Over the last few years, Japanese prefectural assemblies have issued a considerable of resolutions concerning North Korea, but those numbers vary across the Japanese 47 prefectural assemblies. This ...paper attempts to explain the varied number by presence of civic groups in each prefecture. The assessment of the impact of civic groups on local assemblies is undertaken by using original panel data on the 47 prefectures from 1993 to 2018. The panel data analysis empirically shows that grassroots activism exerts significant influence on and facilitates the adoption of resolutions by local legislative bodies and supports the model’s predictions for legislative production.
A single fertilized egg is programmed to differentiate into a multitude of distinct cell types that comprise a multicellular organism. Epigenetic mechanisms such as DNA methylation and histone ...modifications are intricately involved in regulating developmental potential and cellular identity by establishing permissive or repressive chromatin states that are mitotically heritable. Here, we review the dynamics of major epigenetic marks during early mammalian development, and explore the question of whether DNA methylation and chromatin modifications enable or enforce changes that lead to the first cell fate decision.
Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from ...currently under-represented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.
We assembled genomes using public whole-metagenomic shotgun sequencing (WMS) data for 110 and 645 fecal samples from India and Japan, respectively. In addition, we assembled genomes from newly generated WMS data for 90 fecal samples collected from Korea. Expecting genome assembly for low-abundance species may require a much deeper sequencing than that usually employed, so we performed ultra-deep WMS (> 30 Gbp or > 100 million read pairs) for the fecal samples from Korea. We consequently assembled 29,082 prokaryotic genomes from 845 fecal metagenomes for the three under-represented Asian countries and combined them with the Unified Human Gastrointestinal Genome (UHGG) to generate an expanded catalog, the Human Reference Gut Microbiome (HRGM).
HRGM contains 232,098 non-redundant genomes for 5414 representative prokaryotic species including 780 that are novel, > 103 million unique proteins, and > 274 million single-nucleotide variants. This is an over 10% increase from the UHGG. The new 780 species were enriched for the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diets. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. We found that ultra-deep sequencing facilitated the assembly of genomes for low-abundance taxa, and deep sequencing (e.g., > 20 million read pairs) may be needed for the profiling of low-abundance taxa. Importantly, the HRGM significantly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, analysis of human self-antigen homologs on the HRGM species genomes suggested that bacterial taxa with high cross-reactivity potential may contribute more to the pathogenesis of gut microbiome-associated diseases than those with low cross-reactivity potential by promoting inflammatory condition.
By including gut metagenomes from previously under-represented Asian countries, Korea, India, and Japan, we developed a substantially expanded microbiome catalog, HRGM. Information of the microbial genomes and coding genes is publicly available ( www.mbiomenet.org/HRGM/ ). HRGM will facilitate the identification and functional analysis of disease-associated gut microbiota.
Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific ...biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
The success of polymer coatings for biomedical applications is undeniable. Among the very successful examples are poly(dopamine) (PDA) films due to their simplicity in deposition and beneficial ...interaction with biomolecules and cells. The aim of this review is to highlight the findings and achievement of PDA in nanomedicine since 2011. We discuss the progress that has been made to elucidate the structure of PDA and novel aspects considering the assembly of PDA-based films on diverse substrates. We highlight the newest results considering the biological evaluation PDA-based coatings to control cell behavior and the use of PDA in biosensing. The popularity of PDA remains unchanged, but the research efforts start to be consolidated toward more specific aims and clinical applications.
is a fungal genus responsible for a number of major cereal diseases. Although fungi produce many specialised or secondary metabolites for defence and interacting with the surrounding environment, the ...repertoire of specialised metabolites (SM) within
pathogenic species remains mostly uncharted. In this study, an in-depth comparative analysis of the
f.
,
f.
and
potential to produce SMs, based on in silico predicted biosynthetic gene clusters (BGCs), was conducted using genome assemblies from PacBio DNA reads. Conservation of BGCs between the
species included type I polyketide synthases, terpene synthases and the first reporting of a type III polyketide synthase in
f.
.
isolates exhibited substantial expansion of non-ribosomal peptide synthases relative to
, hallmarked by the presence of tailoring cis-acting nitrogen methyltransferase domains.
isolates also possessed unique non-ribosomal peptide synthase (NRPS)-indole and indole BGCs, while a
phytotoxin BGC for triticone production was absent in
. These differences highlight diversification between the pathogens that reflects their different evolutionary histories, host adaption and lifestyles.
Early-diverging fungi harbour unprecedented diversity in terms of living forms, biological traits and genome architecture. Before the sequencing era, non-Dikarya fungi were considered unable to ...produce secondary metabolites (SM); however, this perspective is changing. The main classes of secondary metabolites in fungi include polyketides, nonribosomal peptides, terpenoids and siderophores that serve different biological roles, including iron chelation and plant growth promotion. The same classes of SM are reported for representatives of early-diverging fungal lineages. Encouraged by the advancement in the field, we carried out a systematic survey of SM in
and corroborated the presence of various SM clusters (SMCs) within the phylum. Among the core findings, considerable representation of terpene and nonribosomal peptide synthetase (NRPS)-like candidate SMCs was found. Terpene clusters with diverse domain composition and potentially highly variable products dominated the landscape of candidate SMCs. A uniform low-copy distribution of siderophore clusters was observed among most assemblies.
are highlighted as the most potent SMC producers among the
and as a source of novel peptide products. SMC identification is dependent on gene model quality and can be successfully performed on a batch scale with genomes of different quality and completeness.
Since its discovery in the early days of splicing research, U1snRNP has been recognized as a crucial player in the early stages of the splicing process. In particular, binding of U1snRNP to the ...5'splice site of exons is a fundamental step in the formation of the early splicing complex and directs the subsequent assembly of the functional spliceosome. In recent years, the way that the U1snRNP molecular complexes recognize real 5' ss sequences from a huge background of similar decoy sequences has been extensively studied. In this review, we will provide an account of the latest functional properties of U1snRNP as a splicing factor, its role in transcriptional and mRNA degradation processes, and how these properties can be exploited to act as prospective therapeutic or gene silencing strategies. Finally, we will discuss the latest experimental evidence that challenges the absolute requirement of U1snRNP presence for splicing to take place.
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