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

Md. Shaheed Reza  Nanami Mizusawa  Ayaka Kumano  Chiharu Oikawa  Daisuke Ouchi  Atsushi Kobiyama  Yuichiro Yamada  Yuri Ikeda  Daisuke Ikeda  Kazuho Ikeo  Shigeru Sato  Takehiko Ogata  Toshiaki Kudo  Mitsuru Jimbo  Ko Yasumoto  Kazutoshi Yoshitake  Shugo Watabe 《Fisheries Science》2018,84(3):563-577

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.  相似文献   

Development of a quantitative polymerase chain reaction assay for the detection of skin fluke <Emphasis Type="Italic">Neobenedenia girellae</Emphasis> larvae from environmental water     

Yasuo Agawa  Kazuki Tani  Syuhei Yamamoto  Chihaya Hirano  Sho Shirakashi 《Fisheries Science》2016,82(5):827-833

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Characterization of genes for novel thaumatin-like proteins in Cryptomeria japonica     

Futamura N  Tani N  Tsumura Y  Nakajima N  Sakaguchi M  Shinohara K 《Tree physiology》2006,26(1):51-62

Thaumatin-like proteins (TLPs) are induced by a variety of phytopathogens in many plants and several TLPs are allergenic. Previously, we isolated three TLP-encoding cDNAs (Cry j 3.1, Cry j 3.2 and Cry j 3.3) from a cDNA library derived from the pollen of Cryptomeria japonica D. Don. Here, we describe three new TLP cDNAs (Cry j 3.4, Cry j 3.5 and Cry j 3.6). We compared the sequences, the genetic map location and the expression patterns of the Cry j 3 genes. The amino acid sequence predicted from Cry j 3.5 exhibits only limited similarity to those predicted from the other Cry j 3 genes. Linkage analysis showed that the Cry j 3.1 to Cry j 3.4 genes are located in the same linkage group, but Cry j 3.5 is located in a different group. Organ-specificity and induction by stresses and plant hormones differed among the Cry j 3 mRNAs. In pollen grains, the Cry j 3.5 mRNA expression level was higher than that of the other Cry j 3 genes. Exposure to UV-B and salt stress induced expression of Cry j 3.1. The ethylene-releasing compound ethephon strongly induced expression of Cry j 3.4. Salt stress and salicylic acid also induced expression of Cry j 3.4. Abscisic acid weakly induced expression of Cry j 3.5. Arachidonic acid strongly induced expression of Cry j 3.4 and Cry j 3.6, and weakly induced that of Cry j 3.3, whereas expression of Cry j 3.1 and Cry j 3.5 was unaffected. These results suggest that the roles of TLPs and the cascades that regulate their expression differ among the members of the TLP family in C. japonica.  相似文献   

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan     

Naoki Tani  Hiroshi Yoshimaru  Takayuki Kawahara  Yoshio Hoshi  Fuyuo Nobushima  Takaya Yasui 《BMC ecology》2006,6(1):14-13

Background  

Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards.  相似文献   

Sooty spot of kiwifruit caused by Pseudocercospora actinidiae Deighton     

Kenji Kikuhara  Chiharu Nakashima 《Journal of General Plant Pathology》2008,74(2):185-187

Leaf spots on the lower leaf surface and sunken spots on the fruit of kiwifruit (Actinidia deliciosa and A. chinensis) were found in Fukuoka Prefecture, Japan. The observed fungus was identified as Pseudocercospora actinidiae Deighton. We propose the name sooty spot of kiwifruit (“susuhan-byo” in Japanese) as a new disease fullfilling Koch’s postulates.  相似文献   

Species Composition,Diversity and Productivity of Homesteads in Southeastern Bangladesh     

Md. Abiar Rahman  Masakazu Tani  Kazuo Asahiro  S. M. Asik Ullah 《Small-Scale Forestry》2017,16(3):295-309

A homestead is an integrated production system where trees, crops, livestock and poultry are found in and around the household residence in Bangladesh. It is a potential production unit that provides various product, service and ecological functions. Almost all people in Bangladesh including landless households have homesteads in which they grow trees and crops even in a small piece of land. This study characterizes the species composition, diversity and productivity of the homestead production system in the Teknaf peninsula, southeastern Bangladesh. Survey data collection was from a total of 180 homesteads covering five household categories: large, medium, small, marginal and landless. Vegetable, fruit, timber, and livestock and poultry were common components in the homestead production system. Various types of plants were mainly concentrated in back yards, front yards, boundaries and corners of homesteads. The mean number of tree species per homestead was about 15. In total, 189 tree and shrub species were recorded, and were distinctly high and low in the large (363.7) and landless (55.7) household categories. Species composition, diversity and productivity of homesteads were found to be related to household categories. Richness and diversity of tree and shrub species increased with household size. Betel nut was the dominant tree species followed by mango, jackfruit and coconut. Annual income from homesteads also varied among the household categories, with a mean contribution of the homestead to annual income of about 25 %. A large portion of homestead income came from betel nut trees. There is scope to increase species diversity and income by designing homesteads with the engagement of women and other family members.  相似文献   

