomic and meteorological data, is the most comprehensive method of studying gene expression dynamics in complex environments. However, it is not clear what factors influence the accuracy of field transcriptome models. In this study, a novel simulation system was developed. Using the system, we performed a large-scale simulation to reveal the factors affecting the accuracy of the models. We found that the factors that had the greatest impact on the accuracy are, in order of importance, the expression pattern of the gene, the number of samples in the training data, the diurnal coverage of the training data, and the temperature coverage of the training data. Validation using actually measured transcriptome data showed similar results to the simulations. Our simulation system and the analysis results will be helpful for developing efficient sampling strategies for training data and for generating simulated data for benchmarking new modelling methods. It will also be valuable to dissect the relative importance of various factors behind transcriptome dynamics in the real environment. Key messageNovel simulation system revealed how prediction accuracy of field transcriptome was affected by number and diversity of training data

plant biology↗

bioRxiv2024

A fatal case of peritonitis caused by Dysgonomonas capnocytophagoides harboring the novel metallo-beta-lactamase gene blaDYB-1

Dysgonomonas capnocytophagoides shows multidrug resistance to antibiotics and causes opportunistic infections in immunocompromised hosts. We report a fatal case of peritonitis caused by D. capnocytophagoides in Japan. We identified a novel chromosomally encoded class B1 metallo-beta-lactamase gene designated blaDYB-1 and an ermFS gene that contributed to multidrug resistance.

microbiology↗

bioRxiv2024

The sense of agency from active causal inference

This study investigates the active component of the sense of agency (SoA), positing that SoA is fundamentally an outcome of active causal inference regarding ones own actions and their impact on the environment. Participants controlled visual objects via a computer mouse, with tasks designed to test their ability to judge control or detect controlled objects under varying noise conditions. Our findings reveal that participants formed high-level, low-dimensional action plans that were idiosyncratic across but consistent within individuals to infer their degree of control. Employing transformer-LSTM-based autoencoders, we captured these action plans and demonstrated that the geometrical and dynamical properties of these action plans could predict behavioural profiles in the tasks with remarkable accuracy. This suggests that participants sense of control is shaped by actively altering action plans, viewed as generating causal evidence through intervention. Further, participants proactively expanded the diversity of their action plans, facilitating the exploration of available action plan options while accumulating causal evidence for the inference process. Contrarily, patients with schizophrenia exhibited reduced action plan diversity, suggesting impaired active control inference and detection of self-relevant cues. These findings offer a more comprehensive understanding of the sense of agency, deeply rooted in the process of active causal inference.

neuroscience↗

bioRxiv2023

Genome assembly reconstruction of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae), using homology-based assembly and nanopore long-reads

Honey bees are important for agriculture (e.g., pollination and honey production). Additionally, honey bees are an important insect model species, especially as model social insects. The Japanese honey bee, Apis cerana japonica (a subspecies of the Asian honey bee, Apis cerana), is a Japanese domestic honey bee, which has several subspecies-specific traits. We previously constructed the draft genome sequence data of A. cerana japonica, but it needed to be improved considering the use of the genome sequence data for genome structural analysis and repetitive region analysis, as well as the availability of chromosome-level genome data of A. mellifera and A. cerana. In this study, we constructed the improved A. cerana japonica genome data and new gene set data with functional annotations. The constructed genome data, including 16 pseudochromosomes, was found to be highly contiguous and complete, and the gene set data covered most of the core genes in the BUSCO database. Thus, the constructed genome and gene set data have become more suitable as the reference data of A. cerana japonica.

