Biology subjects

Moriguchi, Y.

Publications and source records attributed to Moriguchi, Y..

13 recordsLinked to original sources

bioRxiv2026

Unsupervised alignment reveals shared but locally refined colour qualia structure from toddlerhood to adulthood

Whether subjective colour experience (e.g., experience of 'red') is shared across children and adults remains a foundational question in developmental psychology and consciousness research. To test this, we compared the relational structures of their colour experiences and identified the mapping that best preserved these structures. Using pairwise similarity judgements for 13 basic colours, we applied Gromov Wasserstein optimal transport (GWOT), an unsupervised method requiring no prespecified stimulus experience correspondence to compare toddlers, preschool children, and adults. Preschoolers' and adults' group-averaged structures perfectly aligned, whereas toddlers' structure did not fully align with either older group. However, removing specific colours, particularly those with relatively late acquired linguistic boundaries, such as light blue-restored near-perfect alignment. Moreover, toddlers with greater colour-word knowledge showed closer correspondence with the adult similarity structure. These findings suggest that the global relational geometry of colour experience is largely established by toddlerhood, with limited local differences linked to colour-language acquisition.

neuroscience↗

bioRxiv2026

Right-lateralized prefrontal signature with successful Stroop-like interference control in early childhood

The Stroop effect is a canonical measure of executive control, yet its neural architecture has been defined largely in literate children and adults, where left frontal mechanisms have long been implicated in resolving verbal conflict. How the developing brain supports Stroop-like interference control before literacy and stable verbal responding are established remains unknown. Here we show that successful interference control in early childhood is associated with the selective engagement of right lateral prefrontal regions. We used multichannel functional near-infrared spectroscopy to measure prefrontal hemodynamics in 94 children aged 35-79 months during a color-pointing Stroop-like task, in which children pointed to colors in response to spoken color names. Stroop-like conflict elicited broad activation across bilateral lateral prefrontal regions, a conflict response already present from around 3 years of age and did not show a detectable age-related increase. By contrast, individual differences in accuracy under conflict were selectively associated with greater activation in the right dorsolateral and right rostrolateral prefrontal cortices, independent of age. These findings suggest that right lateral prefrontal regions play an important role in successful interference control in early childhood, indicating that preschool Stroop-like control is not merely a weaker form of the adult left-lateralized system.

neuroscience↗

bioRxiv2026

Evaluating non-lethal tissue suitability for telomere length measurement in the Japanese eel

Telomere length (TL) is increasingly used in ecology as a biomarker of individual quality and environmental stress, yet research on non-model species with complex life histories remains limited. Because TL varies among tissues and across ages in a species-specific manner, identifying non-lethal tissues that reliably reflect whole-organism telomere dynamics is essential for longitudinal telomere studies in the field. This study aimed to evaluate tissue-specific TL in Japanese eel (Anguilla japonica), an endangered catadromous fish. We first mapped the chromosomal distribution of telomeric sequences using fluorescent in situ hybridization (FISH), the first application of this method in this species. We then tested whether muscle and caudal fin, which can be sampled easily and non-lethally, can serve as suitable proxy tissues for TL measurements in wild individuals. Relative telomere length (RTL) was quantified by qPCR in blood, brain, caudal fin, gonads, heart, liver, and muscle. FISH analysis confirmed telomeric repeats at all chromosomal ends, with only weak interstitial signals on three chromosomal pairs unlikely to affect qPCR-based estimates. A generalized additive mixed model and Wilcoxons signed-rank tests revealed significant inter-tissue differences: RTL was shortest in the brain and muscle and longest in liver, blood and caudal fin. Muscle and caudal fin RTL were significantly correlated with RTL in many other tissues, supporting their use as proxy tissues for longitudinal TL monitoring, including responses to environmental variation. Both total length and age were tested as explanatory variables for RTL, and the model including total length showed a better fit than the age-based model. Non-linear relationships between RTL and total length observed in several tissues suggest physiological shifts associated with growth and sexual differentiation. Overall, these findings advance understanding of telomere dynamics in eels and establish muscle and caudal fin as suitable tissues for repeated, non-lethal TL assessment in ecological and conservation contexts.

