Biology subjects

Hongo, Y.

Publications and source records attributed to Hongo, Y..

4 recordsLinked to original sources

bioRxiv2025

Hypoxia-induced gene expression changes in N. vectensis embryos

Oxygen availability is one of the critical drivers of metazoan evolution and diversification. The earliest metazoans evolved in shallow marine shelves of the Neoproterozoic era, where the redox environment was likely variable and spatially heterogenous. This imposed physiological constraints on the emerging animals, selecting for oxygen-responsive and stress-adaptive traits. Embryogenesis is a novel and highly conserved stage of metazoan development, and its regulatory architecture may hold the key to understanding how adaptive traits arise in response to environmental change. Defining how early metazoan embryos respond to fluctuating oxygen levels will therefore provide essential insights into the adaptive mechanisms that shaped the evolution of metazoans. Here, the embryos of the cnidarian Nematostella vectensis, a representative of early-diverging metazoans, were used to comprehensively investigate the developmental and genetic responses to hypoxia. N. vectensis embryogenesis is oxygen-dependent, with hypoxia inducing a reversible developmental arrest. Transcriptomic profiling reveals that the hypoxia response in N. vectensis embryos is conserved with bilaterians, encompassing core hypoxia-responsive genes and pathways. These findings suggest that the genetic toolkit underlying embryonic hypoxia responses was already established in the common cnidarian-bilaterian ancestor.

evolutionary biology↗

bioRxiv2025

Data-Driven Feed Optimization for Sustainable Aquaculture through Integrated Omics Analysis and Two-stage Bayesian optimization

In aquaculture and livestock farming, developing feed that promotes efficient growth while minimizing environmental impact is crucial for sustainability. We developed a data-driven feed optimization system (DFOS) that integrates omics analysis with machine learning-based optimization technologies. First, DFOS employed Bayesian optimization (BO) to identify the optimal proportions of proteins and lipids, which are crucial feed components. Simultaneously, omics analysis was conducted to assess the physiological response of the targets to a given feed and identify key dietary components essential for growth. Next, BO was used to efficiently modify the combination and proportion of the specific additives identified in the first stage. We demonstrated the efficacy of DFOS by applying it to develop a new feed for the high-demand leopard coral grouper (Plectropomus leopardus) in Southeast Asia. This system provides an efficient data-driven framework for feed optimization across aquaculture and livestock, contributing significantly to more sustainable and productive farming practices.

ecology↗

bioRxiv2021

Seasonal variation in the relative importance of assembly processes in marine fish communities as determined by environmental DNA analyses

Compositional variation among local communities reflects the differences in abiotic environments, though the extent of the influence varies in natural systems. Generally, the environmental filtering is expected to be strong if the environmental gradient encompasses severe habitats where species sorting is highly likely to work. However, this hypothesis has rarely been tested in dynamic systems, where the higher dispersal ability of species allows them to easily respond to stressful environments. Here, with the dynamics of fish communities in a Japanese bay revealed by environmental DNA analyses as a model case, we examined how harmful seasonal hypoxia (low concentration of oxygen in bottom waters in summer) affected the strength of environmental filtering. We found that, in summer, dissolved oxygen (DO) concentration was significantly low and fish species richness decreased in the bottom water compared to the surface, suggesting that the organisms were adversely affected by the hypoxia. At the same time, the between-depths heterogeneity in DO concentration was larger, but species composition was less divergent and the influence of DO on species composition appeared weaker during summer. These results imply that environmental filtering is weakened when the bottom water was characterized by extremely severe environments. Furthermore, there was a shift in the species occurrence from bottom to surface waters in summer that was consistent across species, suggesting that the extremely severe hypoxia adversely affected fish species irrespective of their identity. These results collectively suggest that environmental filtering is weaker during summer despite more severity and heterogeneity in environments, most likely because individual movements to avoid unpreferable environments in the bottom waters occurred quasi-neutrally. By providing evidence against the prevailing understanding that environmental filtering strongly works in severe environments, these findings invoke further investigation on how the filtering acts in various conditions.

ecology↗

bioRxiv2021

Primordial capsid and spooled ssDNA genome structures penetrate ancestral events of eukaryotic viruses

Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the ssDNA viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus, Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.3 [A] resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold, but has additional unique features; a third {beta}-sheet and a long C-terminal tail. Further, low-resolution reconstructions of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organisation.

biophysics↗