genomics↗

bioRxiv2023

Coordinated multiple cellular processes in tongue development

Dysfunction of primary cilia leads to genetic disorder, ciliopathies, which shows various malformations in many vital organs such as brain. Multiple tongue deformities including cleft, hamartoma and ankyloglossia are also seen in ciliopathies, which yield difficulties in fundamental functions such as mastication and vocalization. Here, we found these tongue anomalies in mice with mutation of ciliary protein. Abnormal cranial neural crest-derived cells (CNCC) failed to evoke Hh signal for differentiation of mesoderm-derived cells into myoblasts, which resulted in abnormal differentiation of mesoderm-derived cells into adipocytes. The ectopic adipose subsequently arrested migration of other mesoderm-derived cells and CNCC. Some aberrant CNCC abnormally differentiated into osteoblasts due to the lack of Hh signal, which migrated into tongue to form ectopic bone. Ankyloglossia was caused by aberrant cell migration due to lack of non-canonical Wnt signaling. In addition to ciliopathies, these tongue anomalies are often observed as non-familial condition in human. We found that these tongue deformities could be reproduced in wild-type mice by simple mechanical manipulations in CNCC to disturb cellular processes which were disrupted in mutant mice. Thus, tongue development requires coordinated multiple cellular processes (cell-cell contact, migration and differentiation). Our results provide hints for possible future treatment in ciliopathies.

developmental biology↗

bioRxiv2022

Multi-dimensional antibiotic resistance time series reveals the phenotype-based fitness landscape for Escherichia coli

The fitness landscape represents the complex relationship between genotype or phenotype and fitness under a given environment, the structure of which allows the explanation and prediction of evolutionary trajectories. Although previous studies have constructed fitness landscapes based on comprehensively studying the mutations in specific genes, the high dimensionality of genotypic changes prevents us from developing a fitness landscape capable of predicting evolution for the whole cell. Herein, we address this problem by inferring the fitness landscape for antibiotic resistance evolution by quantifying the phenotypic changes, that is, multi-dimensional time-series measurements of the drug resistance profile. Using the time-series data of drug resistance for multiple drugs, we inferred that the fitness landscape underlies the evolution dynamics of resistance. We showed that different peaks of the landscape correspond to different drug resistance mechanisms, thus supporting the validity of the inferred fitness landscape. We further discuss how inferred phenotype-fitness landscapes could contribute to the prediction and control of evolution. This approach bridges the gap between phenotypic/genotypic changes and fitness while contributing to a better understanding of drug resistance evolution.

evolutionary biology↗

bioRxiv2022

Strategy for selective acquisition of transgenic marmosets using the piggyBac transposon system

Transgenic (Tg) nonhuman primates (NHPs) are excellent potential models due to their physiological similarities with humans. In NHPs, the lentiviral vector is the only available transgenesis method, but transgene sizes are limited. The piggyBac (PB) transposon system is a DNA element sandwiched between two terminal inverted repeats (TRs) that allows transposases to introduce larger genes than lentiviral vectors. However, embryos with integrated transgenes are difficult to distinguish using this system. To address this issue, we placed the Enhanced Green Fluorescent Protein (EGFP) gene inside the TRs and the humanized kusabira orange 1 (hKO1) fluorescent protein gene with the proteolysis-promoting sequence d2PEST outside the TRs to create an indicator for gene integration using fluorescent protein expression. In HEK293T cells, hKO1 and EGFP co-expression after transfection gradually changed to decay of hKO1 expression and enhancement of EGFP expression by transposase within five days. In mouse and marmoset embryos, hKO1 expression was attenuated, while only EGFP expression was observed at the blastocyst stage. All offspring obtained through embryo transfer of EGFP-expressing embryos were Tg; thus, we established a new PB system capable of determining Tg embryos and successfully produced Tg marmosets, for the first time, in NHPs.

