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.     

Entry Inhibition of Influenza Viruses with High Mannose Binding Lectin ESA-2 from the Red Alga Eucheuma serra through the Recognition of Viral Hemagglutinin

Lectin sensitivity of the recent pandemic influenza A virus (H1N1-2009) was screened for 12 lectins with various carbohydrate specificity by a neutral red dye uptake assay with MDCK cells. Among them, a high mannose (HM)-binding anti-HIV lectin, ESA-2 from the red alga Eucheuma serra, showed the highest inhibition against infection with an EC₅₀ of 12.4 nM. Moreover, ESA-2 exhibited a wide range of antiviral spectrum against various influenza strains with EC₅₀s of pico molar to low nanomolar levels. Besides ESA-2, HM-binding plant lectin ConA, fucose-binding lectins such as fungal AOL from Aspergillus oryzae and AAL from Aleuria aurantia were active against H1N1-2009, but the potency of inhibition was of less magnitude compared with ESA-2. Direct interaction between ESA-2 and a viral envelope glycoprotein, hemagglutinin (HA), was demonstrated by ELISA assay. This interaction was effectively suppressed by glycoproteins bearing HM-glycans, indicating that ESA-2 binds to the HA of influenza virus through HM-glycans. Upon treatment with ESA-2, no viral antigens were detected in the host cells, indicating that ESA-2 inhibited the initial steps of virus entry into the cells. ESA-2 would thus be useful as a novel microbicide to prevent penetration of viruses such as HIV and influenza viruses to the host cells.     

Characteristics for Practical Use of Attenuated Isolate UA-Fukushima of <Emphasis Type="Italic">Tomato mosaic virus</Emphasis>

L₁₁A-Fukushima (L₁₁A-F) derived from attenuated isolate LuA of Tomato mosaic virus (ToMV) has the highest ability to cross protect against virulent ToMV among LuA and its derivatives and is stably inherited. Growth, yield, fruit quality and symptom attenuation of inoculated tomato plants did not differ significantly between L₁₁A-F and L₁₁A. The infectivity of progeny viruses in tomato infected with LuA-F was less than 4% of that with virulent ToMV. From these results, L₁₁A-F appears to possess the properties necessary for practical use. To manage L₁₁A-F strictly, a PCR-based assay to detect trace contamination of virulent ToMV in L₁₁A-F preparations was established. Received 10 June 2002/ Accepted in revised form 30 October 2002     

饲喂高亚油酸玉米对奶牛瘤胃发酵、产乳量和乳成分的影响

选用6头经产荷斯坦种乳牛分为对照和HLAC两组,以二乘反转法,研究了高亚油酸玉来(HLAC)对奶牛瘤胃发酵、产乳量和乳成分的影响。HLAC组用HLAC部分替换了对照组饲料中的普通玉米,两组日粮组成和营养成分基本相同。结果表明,HLAC的替换对瘤胃液氨氮浓度、挥发性脂肪酸浓度及其组成无显著影响(P>0.1),但纤毛虫总数显著增加(P>0.05)。两组牛干物采食量和乳量无显著差异,但HLAC组乳脂率有下降趋势(P>0.1)、乳脂肪中C18:2比例小幅提高、C18:1比例显著提高(P<0.05)、乳蛋白质率及其产量小幅增加、乳糖率和无脂固形物率及其产量显著提高(P<0.05)。以上结果显示:奶牛饲料中HLAC的使用可改善乳成分,并对瘤胃发酵产生一定影响。     

In Vitro Suppression of Mycelial Growth of Fusarium oxysporum by Extracellular Chitosanase of Sphingobacterium multivorum and Cloning of the Chitosanase Gene csnSM1

A chitosan-degrading bacterium, isolated from field soil that had been amended with chitin, was identified as Sphingobacterium multivorum KST-009 on the basis of its bacteriological characteristics. The extracellular chitosanase (SM1) secreted by KST-009 was a 34-kDa protein and could be purified through ammonium sulfate precipitation, gel permeation column chromatography and SDS polyacrylamide gel electrophoresis. A chitosanase gene (csnSM1) was isolated from genomic DNA of the bacteria, and the entire nucleotide sequence of the gene and the partial N-terminal amino acid sequence of the purified SM1 were determined. The csnSM1 gene was found to encode 383 amino acids, 72 N-terminal amino acid residues were processed to produce the mature enzyme during the secretion process. Germinated microconidia of four formae speciales (lycopersici, radicis-lycopersici, melonis, and fragariae ) of Fusarium oxysporum were treated with SM1. Chitosanase treatment caused morphological changes, such as swelling of hyphal cells or indistinctness of hyphal cell tips and cessation or reduction of mycelial elongation. Received 2 May 2001/ Accepted in revised form 21 June 2001     

Silicone allergy associated with intraocular silicone ball prosthesis in a dog

A 13-year-old, male Pomeranian dog was presented for scleral rupture with intraocular hemorrhage and retinal detachment in the right eye. After intrascleral silicone ball prosthesis, recurrent swelling and granulomatous blepharitis were observed for 140 d and finally melting keratitis developed. Although an intraorbital prosthesis was implanted, recurrent, serious, erosive, and ulcerative blepharitis developed with high plasma C-reactive protein concentrations. Since the blepharitis could not be controlled, the silicone ball was removed and the affected orbit was debrided. The blepharitis resolved rapidly, and the orbit healed routinely. Positive allergic reactions to silicone were discovered through a patch test.Key clinical message:To the authors’ knowledge, this is the first report on silicone allergy in a dog with positive allergic reactions to silicone in the patch test.     

Estimation of genetic data and breeding values of traits related to wax production in <Emphasis Type="Italic">Rhus succedanea</Emphasis> L. clones using the REML/BLUP method

Rhus succedanea L. is cultivated in Japan for the wax that can be extracted from its fruits. We determined genetic data for specific traits associated with wax production (fruit number per cluster, FN, fruit weight, FW, number of clusters per area, CN, and wax content, WC) in five traditional cultivars and 13 newer clones. Data were collected over 4 years and alternate bearing was observed: 2001 and 2003 were years with high yields; in 2002 and 2004 yields were poor. The restricted maximum likelihood method was used to calculate (co)variance components for analysis. Broad sense heritability was estimated and ranged from low (FN and CN) to high (FW and WC) for the traits examined. There were positive genetic correlations between FW and WC and negative ones between FN and FW throughout the 4 years. Genetic correlations between CN and the other traits were positive in good crop years and negative in bad crop years. For each assessed clone, the four traits in the 4 years were evaluated using best linear unbiased predictors (BLUP) of the clonal breeding values. The BLUP scores for both FW and WC exhibited positive correlations between pairs of years, whereas there were positive BLUP correlations for CN when the high yield and low yield years were examined separately. The traditional cultivars and the newer clones were also characterized. Some of the clones were better than the traditional cultivars with regard to wax yield and reliability of production. The trait characteristics and the future breeding are discussed.