Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus

Genomic imprinting causes parental origin-specific monoallelic gene expression through differential DNA methylation established in the parental germ line. However, the mechanisms underlying how specific sequences are selectively methylated are not fully understood. We have found that the components of the PIWI-interacting RNA (piRNA) pathway are required for de novo methylation of the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus, but not other paternally imprinted loci. A retrotransposon sequence within a noncoding RNA spanning the DMR was targeted by piRNAs generated from a different locus. A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1.     

Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Preparation of Photocrosslinked Fish Elastin Polypeptide/Microfibrillated Cellulose Composite Gels with Elastic Properties for Biomaterial Applications

Photocrosslinked hydrogels reinforced by microfibrillated cellulose (MFC) were prepared from a methacrylate-functionalized fish elastin polypeptide and MFC dispersed in dimethylsulfoxide (DMSO). First, a water-soluble elastin peptide with a molecular weight of ca. 500 g/mol from the fish bulbus arteriosus was polymerized by N,N′-dicyclohexylcarbodiimide (DCC), a condensation reagent, and then modified with 2-isocyanatoethyl methacrylate (MOI) to yield a photocrosslinkable fish elastin polypeptide. The product was dissolved in DMSO and irradiated with UV light in the presence of a radical photoinitiator. We obtained hydrogels successfully by substitution of DMSO with water. The composite gel with MFC was prepared by UV irradiation of the photocrosslinkable elastin polypeptide mixed with dispersed MFC in DMSO, followed by substitution of DMSO with water. The tensile test of the composite gels revealed that the addition of MFC improved the tensile properties, and the shape of the stress–strain curve of the composite gel became more similar to the typical shape of an elastic material with an increase of MFC content. The rheology measurement showed that the elastic modulus of the composite gel increased with an increase of MFC content. The cell proliferation test on the composite gel showed no toxicity.     

Seed quality attributes of food-grade soybeans from the U.S. and Asia

Diversity of food-grade soybeans is critical for utilization of genetic resources in cultivar development, germplasm enhancement, and end-product commercialization. The objective of this study was to assess seed quality attributes and phenotypic variability among 54 U.S. and 51 Asian food-grade cultivars and breeding lines. The results showed greater genetic diversity of protein content, calcium content, seed hardness, and seed size uniformity than other quality traits in both small- and large-seeded genotypes evaluated in this study. Among the small-seeded soybeans, the U.S. genotypes were more diverse and exhibited higher swell ratio and oil content but lower stone seed ratio and protein content than Asian accessions. Among the large-seeded accessions, U.S. genotypes had higher stone seed ratio and oil content but lower swell ratio and protein content, and were less diverse than Asian genotypes. The characterization of diverse food-grade soybeans will facilitate parent selection in specialty soybean breeding.     

Proventricular dilatation disease associated with avian bornavirus infection in a Citron-crested Cockatoo that was born and hand-reared in Japan

A 5-month-old female Citron-crested Cockatoo (Cacatua sulphurea citrinocristata) that was born and hand-reared in Japan died with suspected proventricular dilatation disease (PDD). Macroscopic and microscopic examinations of the bird revealed characteristic features of PDD, i.e., distention of the proventriculus and infiltration of lymphocytes and plasma cells in ganglia of various organs and in central and peripheral nerves. A linkage of this PDD case to infection with avian bornavirus (ABV) was documented by RT-PCR amplification of the virus genomes from the affected bird. Phylogenetic analysis revealed that the ABV identified in this study clustered into the genotype 2, which is one of the dominant ABV genotypes worldwide. To the best of our knowledge, this is the first report of a natural case of PDD associated with ABV infection in Japan.     

Effect of micronutrient application on the growth and occurrence of sterility in barley and rice in a Malaysian deep peat soil

Abstract

Nodule formation in legume crops is a multistep process which involves the interactive gene expression of bacteria and host plants. Attempts to widen the genetic variation of symbiotic bacteria and host plants have led to the isolation of several mutants with a diverse capability of nodulation. The most striking variants in hosts are the supernodulating mutants isolated in pea (Pisum sativum L.) (Jacobsen and Feenstra 1984; Duc and Messager 1989), common bean (Phaseolus vulgaris L.) (Park and Buttery 1988), and soybean (Glycine max (L.) Men.) (Carroll et al. 1985a,b; Gremaud and Harper 1989; Akao and Kouchi 1992), all of which are capable of producing several-fold more nodules than their parental lines in the presence of nitrate. These mutants may be useful materials for analyzing the mechanism controlling nodule formation, and are considered to have a high agronomic potential under certain growing conditions.     

