Chinese HJ-1C SAR And Its Wind Mapping Capability

NASA Astrophysics Data System (ADS)

Huang, Weigen; Chen, Fengfeng; Yang, Jingsong; Fu, Bin; Chen, Peng; Zhang, Chan

2010-04-01

Chinese Huan Jing (HJ)-1C synthetic aperture radar (SAR) satellite has been planed to be launched in 2010. HJ-1C satellite will fly in a sun-synchronous polar orbit of 500-km altitude. SAR will be the only sensor on board the satellite. It operates in S band with VV polarization. Its image mode has the incidence angles 25°and 47°at the near and far sides of the swath respectively. There are two selectable SAR modes of operation, which are fine resolution beams and standard beams respectively. The sea surface wind mapping capability of the SAR has been examined using M4S radar imaging model developed by Romeiser. The model is based on Bragg scattering theory in a composite surface model expansion. It accounts for contributions of the full ocean wave spectrum to the radar backscatter from ocean surface. The model reproduces absolute normalized radar cross section (NRCS) values for wide ranges of wind speeds. The model results of HJ-1C SAR have been compared with the model results of Envisat ASAR. It shows that HJ-1C SAR is as good as Envisat ASAR at sea surface wind mapping.

Taxonomy, virulence and epidemiology of black-pigmented Bacteroides species in relation to oral infections.

PubMed

van Steenbergen, T J; van Winkelhoff, A J; van der Velden, U; de Graaff, J

1989-01-01

Black-pigmented Bacteroides species are recognized as suspected pathogens of oral infections. Developments in the taxonomy of this group include description of a new asaccharolytic species, Bacteroides salivosus, and proposal for the reclassification of the asaccharolytic species into a separate genus, Porphyromonas. Studies on the pathogenicity and virulence of black-pigmented Bacteroides species have identified Bacteroides gingivalis as the most virulent species. B. gingivalis and Bacteroides intermedius have been associated with periodontal diseases; Bacteroides endodontalis is isolated specifically from infections in the oral cavity, and other black-pigmented Bacteroides species are recovered from oral mucous sites. DNA restriction endonuclease analysis was adapted for typing of B. gingivalis and B. intermedius.

H.J. Andrews Experimental Forest.

Treesearch

Art McKee; Pamela Druliner

1998-01-01

The H.J. Andrews Experimental Forest is a world renowned center for research and education about the ecology and management of forests and streams. Located about 50 miles (80 km) east of Eugene, Oregon, the Andrews Experimental Forest lies in the Blue River Ranger District of the Willamette National Forest. Established in 1948, the Experimental Forest is administered...

Selective medium for the isolation of Bacteroides gingivalis.

PubMed

Hunt, D E; Jones, J V; Dowell, V R

1986-03-01

Bacteroides gingivalis has been implicated in various forms of periodontal disease and may be responsible for other diseases in humans. The role of B. gingivalis in disease has been difficult to assess, because it is inhibited by most selective media commonly used by clinical laboratories to aid in isolating gram-negative, nonsporeforming anaerobes. We have developed a new medium, Bacteroides gingivalis agar, which contains bacitracin, colistin, and nalidixic acid as selective agents. This medium allowed B. gingivalis to be isolated from oral specimens with little difficulty and also allowed B. gingivalis to be isolated from phenotypically similar Bacteroides species, such as B. asaccharolyticus and B. endodontalis, with which it can easily be confused.

RNA polymerase beta-subunit gene (rpoB) sequence analysis for the identification of Bacteroides spp.

PubMed

Ko, K S; Kuwahara, T; Haehwa, L; Yoon, Y-J; Kim, B-J; Lee, K-H; Ohnishi, Y; Kook, Y-H

2007-01-01

Partial rpoB sequences (317 bp) of 11 species of Bacteroides, two Porphyromonas spp. and two Prevotella spp. were compared to delineate the genetic relationships among Bacteroides and closely related anaerobic species. The high level of inter-species sequence dissimilarities (7.6-20.8%) allowed the various Bacteroides spp. to be distinguished. The position of the Bacteroides distasonis and Bacteriodes merdae cluster in the rpoB tree was different from the position in the 16S rRNA gene tree. Based on rpoB sequence similarity and clustering in the rpoB tree, it was possible to correctly re-identify 80 clinical isolates of Bacteroides. In addition to two subgroups, cfiA-negative (division I) and cfiA-positive (division II), of Bacteroides fragilis isolates, two distinct subgroups were also found among Bacteroides ovatus and Bacteroides thetaiotaomicron isolates. Bacteroides genus-specific rpoB PCR and B. fragilis species-specific rpoB PCR allowed Bacteroides spp. to be differentiated from Porphyromonas and Prevotella spp., and also allowed B. fragilis to be differentiated from other non-fragilisBacteroides spp. included in the present study.

Plasmid analyses in clinical isolates of Bacteroides fragilis and other Bacteroides species.

PubMed Central

Wallace, B L; Bradley, J E; Rogolsky, M

1981-01-01

Plasmid analyses were performed on Bacteroides strains isolated from clinical specimens. Of 32 Bacteroides strains, 8 were found to contain plasmids. Seven of these eight strains were B. fragilis, and the other one was B. distasonis. Three of these eight strains harbored only a 3.0-megadalton plasmid. Two strains had only a 2.0-megadalton plasmid, and one had 2.0-, 3.0-megadalton plasmid. Of the remaining two strains, one had 2.0-, 3.0-, and 5.0-megadalton plasmids, and the other had 3.0- and 5.0-megadalton plasmids. Beta-Lactamase was produced by 93% of the clinical isolates. Seven of the eight plasmid-carrying strains were cadmium resistant, five were zinc resistant, four were mercury resistant, and two expressed a brick-red fluorescence under ultraviolet light. None of these traits could be associated with a plasmid after performing either curing experiments or genetic transfer experiments by cell-to-cell contact. Images PMID:6974737

Cupriavidus taiwanensis bacteroids in Mimosa pudica Indeterminate nodules are not terminally differentiated.

