Biology subjects

Osada, Y.

Publications and source records attributed to Osada, Y..

6 recordsLinked to original sources

bioRxiv2025

Electrical information flows across the sporocarps of two ectomycorrhizal fungi in the field

We measured the extracellular bioelectrical activities of two ectomycorrhizal basidiomycete species belonging to the genus Hebeloma in a field to examine the potential information flow across the sporocarps and its reponse to artificial stimulation. The 37 sporocarps (29 H. danicum and 8 H. cylindrosporum) occurring within a 5 m x 5 m quadrat on the forest floor of an oak-dominated stand were measured for their electrical potential every second for 3.5 days using subdermal stainless electrodes. Causality analysis of electrical potential during a period without artificial stimulation indicated that the magnitude of potential information flow across the sporocarps was not restricted to the sporocarps belonging to the same genet (clone) nor within a species. Howeverm this was still negatively associated with genetic as well as spatial distances. The effects of artificial stimulation (water and urine addition) on the average magnitude of information flow across the sporocarps were positive when tap water was added locally to a certain sporocarp but were negative when tap water was added to all the sporocarps. In contrast, the addition of urine had minimal effect on the magnitude of information flow. These results indicate the presence of underground electrical information flows across fungal sporocarps which respond vigorously to the environmental conditions.

ecology↗

bioRxiv2025

Astringent flavanol fires the locus-noradrenergic system, regulating neurobehavior and autonomic nerves

Astringent flavanols (FLs) have shown enhanced cognitive function in a large intervention trial, but their mechanism remains unclear due to poor bioavailability. An oral dose of FLs increased spontaneous locomotion and memory, with activation of the sympathetic-adrenergic-medullary (SAM) and hypothalamic-pituitary-adrenal (HPA) axis, as shown by increased urinary catecholamine concentrations and corticotropin-releasing hormone (CRH) mRNA expression in the paraventricular nucleus (PVN) of mice. MS imaging showed high intensity of noradrenaline (NA) in the locus coeruleus (LC), which plays a key role in learning and memory, the hypothalamus lateral preoptic area, which affects sleep and arousal, and the brainstem as the origin of the sympathetic nervous system, immediately after FLs administration. Subsequent in situ hybridization (ISH) analysis showed that these NAs originated from LC. Astringent compounds like FLs influence brain function and physiological changes. Furthermore, the present series of results presents novel mechanisms by which food sensory properties maintain homeostasis. Highlights- A oral dose of astringent flavanols (FLs) immediately fires locus coeruleus-noradrenaline axis - FLs enhance spontaneous locomotion and short-term memory in mice - SAM and HPA axis are also activated by an oral dose of FLs - FLs astringency affects the brain and body, contributing to homeostasis.

synthetic biology↗

bioRxiv2023

A unified framework for nonparametric causality detection

Most complex systems in the real world are driven by multiple interactions among components. Identifying these interactions is critical for understanding, forecasting, and controlling system-level phenomena. Transfer entropy (TE) and convergent cross mapping (CCM) are two widely-used approaches for nonparametric causality detection based on time-series data. However, the theoretical relationship between TE and CCM has not been formally explained. Here, we provide a theoretical formulation that links TE and CCM in an information-theoretic framework, showing that they have different definitions of causal influence. Furthermore, from the formulation, we propose a novel nonparametric causality test, named unified information-theoretic causality (UIC), which has lower data requirements than those of TE (due to robustness to noise) and lower false-positive rates than those of CCM. Numerical experiments confirmed that UIC outperforms TE and CCM in terms of the performance of causality detection for both linear and nonlinear dynamical systems. Finally, we demonstrate the practical importance of the conditional test based on UIC using numerical simulations with indirect causality and empirical data for microbial communities in irrigated water samples from rice fields. Our results contribute to a unified understanding of nonparametric causality tests in time series and the accurate reconstruction of complex real-world systems.

ecology↗

bioRxiv2020

A model ecosystem of twelve cryopreservable microbial species allowing for a non-invasive approach

Simultaneous understanding of both individual and ecosystem dynamics is crucial in an era marked by the degradation of ecosystem services. Herein, we present a high-throughput synthetic microcosm system comprising 12 functionally and phylogenetically diverse microbial species. These species are axenically culturable, cryopreservable, and can be measured noninvasively via microscopy, aided by machine learning. This system includes prokaryotic and eukaryotic producers and decomposers, and eukaryotic consumers to ensure functional redundancy. Our model system displayed both positive and negative interspecific interactions and higher-order interactions that surpassed the scope of any two-species interaction. Although complete species coexistence was not our primary objective, we identified several conditions under which at least one species from the producers, consumers, and decomposers groups, and one functionally redundant species, persisted for over six months. These conditions set the stage for detailed investigations in the future. Given its designability and experimental replicability, our model ecosystem offers a promising platform for deeper insights into both individual and ecosystem dynamics, including evolution and species interactions.

microbiology↗

bioRxiv2019

Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest

Supra-annually synchronized flowering events occurring in tropical forests in Southeast Asia, known as general flowering (GF), are \"spectacular and mysterious\" forest events. Recently, studies that combined novel molecular techniques and model-based theoretical approaches suggested that cool temperature and drought synergistically drove GF. Although the novel approaches advanced our understanding of GF, it is usually difficult to know whether the mathematical formulation reasonably well represents the complex and dynamic processes involved in GF. In the present study, we collected a 17-year set of community-wide phenology data during 1993 to 2011 from Lambir Hills National Park in Borneo, Malaysia, and analyzed it using a model-free approach, empirical dynamic modeling (EDM), that does not rely on specific assumptions about the underlying mechanisms, to overcome and complement the previous limitations. By using EDM, we found that GF in the forest in Lambir Hills National Park is synergistically driven by cool air temperature and drought, which is consistent with the previous studies. Also, we found that cumulative meteorological variables, rather than instantaneous values, drive GF with delayed effects, which is also consistent with the previous studies. Interestingly, the present study showed that effects of cumulative meteorological variables on GF changed through time, which implies that the relationship between GF and meteorological variables may be influenced by other factors such as plant/soil nutrient resource dynamics. Future studies integrating novel mathematical/statistical frameworks, long-term and large spatial scale ecosystem monitoring and molecular phenology data are promising for better understanding and fore-casting of GF events in tropical forests in Southeast Asia.

ecology↗

bioRxiv2018

Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

We propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may o[ff]er a new avenue for population monitoring based on the fast, cost-e[ff]ective, and non-invasive sampling of genetic information.

ecology↗