molecular biology↗

bioRxiv2026

Dissociable pupil-linked arousal during overt and inner speech

Inner (covert) speech, the silent production of language in ones mind, plays a central role in human cognition and is known to activate speech-related cortical regions while also requiring executive and attentional resources. However, the conventional focus on cortical similarity or dissimilarity between inner and overt speech leaves unaddressed the question of whether arousal systems sustain cortical language processing. Here, using pupillometry across three controlled counting experiments, we show a dissociation between inner and overt speech. Overt speech consistently led to pupil dilation across all conditions. Inner speech, by contrast, produced a strikingly different profile: pupil constriction during simple counting, no deviation from baseline during noun-phrase counting, and clear dilation only under a high cognitive load, but with dilation remaining significantly less than that for overt speech in every condition. Covert verbal production thus proceeds at a reduced arousal cost, yet this cost scales flexibly with task demands rather than being fixed. This pupillometric dissociation reveals that inner and overt speech occupy fundamentally distinct arousal states, even when their cortical substrates partially overlap. These findings open a non-invasive window for tracking inner speech physiology across development, individual differences, and clinical populations in whom inner speech is altered.

neuroscience↗

bioRxiv2026

Emergent blink rate in early childhood is associated with neural origins of executive function

Executive function develops rapidly in early childhood and predicts later success in life, yet its neurobiological correlates during this period remain poorly understood. In adults, executive function is supported by prefrontal-striatal circuits under neuromodulatory control, including dopamine. Here, we show that spontaneous eye-blink rate (sEBR), a physiological output influenced by neuromodulatory systems, is associated with the developmental trajectory of executive function and prefrontal functional differentiation. We used fNIRS to monitor prefrontal cortex (PFC) activation in 113 children (35-80 months) during a cognitive flexibility task. With increasing age, the childrens task performance improved, and their PFC activation showed greater right-hemisphere and dorsal bias, reflecting functional differentiation. Importantly, higher sEBR was also associated with this right-dorsal PFC activation and with better task performance. The current findings demonstrate that emergent sEBR is associated with the neural origins of executive function development in young children. This highlights the potential of sEBR to serve as a unique and previously unrecognised indicator of this critical developmental neural mechanism.

neuroscience↗

bioRxiv2025

Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don

BackgroundJapanese cedar (Cryptomeria japonica D. Don) is a major plantation species in Japan, but its abundant pollen production is a primary cause of seasonal allergic rhinitis (pollinosis). To mitigate this public health issue, the use of male-sterile cultivars has been promoted. Five types of recessive male-sterile mutations (ms1-ms5) have been identified, and the causal genes and mutations for MS1 and MS4 have been elucidated. However, the gene responsible for MS2-type male sterility remains unknown. ResultsWe aimed to identify the candidate gene responsible for MS2-type male sterility using a map-based cloning strategy. High-resolution linkage mapping localized the MS2 locus to a 1.56 cM interval on linkage group 5, corresponding to an 8.64 Mb region of the reference genome. Ninety-one genes in this region were subjected to functional annotation, gene expression analysis, and mutation screening. Among these, a single gene, SUGI_0493010, encoding a GDSL-type esterase/lipase protein (GELP), fulfilled all three criteria: it showed homology to pollen development genes in Arabidopsis thaliana, was specifically expressed in male strobili, and carried a deleterious amino acid substitution (S40F) within the predicted catalytic domain in ms2 mutant. The same mutation was also detected in a heterozygous individual (Ms2/ms2) from a separate breeding population, whose genotype was confirmed through progeny testing. Structural annotation revealed that the affected serine residue lies within the conserved GDSL motif, suggesting a functional disruption of enzymatic activity. ConclusionsOur results strongly suggest that SUGI_0493010 (GELP) is the causal gene for MS2-type male sterility in C. japonica. This finding enhances our understanding of male sterility mechanisms in conifers and provides a valuable genetic resource for breeding pollen-free trees. The study also demonstrates the effectiveness of combining genetic mapping with transcriptomic and mutational data in forest tree genomics.