PubMed

Marchetti, Marta; Catrice, Olivier; Batut, Jacques; Masson-Boivin, Catherine

2011-03-01

The beta-rhizobium Cupriavidus taiwanensis forms indeterminate nodules on Mimosa pudica. C. taiwanensis bacteroids resemble free-living bacteria in terms of genomic DNA content, cell size, membrane permeability, and viability, in contrast to bacteroids in indeterminate nodules of the galegoid clade. Bacteroid differentiation is thus unrelated to nodule ontogeny.

Further characterization of Bacteroides endodontalis, an asaccharolytic black-pigmented Bacteroides species from the oral S cavity.

PubMed Central

van Winkelhoff, A J; van Steenbergen, T J; Kippuw, N; De Graaff, J

1985-01-01

In this study, the isolation, characterization, and identification of Bacteroides endodontalis is described. It was found that this asaccharolytic black-pigmented Bacteroides species is associated with infected dental root canals and oral submucous abscesses. B. endodontalis could be differentiated from B. gingivalis by a negative direct hemagglutination test and the absence of trypsin and N-acetyl-beta-glucosamidase. B. endodontalis could be differentiated from B. asaccharolyticus by the absence of alpha-fucosidase, its inability to grow in an atmosphere of 95% N2-5% H2, and a growth requirement for menadione. Immune serum raised against B. endodontalis strain HG 370T agglutinated only B. endodontalis cells. Precautions for the isolation of B. endodontalis are discussed. PMID:3926818

Astrometric Measurements and Proper Motion Analysis for WDS 11582 +0335 HJ 1204

NASA Astrophysics Data System (ADS)

Edwards, Erica; Garcia, Jose; Terronez, Cheyenne; Stuart, Melanie; Calanog, Jae; Boyce, Pat; Boyce, Grady

2018-04-01

We obtained and analyzed CCD images of the double star system WDS 11582 +0335 (HJ 1204) using the iTelescope network and a variety of specialized software. WCS coordinates were attached to each image, and the separation distance (ρ) and mean position angle (θ) were measured at ρ = 7.9" ± 0.03" and θ = 59.3° ± 0.2°. These results were compared to historical data, dating back 200 years and we find that HJ 1204 is currently exhibiting a linearly decreasing ρ and a constant θ. This suggests that HJ 1204 could be a visual double or an edge-on binary. Follow-up spectroscopic observations should resolve the two possibilities.

Cupriavidus taiwanensis Bacteroids in Mimosa pudica Indeterminate Nodules Are Not Terminally Differentiated ▿

PubMed Central

Marchetti, Marta; Catrice, Olivier; Batut, Jacques; Masson-Boivin, Catherine

2011-01-01

The beta-rhizobium Cupriavidus taiwanensis forms indeterminate nodules on Mimosa pudica. C. taiwanensis bacteroids resemble free-living bacteria in terms of genomic DNA content, cell size, membrane permeability, and viability, in contrast to bacteroids in indeterminate nodules of the galegoid clade. Bacteroid differentiation is thus unrelated to nodule ontogeny. PMID:21257807

Evaluation of Fluoretec-M for detection of oral strains of Bacteroides asaccharolyticus and Bacteroides melaninogenicus.

PubMed Central

Mouton, C; Hammond, P; Slots, J; Genco, R J

1980-01-01

Fluoretec-M is a polyvalent conjugate used in direct fluorescent-antibody staining for identification of the Bacteroides asaccharolyticus-Bacteroides melaninogenicus group. The Fluoretec-M reagent detected all oral and nonoral test strains of B. melaninogaenicus subsp. intermedius, all test strains of B. melaninogenicus subsp. melaninogenicus, and the nonoral strains of B. asaccharolyticus. However, the Fluoretec-M polyvalent reagent and the monovalent conjugates which constitute Fluoretec-M did not detect the oral strains B. asaccharolyticus. The use of Fluoretec-M can therefore generate false-negative results in studies of specimens from oral cavity and from nonoral sites in which an infection with B. asacacharolyticus of oral origin may have taken place. It is suggested that antibodies reactive with the oral antigenic type of B. asaccharolyticus be included in the preparative procedure of the Fluoretec-M reagent. PMID:6107305

A study on Nim expression in Bacteroides fragilis

PubMed Central

Leitsch, David; Sóki, József; Kolarich, Daniel; Urbán, Edit; Nagy, Elisabeth

2016-01-01

Summary Members of the genus Bacteroides, mainly Bacteroides fragilis, can cause severe disease in man, especially after intestinal perforation in the course of abdominal surgery. Treatment is based on a small number of antibiotics, including metronidazole which has proved to be highly reliable throughout the last 40 to 50 years. Nevertheless, metronidazole resistance does occur in Bacteroides and has been mainly attributed to Nim proteins, a class of proteins with suggested nitroreductase function. Despite the potentially high importance of Nim proteins for human health, information on the expression of nim genes in Bacteroides fragilis is still lacking. It was the aim of this study to demonstrate expression of nim genes in B. fragilis at the protein level and, further, to correlate the level of Nim levels with the level of metronidazole resistance. By application of two-dimensional gel electrophoresis, Nim proteins could be readily identified in nim-positive strains but their levels were not elevated to a relevant extent after induction of resistance to high doses of metronidazole. Thus, the presented data do not provide evidence for Nim proteins acting as nitroreductases using metronidazole as a substrate because no correlation of Nim levels and level of resistance could be observed. Further, no evidence was found that Nim proteins protect B. fragilis from metronidazole by sequestering activated metronidazole. PMID:24448511

Climatic summaries and documentation for the primary meteorological station, H.J. Andrews Experimental Forest, 1972 To 1984.

