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951.
Shin SH Kim S Kim JY Song HY Cho SJ Kim DR Lee KI Lim HK Park NJ Hwang IT Yang KS 《Journal of bacteriology》2012,194(5):1266
This article reports on the full genome sequence of Paenibacillus terrae HPL-003, which is a gram-positive, endospore-forming, xylanase-producing bacterium isolated from soil found in forest residue on Gara Mountain. The strain HPL-003 contains 6,083,395 bp with a G+C content of 46.77 mol%, 2,633 protein-coding genes, and 117 structural RNAs. 相似文献
952.
A novel Gram-positive, aerobic, motile, hemolytic, endospore-forming and rod-shaped bacterium TW25T was isolated from a dead ark clam during a mass mortality event on the South coast of Korea. The strain grew optimally at
30°C, at pH 8–9, and with 1% (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain TW25T was associated with the genus Ornithinibacillus and that it was most closely related to the type strain of Ornithinibacillus californiensis (98.5% similarity). The dominant cellular fatty acids were iso-C15:0, anteiso-C15:0 and C16:0. The peptidoglycan amino acid
type was A4β, containing l-ornithine and d-aspartic acid. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, four unidentified phospholipids, two unidentified
aminolipids and two unidentified lipids. The major respiratory quinone was menaquinone-7 (MK-7). The G + C content of genomic
DNA was 36.7 mol%. DNA–DNA hybridization experiments with related strains revealed lower than 11 ± 3% relatedness. Based on
this polyphasic taxonomic study, strain TW25T represents a novel species in the genus Ornithinibacillus, for which the name Ornithinibacillus scapharcae sp. nov. is proposed. The type strain is TW25T (=KACC 15116T = JCM 17314T). 相似文献
953.
Kim TY Shin SK Song MY Lee JE Park KS 《Biochemical and biophysical research communications》2012,417(3):1030-1034
Transient receptor potential melastatin 7 (TRPM7) channels are divalent cation-selective ion channels that are permeable to Ca(2+) and Mg(2+). TRPM7 is ubiquitously expressed in vertebrate cells and contains both an ion channel and a kinase domain. TRPM7 plays an important role in regulating cellular homeostatic levels of Ca(2+) and Mg(2+) in mammalian cells. Although studies have shown that the kinase domain of TRPM7 is required for channel activation and can phosphorylate other target proteins, a systematic analysis of intact TRPM7 channel phosphorylation sites expressed in mammalian cells is lacking. We applied mass spectrometric proteomic techniques to identify and characterize the key phosphorylation sites in TRPM7 channels. We identified 14 phosphorylation sites in the cytoplasmic domain of TRPM7, eight of which have not been previously reported. The identification of phosphorylation sites using antibody-based immunopurification and mass spectrometry is an effective approach for defining the phosphorylation status of TRPM7 channels. The present results show that TRPM7 channels are phosphorylated at multiple sites, which serves as a mechanism to modulate the dynamic functions of TRPM7 channels in mammalian cells. 相似文献
954.
Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD(T). 相似文献
955.
Satoshi N. Suzuki Masae I. Ishihara Masahiro Nakamura Shin Abe Tsutom Hiura Kosuke Homma Motoki Higa Daisuke Hoshino Kazuhiko Hoshizaki Hideyuki Ida Ken Ishida Motohiro Kawanishi Kazutaka Kobayashi Koichiro Kuraji Shigeo Kuramoto Takashi Masaki Kaoru Niiyama Mahoko Noguchi Haruto Nomiya Satoshi Saito Takeshi Sakai Michinori Sakimoto Hitoshi Sakio Tamotsu Sato Hirofumi Shibano Mitsue Shibata Maki Suzuki Atsushi Takashima Hiroshi Tanaka Masahiro Takagi Naoaki Tashiro Naoko Tokuchi Toshiya Yoshida Yumiko Yoshida 《Ecological Research》2012,27(6):989-990
This data paper reports litter fall data collected in a network of 21 forest sites in Japan. This is the largest litter fall data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Twenty-three permanent plots in which usually 25 litter traps were installed were established in old-growth or secondary natural forests. Litter falls were collected monthly from 2004, and sorted into leaves, branches, reproductive structures and miscellaneous. The data provide seasonal patterns and inter-annual dynamics of litter falls, and their geographical patterns, and offer good opportunities for meta-analyses and comparative studies among forests. 相似文献
956.
Jung-Joon Park Key-Il Shin Joon-Ho Lee Sung Eun Lee Woo-Kyun Lee Kijong Cho 《Ecological Research》2012,27(1):1-13
Outlier detection and cleaning procedures were evaluated to estimate mathematical restricted variogram models with discrete
insect population count data. Because variogram modeling is significantly affected by outliers, methods to detect and clean
outliers from data sets are critical for proper variogram modeling. In this study, we examined spatial data in the form of
discrete measurements of insect counts on a rectangular grid. Two well-known insect pest population data were analyzed; one
data set was the western flower thrips, Frankliniella occidentalis (Pergande) on greenhouse cucumbers and the other was the greenhouse whitefly, Trialeurodes vaporariorum (Westwood) on greenhouse cherry tomatoes. A spatial additive outlier model was constructed to detect outliers in both the
isolated and patchy spatial distributions of outliers, and the outliers were cleaned with the neighboring median cleaner.
