Biology subjects

Kurita, Y.

Publications and source records attributed to Kurita, Y..

8 recordsLinked to original sources

bioRxiv2025

Systematic measurements of dose-dependent responses for combinatorial treatments of SA and JA led to the development of transcriptomic biomarkers

Plants coordinate defence against pathogens and herbivores through the crosstalk between salicylic acid (SA) and jasmonic acid (JA) signalling pathways. However, little is known about how plants integrate the phytohormone concentration profiles to shape defence states in complex field environments. Here we show that systematically varying combinatorial SA and JA concentrations in Arabidopsis thaliana reveals 43 distinct combination-specific transcriptional signatures beyond SA-JA antagonism. Leveraging these data, we developed and validated machine-learning-based transcriptomic biomarkers that enabled independent quantification of SA and JA response states. By applying these biomarkers to field-grown A. thaliana, we revealed that SA/JA response states were dynamically shaped by abundant and co-occurrence of herbivores on individual plants. Our study provides a strategy to decode hormonal responses to biotic environments from field transcriptomes, bridging the gap between molecular signalling and ecological dynamics.

plant biology↗

bioRxiv2024

Harnessing Dye-induced Photothermal Confinement in Lipid Membranes: A Path to NIR-modulated Artificial Synaptic Vesicles

Optical heating coupled with near-infrared (NIR) light and photothermal materials enables thermal confinement within biospecimens, minimizing undesirable thermal damage. Here, we demonstrated that photothermally heating lipid bilayers embedded with a unique phthalocyanine dye (VPc) efficiently perturbs the bilayers, resulting in increased permeability. Notably, microscopic studies revealed that the mechanism causing changes in membrane permeability may not follow the conventional temperature-sensitive liposome model. Furthermore, the heat generated by NIR laser illumination rarely diffused into the surrounding environment, and the dye was located within the bilayers at the molecular level, where it effectively transferred heat to the lipid bilayer. We prepared VPc-embedded liposomes encapsulating acetylcholine (ACh) and demonstrated the NIR laser-triggered release of ACh, creating a concentration jump across a few cells or within a limited single cell region. This method induced Ca2+ flux through ACh receptor stimulation in thermally delicate biospecimens such as C2C12 myotubes and the Drosophila brain.

bioengineering↗

bioRxiv2023

Millisecond-scale behaviours of plankton quantified in situ and in vitro using the Event-based Vision Sensor (EVS)

The Event-based Vision Sensor (EVS) is a bio-inspired sensor that captures detailed motions of objects, developed with the applicability to become the eyes of machines and especially self-driving cars. Compared to conventional frame-based image sensors as employed in video cameras, EVS has an extremely fast motion capture equivalent to 10,000-fps even with standard optical settings and additionally has high dynamic ranges for brightness and also lower consumption of memory and energy. These features make the EVS an ideal method to tackle questions in biology, such as the fine-scale behavioural ecology. Here, we developed 22 characteristic features for analysing the motions of aquatic particles from the raw data of the EVS, and deployed the EVS system in both natural environments and laboratory aquariums to test its applicability to filming and analysing plankton behaviour. Our EVS monitoring in turbid water at the bottom of Lake Biwa, Japan identified several particles exhibiting distinct cumulative trajectory with periodicities in their motion (up to 16 Hz), suggesting that they were living organisms with rhythmic behaviour. We also carried out EVS monitoring in the deep sea aided by infrared lighting to minimise influence on behaviour, and observed particles with active motion and periodicities over 40 Hz. Furthermore, we used the EVS to observe laboratory cultures of six species of zooplankton and phytoplankton, confirming that they have species-specific motion periodicities of up to 41 Hz. We applied machine learning to automatically classify particles into five categories (four categories of zooplankton plus passive particles), which achieved an accuracy up to 86%. Our attempts to use the EVS for biological observations, especially focusing on its millisecond-scale temporal resolution and wide dynamic range provide a new avenue to investigate rapid and periodical motion and behaviour in small organisms. Given its compact size with low consumption of battery and memory, the EVS will likely be applicable in the near future for the automated monitoring of the behaviour of plankton by edge computing on autonomous floats, as well as quantifying rapid cellular-level activities under microscopy.

animal behavior and cognition↗

bioRxiv2021

Fillable and Unfillable Gaps in Rice Transcriptome under Field and Controlled Environments