Treesearch

Frederick A. Bierlmaler; Arthur McKee

1989-01-01

This report describes the primary meteorological station at the H.J. Andrews Experimental Forest (elev. 426 m, lat. 44°15' N., long. 122°10' W.) in the Willamette National Forest, the automatic digital data logger, sensors, and data-processing procedures used in measuring air temperature, dewpoint temperature, windspeed, precipitation, and solar radiation....

Invertebrates of The H.J. Andrews Experimental Forest, Western Cascades, Oregon: I. An annotated checklist of fleas.

Treesearch

Robert E. Lewis; Chris Maser

1981-01-01

During a trapping survey of small mammals (approximately 3,000 individuals), species of fleas (1,632 specimens) were collected in the H.J. Andrews Experimental Forest, Western Cascades, Oregon. Host mammals were represented by 15 species—6 insectivores and 9 rodents captured from June through September. The collections extend our knowledge of the fauna of Oregon.

First National Survey of Antibiotic Susceptibility of the Bacteroides fragilis Group: Emerging Resistance to Carbapenems in Argentina

PubMed Central

Litterio, Mirta; Legaria, María C.; Castello, Liliana; Predari, Silvia C.; Di Martino, Ana; Rossetti, Adelaida; Rollet, Raquel; Carloni, Graciela; Bianchini, Hebe; Cejas, Daniela; Radice, Marcela; Gutkind, Gabriel

2012-01-01

The antibiotic susceptibility rates of 363 clinical Bacteroides fragilis group isolates collected from 17 centers in Argentina during the period from 2006 to 2009 were as follows: piperacillin-tazobactam, 99%; ampicillin-sulbactam, 92%; cefoxitin, 72%; tigecycline, 100%; moxifloxacin, 91%; and clindamycin, 52%. No metronidazole resistance was detected in these isolates during this time period. Resistance to imipenem, doripenem, and ertapenem was observed in 1.1%, 1.6%, and 2.3% of B. fragilis group strains, respectively. B. fragilis species showed a resistance profile of 1.5% to imipenem, 1.9% to doripenem, and 2.4% to ertapenem. This is the first report of carbapenem resistance in Argentina. The cfiA gene was present in 8 out of 23 isolates, all of them belonging to the B. fragilis species and displaying reduced susceptibility or resistance to carbapenems (MICs ≥ 4 μg/ml). Three out of eight cfiA-positive isolates were fully resistant to carbapenems, while 5 out of 8 isolates showed low-level resistance (MICs, 4 to 8 μg/ml). The inhibition by EDTA was a good predictor of the presence of metallo-β-lactamases in the fully resistant B. fragilis strains, but discrepant results were observed for low-level resistant isolates. B. fragilis was more susceptible to antimicrobial agents than other Bacteroides species. Bacteroides vulgatus species was the most resistant to ampicillin-sulbactam and piperacillin-tazobactam, and B. thetaiotaomicron/ovatus strains showed the highest level of resistance to carbapenems, with an unknown resistance mechanism. B. vulgatus and the uncommon non-Bacteroides fragilis species were the most resistant to moxifloxacin, showing an overall resistance rate of 15.1%. PMID:22232282

The role of black-pigmented Bacteroides in human oral infections.

PubMed

van Winkelhoff, A J; van Steenbergen, T J; de Graaff, J

1988-03-01

Today, 10 black-pigmented Bacteroides (BPB) species are recognized. The majority of these species can be isolated from the oral cavity. BPB species are involved in anaerobic infections of oral and non-oral sites. In the oral cavity, BPB species are associated with gingivitis, periodontitis, endodontal infections and odontogenic abscesses. Cultural studies suggest a specific role of the various BPB species in the different types of infection. Bacteroides gingivalis is closely correlated with destructive periodontitis in adults as well as in juveniles. Bacteroides intermedius seems to be less specific since it is found in gingivitis, periodontitis, endodontal infections and odontogenic abscesses. The recently described Bacteroides endodontalis is closely associated with endodontal infections and odontogenic abscesses of endodontal origin. There are indications that these periodontopathic BPB species are only present in the oral cavity of subjects suffering from periodontal breakdown, being absent on the mucosal surfaces of subjects without periodontal breakdown. BPB species associated with healthy oral conditions are Bacteroides melaninogenicus, Bacteroides denticola and Bacteroides loescheii. There are indications that these BPB species are part of the normal indigenous oral microflora. Many studies in the past have documented the pathogenic potential and virulence of BPB species. This virulence can be explained by the large numbers of virulence factors demonstrated in this group of micro-organisms. Among others, the proteolytic activity seems to be one of the most important features. Several artificial substrates as well as numerous biological proteins are degraded. These include anti-inflammatory proteins such as alpha-2-macroglobulin, alpha-1-antitrypsin, C3 and C5 complement factors and immunoglobulins. B. gingivalis is by far the most proteolytic species, followed by B. endodontalis. Like other bacteria, the lipopolysaccharide of B. gingivalis has shown to be

Research publications of the H.J. Andrews Experimental Forest, Cascade Range, Oregon: 1998 supplement.

