Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria

The prevalence of antibiotic resistance and the decrease in novel antibiotic discovery in recent years necessitates the identification of potentially novel microbial resources to produce natural products. Ktedonobacteria, a class of deeply branched bacterial lineage in the ancient phylum Chloroflexi, are ubiquitous in terrestrial environments and characterized by their large genome size and complex life cycle. These characteristics indicate Ktedonobacteria as a potential active producer of bioactive compounds. In this study, we observed the existence of a putative “megaplasmid,” multiple copies of ribosomal RNA operons, and high ratio of hypothetical proteins with unknown functions in the class Ktedonobacteria. Furthermore, a total of 104 antiSMASH-predicted putative biosynthetic gene clusters (BGCs) for secondary metabolites with high novelty and diversity were identified in nine Ktedonobacteria genomes. Our investigation of domain composition and organization of the non-ribosomal peptide synthetase and polyketide synthase BGCs further supports the concept that class Ktedonobacteria may produce compounds structurally different from known natural products. Furthermore, screening of bioactive compounds from representative Ktedonobacteria strains resulted in the identification of broad antimicrobial activities against both Gram-positive and Gram-negative tested bacterial strains. Based on these findings, we propose the ancient, ubiquitous, and spore-forming Ktedonobacteria as a versatile and promising microbial resource for natural product discovery

Genomic and Phenotypic Characterization of a Wild Medaka Population : Towards the Establishment of an Isogenic Population Genetic Resource in Fish

Oryzias latipes (medaka) has been established as a vertebrate genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel

Study protocol for a multi-center, randomized controlled trial to develop Japanese denture adhesive guidelines for patients with complete dentures : the Denture Adhesive Guideline trial : study protocol for a randomized controlled trial

Background: Denture adhesives, characterized as medical products in 1935 by the American Dental Association, have been considered useful adjuncts for improving denture retention and stability. However, many dentists in Japan are hesitant to acknowledge denture adhesives in daily practice because of the stereotype that dentures should be inherently stable, without the aid of adhesives. The aim of this study is to verify the efficacy of denture adhesives to establish guidelines for Japanese users. The null hypothesis is that the application of denture adhesives, including the cream and powder types, or a control (isotonic sodium chloride solution) would not produce different outcomes nor would they differentially improve the set outcomes between baseline and day 4 post-application. Methods: This ten-center, randomized controlled trial with parallel groups is ongoing. Three hundred edentulous patients with complete dentures will be allocated to three groups (cream-type adhesive, powder-type adhesive, and control groups). The participants will wear their dentures with the denture adhesive for 4 days, including during eight meals (three breakfasts, two lunches, and three dinners). The baseline measurements and final measurements for the denture adhesives will be performed on the first day and after breakfast on the fourth day. The primary outcome is a general satisfaction rating for the denture. The secondary outcomes are denture satisfaction ratings for various denture functions, occlusal bite force, resistance to dislodgement, masticatory performance, perceived chewing ability, and oral health-related quality of life. Between-subjects comparisons among the three groups and within-subjects comparisons of the pre- and post-intervention measurements will be performed. Furthermore, a multiple regression analysis will be performed. The main analyses will be based on the intention-to-treat principle. A sample size of 100 subjects per group, including an assumed dropout rate of 10 %, will be required to achieve 80 % power with a 5 % alpha level. Discussion: This randomized clinical trial will provide information about denture adhesives to complete denture wearers, prosthodontic educators, and dentists in Japan. We believe this new evidence on denture adhesive use from Japan will aid dentists in their daily practice even in other countries

A genome database for a Japanese population of the larvacean Oikopleura dioica

The larvacean Oikopleura dioica is a planktonic chordate, and is tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of five days make it a promising model organism for developmental biology research. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for three years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 Mb and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named as OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. Moreover, screening of the male-specific scaffolds revealed that over 2.6 Mb of sequence were included in the male-specific Yregion. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism

Mining of the Uncharacterized Cytochrome P450 Genes Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence

