Biology subjects

Okamoto, C.

Publications and source records attributed to Okamoto, C..

3 recordsLinked to original sources

bioRxiv2023

Molecular Dynamics Simulation Analysis of Structural Dynamic Cross Correlation Induced by Odorant Hydrogen-Bonding in Mouse Eugenol Olfactory Receptor

Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlfaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the -carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 [->] Phe182 [->] (Leu259 or Tyr260) [->] Tyr291 induced by the ligand binding with a time scale of 4-6 ns.

biophysics↗

bioRxiv2023

A stress sensor IRE1α is required for bacterial exotoxin-induced inflammasome activation in tissue-resident macrophages

Cholera toxin (CT), a bacterial exotoxin composed of one A subunit (CTA) and five B subunits (CTB), functions as an immune adjuvant. CTB can induce production of interleukin-1{beta} (IL-1{beta}), a proinflammatory cytokine, in synergy with a lipopolysaccharide (LPS), from resident peritoneal macrophages (RPMs) through the pyrin and NLRP3 inflammasomes. However, how CTB or CT activates these inflammasomes in the macrophages has been unclear. Here, we clarified the roles of IRE1, an endoplasmic reticulum (ER) stress sensor, in CT-induced IL-1{beta} production from RPMs. In RPMs, CTB is incorporated into ER and induced ER stress responses, depending on GM1, a cell membrane ganglioside. IRE1-deficient RPMs showed a significant impairment of CT- or CTB-induced IL-1{beta} production, indicating that IRE1 was required for CT- or CTB-induced IL-1{beta} production from RPMs. This study first demonstrates the critical roles of IRE1 in activation of both NLRP3 and pyrin inflammasomes in tissue-resident macrophages. One sentence summaryIRE1 is required for NLRP3 and pyrin-mediated IL-1{beta} production

immunology↗

bioRxiv2021

Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

O_LIAssessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics and can help distinguish between anthropogenic and natural causes for population decline. C_LIO_LIJapanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. Here we assess the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods. C_LIO_LIThe analyses indicate a reduction in effective population size (Ne) from 38 000 to 10 000 individuals between 4 and 1 Ma, followed by an increase to 80 000 individuals, between 1 Ma and 22-30 kya. Approximately 22-30 kya there is evidence for a reduction in Ne to approximately 60 000 individuals. These events are likely due to changes in environmental conditions, such as sea level and oceanic currents, especially around the last glacial maximum (19-33 kya). C_LIO_LIThe results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. This pattern of demographic history may make Japanese eel sensitive to current and future population declines. Conservation management of Japanese eel should focus on practical ways to prevent further population decline and the loss of genetic diversity that is essential for the species to adapt to changing environmental conditions such as climate change. C_LI

evolutionary biology↗