Treesearch

Donald L. Henshaw; Sarah E. Greene; Tami Lowry

1998-01-01

This bibliography updates the list of publications, abstracts, theses, and unpublished reports included in "Research Publications of the H.J. Andrews Experimental Forest, Cascade Range, Oregon, 1948 to 1986" (General Technical Report PNW-GTR-201) and "Research Publications of the H.J. Andrews Experimental Forest, Cascade Range, Oregon: 1988 Supplement...

Activity of semisynthetic penicillins and synergism with mecillinam against Bacteroides species.

PubMed Central

Trestman, I; Kaye, D; Levison, M E

1979-01-01

The minimal inhibitory concentrations (MIC) of six penicillins (ampicillin, carbenicillin, ticarcillin, piperacillin, mezlocillin, and Bay k 4999) against 29 clinical isolates of Bacteriodes spp. (including Bacteroides fragilis, Bacteroides thetaiotaomicron, and Bacteroides vulgatus) were determined by an agar dilution method. Bay k 4999 was most active, followed in descending order by ampicillin, piperacillin, mezlocillin, ticarcillin, and carbenicillin. Mecillinam, a 6 beta-amidino-penicillanic acid, inhibited no strains at 50 micrograms/ml, but when compared with ampicillin, a fourfold or greater increase in MIC for ampicillin (antagonism) was noted in 3 of 29 strains, with no effect on MIC for 26 strains, whereas when combined with carbenicillin, a fourfold or greater decrease in MIC for both antibiotics (synergism) was noted in 12 strains, 4 of which had an MIC of greater than or equal to 250 micrograms/ml for carbenicillin alone. These studies demonstrate the increased activity of some newer semisynthetic penicillins and the potential synergy obtained with mecillinam and carbenicillin against Bacteroides sp. PMID:228593

Use of synthetic oligonucleotide DNA probes for the identification of Bacteroides gingivalis.

PubMed Central

Moncla, B J; Braham, P; Dix, K; Watanabe, S; Schwartz, D

1990-01-01

Six different oligonucleotide probes complementary to the hypervariable regions of 16S rRNA of Bacteroides gingivalis were tested for specificity and sensitivity against 77 field strains of B. gingivalis and 105 strains of 12 other Bacteroides species. The data demonstrated that these probes were very specific (range, 0.85 to 1.00) and sensitive (1.00). Some limited cross-reactions with other Bacteroides species were observed. Four of these probes should be useful for rapid detection and identification of B. gingivalis. Images PMID:1690217

Mode of Birth Influences Preterm Infant Intestinal Colonization with Bacteroides Over the Early Neonatal Period

PubMed Central

Gregory, Katherine E.; LaPlante, Rose D.; Shan, Gururaj; Kumar, Deepak Vijaya; Gregas, Matt

2015-01-01

Background Intestinal colonization during infancy is important to short and long term health outcomes. Bacteroides, an early member of the intestinal microbiome, are necessary for breaking down complex molecules within the intestine and function to assist the body’s immune system in fighting against potentially harmful pathogens. Little is known about the colonization pattern of Bacteroides in preterm infants during the early neonatal period. Purpose This study measured Bacteroides colonization during the early neonatal period in a population of preterm infants based on clinical factors including mode of birth, antibiotics, and nutrition. Methods Bacterial DNA was isolated from 144 fecal samples from 29 preterm infants and analyzed using quantitative real time polymerase chain reaction (PCR). Analyses included liner mixed models to determine which clinical factors affect Bacteroides colonization of the infant gut. Results We found that infants born via vaginal canal had a higher rate of increase in Bacteroides than infants born via Cesarean section (p<.001). We did not find significant associations between antibiotic administration and differences in nutritional exposures with Bacteroides colonization. Implications for Practice These findings highlight the significant influence of mode of birth on Bacteroides colonization. While mode of birth is not always modifiable, these study findings may help develop interventions for preterm infants born via Cesarean section aimed at overcoming delayed Bacteroides colonization. Implications for Research Greater study of the intestinal microbiome and the clinical factors relevant to the preterm infant is needed so that interventions may be developed and tested, resulting in optimal microbial and immune health. PMID:26551793

[Feasibility of prismatic correction of microesotropia using the measuring and correcting methodology by H.-J. Haase].

PubMed

Kromeier, M; Kommerell, G

2006-01-01

The "Measuring and Correcting Methodology after H.-J. Haase" is based on the assumption that a minute deviation from the orthovergence position (fixation disparity) indicates a difficulty to overcome a larger "vergence angle of rest". Objective recordings have, however, revealed that the subjective tests applied in the "Measuring and Correcting Methodology after H.-J. Haase" can mislead to the assumption of a fixation disparity, although both eyes are aligned exactly to the fixation point. How do patients with an inconspicuously small, yet objectively verified strabismus react to the "Measuring and Correcting Methodology by H.-J. Haase"? Eight patients with a microesotropia between 0.5 and 3 degrees were subjected to the "Measuring and Correcting Methodology after H.-J. Haase. In all 8 patients, the prisms determined with the Cross-, Pointer- and Rectangle Tests increased the angle of squint, without reaching a full correction: the original angle prevailed. In the Stereobalance Test, prisms did not reduce the 100 % preponderance of the non-squinting eye. The stereoscopic threshold was between 36 and 1170 arcsec in 7 out of the 8 subjects, and above 4000 arcsec in 1 subject. (1) In all 8 patients, prisms determined with the "Measuring and Correcting Methodology by H.-J. Haase" increased the angle of strabismus, without reaching bifoveal vision. This uniform result suggests that primary microesotropia cannot be corrected with the "Measuring and Correcting Methodology after H.-J. Haase" (2) A lacking contribution of the strabismic eye to the recognition of a lateral offset between stereo objects, as determined with the Stereobalance Test, does not imply a lack of binocular stereopsis.

