Biology subjects

Miyamoto, K.

Publications and source records attributed to Miyamoto, K..

18 recordsLinked to original sources

bioRxiv2026

Photosynthesis-derived carbohydrate supply sustains CuCl2-induced phytoalexin production in rice leaves

Phytoalexins are antimicrobial metabolites whose biosynthesis is triggered by signaling activated by both biotic and abiotic elicitors, but the physiological conditions that sustain their production remain poorly understood. Here, we examined how light and carbohydrate availability affect CuCl2-induced production of diterpenoid (phytocassanes and momilactones) and flavonoid (sakuranetin) phytoalexins in rice (Oryza sativa L.) leaf disks. Darkness strongly suppressed both the accumulation of all three phytoalexin groups and the induction of their biosynthetic genes. In darkness, endogenous sucrose, glucose, and fructose declined to 3%-8% of the levels in the light, whereas early accumulation of jasmonic acid and jasmonoyl-L-isoleucine (JA-Ile) was not detectably reduced. Exogenous sucrose restored phytoalexin accumulation in darkness in a dose-dependent manner, together with the expression of the suppressed biosynthetic genes, whereas equimolar mannitol had no effect. Glucose also restored sakuranetin accumulation in darkness but only partially restored diterpenoid accumulation, whereas the glucose analog 2-deoxy-D-glucose did not, and it suppressed CuCl2-induced accumulation in the light in a dose-dependent manner. In the light, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosynthetic electron transport, depleted soluble sugars and suppressed phytoalexin accumulation, and sucrose reversed this suppression. Sugars alone induced little phytoalexin accumulation, indicating that carbohydrates act permissively rather than as elicitors. Diterpenoid phytoalexins depended more strongly on light than sakuranetin, yet both classes depended on carbohydrate availability. These results indicate that photosynthesis-derived carbohydrate supply sustains elicitor-induced phytoalexin production in rice leaves and largely accounts for its light dependence.

plant biology↗

bioRxiv2026

Near-atomic structures of human astrovirus capsids reveal a subunit-specific maturation mechanism

Human astrovirus (HAstV) is a major cause of acute gastroenteritis, yet the structural basis of capsid maturation and infectivity remains poorly understood. Here, we report near-atomic cryo-electron microscopy structures of HAstV serotype 4 in immature and mature states at 1.79 [A] and 1.73 [A] resolution, respectively. These structures reveal a subunit-specific maturation mechanism in which differential protease accessibility drives selective removal of spike (P2) domains. Structural comparisons show that only A-B dimers form a broad cavity beneath the P2 domains that is permissive for trypsin entry, whereas the corresponding region in C-C dimers is sterically restricted. Proteolytic maturation induces pronounced conformational rearrangements, particularly in subunit B, linking capsid geometry to asymmetric protease susceptibility. Despite these changes, the inner capsid architecture and presumptive RNA-associated densities remain conserved, indicating that genome release occurs at a later stage of infection. Together, our findings establish a mechanistic framework in which capsid geometry governs proteolysis-driven activation.

microbiology↗

bioRxiv2026

Minimally invasive measurement of maternal transcripts enables predicting the developmental potential of mammalian zygotes

Maternal transcripts are stored in the oocyte cytoplasm during oogenesis and play a pivotal role in early embryonic development after fertilization. However, specific maternal transcripts that reflect the developmental potential of embryos have not been systematically identified, and the use of maternal transcript levels as an indicator of successful development has not been explored. Here, we link the maternal transcriptome to the zygotes developmental potential by examining transcripts in a single polar body. The transcriptome of a zygote or an oocyte was highly similar to that of its accompanying polar body in mouse, cow, and human. We have identified a set of maternal transcripts whose expression levels fluctuate between poor- and good-quality zygotes. Specifically, Sipa1and Zmym6 were identified as marker transcripts that accurately reflect the developmental potential of zygotes. Using these marker genes, combined with machine learning, the development of zygotes to the blastocyst stage was successfully predicted with more than 80% specificity as early as 12 hours after fertilization. Furthermore, our prediction platform significantly improved implantation rates and live births to term. Thus, we have demonstrated a minimally invasive method for identifying maternal transcripts associated with zygote developmental potential. Our developed prediction system provides a generalizable conceptual framework for human infertility treatment to reduce the risk of implantation failure by excluding embryos with low developmental potential, especially when early embryos are transferred, and for livestock propagation to assess selected expressed maternal trait-associated variants before embryo transfer.