Survey and molecular characterization of Cryptosporidium and Giardia spp. in owned companion animal, dogs and cats, in Japan     

Yoshiuchi R  Matsubayashi M  Kimata I  Furuya M  Tani H  Sasai K 《Veterinary parasitology》2010,174(3-4):313-316

Compared with other countries, surveys of these parasites have been rarely performed in companion animals of Japan in spite of their significance for public health. Here, we investigated pet dogs and cats in Japan for the first time, and genetically analyzed the isolates to evaluate the risk of zoonotic infections. Seventy-seven fecal samples were collected from privately owned dogs and 55 samples from owned cats in Osaka city, Japan. Cryptosporidium oocysts were identified in 3/77 dogs (3.9%) and 7/55 cats (12.7%), and Giardia infection in 2/77 dogs (2.6%) and 1/55 cats (1.8%). Amplification of the target regions for genotyping was successful, Cryptosporidium isolates in dogs and cats were identified as C. canis and C. felis, respectively, and those of Giardia in dogs and cats were G. intestinalis Assemblages D and F. The discharge period of the oocysts varied within 3-16 weeks and that of the cysts was 12 weeks. To date, zoonotic types of both parasites have been identified in other animals in Japan, and further large-scale studies are needed to determine the distribution of zoonotic genotypes in these animals, especially those closely associated with humans.  相似文献   

Cytotoxicity of benzyl isothiocyanate in normal renal proximal tubular cells and its modulation by glutathione     

Abe N  Okuhira M  Tsutsui C  Murata Y  Nakamura Y 《Journal of agricultural and food chemistry》2012,60(7):1887-1892

In the present study, we examined the toxicity of benzyl ITC (BITC) and its urinary mercapturic acid metabolite (BITC-NAC), using a normal renal proximal tubular cell line, pig LLC-PK1. BITC increased cell death with an IC(50) value of about 7 μM, whereas the cytotoxic effect of BITC-NAC was five times weaker than that of BITC. We observed a significant necrosis of the compounds on LLC-PK1 cells with oxidative stress. In the presence of 5 mM glutathione (GSH), comparable to physiological levels, the cytotoxicity of BITC-NAC as well as BITC was significantly reduced. Furthermore, the increase in intracellular GSH levels by pretreatment with NAC before the BITC treatment resulted in inhibition of the BITC-induced necrotic events as well as intracellular oxidative stress. These results suggest that GSH is a determinant of cellular resistance against the BITC-mediated and oxidative stress-dependent cytotoxicity in renal proximal tubular cells.  相似文献   

Phylogenetic identification of Cystoisospora spp. from dogs, cats, and raccoon dogs in Japan     

Matsubayashi M  Carreno RA  Tani H  Yoshiuchi R  Kanai T  Kimata I  Uni S  Furuya M  Sasai K 《Veterinary parasitology》2011,176(2-3):270-274

Cystoisospora spp. from feces in dogs, cats, and raccoon dogs were isolated, sequenced at the small subunit ribosomal RNA gene locus and compared to other Cystoisospora spp. Cystoisospora oocysts from dogs and raccoon dogs were morphologically similar with those of C. ohioensis, and cat isolates were similar with those of C. felis. The sequences from dogs and raccoon dogs, and cats have a homology with C. ohioensis and C. felis, respectively. Phylogenetic analysis of the DNA sequences showed that the dog and raccoon dog isolates were nested in a clade with other Cystoisospora spp. including C. ohioensis, C. belli, and C. orlovi. The cat isolate formed a sister group with C. felis that was a separate clade from the dog and raccoon dog group. We report sequence variation in these Cystoisospora sequences and have identified raccoon dogs as another carnivore host for Cystoisospora spp. infecting dogs.  相似文献   

Characterization and expression analysis of FRUITFULL- and SHATTERPROOF-like genes from peach (Prunus persica) and their role in split-pit formation   总被引：1，自引：0，他引：1  

Tani E  Polidoros AN  Tsaftaris AS 《Tree physiology》2007,27(5):649-659

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