Bacillus subtilis HJ18-4 from traditional fermented soybean food inhibits Bacillus cereus growth and toxin-related genes.

PubMed

Eom, Jeong Seon; Lee, Sun Young; Choi, Hye Sun

2014-11-01

Bacillus subtilis HJ18-4 isolated from buckwheat sokseongjang, a traditional Korean fermented soybean food, exhibits broad-spectrum antimicrobial activity against foodborne pathogens, including Bacillus cereus. In this study, we investigated the antibacterial efficacy and regulation of toxin gene expression in B. cereus by B. subtilis HJ18-4. Expression of B. cereus toxin-related genes (groEL, nheA, nheC, and entFM) was downregulated by B. subtilis HJ18-4, which also exhibited strong antibacterial activity against B. cereus. We also found that water extracts of soy product fermented with B. subtilis HJ18-4 significantly inhibited the growth of B. cereus and toxin expression. These results indicate that B. subtilis HJ18-4 could be used as an antimicrobial agent to control B. cereus in the fermented soybean food industry. Our findings also provide an opportunity to develop an efficient biological control agent against B. cereus. © 2014 The Authors. Journal of Food Science published by Wiley Periodicals, Inc. on behalf of Institute of Food Technologists®

Evidence for free-living Bacteroides in Cladophora along the shores of the Great Lakes

USGS Publications Warehouse

Whitman, Richard L.; Byappanahalli, Muruleedhara; Spoljaric, Ashley; Przybyla-Kelly, Katarzyna; Shively, Dawn A.; Nevers, Meredith

2014-01-01

Bacteroides is assumed to be restricted to the alimentary canal of animals and humans and is considered to be non-viable in ambient environments. We hypothesized that Bacteroides could persist and replicate within beach-stranded Cladophora glomerata mats in southern Lake Michigan, USA. Mean Bacteroides concentration (per GenBac3 Taqman quantitative PCR assay) during summer 2012 at Jeorse Park Beach was 5.2 log calibrator cell equivalents (CCE) g-1 dry weight (dw), ranging from 3.7 to 6.7. We monitored a single beach-stranded mat for 3 wk; bacterial concentrations increased by 1.6 log CCE g-1 dw and correlated significantly with ambient temperature (p = 0.003). Clonal growth was evident, as observed by >99% nucleotide sequence similarity among clones. In in vitro studies, Bacteroides concentrations increased by 5.5 log CCE g-1 after 7 d (27°C) in fresh Cladophora collected from rocks. Partial sequencing of the 16S rRNA gene of 36 clones from the incubation experiment showed highly similar genotypes (≥97% sequence overlap). The closest enteric Bacteroides spp. from the National Center for Biotechnology Information database were only 87 to 91% similar. Genomic similarity, clonality, growth, and persistence collectively suggest that putative, free-living Bacteroides inhabit Cladophora mats of southern Lake Michigan. These findings may have important biological, medical, regulatory, microbial source tracking, and public health implications.

Fine Structure of Bacteroids in Root Nodules of Vigna sinensis, Acacia longifolia, Viminaria juncea, and Lupinus angustifolius

PubMed Central

Dart, P. J.; Mercer, F. V.

1966-01-01

Dart, P. J. (University of Sydney, Sydney, Australia), and F. V. Mercer. Fine structure of bacteroids in root nodules of Vigna sinensis, Acacia longifolia, Viminaria juncea, and Lupinus angustifolius. J. Bacteriol. 91:1314–1319.—In nodules of Vigna sinensis, Acacia longifolia, and Viminaria juncea, membrane envelopes enclose groups of bacteroids. The bacteroids often contain inclusion granules and electron-dense bodies, expand little during development, and retain their rod form with a compact, central nucleoid area. The membrane envelope may persist around bacteroids after host cytoplasm breakdown. In nodules of Lupinus angustifolius, the membrane envelopes enclose only one or two bacteroids, which expand noticeably during development and change from their initial rod structure. Images PMID:5929757

Improving HJ-1B IRS land surface temperature product using ASTER global emissivity database

NASA Astrophysics Data System (ADS)

Li, H.; Hu, T.; Meng, X.; Yongming, D.; Cao, B.; Liu, Q.

2015-12-01

Land surface temperature (LST) is a key parameter for hydrological, meteorological, climatological and environmental studies. Currently many operational LST products have been generated using European and American satellite data, i.e., the Advanced Very High Resolution Radiometer (AVHRR), Advanced Along-Track Scanning Radiometer (AATSR) and Moderate Resolution Imaging Spectroradiometer (MODIS). However, few LST product has been produced using Chinese satellite data. Thus, the objective of this study is to generate reliable LST product using Chinese HJ-1B satellite data. The HJ-1B satellite of China, were launched on September 6, 2008, which are used for disaster and environment monitoring. IRS (Infrared Scanner) is one of the key instruments onboard HJ-1B satellite, it can scan the earth every four days, has four spectral bands ranging from the near-infrared to thermal infrared bands (band 1 0.75 - 1.10μm, band 2 1.55-1.75μm, MIR band 3 3.50 - 3.90μm, band 4 10.5-12.5μm) with 720 km swath. It scans ±29° from nadir and the spatial resolution for band1-3 is 150m and 300m for band4. In this study, a single-channel parametric model (SC-PM) algorithm were used to produce 300m LST product from HJ-1B IRS data. The NCEP atmospheric profiles and a parametric model were used for atmospheric correction. In order to improve the accuracy of the land surface emissivity (LSE), the 1km ASTER Global Emissivity Database (GED) and self-developed 5-day 1km vegetation cover product were used for estimating the LSE based on the Vegetation Cover Method. Two years of HJ-1B IRS LST product in Heihe River basin (Gansu province, China) from June 2012 to June 2014 were generated. The LST products were evaluated against ground observations in an arid area of northwest China during the Heihe Watershed Allied Telemetry Experimental Research (HiWATER) experiment. Four barren surface sites and ten vegetated sites were chosen for the evaluation. The results show that the developed HJ-1B IRS