developmental biology↗

bioRxiv2026

Hydrophobic pocket engineering of arylmalonate decarboxylase expands its substrate scope towards the synthesis of the (R)-enantiomers of sterically hindered carboxylic acids

Arylmalonate decarboxylase (AMDase) stereoselectively converts disubstituted malonates to chiral carboxylic acids, but its substrate spectrum is very limited regarding the size of the smaller substituent. Inspired by the observation that (S)-selective AMDase variants also convert larger substrates, we unlocked the synthesis of the (R)-enantiomers of -aryl and -alkenyl n-butanoic and n-pentanoic acids, respectively, in exquisite enantiopurity.

biochemistry↗

bioRxiv2026

A collagen orientation switch reshapes fin architecture

The orientation and distribution of fibrillar collagen are critical determinants of the shape and mechanical properties of bones and organs.1-3 However, how they are spatially organized within tissues is still poorly understood,4-7 as visualizing these collagen architectures remains challenging. Actinotrichia (AT), the spear-shaped fibrillar collagen structures located at the distal tips of fish fins, are easily observable due to their large size and distinctive morphology8-14 and have recently emerged as a model system for studying collagen fiber organization.15-19 In this study, we generated knockout lines for the fish-specific extracellular matrix (ECM) genes actinodin1 and actinodin2 (and1/2), which are lost in tetrapods.12 Loss of these genes dramatically altered the orientation of collagen fibers, thereby inducing changes in fin morphology. In the wild-type fins, AT are orderly arranged beneath the epidermis, forming layers parallel to the fin surface, and their individual fibers radiate distally toward the fin tip. In contrast, double knockout (dKO) of and1/2 results in overall fin reduction accompanied by increased thickness. Examination of the collagen structure distribution revealed the presence of aberrant collagen fibers oriented perpendicular to the fin epidermis. Moreover, the vertically oriented fibers contributed to thickening of the mesenchymal region in which they were distributed. The number of abnormal fibers increased with the severity of and1/2 deficiency, suggesting that collagen fibers in fins inherently tend to align perpendicular to the epidermis when these genes are absent. Furthermore, in tetrapods lacking the and gene family--specifically amphibians, the tetrapod group most closely related to fish20--examination of the developing limb, the organ homologous to paired fins in fish,21 revealed collagen fibers oriented perpendicular to the epidermis. The distribution pattern also resembled that observed in the fin buds of and1/2 dKO fish. Together, these findings highlight collagen patterning alterations as a previously unrecognized factor contributing to the evolutionary divergence between thinned fins and thickened limbs. Moreover, the identification of mutants that dramatically alter collagen fiber orientation is unprecedented, suggesting that analysis of Actinodin (And) function unveil the mechanisms underlying collagen matrix formation.22-28

developmental biology↗

bioRxiv2025

Two phytohormones synergistically induce parasitic weeds seed germination via KAI2d receptors

Root parasitic plants can severely decrease global crop production. The germination of their seeds is induced by host root-derived strigolactones (SLs). Considering this unique germination system, a "suicidal germination" method has been proposed to control root parasitic plants. However, this method requires the cost-effective production of germination inducers. In this study, we determined that jasmonates and SLs can synergistically induce the seed germination of root parasitic plants (Orobanche minor and Striga hermonthica). Biochemical analyses indicated that jasmonates and SLs cooperatively activate multiple divergent KARRIKIN INSENSITIVE 2 receptors. Our findings have elucidated the host recognition systems associated with these highly duplicated promiscuous receptors, with potential implications for developing a new strategy to protect crops against root parasitic plants.

plant biology↗

bioRxiv2025

Human-specific fast synaptic kinetics enable rapid detection of predictive features

Humans can discern the underlying principles in complex environments, but the cellular basis of this ability is unclear. By comparing layer 2/3 cortical pyramidal neurons in five mammals (mouse, rat, marmoset, macaque and human), we found that human neurons exhibited distinctively faster kinetics of excitatory synaptic transmissions. In a computational model, neurons with human-type synapses detected hidden patterns more quickly in noise, and this superiority was only evident in unsupervised learning. Tracking synaptic weights revealed that human synapses were potentiated sharply and persistently by the patterns, while macaque-type synapses were broadly potentiated, which were easily eroded. These data suggest that the human-specific acceleration of synaptic kinetics enables the rapid extraction of latent structures in complex environments, providing a cellular basis for our efficient cognitive abilities.

