Biology subjects

Soga, K.

Publications and source records attributed to Soga, K..

8 recordsLinked to original sources

bioRxiv2026

Hygrochastic Seedpods: Engineering Microclimates for Forest Restoration

Forest restoration at scale depends on sowing seeds directly onto the land, yet seedling establishment is often poor and inconsistent. Seed enhancement technologies, such as priming, coating, and pelleting, improve germination under water, temperature, and salinity stress by supplying polymers, nutrients, or microorganisms at the seed surface. Being mainly conformal films, they act continuously once wetted and cannot gate when a seed is exposed to the soil. They also enclose no air volume, so the microenvironment they create is inseparable from the surrounding soil and has been inferred from plant performance rather than measured directly. Whether an engineered carrier can instead set both the state and the duration of the post-dispersal microenvironment, and how such an effect can be directly quantified, remains unexplored. Here we show that hygrochastic seedpods hold seeds in a timed, directly measurable microclimate and accelerate seedling emergence. The pods are programmable, responsive conical shells enclosing an air cavity around the seed. Two design solutions were investigated in parallel: wooden seedpods that crack open upon hydration, and poly(vinyl alcohol)/boric acid seedpods that gradually disintegrate after sustained wetting. In both, wax coatings act as a programmable diffusion-limited timer that sets activation from hours to days. The pod cavity permits direct sensing and monitoring, which no coating geometries allow. As directly measured during the initial phase after deployment, seedpod interiors ran 2 - 3 C warmer and drier than the surrounding soil, and these differences persisted after opening. Across indoor and field trials in several tree species, pods accelerated early seedling emergence without penalizing subsequent growth. These results identify artificial hygrochastic seedpods as a transient ecological mediator that regulates both the timing of seed exposure and the microclimate around the seed, offering a strategy for improving forest restoration under variable environmental conditions.

bioengineering↗

bioRxiv2025

Artificial hibernation uncovers distinct synaptic engram architecture for memory retention

The memory trace at the neuronal and synaptic levels remains controversial. Stable, larger spines are thought to support memory, but the high turnover of dendritic spines and the drifting of neuronal representations following memory formation suggest alternative possibilities. To elucidate a structural trace underlying memory retention, we utilize a mouse model of artificial hibernation. During hibernation, hippocampal neurons exhibited a substantial reduction in their activity and an extensive elimination of dendritic spines and synapses. Despite these changes, their memory and associated hippocampal neuronal representations are intact after arousal. We find that a subset of spines is maintained during hibernation. These spatially clustered engram-engram synapses are exclusively protected from elimination and characterized by synaptic contacts with multi-synaptic boutons. These findings suggest that synaptic engram architecture, rather than larger spines per se, is resilient to network remodeling and underlies long-term memory retention.

neuroscience↗

bioRxiv2025

TCP3-mediated regulation of cell expansion in Arabidopsis thaliana

(1) Cell expansion is crucial for organ morphogenesis in multicellular organisms. Apoplast acidification triggers plant cell expansion. Plant hormones and transcription factors such as TEOSINTE BRANCHED, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTORs (TCPs) control cell expansion. However, details regarding the regulatory mechanism of cell expansion for organ morphogenesis remain unclear. (2) In this study, we used molecular, biochemical, cellular, genetic, atomic force microscopy, and tensile testing analyses and showed that miR319-targeted TCPs integrated cell expansion with organ morphogenesis in Arabidopsis thaliana. (3) We found that TCPs directly induce the expression of genes encoding cell wall loosening proteins and SMALL AUXIN UP RNAs (SAURs), activators of plasma membrane-localized H+-ATPases. TCP-mediated activation of plasma membrane- localized H+-ATPases stimulates apoplast acidification, reduce cell stiffness, promote cell expansion, and thus exaggerate elongation of the hypocotyl. Ectopic expression of a SAUR gene in sextuple tcp mutant plants substantially recovered the hypocotyl morphology of the tcp mutant, providing genetic evidence of TCP-mediated SAUR regulation. (4) Collectively, our data show that TCPs regulate apoplast acidification for cell expansion.

plant biology↗

bioRxiv2025

Defective pollen meiosis in Arabidopsis due to combined arabinan and galactan insufficiency

The development of pollen is critical or seed plants, and depends on precise cellular and molecular mechanisms. It is known that the cell wall plays a key role in the progression of pollen maturation. An earlier phase in pollen development is the meiosis of pollen mother cells (PMCs), the fundamental process for producing viable pollen grains. However, the significance of the cell wall during pre-meiosis processes has remained unclear. Pectin, a major component of the cell wall, is known to accumulate abundantly in pollen. To investigate the significance of the cell wall during pollen meiosis, we generated an arad1 gals2 gals3 triple mutant of Arabidopsis thaliana, lacking the genes responsible for normal synthesis of arabinan and galactan, which constitute the side chains of pectin. Although vegetative growth and cell wall properties were comparable in wild-type (WT) and arad1 gals2 gals3, the pollen development in the mutant failed during meiosis. Immunohistochemical analysis showed that pectic arabinan and galactan accumulated in WT PMCs before meiosis, but this was not observed in mutant PMCs. We believe that this study is the first to demonstrate the critical role of cell wall components, specifically pectic arabinan and galactan, in the pre-meiosis processes of pollen development. HighlightPectic arabinan and galactan accumulate on the surface of pollen mother cells and this accumulation is essential for pollen meiosis.