To analyze the effect of outliers, we compared the relative nugget effects of data cleaned of outliers and data still containing
outliers after transformation. In addition, the correlation coefficients between the actual and predicted values were compared
using the leave-one-out cross-validation method with data cleaned of outliers and non-cleaned data after unbiased back transformation.
The outlier detection and cleaning procedure improved geostatistical analysis, particularly by reducing the nugget effect,
which greatly impacts the prediction variance of kriging. Consequently, the outlier detection and cleaning procedures used
here improved the results of geostatistical analysis with highly skewed and extremely fluctuating data, such as insect counts. 相似文献
957.
JY Cho JY Kang YK Hong HH Baek HW Shin MS Kim 《Bioscience, biotechnology, and biochemistry》2012,76(6):1116-1121
Marine derived actinomycetes constituting 185 strains were screened for their antifouling activity against the marine seaweed, Ulva pertusa, and fouling diatom, Navicula annexa. Strain 291-11 isolated from the seaweed, Undaria pinnatifida, rhizosphere showed the highest antifouling activity and was identified as Streptomyces praecox based on a 16S rDNA sequence analysis. Strain 291-11 was therefore named S. praecox 291-11. The antifouling compounds from S. praecox 291-11 were isolated, and their structures were analyzed. The chemical constituents representing the antifouling activity were identified as (6S,3S)-6-benzyl-3-methyl-2,5-diketopiperazine (bmDKP) and (6S,3S)-6-isobutyl-3-methyl-2,5-diketopiperazine (imDKP) by interpreting the nuclear magnetic resonance and high-resolution mass spectroscopy data. Approximately 4.8 mg of bmDKP and 3.1 mg of imDKP were isolated from 1.2 g of the S. praecox 291-11 crude extract. Eight different compositions of culture media were investigated for culture, the TBFeC medium being best for bmDKP and TCGC being the optimum for imDKP production. Two compounds respectively showed a 17.7 and 21 therapeutic ratio (LC50/EC50) to inhibit zoospores, and two compounds respectively showed a 263 and 120.2 therapeutic ratio to inhibit diatoms. 相似文献
958.
Inflammation is a system used by a host to defend against the presence of bacteria, viruses, or yeasts. Toll-like receptors (TLRs) in the plasma membranes of macrophages are activated when they recognize the molecular structure of a virus or bacterium. Lipopolysaccharide (LPS), an outer cell-wall component of Gram-negative bacteria, initiates an inflammatory process via TLR4. We investigated the effect of the extract of Anethum graveloens flowers (AGFs) on LPS-mediated inflammation in RAW 264.7 cells. The extract markedly suppressed nitric oxide generation in a concentration-dependent manner in LPS-stimulated RAW 264.7 cells. It inhibited inducible nitric oxide synthase (iNOS) and the mRNA expression of cytokines such as interleukin-1 beta and interleukin-6 in LPS-stimulated RAW 264.7 cells. It also inhibited iNOS protein levels in LPS-stimulated RAW 264.7 cells. In addition, AGF decreased the LPS-induced phosphorylation of mitogen-activated protein kinases in LPS-stimulated RAW 264.7 cells. AGF inhibited the phosphorylation of Akt, an upstream molecule of the nuclear factor kappa B (NF-κB) pathway, and thus inhibited NF-κB activity in LPS-stimulated RAW 264.7 cells. These results suggest that AGF exerts an anti-inflammatory effect in LPS-stimulated RAW 264.7 cells by inhibiting iNOS expression and blocking the NF-κB pathway. 相似文献
959.
The therapeutic benefits of L-arginine (ARG) supplementation in humans, often clearly observed in short-term studies, are not evident after long-term use. The mechanisms for the development of ARG tolerance are not known and cannot be readily examined in humans. We have developed a sensitive in vitro model using a low glucose/low arginine culture medium to study the mechanisms of ARG action and tolerance using two different human endothelial cells, i.e., Ea.hy926 and human umbilical venous endothelial cells. Cultured cells were incubated with different concentrations of ARG and other agents to monitor their effects on endothelial nitric oxide synthase (eNOS) expression and function, as well as glucose and superoxide (O2(·-) ) accumulation. Short-term (2 h) exposure to at least 50 μM ARG moderately increased eNOS activity and intracellular glucose (p < 0.05), with no change in eNOS mRNA or protein expression. In contrast, 7-day continuous ARG exposure suppressed eNOS expression and activity. This was accompanied by increase in glucose and O2(·-) accumulation. Co-incubation with 100 μM ascorbic acid, 300 U/ml polyethylene glycol-superoxide dismutase (PEG-SOD), 100 μM L-lysine or 30 μM 5-chloro-2-(N-2,5-dichlorobenenesulfonamido)-benzoxazole (a fructose-1,6-bisphosphatase inhibitor) prevented the occurrence of cellular ARG tolerance. Short-term co-incubation of ARG with PEG-SOD improved cellular nitrite accumulation without altering cellular ARG uptake. These studies suggest that ARG-induced oxidative stress may be a primary causative factor for the development of cellular ARG tolerance. 相似文献
960.
A new type of alkyne dye, 6-dimethylaminobenzothiazole alkyne (1), was developed for Cu sensing in biological system. Dye (1) offered excellent selective over a panel of ions, only Cu(I) could change the fluorescence of dye (I) by forming copper acetylide between the terminal alkyne and Cu(I). Its potential of detecting Cu in biological system was demonstrated in cell culture. 相似文献