Biology subjects

Akiyama, R.

Publications and source records attributed to Akiyama, R..

8 recordsLinked to original sources

bioRxiv2026

Fgf3 and Fgf10a regulate neuronal fasciculation through Schwann cell proliferation and infiltration in zebrafish posterior lateral line

BackgroundDuring development, axons are organized into bundles, a process known as axonal fasciculation. The zebrafish lateral line nerve has been used as a model to study axonal fasciculation; however, the underlying mechanisms are not yet fully understood. Although Fgf3 and Fgf10a are well known to regulate the migration of the lateral line primordium along which the lateral line nerve projects, their roles in the organization of the lateral line nerve itself have not been clarified. Resultsfgf3,10a double mutants exhibited lateral line axonal defasciculation accompanied by an increased number of Schwann cells. Live imaging revealed a marked increase in Schwann cell proliferation and demonstrated that newly divided Schwann cells migrate along axons and infiltrate interaxonal spaces, thereby expanding these spaces and disrupting axonal fasciculation. Pharmacological manipulations further implicated a contribution of Nrg1-ErbB signaling to this phenotype. ConclusionsOur findings suggest that Fgf3 and Fgf10a are required to restrict Schwann cell proliferation and infiltration, thereby ensuring axonal fasciculation during lateral line development.

developmental biology↗

bioRxiv2025

Short-chain fatty acids modulate the development and the cell surface molecule expression of dendritic cells by epigenetic regulation

BackgroundShort-chain fatty acids (SCFAs) are produced by the gut microbiota as secondary metabolites during fermentation process of dietary fibers. Although SCFAs are beneficial for immuno-related diseases because they regulate the gene expression and functions of myeloid cells, the effects of SCFAs on the development of DCs remain unclear. MethodsWe analyzed the effect of SCFAs on the expression levels of surface proteins and mRNAs, and histone modification in Flt3L-induced bone marrow-derived DCs. ResultsSCFAs, particularly butyrate, regulated the expression of surface molecules on mouse bone marrow-derived dendritic cells (DCs): increases in MHCII, CD86, CD11b, and LPAM-1 (4{beta}7) levels and the ratio of CD11c+/PDCA-1-/B220- conventional DCs (cDCs) to CD11c+/PDCA-1+/B220+ plasmacytoid DCs (pDCs). Experiments using inhibitors of histone deacetylase (HDAC) and Gi proteins, and GPR109A deficient mice indicated that butyrate regulated DCs by suppression of HDACs and not through a stimulatory effect on G protein-coupled receptors. Butyrate and the HDAC inhibitor, trichostatin A (TSA), increased the cDC/pDC ratio, surface LPAM-1 and Itga4 mRNA, while the mRNA level of Itgb7 was not affected by butyrate and was reduced by TSA. ChIP assays showed that butyrate and TSA increased histone acetylation in the Itga4 and Spi1 genes. Furthermore, the butyrate treatment increased the levels of Spi1 mRNA and PU.1 protein and decreased those of Spib/SpiB in DCs. In knockdown (KD) experiments using siRNAs, the gene expression of Itga4 was decreased by KD of Spi1 or Irf8, and cDC/pDC ratio decreased by Spi1 KD. ConclusionsButyrate controls the gene expression and development of DCs through epigenetic regulation and DC-related transcription factors.

immunology↗

bioRxiv2022

PlantServation: time-series phenotyping using machine learning revealed seasonal pigment fluctuation in diploid and polyploid Arabidopsis

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers, but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software to analyze field images, where the plant shape, color, and background vary over months. We estimated the anthocyanin contents of small individuals of four Arabidopsis species using color information and verified the results experimentally. We obtained >4 million plant images over three field seasons to study anthocyanin fluctuations. We found significant effects of past radiation, coldness, and precipitation on the anthocyanin content in the field. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation pipeline facilitates the study of plant responses to complex environments termed "in natura."

plant biology↗

bioRxiv2021

The UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME1 For Plant Survival Under Sunlight In The Field

