Biology subjects

Higuchi, N.

Publications and source records attributed to Higuchi, N..

4 recordsLinked to original sources

bioRxiv2026

Gata.a, Tbx21, and Klf6/7 function cooperatively for zygotic genome activation in ascidian embryos

In ascidian embryos, gene expression from the zygotic genome begins between the 8- and 16-cell stages. While most zygotic genes are expressed in specific cell lineages at these stages, transcription factors that provide spatial cues for establishing specific expression patterns are insufficient to activate target genes at normal physiological levels. Gata.a is a transcription factor that provides spatial cues for targets expressed specifically in the animal hemisphere. Intriguingly, it is also required for physiological-level expression of many zygotic genes expressed in the vegetal hemisphere. In the present study, we found that Tbx21 and Klf6/7 augment the latter function of Gata.a. To determine the global extent of genes under control of these factors, we identified genes zygotically activated in early embryos using RNA-sequencing of BrU-labelled zygotic mRNAs. Our results revealed that approximately 80% of all zygotically activated genes were under control of these three factors. That is, together, Gata.a, Tbx21, and Klf6/7 are necessary to regulate target gene expression at physiological levels. This requirement for a specific set of broadly distributed factors resembles those of pioneer transcription factors that trigger zygotic genome activation (ZGA) in other animals, including flies and vertebrates. Regulatory factors involved in ZGA vary among animals, and our results indicate that ascidians use a distinct set of transcription factors for ZGA.

developmental biology↗

bioRxiv2025

Mapping giant-tree density in the Amazon

Tall trees are pivotal in maintaining tropical forests biodiversity and regulating biogeochemical cycles, mainly through their influence on carbon storage, nutrient cycling, and habitat structuring. Despite their ecological importance, the drivers behind their spatial distribution and the environmental factors driving the density of these emergent trees remain unexplained. Here we analyzed tall-tree density data derived from airborne LiDAR across 900 randomly distributed transects throughout the Brazilian Amazon. We paired each transect location with climatic, topographic, atmospheric, and soil metrics to investigate regional-level environmental drivers of large tree density using spatial modeling. Water availability and stable climatic conditions (low incidence of storms and of lightning) were the main drivers of tall-tree density at the regional level. The occurrence of tall trees is aggregated along the Amazon, with 14% occurring within 1.3% of the Amazon and 50% concentrated in 11.2% of the area. These patterns suggest that tall trees dominate localized regions of the biome and that high densities of tall trees are primarily dependent on mechanical rather than physiological drivers. Understanding the dynamics of 55.5 million emergent trees is imperative for advancing research in biogeochemistry, ecology, and climate resilience. Our results are especially relevant in the context of conserving nature and carbon stocks under increasing anthropogenic and environmental pressures.

ecology↗

bioRxiv2020

Resource availability and availability and disturbance shape maximum tree height across the Amazon

The factors shaping the distribution of giant tropical trees are poorly understood, despite its importance as a link between evolutionary biology and ecosystem biogeochemistry. The recent discovery of clusters of trees over 80 metres tall in the Guiana Shield region of the Amazon rainforest challenges the current understanding of the factors controlling the growth and survival of giant trees. The new discovery led us to revisit the question: what determines the distribution of the tallest trees of the Amazon? Here, we used high-resolution airborne LiDAR (Light Detection and Ranging) surveys to measure canopy height across 282,750 ha of primary old-growth and secondary forests throughout the entire Brazilian Amazon to investigate the relationship between the occurrence of giant trees and the environmental factors that influence their growth and survival. Our results suggest that the factors controlling where trees grow extremely tall are distinct from those controlling their longevity. Trees grow taller in areas with high soil clay content (> 42%), lower radiation (< 130 clear days per year) and wind speeds, avoiding alluvial areas (elevations higher than 40 m a.s.l), and with an optimal precipitation range of 1,500 to 2,500 mm yr-1. We then used an envelope model to determine the environmental conditions that support the very tallest trees (i.e. over 70 m height). We found that, as opposed to the myriad of interacting factors that control the maximum height at a large scale, wind speed had by far the largest influence on the distribution of these sentinel trees, and explained 67% of the probability of finding trees over 70 m in the Brazilian Amazon forest. The high-resolution pan-Amazon LiDAR data showed that environmental variables that drive growth in height are fundamentally different from environmental variables that support their survival. While precipitation and temperature seem to have lower importance for their survival than expected from previous studies, changes in wind and radiation regimes could reshape our forested biomes. This should be carefully considered by policy-makers when identifying important hotspots for the conservation of biodiversity in the Amazon.

ecology↗

bioRxiv2020

Volatiles defenses of Amazon Azteca ants (repellent ants)

Azteca ants are widely distributed in the neotropics and have been utilized as natural insect repellent for centuries. Azteca oils provide natural defense against herbivores in mutualistic interactions between ants and their host trees. While chemical characterization of oil secretions revealed a composition dominated by iridoids and ketones, the volatile emissions from Azteca ants, and therefore the active gas-phase semiochemicals, remain uncharacterized. In this study, we determined the composition of volatile emissions from a sample of an Azteca ant nest near the Rio Negro in the central Amazon. We found Azteca emissions were composed of a blend of methyl cyclopentyl and methyl cyclopentenyl based volatiles previously identified in Azteca oil extracts as potent alarm pheromones. The ketone 6-methyl-5-hepten-2-one, which also waspreviously identified as a major component of the Azteca oil, was found to be the dominant volatile emitted. For the first time, we report emissions of the highly volatile ketones 2,3-butadione and acetoin from the Azteca nest. Our study has important implications for the better understanding of the ecology and defense strategies of Azteca ants in herbivore defense and provides a base for future commercial applications involving Azteca ant essential oils as natural insect repellents.

plant biology↗