A comparison of physical properties, oxalate-oxalic acid soluble substances, protein content, and in vitro protein digestibility of the blue-green algaNostoc commune Vauch. from the Philippines and Japan

The physical properties, amount of oxalate-oxalic acid soluble substances (OOSS), protein and in vitro protein digestibility ofNostoc commune from the Philippines and Japan were determined. The samples were the spherical type from the Philippines (PS), the dry field discoid type from the Philippines (PD), and the dry field discoid type from Japan (JD). The discoid types, PD and JD, regardless of origin showed higher settling volume in water (SV) and bulk density than PS. The OOSS values obtained for all samples were directly related to SV and bulk density. The WHC level was highest in PS. This desirable characteristic makes PS a technologically potential sample for large-scale food production applications in the future. Protein and in vitro protein digestibility varied significantly among all samples. In general, the algal samples examined posses desirable physical properties which are expected to be related to physiological functions.     

At5g54160 gene encodes <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> 5-hydroxyconiferaldehyde <Emphasis Type="Italic">O</Emphasis>-methyltransferase

The function of an Arabidopsis thaliana gene, At5g54160 annotated as a caffeic acid O-methyltransferase CAOMT gene was characterized. The recombinant enzyme of this gene (AtOMT1) catalyzed the O-methylation of phenylpropanoid and flavonoid substrates. The specificity constants (k _cat/K _m) for 5-hydroxyconiferaldehyde (5-HCAld) and quercetin were both 0.11 μM⁻¹·min⁻¹. On the other hand, lignins of At5g54160-knockout Arabidopsis mutants lacked syringyl units. In addition, we showed that the gene silencing also resulted in significant accumulation of caffeyl alcohol (CaAlc). These results strongly suggested that At5g54160 gene is involved in syringyl lignin synthesis for the methylation of both 5-hydroxyconiferaldehyde and 3,4-dihydroxyphenyl compound(s). Part of this work was presented at the Annual Meeting of Japan Society for Bioscience, Biotechnology, and Agrochemistry, March 24–27, 2007     

Enantiomeric compositions and biosynthesis ofWikstroemia sikokiana lignans

Thymelaeaceae plants produce dextrorotatory dibenzylbutyrolactone lignans, which are opposite enantiomers to the lignans isolated from other plants (e.g.,Forsythia spp.). In our previous paper, (–)-pinoresinol (74% enantiomer excess), (+)-matairesinol (optically pure), and (+)-wikstromol (optically pure) were isolated fromWikstroemia sikokiana (Thymelaeaceae). In the present investigation, a survey of lignans and the determination of their enantiomeric compositions were continued. Four lignans, (–)-lariciresinol, (–)-secoisolariciresinol, (+)-kusunokinin, and (+)-methyltrachelogenin, were isolated from MeOH extracts ofW. sikokiana stem. To our knowledge, we have isolated (+)-methyltrachelogenin from plants for the first time. Chiral high-performance liquid chromatographic analysis showed that (+)-kusunokinin and (+)-methyltrachelogenin were optically pure, whereas (–)-lariciresinol and (–)-secoisolariciresinol were not (39% and 45% enantiomer excess, respectively). Feeding experiments with deuterium-labeled substrates demonstrated conversion of coniferyl alcohol to the lignans and interconversion of lignans. These reaction sequences are similar to the sequence catalyzed byForsythia enzymes. However, predominant enantiomers of the lignans, except for secoisolariciresinol isolated fromW. sikokiana, have absolute configurations opposite to those of the corresponding lignans isolated fromForsythia spp. Based on the results of the isolation and the feeding experiments, several differences betweenW. sikokiana andForsythia spp. are pointed out regarding stereochemical mechanisms for lignan biosynthesis.Parts of this report were presented at the 46th annual meeting of the Japan Wood Research Society, Kumamoto, April 1996; and the 47th annual meeting of the Japan Wood Research Society, Kochi, April 1997