plant biology↗

bioRxiv2024

A fluorophore-ligand conjugate for the rapid and reversible staining of native AMPA receptors in living neurons

The subcellular localizations of neurotransmitter receptors are strictly regulated in neurons. Changes in the trafficking of -amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA)-type glutamate receptors (AMPARs) play an essential role in synaptic plasticity, which is the cellular basis of learning and memory. To explore receptor trafficking, genetically encoded approaches (e.g., the fusion of fluorescent proteins to receptors) are often used. However, concerns remain that genetic approaches cannot fully reproduce the receptor function that is inherent to neurons. Herein, we report a chemical probe, PFQX1(AF488), for the visualization of cell-surface AMPARs without any genetic manipulation to neurons. The rapid and reversible staining features of this probe allowed the visualization of AMPAR accumulation in dendritic spines during synaptic plasticity in living hippocampal neurons. Moreover, the mechanisms of this synaptic accumulation, for which genetically encoded approaches have given controversial results, were revealed by integrating two chemical methods: PFQX1(AF488) and covalent chemical labeling.

neuroscience↗

bioRxiv2023

Cell wall pectic β-1,4-galactan contributes to increased plant freezing tolerance induced by cold acclimation

Subzero temperatures are often lethal to plants. Many temperate plants have a mechanism called cold acclimation that allows them to sense a drop in temperature and prepare for freezing stress through accumulation of soluble sugars and cryoprotective proteins. Plant cells are surrounded by a cell wall and as ice formation primarily occurs in the extracellular matrix (the apoplast), cell wall properties are important for plant freezing tolerance. Although previous studies have shown that the amounts of constituent sugars of the cell wall, in particular those present in pectic polysaccharides, are altered by cold acclimation, the significance of this change during cold acclimation has not been clarified. We found that {beta}-1,4-galactan, which forms neutral side chains of pectin, accumulates in the cell walls of Arabidopsis and various freezing tolerant vegetables during cold acclimation. The gals1 gals2 gals3 triple mutant, which has reduced {beta}-1,4-galactan in the cell wall, exhibited reduced freezing tolerance compared with wild-type Arabidopsis during initial stages of cold acclimation. Expression of genes involved in the galactan biosynthesis pathway such as GALACTAN SYNTHASES and UDP-glucose 4-epimerases were induced during cold acclimation in Arabidopsis explaining galactan accumulation. Cold acclimation resulted in a decrease in extensibility and an increase in rigidity of the cell wall in the wild type, whereas these changes were not observed in the gals1 gals2 gals3 triple mutant. These results indicate that the accumulation of pectic {beta}-1,4-galactan contributes to acquired freezing tolerance by cold acclimation via changes in cell wall mechanical properties.

plant biology↗

bioRxiv2021

Strategy for detecting off-target sites in genome-edited rice

Genome-editing using the CRISPR-Cas9 system can substantially accelerate crop breeding. Because off-target editing is the main problem with this system, a reliable method for comprehensively detecting off-target sites is required for the editing of food crop genomes. However, a method that accurately predicts off-target sites has not been established. In this study, we performed a SITE-Seq analysis to predict potential off-target sites. SITE-Seq is an unbiased method applicable for the in vitro detection of double-strand breaks (DSBs). To analyze SITE-Seq data, we developed a novel Galaxy system, which can perform simple and reproducible analyses without a command line operation. We conducted a SITE-Seq analysis of a rice genome modified by OsFH15 gRNA-Cas9, and identified 41 DSB sites in the annotated regions. Amplicon-sequencing revealed mutations at one off-target site in the genome-edited rice. The presence of an uncommon protospacer adjacent motif (NTG PAM) likely makes this off-target site difficult to identify using in silico methods. Of the six tested programs, only CRISPRdirect predicted this off-target site, but it also predicted 6,080 off-target sites in total. These results suggest the SITE-Seq method presented herein can efficiently predict off-target sites and is useful for assessing the safety of genome-edited food.

bioinformatics↗

bioRxiv2018

Rapid clearing of biological organs by using phosphoric acid, a hydrophilic solution with high refractive index

Tissue clearing is a fundamental challenge in biology and medicine to achieve high-resolution optical imaging of tissues deep inside intact organs. The clearing methods, reported up to now, require long incubation time or physical/electrical pressure to achieve tissue clearing, which is done by matching the refractive indices of the whole sample and medium to that of the lipid layer. Here we show that phosphoric acid increases the refractive index of the medium and can increase the transparency of formalin-fixed tissue samples rapidly. Immersion of fixed tissues of mice in phosphoric acid solutions increased their transparency within 60 min in the case of 3-mm-thick fixed tissue specimens. While phosphoric acid suppresses bright signals on the boundary of cells in their phase-contrast images, it does not damage the morphology of cell membrane with phospholipid bilayer. The protocol presented herein may contribute to develop better and faster soaking methods for tissue clearing than previously reported protocols.\n\nHighlights{blacksquare} Phosphoric acid can reduce light scattering by tissue samples.\n{blacksquare}Tissue clearing effect of phosphoric acid is fast and needs only 60-min incubation.\n{blacksquare}Cell membrane was preserved during incubation using phosphoric acid.

cancer biology↗