Ultrafast exciton migration in an HJ-aggregate: Potential surfaces and quantum dynamics

NASA Astrophysics Data System (ADS)

Binder, Robert; Polkehn, Matthias; Ma, Tianji; Burghardt, Irene

2017-01-01

Quantum dynamical and electronic structure calculations are combined to investigate the mechanism of exciton migration in an oligothiophene HJ aggregate, i.e., a combination of oligomer chains (J-type aggregates) and stacked aggregates of such chains (H-type aggregates). To this end, a Frenkel exciton model is parametrized by a recently introduced procedure [Binder et al., J. Chem. Phys. 141, 014101 (2014)] which uses oligomer excited-state calculations to perform an exact, point-wise mapping of coupled potential energy surfaces to an effective Frenkel model. Based upon this parametrization, the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method is employed to investigate ultrafast dynamics of exciton transfer in a small, asymmetric HJ aggregate model composed of 30 sites and 30 active modes. For a partially delocalized initial condition, it is shown that a torsional defect confines the trapped initial exciton, and planarization induces an ultrafast resonant transition between an HJ-aggregated segment and a covalently bound "dangling chain" end. This model is a minimal realization of experimentally investigated mixed systems exhibiting ultrafast exciton transfer between aggregated, highly planarized chains and neighboring disordered segments.

Transcriptomic dissection of Bradyrhizobium sp. strain ORS285 in symbiosis with Aeschynomene spp. inducing different bacteroid morphotypes with contrasted symbiotic efficiency.

PubMed

Lamouche, Florian; Gully, Djamel; Chaumeret, Anaïs; Nouwen, Nico; Verly, Camille; Pierre, Olivier; Sciallano, Coline; Fardoux, Joël; Jeudy, Christian; Szücs, Attila; Mondy, Samuel; Salon, Christophe; Nagy, István; Kereszt, Attila; Dessaux, Yves; Giraud, Eric; Mergaert, Peter; Alunni, Benoit

2018-06-19

To circumvent the paucity of nitrogen sources in the soil legume plants establish a symbiotic interaction with nitrogen-fixing soil bacteria called rhizobia. During symbiosis, the plants form root organs called nodules, where bacteria are housed intracellularly and become active nitrogen fixers known as bacteroids. Depending on their host plant, bacteroids can adopt different morphotypes, being either unmodified (U), elongated (E) or spherical (S). E- and S-type bacteroids undergo a terminal differentiation leading to irreversible morphological changes and DNA endoreduplication. Previous studies suggest that differentiated bacteroids display an increased symbiotic efficiency (E>U and S>U). In this study, we used a combination of Aeschynomene species inducing E- or S-type bacteroids in symbiosis with Bradyrhizobium sp. ORS285 to show that S-type bacteroids present a better symbiotic efficiency than E-type bacteroids. We performed a transcriptomic analysis on E- and S-type bacteroids formed by Aeschynomene afraspera and Aeschynomene indica nodules and identified the bacterial functions activated in bacteroids and specific to each bacteroid type. Extending the expression analysis in E- and S-type bacteroids in other Aeschynomene species by qRT-PCR on selected genes from the transcriptome analysis narrowed down the set of bacteroid morphotype-specific genes. Functional analysis of a selected subset of 31 bacteroid-induced or morphotype-specific genes revealed no symbiotic phenotypes in the mutants. This highlights the robustness of the symbiotic program but could also indicate that the bacterial response to the plant environment is partially anticipatory or even maladaptive. Our analysis confirms the correlation between differentiation and efficiency of the bacteroids and provides a framework for the identification of bacterial functions that affect the efficiency of bacteroids. This article is protected by copyright. All rights reserved. © 2018 Society for Applied

Relative adherence of Bacteroides species and strains to Actinomyces viscosus on saliva-coated hydroxyapatite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, J.; Ellen, R.P.

1989-09-01

The study was designed to compare the adherence of several Bacteroides species to A. viscosus. Using 3H, we labeled 24 laboratory strains, including 13 Bacteroides species and 11 fresh clinical isolates of three Bacteroides species. Their adherence to A. viscosus bound to a saliva-coated mineral surface was quantified by liquid scintillation. Adherence relative to a standard strain, B. gingivalis 2561, was compared. Among the lab bacteroides, those of B. gingivalis (eight strains) were the greatest binders (mean, 80.5 {plus minus} 12.4%). Strains of other lab bacteroides bound less well (mean, 33.4 {plus minus} 6.3%). The difference in means was statisticallymore » significant (p less than 0.01). The mean for B. gingivalis strains was also significantly greater than that for strains of B. intermedius (51.7 {plus minus} 6.2%). Attachment of B. gingivalis was saturable in experiments in which either input concentration or time was the independent variable, indicating that B. gingivalis cells do not accumulate in this vitro simulation of plaque formation by binding to each other. Subculture did not seem to affect the degree of binding.« less

Lincomycins in the Treatment of Bacteroides Infections

PubMed Central

Tracy, Oonagh; Gordon, A. M.; Moran, F.; Love, W. C.; McKenzie, Peter

1972-01-01

Lincomycin, or the closely related derivative clindamycin, was used to treat six patients with bacteroides infection. In five of the six there was a rapid clinical response to the treatment. Lincomycin and clindamycin seem to be the antibiotics of choice for such infections. PMID:5008478

Radioactive quality evaluation and cross validation of data from the HJ-1A/B satellites' CCD sensors.