As sessile organisms, plants are subjected to fluctuating sunlight including potentially detrimental ultraviolet-B radiation (UV-B). In Arabidopsis thaliana, experiments under controlled conditions have shown that UV RESISTANCE LOCUS 8 (UVR8) controls photomorphogenic responses for acclimation and tolerance to UV-B; however, its long-term impacts on plant performance remain poorly understood in naturally fluctuating environments. Here we quantified the survival and reproduction of different Arabidopsis mutant genotypes in diverse field and laboratory conditions. We found that uvr8 mutants produced more fruits than wild type in growth chambers with artificial low UV-B conditions but not in natural field conditions. Importantly, independent double mutants of UVR8 and the blue-light photoreceptor gene CRYPTOCHROME 1 (CRY1) in two genetic backgrounds showed a drastic reduction in fitness in the field. UV-B attenuation experiments in field conditions and supplemental UV-B in growth chambers demonstrated that UV-B caused the conditional cry1 uvr8 lethality phenotype. RNA sequencing in different conditions revealed a large number of genes with statistical interaction of UVR8 and CRY1 mutations in the presence of UV-B in the field. Among them, Gene Ontology analysis identified enrichment of categories related to UV-B response, oxidative stress, photoprotection and DNA damage repair. Our study demonstrates the functional importance of the UVR8-mediated response across life stages in natura, which is partially redundant with CRY1, and provides an integral picture of gene expression associated with plant environmental responses under diverse environmental conditions.

plant biology↗

bioRxiv2019

Experimental and field data support habitat expansion of the allopolyploid Arabidopsis kamchatica owing to parental legacy of heavy metal hyperaccumulation

Little empirical evidence is available whether allopolyploid species combine or merge adaptations of parental species. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the diploid parents A. halleri, a heavy metal hyperaccumulator, and A. lyrata, a non-hyperaccumulating species. Zinc and cadmium were measured in native soils and leaf tissues in natural populations, and in hydroponic cultures of A. kamchatica and A. halleri. Pyrosequencing was used to estimate homeolog expression ratios. Soils from human modified sites showed significantly higher Zn concentrations than non-modified sites. Leaf samples of A. kamchatica collected from 40 field localities had > 1,000 {micro}g g-1 Zn in over half of the populations, with significantly higher amounts of Zn concentrations in plants from human modified sites. In addition, serpentine soils were found in two populations. Most genotypes accumulated >3000 {micro}g g-1 of Zn in hydroponic culture with high variability among them. Genes involved in hyperaccumulation showed a bias in the halleri-derived homeolog. A. kamchatica has retained constitutive hyperaccumulation ability inherited from A. halleri. Our field and experimental data provides a compelling example in which the inheritance of genetic toolkits for soil adaptations likely contributed to the habitat expansion of an allopolyploid species.

evolutionary biology↗

bioRxiv2019

Myristate as a carbon and energy source for the asymbiotic growth of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal (AM) fungi, forming symbiotic associations with land plants, are obligate symbionts that cannot complete their natural life cycle without a host. Recently, fatty acid auxotrophy of AM fungi is supported by studies showing that lipids synthesized by the host plants are transferred to the fungi and that the latter lack genes encoding cytosolic fatty acid synthases (1-7). Therefore, to establish an asymbiotic cultivation system for AM fungi, we tried to identify the fatty acids that could promote biomass production. To determine whether AM fungi can grow on medium supplied with fatty acids or lipids under asymbiotic conditions, we tested eight saturated or unsaturated fatty acids (C12-C18) and two {beta}-monoacylglycerols. Only myristate (C14:0) led to an increase in biomass of Rhizophagus irregularis, inducing extensive hyphal growth and formation of infection-competent secondary spores. However, such spores were smaller than those generated symbiotically. Furthermore, we demonstrated that R. irregularis can take up fatty acids in its branched hyphae and use myristate as a carbon and energy source. Myristate also promoted the growth of Rhizophagus clarus and Gigaspora margarita. Finally, mixtures of myristate and palmitate accelerated fungal growth and induced a substantial change in fatty acid composition of triacylglycerol compared with single myristate application, although palmitate was not used as a carbon source for cell wall biosynthesis in this culture system. In conclusion, here we demonstrate that myristate boosts asymbiotic growth of AM fungi and can also serve as a carbon and energy source. Significance statementThe origins of arbuscular mycorrhizal (AM) fungi, which form symbiotic associations with land plants, date back over 460 million years ago. During evolution, these fungi acquired an obligate symbiotic lifestyle, and thus depend on their host for essential nutrients. In particular, fatty acids are regarded as crucial nutrients for the survival of AM fungi owing to the absence of genes involved in de novo fatty acid biosynthesis in the AM fungal genomes that have been sequenced so far. Here, we show that myristate initiates AM fungal growth under asymbiotic conditions. These findings will advance pure culture of AM fungi.

