Evaluation of genomic prediction considering non-additive genetic effects on fatty acid traits of Japanese Black cattle.

Genomic prediction was conducted using 2494 Japanese Black cattle from Hiroshima Prefecture and both single-nucleotide polymorphism information and phenotype data on monounsaturated fatty acid (MUFA) and oleic acid (C18:1) analyzed with gas chromatography. We compared the prediction accuracy for four models (A, additive genetic effects; AD, as for A with dominance genetic effects; ADR, as for AD with the runs of homozygosity (ROH) effects calculated by ROH-based relationship matrix; and ADF, as for AD with the ROH-based inbreeding coefficient of the linear regression). Bayesian methods were used to estimate variance components.

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf-production methods.

In ruminants, the overgrowth of offspring produced by in vitro fertilization (IVF) is a common problem. Abnormal epigenetic modifications caused by environmental factors during the early embryonic period are suspected as an aetiology of overgrowth. In this study, we investigated the genome-wide histone H3K4me3 profiles of bovine placentae that play a pivotal role in foetal development and compared their characteristics between artificial insemination (AI)- and IVF-derived samples.

Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle.

We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP.

Quantitative prediction of rice starch digestibility using Raman spectroscopy and multivariate calibration analysis.

Digestibility is an important characteristic of rice starch. It is affected by the growing environment, such as temperature and soil, so that even in the same genetic cultivar the digestibility of each product will be different. Here, we predicted rice starch digestibility by Raman scattering spectroscopy.

A Novel Hemostatic Belt Allowing Ambulation Soon After Atrial Fibrillation Ablation.

We aimed to develop a hemostatic device with physiological evidence that allows ambulation soon after atrial fibrillation (AF) ablation. We measured right femoral vein pressure in 57 participants to clarify why groin post-venipuncture rebleeding often occurs during the transition from supine to sitting under compression bandage application and found that it increased more than threefold when raising the upper body (8.6 ± 4.

Distribution of Human Sapovirus Strain Genotypes over the Last Four Decades in Japan: a Global Perspective.

Sapovirus (SaV) infections are a public health problem because they cause acute gastroenteritis in humans of all ages, both sporadically and as outbreaks. However, only a limited amount of SaV sequence information, especially whole-genome sequences for all the SaV genotypes, is publicly available. Therefore, in this study, we determined the full/near-full-length genomic sequences of 138 SaVs from the 2001 to 2015 seasons in 13 prefectures across Japan.

Cloning, DNA sequence, and expression of flagellins from high and low virulence strains of Edwardsiella tarda and their macrophage-stimulating activities.

Edwardsiella tarda is a causative pathogen of edwardsiellosis in fish. Our previous studies on high (NUF251) and low (NUF194) virulent strains of E. tarda demonstrated that NUF251 strain induced significantly higher levels of NO and TNF-α from fish and mouse macrophages than NUF194 strain.

Density estimations and comparisons of a fragmented single fiber using X-ray computed tomography.

A commercial X-ray computed tomography (CT) apparatus using a quasi-monochromatic beam was utilized for density estimations and comparisons of a fragmented single fiber. The validation of quasi-monochromaticity of the X-ray source was investigated by radiograph measurements. For the case of a transmittance higher than 50%, the contribution of Cu Kα characteristic X-rays was dominant.

A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan.

Perilla frutescens (Lamiaceae) is an important herbal plant with hundreds of bioactive chemicals, among which perillaldehyde and rosmarinic acid are the two major bioactive compounds in the plant. The leaves of red perilla are used as traditional Kampo medicine or food ingredients. However, the medicinal and nutritional uses of this plant could be improved by enhancing the production of valuable metabolites through the manipulation of key enzymes or regulatory genes using genome editing technology.

New microbial electrosynthesis system for methane production from carbon dioxide coupled with oxidation of sulfide to sulfate.

Microbial electrosynthesis system (MES) is a promising method that can use carbon dioxide, which is a greenhouse gas, to produce methane which acts as an energy source, without using organic substances. However, this bioelectrical reduction reaction can proceed at a certain high applied voltage when coupled with water oxidation in the anode coated with metallic catalyst. When coupled with the oxidation of HS to SO, methane production is thermodynamically more feasible, thus implying its production at a considerably lower applied voltage.

The Role of Mycangial Fungi Associated with Ambrosia Beetles () in Fig Wilt Disease: Dual Inoculation of and Can Bring Fig Saplings to Early Symptom Development.