PubMed

Zhang, Xin; Zhao, Xiang; Liu, Guodong; Kang, Qian; Wu, Donghai

2013-07-05

Data from multiple sensors are frequently used in Earth science to gain a more complete understanding of spatial information changes. Higher quality and mutual consistency are prerequisites when multiple sensors are jointly used. The HJ-1A/B satellites successfully launched on 6 September 2008. There are four charge-coupled device (CCD) sensors with uniform spatial resolutions and spectral range onboard the HJ-A/B satellites. Whether these data are keeping consistency is a major issue before they are used. This research aims to evaluate the data consistency and radioactive quality from the four CCDs. First, images of urban, desert, lake and ocean are chosen as the objects of evaluation. Second, objective evaluation variables, such as mean, variance and angular second moment, are used to identify image performance. Finally, a cross validation method are used to ensure the correlation of the data from the four HJ-1A/B CCDs and that which is gathered from the moderate resolution imaging spectro-radiometer (MODIS). The results show that the image quality of HJ-1A/B CCDs is stable, and the digital number distribution of CCD data is relatively low. In cross validation with MODIS, the root mean square errors of bands 1, 2 and 3 range from 0.055 to 0.065, and for band 4 it is 0.101. The data from HJ-1A/B CCD have better consistency.

Identification of feces by detection of Bacteroides genes.

PubMed

Nakanishi, Hiroaki; Shojo, Hideki; Ohmori, Takeshi; Hara, Masaaki; Takada, Aya; Adachi, Noboru; Saito, Kazuyuki

2013-01-01

In forensic science, the identification of feces is very important in a variety of crime investigations. However, no sensitive and simple fecal identification method using molecular biological techniques has been reported. Here, we focused on the fecal bacteria, Bacteroides uniformis, Bacteroides vulgatus and Bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, urine, vaginal fluids and skin surfaces) and forensic (anal adhesions) specimens. Bacterial gene detection was performed by real-time PCR using a minor groove binding probe to amplify the RNA polymerase β-subunit gene of B. uniformis and B. vulgatus, and the α-1-6 mannanase gene of B. thetaiotaomicron. At least one of these bacteria was detected in the feces of 20 donors; the proportions of B. uniformis, B. vulgatus and B. thetaiotaomicron were 95, 85 and 60%, respectively. Bacteroides vulgatus was also detected in one of six vaginal fluid samples, but B. thetaiotaomicron and B. uniformis were not detected in body samples other than feces. Further, we applied this method to forensic specimens from 18 donors. Eighteen anal adhesions also contained at least one of three bacteria; B. uniformis, B. vulgatus and B. thetaiotaomicron were detected in 89, 78 and 56%, respectively, of the specimens. Thus, these bacteria were present at a high frequency in the fecal and forensic specimens, while either B. uniformis or B. vulgatus was detected in all samples. Therefore, B. uniformis and B. vulgatus represent more appropriate target species than B. thetaiotaomicron for the identification of fecal material. If B. vulgatus and/or B. uniformis are detected, it is likely that the sample contains feces. Taken together, our results suggest that the use of molecular biological techniques will aid the detection of feces in forensic practice, although it is possible that the samples contained

Comparative analysis of data quality and applications in vegetation of HJ-1A CCD images

NASA Astrophysics Data System (ADS)

Wei, Hongwei; Tian, Qingjiu; Huang, Yan; Wang, Yan

2014-05-01

To study the data quality and to find the differences in vegetation monitoring applications, the same region at Chuzhou Lai 'an, the data of HJ-1A CCD1 on the April 1st, 2012 and the data of HJ-1A CCD2 on the March 31, 2012 have being comparative analysis by the method of objective quality (image)assessment which selecting over five spectral image evaluation parameters: radiation precision (mean, variance, inclination, steepness), information entropy, signal-to-noise ratio, sharpness, contrast, and normalized differential vegetation index. The results show that there is little differences between the HJ-1A CCD1 and CCD2 by objective evaluation of data quality except radiation precision conform to their design theory, so the conclusion is that the difference of them without considering on the usual unless continuation;and Combination of field observation data Lai'an spectral data and GPS data (each point),selecting the normalized difference vegetation index as CCD1, CCD2 in vegetation monitoring application on the evaluation of the differences, and the specific process is based on GPS data is divided into nine small plots of spectral data ,and image data of nine one-to-one correspondence plots, and their normalized difference vegetation index values were calculated ,and measured spectra data resampling HJ-1A CCD1, CCD2 spectral response function calculated NDVI, and the results show that there is little differences between the HJ-1A CCD1 and CCD2 by objective evaluation of data quality, and, the differences of wheat `s reflection and normalized vegetation index is mainly due to calibration coefficients of CCD1 and CCD2, the differences of the solar elevation angle when obtaining the image and atmospheric conditions, so it has to consider the performance indicators as well as access conditions of CCD1 and CCD2, and to be take the normalization techniques for processing for the comparison analysis in the use of HJ-1A CCD Data to surface dynamic changes; Finally, in

