Biology subjects

Yoshikawa, K.

Publications and source records attributed to Yoshikawa, K..

4 recordsLinked to original sources

bioRxiv2018

Self-Organized Critical Control of Genome Expression: Novel Scenario on Cell-Fate Decision

In our current studies on whole genome expression in several biological processes, we have demonstrated the actual existence of self-organized critical control (SOC) of gene expression at both population and single cell level. SOC allows for cell-fate change by critical transition encompassing the entire genome expression that, in turn, is partitioned into distinct response domains (critical states).\n\nIn this paper, we go more in depth into the elucidation of SOC control of genome expression focusing on the determination of critical point (CP) and associated distinct critical states in single-cell genome expression. This leads us to the proposal of a potential universal model with genome-engine mechanism for cell-fate change. Our findings suggest that the CP is fixed point in terms of temporal expression variance, where the CP (set of critical genes) becomes active (ON) for cell-fate change ( super-critical in genome-state) or else inactive (OFF) state ( sub-critical in genome-state); this may lead to a novel scenario of the cell-fate control through activating or inactivating CP.

genomics↗

bioRxiv2018

Cytokine profile in human olfactory cleft mucus and associated changes in olfactory function

Multiple factors, including physical changes of the nasal mucosa and epithelium and exposure to air-borne environmental agents, appear to contribute to age-related olfactory loss. However, the molecular aspects of aging-associated olfactory loss in humans are not well understood. Although inflammation can be a significant underlying cause for olfactory impairment, whether aging increases the levels of inflammatory cytokines in the human olfactory mucosa and whether any inflammatory markers are associated with age-related olfactory loss remain unclear. Using a noninvasive method for collecting human olfactory mucus, we characterized and compared inflammatory cytokines, chemokines, and some growth factors, in the mucus collected from the olfactory cleft or the anterior nasal cavity from 12 healthy, young (18-40 years old) and 12 elderly (60-85 years old) individuals. We also hoped to identify candidate molecular biomarkers associated with age-associated olfactory loss in humans. Olfactory thresholds were obtained for two odorants and individual mucus samples were analyzed using multiplex assays for the levels of 30 cytokines. Results indicated elevated levels of certain inflammatory cytokines (IL-12, MCP-1) in olfactory mucus of the elderly, and high levels of some inflammatory factors (MCP-1, IL-8, IL-13 and VEGF) were associated with reduced olfactory sensitivity, suggesting that inflammation may play a role in olfactory decline associated with aging.

neuroscience↗

bioRxiv2017

Single-Cell Reprogramming Of Mouse Embryo Development Through A Critical Transition State

Our work dealing with the temporal development of the genome-expression profile in single-cell mouse early embryo indicated that reprogramming occurs via a critical transition state, where the critical-regulation pattern of the zygote state disappears. In this report, we unveil the detailed mechanism of how the dynamic interaction of thermodynamic states (critical states) enables the genome system to pass through the critical transition state to achieve genome reprogramming.\n\nSelf-organized criticality (SOC) control of overall expression provides a snapshot of self-organization and explains the coexistence of critical states at a certain experimental time point. The time-development of self-organization is dynamically modulated by exchanges in expression flux between critical states through the cell nucleus milieu, where sequential global perturbations involving activation-inhibition of multiple critical states occur from the early state to the late 2-cell state. Two cyclic fluxes act as feedback flow and generate critical-state coherent oscillatory dynamics. Dynamic perturbation of these cyclic flows due to vivid activation of the ensemble of low-variance expression (sub-critical state) genes allows the genome system to overcome a transition state during reprogramming.\n\nOur findings imply that a universal mechanism of long-term global RNA oscillation underlies autonomous SOC control, and the critical gene ensemble at a critical point (CP) drives genome reprogramming. Unveiling the corresponding molecular players will be essential to understand single-cell reprogramming.

developmental biology↗

bioRxiv2017

Single-Cell Statistical Thermodynamics In Early Embryo Development

A statistical thermodynamics approach to the temporal development of biological regulation provides a phenomenological description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC). In early mouse embryo development, the dynamical change in the self-organization of overall expression determines how and when reprogramming of the genome-expression state occurs. Reprogramming occurs via a transition state (climbing over an epigenetic landscape), where the critical-regulation pattern of the zygote state disappears. A critical transition is well captured in terms of the bimodality of expression ensembles, which reflects distinct thermodynamic states (critical states). These critical states exhibit a genome avalanche pattern: competition between order (scaling) and disorder (divergence) around a critical point. The genome avalanche in mouse embryo development, which is committed to erase a previous ordered state, reveals that the direction of early embryo single-cell development traverses the same steps as in differentiation, but in the opposite order of self-organization.

genomics↗