Biology subjects

Yamagishi, Y.

Publications and source records attributed to Yamagishi, Y..

4 recordsLinked to original sources

bioRxiv2025

Enhanced axonal transport in large vertebrates: KIF5A adaptations in giraffes and pythons

Efficient axonal transport is essential for neuronal function, particularly in species with exceptionally long axons. The Kinesin-1 motor protein KIF5A plays a key role in this process, but whether and how it adapts to the transport demands of large vertebrates remains unclear. Here, we show that KIF5A from giraffes (GcKIF5A) and pythons (PbKIF5A), moves 25% faster than its mouse counterpart (MmKIF5A) on neuronal microtubules in vitro and within axons of cultured mouse hippocampal neurons. This enhanced velocity, driven by three unique amino acid substitutions (R114Q, S155A and Y309F), facilitates long-distance transport in these species and represents a case of convergent evolution. Our structural analysis reveals that accelerated ADP release underlies the increased speed of GcKIF5A. Despite exhibiting a reduced force generation, GcKIF5A maintains efficient cargo transport under load. Furthermore, GcKIF5A exerts less drag in mixed-motor environments, an adaptation particularly beneficial for multiple motor-driven long-distance axonal transport. These findings reveal that KIF5A has evolved specific adaptations to facilitate efficient axonal transport in large vertebrates, highlighting the evolutionary plasticity of kinesin motors.

biophysics↗

bioRxiv2024

Extracellular rRNA profiling reveals the sinking and cell lysis dynamics of marine microeukaryotes

Marine plankton communities consist of numerous species, and their composition and physiological states are closely linked to ecosystem functions. Understanding biogeochemical cycles requires measuring taxon-specific mortality due to viral lysis or sloppy feeding, as the dissolved organic matter released contributes to rapid nutrient recycling and long-term carbon sequestration following microbial transformation. This study introduces a quantitative and comprehensive analysis of microeukaryotes in the dissolved constituents of seawater by using Mortality by Ribosomal Sequencing (MoRS) method. Our experimental pipeline successfully recovered 83% of cell-free rRNA. The ratio of cell-free rRNA to cell-associated rRNA was more than 10-fold higher in the mesopelagic layer than in the upper epipelagic layer, suggesting the mesopelagic zone as a hotspot for eukaryotic cell lysis. Many protist lineages, including phytoplankton such as haptophytes, are less susceptible to cell lysis in the epipelagic layer yet are actively lysed in the mesopelagic zone. Notably, over 86% of the significantly lysed species in the mesopelagic layer showed a habitat preference for the epipelagic layer. These findings indicate that sinking from the surface and lysis in the mesopelagic are prevalent dynamics for various eukaryotes.

ecology↗

bioRxiv2022

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus.

The Kimoto-style fermentation starter is a traditional preparation method of sake brewing. In this process, specific microbial transition patterns have been observed within nitrate-reducing bacteria and lactic acid bacteria during the production process of the fermentation starter. We have characterized phylogenetic compositions and diversity of the bacterial community in a sake brewery performing the Kimoto-style fermentation. Comparing the time-series changes with other sake breweries previously reported, we found a novel type of Kimoto-style fermentation in which the microbial transition differed significantly from other breweries during the fermentation step. Specifically, the lactic acid bacteria, Leuconostoc spp. was a predominant species in the late stage in the preparation process of fermentation starter, on the other hand, Lactobacillus spp., which plays a pivotal role in other breweries, was not detected in this analysis. The discovery of this new variation of microbiome transition in Kimoto-style fermentation has further deepened our understanding of the diversity of sake brewing.

microbiology↗

bioRxiv2021

The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines

mRNA-based vaccines provide effective protection against most common SARS-CoV-2 variants. However, identifying likely breakthrough variants is critical for future vaccine development. Here, we found that the Delta variant completely escaped from anti-N-terminal domain (NTD) neutralizing antibodies, while increasing responsiveness to anti-NTD infectivity-enhancing antibodies. Although Pfizer-BioNTech BNT162b2-immune sera neutralized the Delta variant, when four common mutations were introduced into the receptor binding domain (RBD) of the Delta variant (Delta 4+), some BNT162b2-immune sera lost neutralizing activity and enhanced the infectivity. Unique mutations in the Delta NTD were involved in the enhanced infectivity by the BNT162b2-immune sera. Sera of mice immunized by Delta spike, but not wild-type spike, consistently neutralized the Delta 4+ variant without enhancing infectivity. Given the fact that a Delta variant with three similar RBD mutations has already emerged according to the GISAID database, it is necessary to develop vaccines that protect against such complete breakthrough variants.

microbiology↗