neuroscience↗

bioRxiv2025

Generative AI-driven artificial DNA design for enhancing inter-species gene activation and enzymatic degradation of PET

Conventional approaches to heterologous gene expression rely on codon optimization, which is limited to swapping synonymous codons and often fails to capture deeper adaptive changes. In contrast, naturally evolved orthologous genes between species often differ by more than just synonymous substitutions - they can include non-synonymous mutations, insertions, and deletions that confer functional adaptation to different host contexts. Here we present OrthologTransformer, a Transformer-based deep learning model that converts orthologous genes between species by learning from large-scale orthologous gene datasets curated for high-quality sequence alignments. The model recapitulates the full spectrum of evolutionary differences - from synonymous codon swaps to amino acid-changing mutations and indels - to predict a coding sequence optimized for a target species while preserving the proteins function. In extensive validation across diverse bacterial species pairs, OrthologTransformer significantly increased the conversion accuracy of generated genes to native target sequences compared to the original source genes, even for pairs with stark disparities in GC content and optimal growth temperature. The Transformers context-aware designs also favored conservative amino acid substitutions, maintaining protein functional integrity. As a proof-of-concept, an OrthologTransformer-designed PETase gene for Bacillus subtilis from the host species Ideonella sakaiensis was synthesized and expressed, yielding robust PET plastic-degradation activity that surpassed synonymous codon-optimized controls. These results establish OrthologTransformer as a powerful tool for de novo cross-species gene adaptation, transcending the limits of traditional codon optimization and enabling more effective heterologous gene performance in synthetic biology applications.

bioinformatics↗

bioRxiv2025

Actinotrichia-independent developmental mechanisms of spiny rays facilitate the morphological diversification of Acanthomorpha fish fins

Skeletal forms in vertebrates have been regarded as good models of morphological diversification. Fish fin forms are greatly diversified, and their bone structure is classified into soft rays and spiny rays. In fish evolution, spiny-ray morphologies are known to be sometimes extremely modified; however, it remains unknown how the developmental mechanisms of spiny-rays have contributed to their morphological diversification. By using the rainbowfish Melanotaenia praecox for examination of the extracellular matrix (ECM) and cell dynamics of spiny-ray development, we demonstrate that spiny-ray developments are independent of the actinotrichia (needle-shaped collagen polymers at the tip of fish fins), which are known as an important ECM in soft-ray morphogenesis. Furthermore, we found that in the thorny spiny-ray of the filefish Stephanolepis cirrhifer, the lateral protrusions equip the BMP positive osteoblast condensation, as in the state of the spiny-ray tips in M. praecox and S. cirrhifer. Taken together, our findings reveal that osteoblast distribution and signaling-molecule intensity would contribute to spiny-ray modification. In comparison to soft rays development, the independence from actinotrichia in spiny-rays would facilitate growth direction change, leading to their morphological diversification. This indicates that the cell distribution and ECM usage would be major factors driving the morphological diversification in animals.

evolutionary biology↗

bioRxiv2024

Evolutionary conserved cis-trans regulation machinery for diterpenoid phytoalexin production in Poaceae

O_LIMomilactones and phytocassanes are diterpenoid phytoalexins involved in plant chemical defense. These metabolites, along with biosynthetic gene clusters (BGCs), are conserved in wild rice. However, the mechanisms by which phytoalexins are regulated in wild rice are unclear. Thus, we aimed to investigate the regulatory mechanisms for biosynthetic genes within the BGCs of diterpenoid phytoalexins. C_LIO_LIWe conducted a transcriptome analysis of five wild rice species, Oryza rufipogon, Oryza punctata, Oryza officinalis, Oryza brachyantha, and Leersia perrieri, after CuCl2 treatment. C_LIO_LIAmong the CuCl2-responsive transcription factors, diterpenoid phytoalexin factor (DPF), which regulates phytoalexin production in cultivated rice (Oryza sativa), was broadly conserved in wild rice and showed phytoalexin-inducing activity when introduced into cultivated rice. Highly conserved genomic regions containing N-boxes (5'-CACGAG-3'), the potential binding motif of DPF, were found. CRISPR/Cas9 genome editing to remove these regions showed that biosynthetic gene expression and phytoalexin production were significantly attenuated after CuCl2 treatment in the leaves of the edited plants. Thus, the cis-trans factor combination of DPF and N-boxes is a key determinant of regulation. C_LIO_LIDPF has evolved as a strong cis-trans regulatory system for diterpenoid phytoalexin production, with N-boxes generated within the cluster region during the evolution from wild rice to cultivated rice. C_LI

