Biology subjects

Koyama, A.

Publications and source records attributed to Koyama, A..

5 recordsLinked to original sources

bioRxiv2026

Genetic legacy in soil seedbanks after grassland conversion to plantation forests: evidence from Potentilla freyniana

Semi-natural grasslands are important ecosystems supporting biodiversity in Japan, but their area has declined rapidly due to land-use change and abandonment of traditional management practices such as mowing and burning. Although the conservation of genetic diversity is essential for the long-term persistence of grassland plants, little is known about the genetic diversity retained in soil seedbanks following conversion of grasslands to plantation forests. In this study, we compared the genetic diversity and population structure of above-ground and soil seedbank populations of the grassland perennial forb Potentilla freyniana across three sites in each of three land-use types: burned grasslands, deciduous plantation forests, and evergreen plantation forests (plantation ages approximately 21-62 years) on the Kaida Plateau, central Japan. Soil seedbank populations were obtained from soil samples through germination experiments, and genetic analyses were conducted using newly developed simple sequence repeat (SSR) markers. Genetic diversity was assessed using expected heterozygosity, allelic richness, and private allelic richness, population structure was evaluated using analysis of molecular variance (AMOVA), STRUCTURE analyses, and pairwise FST. Soil seedbank populations maintained levels of genetic diversity comparable to those of above-ground populations, and no significant differences were detected between the two population types. Furthermore, soil seedbank populations in evergreen plantation forests, where above-ground individuals of P. freyniana were absent, retained genetic diversity comparable to that observed in burned grasslands. AMOVA detected no significant genetic differentiation between above-ground and soil seedbank populations. These results suggest that high levels of genetic diversity can persist in soil seedbank populations for decades after forest establishment and highlight the potential importance of soil seedbanks as genetic resources for grassland restoration.

ecology↗

bioRxiv2025

Speed-controlled visual stimuli modulate fish collective dynamics

Fish navigation is modulated by visual stimulation and associated parameters, such as size, speed, and orientation, yet the regulatory mechanisms remain unclear. Here, we experimentally investigate how systematically controlled stimulus speed influences the temporal and spatial collective dynamics of Hemigrammus bleheri. Using a simple and customisable top-down projection setup, we displayed clockwise-rotating black-dot patterns at three distinct speeds to simulate complex environmental motion cues. We quantified individual temporal responsiveness through angular movements, and evaluated group-level spatial organisation. Fish angular movements positively tracked the rotation direction of the visual patterns. Lower stimulus speeds elicited predominantly exploratory behaviour, while higher speeds induced a transition to strong motion-tracking behaviour, aligning fish orientation with the rotating patterns. Increasing stimulus speed also corresponded with greater nearest-neighbour distance, indicating reduced spatial cohesion. Notably, we observed transient schooling episodes not aligned with the rotational stimulus, reflecting periods in which internal social interactions outweighed stimulus-driven coordination. Using a newly defined free-schooling index, we show that such internally driven episodes were frequent at lower stimulus speeds but markedly reduced at higher speeds. Overall, these results demonstrate that speed-controlled visual stimuli modulate both individual navigation and group coherence, offering new insights into how visual cues shape fish collective behaviour dynamics.

animal behavior and cognition↗

bioRxiv2023

Warming alters cascading effects of a dominant arthropod predator on microbial community composition in the Arctic

Warming is expected to increase abundances of wolf spider, the top predator in soil communities in the Arctic, but we have little understanding on how increased wolf spider density under warmer conditions affects soil microbial structure through trophic cascades. We tested the effects of wolf spider density and warming on bacterial and fungal community structure in litter through a fully factorial mesocosm experiment in Arctic tundra over two summers. Replicated litter bags were deployed at the soil surface and underground in the organic soil profile and collected at 2- and 14-month incubation. The litter samples were analyzed for community structure of bacteria and fungi and mass weight loss. After 2-month incubation, bacterial and fungal community compositions were already structured interactively by the spider density and warming treatments. Such interaction effect was also found in litter microbial community structure as well as litter mass loss rates after 14-month incubation. Our results show that wolf spiders have indirect, cascading effects on microbial community structure but that warming can alter these effects. The non-linear responses of microbial communities and litter decomposition to warming and increased spider density cast uncertainty in predicting structure and function of Arctic terrestrial ecosystem under warmer conditions in the future. IMPORTANCEThis is one of the first studies demonstrating that predator abundances and increased temperature interactively structure litter microbial communities in the Arctic. The Arctic is one of the fastest warming regions due to climate change and contains disproportionately large amounts of soil organic matter, including thick litter which accumulated over the long time because of slow decomposition. The accelerated soil organic matter decomposition due to the rapid warming can cause positive feedback where resulting greenhouse gas emission contribute to further global warming. Since microbial structure can affect decomposition rates of litter, the observed non-linear responses of soil microbial community compositions and litter decomposition rates indicate challenges in predicting Arctic ecosystem responses in the future.

ecology↗

bioRxiv2022

FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD

Abnormal expansions of GGGGCC repeat sequence in the noncoding region of the C9orf72 gene is the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). The expanded repeat sequence is translated into dipeptide repeat proteins (DPRs) by noncanonical repeat-associated non-AUG (RAN) translation. Since DPRs play central roles in the pathogenesis of C9-ALS/FTD, we here investigate the regulatory mechanisms of RAN translation, focusing on the effects of RNA-binding proteins (RBPs) targeting GGGGCC repeat RNAs. Using C9-ALS/FTD model flies, we demonstrated that the ALS/FTD-linked RBP FUS suppresses RAN translation and neurodegeneration in an RNA-binding activity-dependent manner. Moreover, we found that FUS directly binds to and modulates the G-quadruplex structure of GGGGCC repeat RNA as an RNA chaperone, resulting in the suppression of RAN translation in vitro. These results reveal a previously unrecognized regulatory mechanism of RAN translation by G-quadruplex-targeting RBPs, providing therapeutic insights for C9-ALS/FTD and other repeat expansion diseases.

neuroscience↗

bioRxiv2019

Highly efficient direct conversion of human monocytes into neuronal cells using a small molecule combination

Previous studies reported that human fibroblasts and astrocytes were successfully converted into neuronal cells by small molecules without introducing ectopic transgenes. Induced neuronal cells--reprogrammed directly from dermal fibroblasts or brain astrocytes--were obtained from some donors; however, the clinical applications of this approach would be limited because it requires an invasive biopsy to harvest enough cells for derivation. Here, we report that adult human peripheral blood monocytes may be directly converted into neuron-like cells using only a combination of small molecules without transgene integration. This method enables neuronal cell generation from TUJ1-positive cells after 3 days of induction (at over 80% conversion efficacy). These cells presented neuronal morphologies and markers, suggesting that terminally differentiated human cells may be efficiently transdifferentiated into a distantly related lineage. Overall, our study provides a strategy to develop neuronal cells directly from human adult peripheral blood monocytes using a generate transgene-free, chemical-only approach.

cell biology↗