Biology subjects

Sato, H.

Publications and source records attributed to Sato, H..

7 recordsLinked to original sources

bioRxiv2018

Evaluating intraspecific diversity of a fish population using environmental DNA: An approach to distinguish true haplotypes from erroneous sequences

Recent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) provide a non-invasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate such erroneous sequences when evaluating intraspecific genetic diversity using eDNA metabarcoding. In this study, we propose an approach combining denoising using amplicon sequence variant (ASV) method and the removal of haplotypes with low detection rates. A mixture of rearing water of Ayu (Plecoglossus altivelis altivelis) was used as an eDNA sample. In total, nine haplotypes of Ayu mitochondrial D-loop region were contained in the sample and amplified by two-step tailed PCR. The 15 PCR replicates indexed different tags were prepared from the eDNA sample to compare the detection rates between true haplotypes and false positive haplotypes. All PCR replications were sequenced by HTS, and the total number of detected true haplotypes and false positive haplotypes were compared with and without denoising using the two types of ASV methods, Divisive Amplicon Denoising Algorithm 2 (DADA2) and UNOISE3. The use of both ASV methods considerably reduced the number of false positive haplotypes. Moreover, all true haplotypes were detected in all 15 PCR, whereas false positive haplotypes had detection rates varying from 1/15 to 15/15. Thus, by removing haplotypes with lower detection rates than 15/15, the number of false positive haplotypes were further reduced. The approach proposed in this study successfully eliminated most of false positive haplotypes in the HTS data obtained from eDNA samples, which allowed us to improve the detection accuracy for evaluating intraspecific genetic diversity using eDNA analysis.

molecular biology↗

bioRxiv2018

In vitro characterization of multidrug-resistant influenza A(H1N1)pdm09 viruses carrying a dual amino acid substitution associated with reduced susceptibility to neuraminidase inhibitors

We detected influenza A(H1N1)pdm09 viruses carrying dual H275Y/I223R, H275Y/I223K, or H275Y/G147R substitutions in their neuraminidase protein, respectively. These viruses showed cross-resistance to oseltamivir and peramivir and reduced susceptibility to zanamivir. The H275Y/G147R virus retained its replication capability at least in vitro, but the H275Y/I223R and H275Y/I223K viruses did not.

microbiology↗

bioRxiv2018

Re-targeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

The heritability of chromatin states through cell division is a potential contributor to the epigenetic maintenance of cellular memory of prior states. The macroH2A histone variant has properties of a regulator of epigenetic cell memory, including roles controlling gene silencing and cell differentiation. Its mechanisms of regional genomic targeting and maintenance through cell division are unknown. Here we combined in vivo imaging with biochemical and genomic approaches to show that human macroH2A is incorporated into chromatin in the G1 phase of the cell cycle following DNA replication. The newly-incorporated macroH2A re-targets the same, large heterochromatic domains where macroH2A was already enriched in the previous cell cycle. It remains heterotypic, targeting individual nucleosomes that do not already contain a macroH2A molecule. The pattern observed resembles that of new deposition of centromeric histone variants during the cell cycle, indicating mechanistic similarities for macrodomain-scale regulation of epigenetic properties of the cell.

biochemistry↗

bioRxiv2018

Network hubs in root-associated fungal metacommunities

BackgroundAlthough a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring \"hub\" microbial species, which potentially organize community-scale processes of plant-microbe interactions.\n\nMethodsBy compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within \"metacommunity-scale\" networks of plant-fungus associations. In total, the metadata included 8,080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.\n\nResultsFew fungal OTUs were common across all the eight forests. However, in each metacommunity-scale network representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as \"metacommunity hubs\", which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.\n\nConclusionsThe network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to increase the growth and pathogen resistance of host plants, further studies elucidating their functional roles are awaited.

microbiology↗

bioRxiv2018

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks

BackgroundBelow-ground linkage between plant and fungal communities is one of the major drivers of terrestrial ecosystem dynamics. However, we still have limited knowledge of how such plant-fungus associations vary in their community-scale properties depending on fungal functional groups and geographic locations.\n\nMethodsBased on high-throughput sequencing of root-associated fungi in eight forests along the Japanese Archipelago, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.\n\nResultsIn most of the plant-fungus networks analyzed, host-symbiont associations were significantly specialized but lacked \"nested\" architecture, which has been commonly reported in plant-pollinator and plant-seed disperser networks. Meanwhile, the structure of arbuscular mycorrhizal networks was differentiated from that of ectomycorrhizal and saprotrophic/endophytic networks, characterized by high connectance. Our data also suggested that geographic factors affected the organization of plant-fungus network structure. For example, the southernmost subtropical site analyzed in this study displayed lower network-level specificity of host-symbiont associations and higher (but still low) nestedness than northern localities.\n\nConclusionsOur comparative analyses suggest that arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic plant-fungus associations often lack nested network architecture, while those associations can vary, to some extent, in their community-scale properties along a latitudinal gradient. Overall, this study provides a basis for future studies that will examine how different types of plant-fungus associations collectively structure terrestrial ecosystems.

microbiology↗

bioRxiv2017

Plant-soil feedbacks between arbuscular- and ecto-mycorrhizal communities

Soil microbiomes of adult trees exert species-specific effects on the survival and growth of seedlings1-6, yet empirical evidence that such plant-soil microbiome interaction drives seedling community assembly remains scarce. Here we show that mycorrhizal fungal communities determine seedling community assembly by controlling how resident plant communities alter the growth of newly established seedlings. We reciprocally introduced seedling communities of arbuscular-and ecto-mycorrhizal plant species to replicated mesocosms to follow the effects of mycorrhizal type match/mismatch with resident plant communities on seedling growth rates. The growth rates of recruited seedlings were generally higher under resident trees of the same mycorrhizal types than under those of different mycorrhizal types, generating positive plant-soil feedbacks through mycorrhizal-type matching. Such positive effects of matching were linked with seedlings greater acquisition rates of mycorrhizal symbionts from matched resident plants than from mismatched plants, and such linkage was pronounced for ecto-mycorrhizal plant species. In contrast, under the condition of mycorrhizal-type matching between resident plants and seedlings (i.e., within-mycorrhizal-type comparison), plant-soil feedback effects varied considerably in their sign and strength among resident-seedling species combinations. Consequently, the assembly of a temperate tree seedling community is driven by a combination of species-specific plant-soil feedbacks and the match/mismatch of mycorrhizal type between resident plants and seedlings.

ecology↗

bioRxiv2017

System-level studies of a cell-free transcription-translation platform for metabolic engineering

Current methods for assembling biosynthetic pathways in microorganisms require a process of repeated trial and error and have long design-build-test cycles. We describe the use of a cell-free transcription-translation (TX-TL) system as a biomolecular breadboard for the rapid engineering of the 1,4-butanediol (BDO) pathway. We demonstrate the reliability of TX-TL as a platform for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Using TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied to in vivo strain development.

bioengineering↗