microbiology↗

bioRxiv2019

Fine-scale ecological and transcriptomic data reveal niche differentiation of an allopolyploid from diploid parents in Cardamine

Polyploidization, or whole genome duplication, is one of the major mechanisms of plant speciation. Allopolyploids (species that harbor polyploid genomes originating from hybridization of different diploid species) have been hypothesized to occupy a niche with intermediate, broader, or fluctuating environmental conditions compared with parental diploids. It remains unclear whether empirical data support this hypothesis and whether specialization of expression patterns of the homeologs (paralogous gene copies resulting from allopolyploidization) relates to habitat environments. Here, we studied the ecology and transcriptomics of a wild allopolyploid Cardamine flexuosa and its diploid parents C. hirsuta and C. amara at a fine geographical scale in their native area in Switzerland. We found that the diploid parents favored opposite extremes in terms of soil moisture, soil carbon-to-nitrogen ratios, and light availability. The habitat of the allopolyploid C. flexuosa was broader compared with those of its parental species and overlapped with those of the parents, but not at its extremes. In C. flexuosa, the genes related to water availability were overrepresented among those at both the expression level and the expression ratio of homeolog pairs, which varied among habitat environments. These findings provide empirical evidence for niche differentiation between an allopolyploid and its diploid parents at a fine scale, where both ecological and transcriptomic data indicated water availability to be the key environmental factor for niche differentiation.Significance statement Polyploidization, or whole genome duplication, is common in plants and may contribute to their ecological diversification. However, little is known about the niche differentiation of wild allopolyploids relative to their diploid parents and the gene expression patterns that may underlie such ecological divergence. We detected niche differentiation between the allopolyploid Cardamine flexuosa and its diploid parents C. amara and C. hirsuta along water availability gradient at a fine scale. The ecological differentiation was mirrored by the dynamic control of water availability-related gene expression patterns according to habitat environments. Thus, both ecological and transcriptomic data revealed niche differentiation between an allopolyploid species and its diploid parents.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2018

Noise-resistant developmental reproducibility in vertebrate somite formation

The reproducibility of embryonic development is remarkable, although molecular processes are intrinsically stochastic at the single-cell level. How the multi-cellular system resists the inevitable noise to acquire developmental reproducibility constitutes a fundamental question in developmental biology. Toward this end, we focused on vertebrate somitogenesis as a representative system, because somites are repeatedly reproduced within a single embryo whereas such reproducibility is lost in segmentation clock gene-deficient embryos. However, the effect of noise on developmental reproducibility has not been fully investigated, because of the technical difficulty in manipulating the noise intensity in experiments. In this study, we developed a computational model of ERK-mediated somitogenesis, in which bistable ERK activity is regulated by an FGF gradient, cell-cell communication, and the segmentation clock, subject to the intrinsic noise. The model simulation generated our previous in vivo observation that the ERK activity was distributed in a step-like gradient in the presomitic mesoderm, and its boundary was posteriorly shifted by the clock in a stepwise manner, leading to regular somite formation. Here we showed that this somite regularity was robustly maintained against the noise. Removing the clock from the model predicted that the stepwise shift of the ERK activity occurs at irregular timing with irregular distance owing to the noise, resulting in somite size variation. Through theoretical analysis, we presented a mechanism by which the clock reduces the inherent somite irregularity observed in clock-deficient embryos. Therefore, this study indicates a novel role of the segmentation clock in noise-resistant developmental reproducibility.

developmental biology↗