molecular biology↗

bioRxiv2021

Transcriptional regulation of sphingolipid metabolism in budding yeast

Global control for the synthesis of lipids constituting a bilayer of cell membranes is known to be with a small number of transcription factors called master transcriptional regulators, which target a wide range of genes encoding lipid metabolism enzymes and/or their regulators. Although master transcriptional regulators of glycerophospholipids and sterols have been identified in both yeast and mammals, this aspect of sphingolipid metabolism is not yet understood. In the present study, we identified the C2H2-type zinc finger transcription factor, Com2, as a master transcriptional regulator of sphingolipid metabolism in the budding yeast, Saccharomyces cerevisiae. The target of rapamycin complex 2 (TORC2)-activated protein kinase Ypk1 is known to regulate sphingolipid metabolism. Activated Ypk1 stimulates the activity of serine palmitoyl transferase (SPT), the first-step enzyme in sphingolipid biosynthesis, by phosphorylating and inhibiting Orm1/2, a negative regulator of SPT. This regulation of SPT activity is thought to be a major pathway in the regulation of sphingolipid metabolism. In the present study, we found that inhibition of sphingolipid synthesis upregulates the expression of Com2, which in turn leads to the concomitant expression of Ypk1. The upregulation of Ypk1 expression was found to be dependent on a putative Com2-binding site in the YPK1 promoter. Our results also suggested that Com2 senses intracellular sphingolipid levels through a pathway independent of TORC2-Ypk1-mediated sensing of sphingolipids. Our results revealed an additional layer of mechanistic regulation that allows cells to maintain appropriate levels of sphingolipid biosynthesis and to rapidly induce this process in response to environmental stresses. Significance StatementOne of the major regulatory mechanisms involved in the control of lipid metabolism in bilayers of biological membranes is regulation at the transcriptional level by master transcriptional regulators that control the transcription of genes encoding lipid metabolism enzymes and/or their regulators. In the present study, we identified the C2H2-type zinc finger transcription factor Com2 as a master transcriptional regulator in sphingolipid metabolism. We found that Com2 regulates sphingolipid metabolism by transcriptionally controlling the expression of Ypk1, which regulates Orm1/2, a negative regulator of serine palmitoyl transferase, the first-step enzyme in sphingolipid biosynthesis, through phosphorylation. Our study revealed a new layer of regulation that allows the maintenance of an appropriate level of sphingolipid biosynthesis for a rapid response to environmental stresses.

cell biology↗

bioRxiv2021

Self-organized yolk sac-like organoids allow for scalable generation of multipotent hematopoietic progenitor cells from human induced pluripotent stem cells

The human definitive yolk sac is an important organ supporting the early developing embryo through nutrient supply and by facilitating the establishment of the embryonic circulatory system. However, the molecular and cellular biology of the human yolk sac remains largely obscure due to the lack of suitable in vitro models. Here, we show that human induced pluripotent stem cells (hiPSCs) co-cultured with various types of stromal cells as spheroids self-organize into yolk sac-like organoids without the addition of exogenous factors. Yolk sac-like organoids recapitulated a yolk sac specific cellular complement and structures as well as the functional ability to generate definitive hematopoietic progenitor cells (HPCs). Furthermore, sequential hemato-vascular ontogenesis could be observed during organoid formation. Notably, our organoid system can be performed in a scalable, autologous, and xeno-free condition, thereby providing an important model of human definitive yolk sac development and allows for efficient bulk generation of hiPSC-derived HPCs.

cell biology↗

bioRxiv2021

Behavioural synchronization in a multilevel society of feral horses

AO_SCPLOWBSTRACTC_SCPLOWBehavioural synchrony among individuals is essential for group-living organisms. It is still largely unknown how synchronization functions in a multilevel society, which is a nested assemblage of multiple social levels between many individuals. Our aim was to build a model that explained the synchronization of activity in a multilevel society of feral horses. We used multi-agent based models based on four hypotheses: A) horses do not synchronize, B) horses synchronize with any individual in any unit, C) horses synchronize only within units and D) horses synchronize across and within units, but internal synchronization is stronger. Our empirical data obtained from drone observations best supported hypothesis D. This result suggests that animals in a multilevel society coordinate with other conspecifics not only within a unit but at an inter-unit level. In this case, inter-individual distances are much longer than those in most previous models which only considered local interaction within a few body lengths.

animal behavior and cognition↗