genomics↗

bioRxiv2024

Developing simple DNA extraction and PCR-RFLP for MALE STERILITY 4 (MS4) gene in Cryptomeria japonica D. Don: Toward an environmentally friendly protocol

This study presents the development of a simple DNA extraction method and a novel PCR-RFLP protocol for genotyping the MALE STERILITY 4 (MS4) gene in Cryptomeria japonica as a proof of concept. Traditional CTAB-based DNA extraction methods, while effective, involve hazardous chemicals and require high-speed centrifugation, which are impractical in many field settings. Our approach utilizes a household dish detergent-based buffer, sodium chloride, and polyvinylpyrrolidone K-30 to extract DNA from C. japonica needle leaf tissues--without the need for liquid nitrogen. The simplicity of this method makes it more accessible and environmentally friendly. The extracted DNA was successfully used in PCR-RFLP analysis, targeting a single nucleotide polymorphism in the MS4 gene, demonstrating its efficacy for genotyping. The PCR-RFLP markers reliably discriminated between individual genotypes, confirming the practical application of our simple extraction method, even for conifers containing inhibitory substances. This technique is particularly advantageous for use in arboretums and field stations, where the use of hazardous chemicals, specialized equipment, and a draft chamber is limited. Our study contributes to genetic resource management by providing an easy, reliable, and safer method for DNA extraction and genetic analysis.

genetics↗

bioRxiv2023

A chromosome-level genome assembly of amodel conifer plant, the Japanese cedar,Cryptomeria japonica D. Don

Japanese cedar (Cryptomeria japonica D. Don) is the most important Japanese forest tree, occupying about 44% of artificial forests in Japan, and planted in East Asia, Azores Archipelago, and some islands in the Indian Ocean. Although the huge genome of the species (ca. 11 Gb) with abundant repeat elements might have been an obstacle for genetic analysis, the species is easily propagated by cutting, flowered by plant hormones like gibberellic acid, transformed by agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica are preferable to make the species a model conifer for which reference genome sequences are necessary. In this study, we report the first chromosome-level assembly for C. japonica (2n = 22) using a third generation selfed progeny with an estimated homozygosity of 0.96. Young leaf tissue was used to extract high-molecular-weight DNA (>50 kb) for HiFi PacBio long read sequencing and to construct Hi-C/Omni-C library for Illumina short read sequencing. Using the 29x and 26x genome coverage of HiFi and Illumina reads, respectively, de novo assembly resulted in 2,650 contigs (9.1 Gb in total) with N50 contig size of 12.0 Mb. The Hi-C analysis mapped 97% of the nucleotides on the 11 chromosomes. The assembly was verified by comparing with a consensus linkage map of 7,785 markers. The BUSCO analysis confirmed ~91% of conserved genes. Annotations of genes, repeat elements and synteny with other Cupressaceae and Pinaceae species were performed, providing fundamental resources for genomic research of conifers.

genomics↗

bioRxiv2022

Single-nucleotide substitution determines pollen production in Japanese cedar

Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species1-6. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades7. The MS4 (MALE STERILITY 4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TKPR1 (TETRAKETIDE -PYRONE REDUCTASE) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plant not only for Japanese cedar but also for broader plant species.

plant biology↗

bioRxiv2020

Marker-assisted selection of trees with MALE STERALITY 1 in Cryptomeria japonica D. Don

Practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among breeding material collections. First, in this study, two families were produced by artificial crossing between two male-sterile trees, Shindai11 and Shindai12, and a plus tree, Suzu-2 (Ms1/ms1) (S11-S and S12-S families, respectively). The segregation ratio between male-sterile and male-fertile trees did not deviate significantly from the expected 1:1 ratio in either family. These results clearly suggested that the male-sterile gene of Shindai11 and Shindai12 is MALE STERALITY 1 (MS1). Because some markers reported previously have not been linkage mapped, we constructed a partial linkage map of the region encompassing MS1 using the S11-S and S12-S families. For the S11-S and S12-S families, 19 and 18 markers were mapped onto the partial linkage maps of MS1 region, respectively. There was collinearity (conserved gene order) between the two partial linkage maps. Two markers (CJt020762_ms1-1 and reCj19250_2335) were mapped to the same position as the MS1 locus on both maps. Of these markers, we used CJt020762 for MAS in this study. According to the MAS results for 650 trees from six prefectures of Japan (603 trees from breeding materials and 47 trees from the Ishinomaki natural population), five trees in Niigata Prefecture and one tree in Yamagata Prefecture had heterozygous ms1-1, and three trees in Miyagi Prefecture had heterozygous ms1-2. The results obtained in this study suggested that there may be geographical hotspots for the ms1-1 and ms1-2 alleles. Because MAS can be used effectively to reduce the labor and time required for selection of trees with a male-sterile gene, the number of breeding materials should increase in the future.

genetics↗

bioRxiv2020

Development of diagnostic PCR and LAMP markers for MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don

ObjectiveDue to the allergic nature of the pollen of Cryptomeria japonica, the most important Japanese forestry conifer, a pollen-free cultivar is preferred. Mutant trees detected in nature have been used for the production of a pollen-free cultivar. In order to reduce the time and cost needed for the production and breeding, we aimed to develop simple diagnostic molecular markers for mutant alleles of the causative gene MALE STERILITY 1 (MS1) in C. japonica. The expected function of this gene, its two dysfunctional mutations, and genetic diversity were described recently in a related study. ResultsWe have developed PCR and LAMP markers to detect mutant alleles and to present experimental options depending on available laboratory equipment. At field stations, where PCR machines are not available, LAMP markers were developed. LAMP only needs heat-blocks or a water bath to perform the isothermal amplification and assay results can be easily seen by eye. Because the causative mutations were deletions, two kinds of PCR markers, amplified length polymorphism (ALP) and allele specific PCR (ASP) markers, were developed. These assays can be carried out by capillary or agarose gel electrophoresis.

genetics↗

bioRxiv2020

Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don)

Identifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) in Cryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterile C. japonica to reduce the pollinosis caused by pollen dispersal from artificial C. japonica forests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with the ms1. All nine breeding materials with the allele ms1 had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene of MS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials of C. japonica with the allele ms1 adapted to the unique environment of each region of the Japanese archipelago.

genetics↗

bioRxiv2020

Inspecting abundantly expressed genes in male strobili in sugi (Cryptomeria japonica D. Don) via a highly accurate cDNA assembly

Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. The field of functional genomics is rapidly developing. The genomics of this gymnosperm species is currently being studied. Although its genomic size is 11 Gbps, it is still too large to assemble well within a short period of time. Transcriptomics is the one another approach to address this. Moreover, it is a necessary step in obtaining the complete genomic data. Here we designed a three stages assembling workflow using the de novo transcriptome assembly tools, Oases and Trinity. The three stages in transcriptomics are independent assembly, automatic and semi-automatic integration, and refinement by filtering out potential contamination. We found a set of 49,795 cDNA and an equal number of translated proteins (CJ3006NRE). According to the benchmark of BUSCO, 87.01 % were complete genes, including very high "Complete and single-copy" genes-78.47%. Compared to other full-length cDNA resources, the extent of the coverage in CJ3006NRE suggests that it may be used as the standard for further studies. When two tissue-specific libraries were compared, principal component analysis (PCA) showed that there were significant differences between male strobili and leaf and bark sets. The highest three upregulated transcription factors stood out as orthologs to angiosperms. The identified signature-like domain of the transcription factors demonstrated the accuracy of the assembly. Based on the evaluation of different resources, we demonstrate that our transcriptome assembly output is valuable and useful for further studies in functional genomics and evolutionary biology.

bioinformatics↗