plant biology↗

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

Quantum algorithm for position weight matrix matching

We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The two proposed algorithms, the naive iteration method and the Monte-Carlo-based method, output matched segments, given the oracular accesses to the entries in the biological sequence and the PWM. The former uses quantum amplitude amplification (QAA) for sequence motif search, resulting in the query complexity scaling on the sequence length n, the sequence motif length m and the number of the PWMs K as [Formula], which means speedup over existing classical algorithms with respect to n and K. The latter also uses QAA, and further, quantum Monte Carlo integration for segment score calculation, instead of iteratively operating quantum circuits for arithmetic in the naive iteration method; then it provides the additional speedup with respect to m in some situation. As a drawback, these algorithms use quantum random access memories and their initialization takes O(n) time. Nevertheless, our algorithms keep the advantage especially when we search matches in a sequence for many PWMs in parallel.

bioinformatics↗

bioRxiv2023

Transition to the structurally vulnerable nuclear state is an integral part of mouse embryonic development

Upon fertilization, germ cells are reprogrammed to acquire the ability to develop into an entire organism. Whereas extensive studies have focused on epigenetic reprogramming of chromatin states during development, changes of the nucleus that surrounds chromatin are ill-defined. Here, we show that nuclei become structurally and mechanically vulnerable at the 2-cell stage during mouse embryonic development. The 2-cell stage nuclei are extraordinarily plastic and deformable in contrast to those of 1-cell and 4-cell stages. The mechanically vulnerable nuclear state is attained by autophagy-mediated loss of lamin B1 from the nuclear membrane. This developmentally programmed lamin B1 dynamics is required for chromatin organization and major zygotic genome activation. We thus demonstrate that structural reprogramming of nuclei is a major determinant of embryonic gene expression and acquisition of totipotency.

cell biology↗

bioRxiv2022

Incomplete activation of developmentally required genes Alyref1 and Gabpb1 leads to preimplantation arrest in cloned mouse embryos

Differentiated cell nuclei can be reprogrammed after nuclear transfer (NT) to oocytes and the produced NT embryos can give rise to cloned animals. However, development of NT embryos is often hampered by recurrent reprogramming failures, including the incomplete activation of developmental genes, yet specific genes responsible for the arrest of NT embryos are not well understood. Here, we searched for developmentally important genes among the reprogramming-resistant H3K9me3-repressed genes, and identified Alyref and Gabpb1 by siRNA screening. Gene knockout of Alyref and Gabpb1 by the CRISPR/Cas9 system resulted in early developmental arrest in mice. Single embryo RNA-seq revealed that Alyref is needed for the formation of inner cell mass. The supplement of Alyref and Gabpb1 by mRNA injection supported efficient preimplantation development of cloned embryos. Thus, our study shows that the H3K9me3-repressed genes contain developmentally required genes and the incomplete activation of such genes results in preimplantation arrest of cloned embryos.

developmental biology↗

bioRxiv2020

Heterogeneous relationships between white matter and behaviour

Several studies have established specific relationships between White Matter (WM) and behaviour. However, these studies have typically focussed on fractional anisotropy (FA), a neuroimaging metric that is sensitive to multiple tissue properties, making it difficult to identify what biological aspects of WM may drive such relationships. Here, we carry out a pre-registered assessment of WM-behaviour relationships in 50 healthy individuals across multiple behavioural and anatomical domains, and complementing FA with myelin-sensitive quantitative MR modalities (MT, R1, R2*). Surprisingly, we only find support for predicted relationships between FA and behaviour in one of three pre-registered tests. For one behavioural domain, where we failed to detect an FA-behaviour correlation, we instead find evidence for a correlation between behaviour and R1. This hints that multimodal approaches are able to identify a wider range of WM-behaviour relationships than focusing on FA alone. To test whether a common biological substrate such as myelin underlies WM-behaviour relationships, we then ran joint multimodal analyses, combining across all MRI parameters considered. No significant multimodal signatures were found and power analyses suggested that sample sizes of 40 to 200 may be required to detect such joint multimodal effects, depending on the task being considered. These results demonstrate that FA-behaviour relationships from the literature can be replicated, but may not be easily generalisable across domains. Instead, multimodal microstructural imaging may be best placed to detect a wider range of WM-behaviour relationships, as different MRI modalities provide distinct biological sensitivities. Our findings highlight a broad heterogeneity in WMs relationship with behaviour, suggesting that variable biological effects may be shaping their interaction. HighlightsO_LIPre-registered testing of microstructural imaging across modalities (FA, MT, R1, R2*) to test WM-behaviour relationships. C_LIO_LIPartial support for FA-behaviour relationships hypothesised based on previous literature. C_LIO_LIMultimodal approaches can help detect WM-behaviour relationships that are not detected with FA alone. C_LIO_LISample sizes of 40 to 200 may be needed to detect myelin-behaviour relationships in joint multimodal analyses. C_LIO_LIVariable biological effects may be shaping WM-behaviour relationships. C_LI