The ambrosia beetle, , is a wood-boring pest and a vector of , a pathogenic fungus causing fig () wilt disease (FWD) in Japan. The ambrosia fungi, and , have been frequently isolated from heads (including mycangia) of wild and reared adult female , respectively. However, the exact mechanisms driving FWD as well as the interactions between and in fig orchard remain unclear.

Isolation and characterization of Zygosaccharomyces sp. yeast strains from miso.

There is currently great interest in the salt-tolerant yeast strains used to produce miso and soy sauce. Since the isolation of Zygosaccharomyces sp. strain from Japanese miso more than 60 years, several hybrid strains have been identified in fermented foods.

Non-destructive analysis of hollow-shaped single fibers using X-ray computed tomography.

A commercial high-resolution X-ray computed tomography (CT) was utilized for non-destructive analysis of single fibers. The micro-CT apparatus was employed because it is applicable to both colored and colorless fibers. A sample preparation using adhesive sheets was demonstrated, and the method is similar to typical tape-lift sample collection method in crime cases.

Exercising the Sanger Sequencing Strategy for Variants Screening and Full-Length Genome of SARS-CoV-2 Virus during Alpha, Delta, and Omicron Outbreaks in Hiroshima.

This study aimed to exercise the Sanger sequencing strategy for screening of variants among confirmed COVID-19 cases and validate our strategy against NGS strains in Hiroshima retrieved from GISAID. A total of 660 samples from confirmed COVID-19 cases underwent screening for variants by Sanger-based partial sequencing to the targeted spike gene (nt22,735~nt23,532) using an in-house-developed primer set. The identification of variants was done by unique checkpoints of base nucleotide changes in the targeted spike gene.

Environmental Factors Affecting the Community of Methane-oxidizing Bacteria.

Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB.

Enhanced Protein Adsorption Capacity of Macroporous Pectin Particles with High Specific Surface Area and an Interconnected Pore Network.

There has been much interest in developing protein adsorbents using nanostructured particles, which can be engineered porous materials with fine control of the surface and pore structures. A significant challenge in designing porous adsorbents is the high percentage of available binding sites in the pores owing to their large surface areas and interconnected pore networks. In this study, continuing the idea of using porous materials derived from natural polymers toward the goal of sustainable development, porous pectin particles are reported.

Biological methane production coupled with sulfur oxidation in a microbial electrosynthesis system without organic substrates.

Methane is produced in a microbial electrosynthesis system (MES) without organic substrates. However, a relatively high applied voltage is required for the bioelectrical reactions. In this study, we demonstrated that electrotrophic methane production at the biocathode was achieved even at a very low voltage of 0.

Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle.

Background: Size of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus, extent to which traits of interest affect accuracy of genomic prediction in Japanese Black cattle remains obscure.

Assessment of the risk posed by three antifouling biocides to Pacific oyster embryos and larvae in Hiroshima Bay, Japan.

The Pacific oyster (Crassostrea gigas) is an important species in oyster farming worldwide, including in Japan. Hiroshima Bay is one of the most important oyster farming areas in Japan. We investigated the occurrence of antifouling biocides used worldwide including diuron, Irgarol 1051 (Irgarol), and 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT), which have been detected at sub-ppb levels in seawater in Japan, and estimated their no observed effect concentrations (NOECs).

First Report of Cluster B2a Species Causing Root Rot in Welsh Onion.

Hiroshima Prefecture has the highest production area of hydroponically grown Welsh onions ( L.) in Japan. Since the cultivation began in 1988, root rot (Fig.

Bioelectrical Methane Production with an Ammonium Oxidative Reaction under the No Organic Substance Condition.

The present study investigated bioelectrical methane production from CO without organic substances. Even though microbial methane production has been reported at relatively high electric voltages, the amount of voltage required and the organisms contributing to the process currently remain unknown. Methane production using a biocathode was investigated in a microbial electrolysis cell coupled with an NH oxidative reaction at an anode coated with platinum powder under a wide range of applied voltages and anaerobic conditions.

Subtype Screening of bla Genes Using Bipartite Primers for DNA Sequencing.

Genes conferring carbapenem resistance have spread worldwide among gram-negative bacteria. Subtyping of these genes has epidemiological value due to the global cross-border movement of people. Subtyping of bla genes that frequently detected in Japan appears to be important in public health settings; however, there are few useful tools for this purpose.