The differences between plants grown in field and controlled environments have long been recognised; however, few studies have addressed the underlying molecular mechanisms. Here, we show fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments by utilising SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature, and humidity of field environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening; those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature only affects transcriptome dynamics in the morning. We found upregulation of genes related to biotic and abiotic stress, whose expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results accelerate the understanding of plant responses to field environments for both field and laboratory studies.

plant biology↗

bioRxiv2021

Artificial mimicry of seasonal transcriptome dynamics in Arabidopsis thaliana reveals short- and long-term responses to environmental conditions

Plants must respond to various seasonally changing environmental stimuli. In a previous study, seasonally oscillating genes were identified by a massive time-series transcriptome analysis for the wild population of Arabidopsis halleri ssp. gemmifera, a sister species to Arabidopsis thaliana. It was not clear how environmental stimuli shaped the seasonal expression pattern of these seasonally oscillating genes. In this study we show that responses in different time-scales contributed to the formation of seasonal expression patterns for several genes. To analyze the seasonally oscillating genes, we established an experimental system to mimic seasonal expression trends using A. thaliana and a "smart growth chamber mini," a hand-made low-cost small chamber. Arabidopsis thaliana plants were cultured under conditions that mimicked the average monthly temperatures and daylengths under different day-scale incubation. In total, the seasonal trends of 1627 seasonally oscillating genes were mimicked, and they showed varying temporal responses (constant, transient, and incremental) to environmental stimuli. Our results suggest that plants perceive and integrate information regarding environmental stimuli in the field by combining seasonally oscillating genes with different temporal responsiveness.

plant biology↗

bioRxiv2020

Removal of repressive histone marks creates epigenetic memory of recurring heat in Arabidopsis

Acclimation to high temperature increases plants tolerance of subsequent lethal high temperatures1-3. Although epigenetic regulation of plant gene expression is well studied, how plants maintain a memory of environmental changes over time remains unclear. Here, we show that JUMONJI (JMJ) proteins4-8, demethylases involved in histone H3 lysine 27 trimethylation (H3K27me3), are necessary for Arabidopsis thaliana heat acclimation. Acclimation induces sustained H3K27me3 demethylation at key HEAT SHOCK PROTEIN (HSP) loci by JMJs, poising the HSP genes for subsequent activation. Upon sensing heat after a 3-day interval, JMJs directly reactivate HSP genes. Finally, jmj mutants fail to maintain heat memory under fluctuating field temperature conditions. Our findings of an epigenetic memory mechanism involving histone demethylases may have implications for environmental adaptation of field plants.

plant biology↗

bioRxiv2020

Visualization of seasonal shifts of phosphorus re-translocation and overwintering recycling in a shortened annual cycle system of the deciduous poplar tree (Populus alba L.).

Phosphorus (P) is an essential macronutrient for plant growth. In deciduous trees, P is remobilized from senescing leaves and stored in perennial tissues during winter for further growth. Annual internal recycling and accumulation of P is considered an important strategy to support vigorous growth of trees. However, the pathways of seasonal re-translocation of P and the molecular mechanisms of this transport have not been clarified. Here we show the seasonal P re-translocation route visualized using the real-time radioisotope imaging and the macro- and micro-autoradiography. We analyzed the seasonal re-translocation P in poplar (Populus alba. L) cultivated under "a shortened annual cycle system", which mimicked seasonal phenology in a laboratory. From growing to senescing season, sink tissues of 32P and/or 33P shifted from young leaves and the apex to the lower stem and roots. The radioisotope P re-translocated from a leaf was stored in phloem and xylem parenchyma cells and redistributed to new shoots after dormancy. Seasonal expression profile of phosphate transporters (PHT1, PHT5 and PHO1 family) was obtained in the same system. Our results reveal the seasonal P re-translocation routes at the organ and tissue levels and provide a foothold for elucidating its molecular mechanisms.

plant biology↗

bioRxiv2018

Prediction of environmental response in field-grown rice using expression-dynamics-QTL

How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Using statistical analysis of large-scale time-series RNA-sequencing of field-grown rice from chromosome segment substitution lines (CSSLs), we identified 1675 expression dynamics quantitative trait loci (edQTLs) leading to polymorphisms in expression dynamics under field conditions. Based on the edQTL and environmental information, we successfully predicted gene expression under environments different from training environments, and in rice cultivars with more complex genotypes than the CSSLs. Overall, edQTL identification helped understanding the genetic architecture of expression dynamics under field conditions, which is difficult to assess with laboratory experiments1.The prediction of expression based on edQTL and environmental information will contribute to crop breeding by increasing the accuracy of trait prediction under diverse conditions.

bioinformatics↗