neuroscience↗

bioRxiv2020

Environmental DNA metabarcoding for biodiversity monitoring of a highly-diverse tropical fish community in a coral-reef lagoon: Estimation of species richness and detection of habitat segregation

An environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic ecosystems, where species diversity is remarkably high. This study examined the extent to which species richness can be estimated in a small coral reef lagoon (1500 x 900 m) near Okinawa Island, southern Japan, where the surrounding waters are likely to harbor more than 1500 species of fish. During 2015-2017, a total of 16 capture-based surveys were conducted to create a faunal list of fish species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect differences between adjacent fish communities inhabiting the offshore reef edge and shore-side seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture-based samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the total) were commonly identified by both methods, indicating that capture-based surveys failed to collect a number of species detected by eDNA metabarcoding. Interestingly, two different approaches to estimate species richness based on eDNA data yielded values close to the 410 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 samples) would detect 90% of the 410 species. In addition, non-metric multi-dimensional scaling for fish assemblages clearly distinguished between the fish communities of the offshore reef edge and those of the shore-side seagrass beds.

ecology↗

bioRxiv2019

A slight decrease in serum albumin level is associated with rapid progression of kidney dysfunction even within the normal range: The Yuport Health Checkup Center Cohort Study

ObjectiveA low-normal albumin level is associated with a high risk of cardiovascular disease and mortality in the general population. However, the relationship between serum albumin level and future decline of kidney function is unclear. We aimed to clarify the effect of serum albumin level on the decline of kidney function in the general population.\n\nMethodsThe data used were from 11,000 participants of a voluntary health checkup program between 1998 and 2006 conducted in Japan. The primary outcome for kidney function was a difference in estimated glomerular filtration rate ({Delta}eGFR) of [≥]3 mL/min/1.73 m2/year. The association of the risk of decreased kidney function with albumin level was determined using a logistic regression analysis. We fit separate multivariable logistic regressions for serum albumin levels (g/dL) as a continuous variable and as categorical data, classified as [≤]4.3 (n=2,530), 4.4- 4.6 (n=5,427), and [≥]4.7 (n=3,043).\n\nResultsOf 11,000 participants, 346 had a {Delta}eGFR/year of [≥]3. As compared with the participants with albumin levels of [≥]4.7 g/dL, the risk of decline in kidney function was higher not only in those with albumin levels of [≤]4.3 g/dL (adjusted OR = 2,29, 95% CI: 1.65-3.18) but also in 4.4-4.6 g/dL (adjusted OR = 1.60, 95% CI: 1.20-2.14).\n\nConclusionDecreased albumin level is an independent risk factor for rapid decline in kidney function even within the normal range.

epidemiology↗

bioRxiv2017

Predation Of Stocked Masu Salmon (Oncorhynchus masou) By Riparian Wildlife

Predation after release is one of the major concerns of hatchery fish conservation and propagation. However, the relationship among the size of hatchery fish, the predator species, and their behaviors in natural environments is largely unknown. To understand the relationship, we conducted predation experiments in outdoor tanks and a semi-natural stream with exposure to local predators. Two different ranges of fork lengths of masu salmon (Oncorhynchus masou) were examined as prey sizes. Camera trap data showed that grey herons (Ardea cinerea) were the primary predator animal in the system, and that most herons utilized shallow areas in the morning or evening. Increasing the density of stocked salmon brought in more grey herons. More importantly, predation by grey herons resulted in the survival rate of larger salmon being significantly lower than that of the smaller salmon. Our results suggest that it is important to understand local predators, adjust the optimum body size of hatchery fish at release, and choose the appropriate stocking site and time of day for maximizing the effectiveness of fish stocking.

ecology↗