ハナビシソウゲノムの解読から見えてきたイソキノリンアルカロイド生合成酵素遺伝子の進化 --植物が有用物質生産系を進化させる仕組みの解読--. 京都大学プレスリリース. 2018-01-26.Land plants produce specialized low molecular weight metabolites to adapt to various environmental stressors, such as UV radiation, pathogen infection, wounding and animal feeding damage. Due to the large variety of stresses, plants produce various chemicals, particularly plant species-specific alkaloids, through specialized biosynthetic pathways. In this study, using a draft genome sequence and querying known biosynthetic cytochrome P450 (P450) enzyme-encoding genes, we characterized the P450 genes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in California poppy (Eschscholzia californica), as P450s are key enzymes involved in the diversification of specialized metabolism. Our in silico studies showed that all identified enzyme-encoding genes involved in BIA biosynthesis were found in the draft genome sequence of approximately 489 Mb, which covered approximately 97% of the whole genome (502 Mb). Further analyses showed that some P450 families involved in BIA biosynthesis, i.e. the CYP80, CYP82 and CYP719 families, were more enriched in the genome of E. californica than in the genome of Arabidopsis thaliana, a plant that does not produce BIAs. CYP82 family genes were highly abundant, so we measured the expression of CYP82 genes with respect to alkaloid accumulation in different plant tissues and two cell lines whose BIA production differs to estimate the functions of the genes. Further characterization revealed two highly homologous P450s (CYP82P2 and CYP82P3) that exhibited 10-hydroxylase activities with different substrate specificities. Here, we discuss the evolution of the P450 genes and the potential for further genome mining of the genes encoding the enzymes involved in BIA biosynthesis

Factors Associated with Selection of Denture Adhesive Type: A Cross-Sectional Survey

The type of denture adhesive, cream or home-liner, chosen by regular denture adhesive users and oral conditions contributing to this selection require elucidation. The factors associated with denture adhesive selection were investigated through a face-to-face survey on oral and denture conditions. Age, sex, oral moisture, masticatory performance, retention and stability of the removable denture, ridge shape, mucosal thickness, and duration of denture use were examined in cream and home-liner-type denture adhesive users who did not regularly visit a dentist. Univariate analysis and multivariate analyses were performed. There were 38 and 40 cream-type and home-liner-type adhesive users, respectively. The type of denture adhesive was significantly associated with the oral moisture value, retention, ridge shape, mucosal thickness, and duration of denture use in univariate analyses. The residual ridge conditions with large factor loadings for ridge shape and mucosal thickness and duration of denture use were significantly related to the denture adhesive selection in multivariate logistic analysis. The residual ridge conditions and duration of denture use were significant factors in the selection of cream- and home-liner-type denture adhesives. These results can provide appropriate guidance based on the adhesives patients without dental supervision are more likely to choose

Initial curing characteristics of composite cements under ceramic restorations.

PURPOSE: To assess the degree of conversion (DC) of dual-curing composite cements when cured through ceramic-veneered zirconia disks. METHODS: Portions of mixed cement, either G-CEM LinkForce (GC), Panavia V5 (Kuraray Noritake) or ResiCEM (Shofu), were placed on the ATR crystal of a Fourier Transform Infrared Spectroscope (FTIR; iS50, Thermo Scientific) and squeezed to a 100-µm film thickness using a microscopy cover glass. DC (%) of the composite cements applied in self-curing mode was measured in the dark at 37°C. Following the dual-curing mode, the cements were light-cured directly (positive control) or through a ceramic-veneered zirconia disk (0.5-mm thick zirconia with a 1.0-mm thick veneering ceramic) for 40 sec using two light-curing units (G-Light Prima 2, GC; PenCure, Morita). Per experimental group, 5 tests were conducted to measure DC in self-cure and dual-cure mode (n=5). FTIR spectra of the composite cement films were acquired to determine DC every min up to 30 min. DC of the composite cements was statistically compared using two-way repeated-measures ANOVA (α=0.05). RESULTS: For all cements investigated, the self-curing mode resulted in significantly lower DC at 10, 20 and 30 min than the light-curing mode. When the composite cements were light-cured through the zirconia disk, DC at 30 min dropped significantly for ResiCem (Shofu), while not for Panavia V5 (Kuraray Noritake) and G-CEM LinkForce (GC). CONCLUSIONS: Self-curing slows down polymerization but does not reach for all composite cements the highest (light-cured) DC. Ceramic-veneered zirconia-based restorations may affect DC of some composite cements.status: Published onlin