Putative Porin of Bradyrhizobium sp. (Lupinus) Bacteroids Induced by Glyphosate▿

PubMed Central

de María, Nuria; Guevara, Ángeles; Serra, M. Teresa; García-Luque, Isabel; González-Sama, Alfonso; de Lacoba, Mario García; de Felipe, M. Rosario; Fernández-Pascual, Mercedes

2007-01-01

Application of glyphosate (N-[phosphonomethyl] glycine) to Bradyrhizobium sp. (Lupinus)-nodulated lupin plants caused modifications in the protein pattern of bacteroids. The most significant change was the presence of a 44-kDa polypeptide in bacteroids from plants treated with the higher doses of glyphosate employed (5 and 10 mM). The polypeptide has been characterized by the amino acid sequencing of its N terminus and the isolation and nucleic acid sequencing of its encoding gene. It is putatively encoded by a single gene, and the protein has been identified as a putative porin. Protein modeling revealed the existence of several domains sharing similarity to different porins, such as a transmembrane beta-barrel. The protein has been designated BLpp, for Bradyrhizobium sp. (Lupinus) putative porin, and would be the first porin described in Bradyrhizobium sp. (Lupinus). In addition, a putative conserved domain of porins has been identified which consists of 87 amino acids, located in the BLpp sequence 30 amino acids downstream of the N-terminal region. In bacteroids, mRNA of the BLpp gene shows a basal constitutive expression that increases under glyphosate treatment, and the expression of the gene is seemingly regulated at the transcriptional level. By contrast, in free-living bacteria glyphosate treatment leads to an inhibition of BLpp mRNA accumulation, indicating a different effect of glyphosate on BLpp gene expression in bacteroids and free-living bacteria. The possible role of BLpp in a metabolite interchange between Bradyrhizobium and lupin is discussed. PMID:17557843

5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

NASA Technical Reports Server (NTRS)

Van den Eynde, H.; De Baere, R.; Shah, H. N.; Gharbia, S. E.; Fox, G. E.; Michalik, J.; Van de Peer, Y.; De Wachter, R.

1989-01-01

The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

Radioactive Quality Evaluation and Cross Validation of Data from the HJ-1A/B Satellites' CCD Sensors

PubMed Central

Zhang, Xin; Zhao, Xiang; Liu, Guodong; Kang, Qian; Wu, Donghai

2013-01-01

Data from multiple sensors are frequently used in Earth science to gain a more complete understanding of spatial information changes. Higher quality and mutual consistency are prerequisites when multiple sensors are jointly used. The HJ-1A/B satellites successfully launched on 6 September 2008. There are four charge-coupled device (CCD) sensors with uniform spatial resolutions and spectral range onboard the HJ-A/B satellites. Whether these data are keeping consistency is a major issue before they are used. This research aims to evaluate the data consistency and radioactive quality from the four CCDs. First, images of urban, desert, lake and ocean are chosen as the objects of evaluation. Second, objective evaluation variables, such as mean, variance and angular second moment, are used to identify image performance. Finally, a cross validation method are used to ensure the correlation of the data from the four HJ-1A/B CCDs and that which is gathered from the moderate resolution imaging spectro-radiometer (MODIS). The results show that the image quality of HJ-1A/B CCDs is stable, and the digital number distribution of CCD data is relatively low. In cross validation with MODIS, the root mean square errors of bands 1, 2 and 3 range from 0.055 to 0.065, and for band 4 it is 0.101. The data from HJ-1A/B CCD have better consistency. PMID:23881127

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk

PubMed Central

Lange, Anna; Beier, Sina; Steimle, Alex; Autenrieth, Ingo B.; Huson, Daniel H.; Frick, Julia-Stefanie

2016-01-01

Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota. PMID:27071651

Associated phoria and the measuring and correcting methodology after H.-J. Haase (MKH).

PubMed

Brautaset, R L; Jennings, J A

2001-09-01

The test charts included in the Polatest, designed by H.-J. Haase and manufactured by Zeiss, are used in Germany, Switzerland and Scandinavia for prism correction of 'associated phoria.' From clinical experience with the Polatest Haase developed a motor and sensory theory of the different stages of decompensation of 'associated phoria ' and a strategy for its prismatic correction - the MKH (Measuring and Correcting Methodology after H.-J. Haase). The theory challenges many accepted ideas about the plasticity of the visual system and the use of prisms in the treatment of sensory abnormalities. This article, the first full description in English, describes and critically discusses the MKH.

Complete Genome Sequence of Bacteroides ovatus V975

PubMed Central

Goesmann, Alexander; Carding, Simon R.

2016-01-01

The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of a single circular chromosome of 6,475,296 bp containing five rRNA operons, 68 tRNA genes, and 4,959 coding genes. PMID:27908995

Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon.

PubMed Central

Salyers, A A; Vercellotti, J R; West, S E; Wilkins, T D

1977-01-01

Ten Bacteroides species found in the human colon were surveyed for their ability to ferment mucins and plant polysaccharides ("dietary fiber"). A number of strains fermented mucopolysaccharides (heparin, hyaluronate, and chondroitin sulfate) and ovomucoid. Only 3 of the 188 strains tested fermented beef submaxillary mucin, and none fermented porcine gastric mucin. Many of the Bacteroides strains tested were also able to ferment a variety of plant polysaccharides, including amylose, dextran, pectin, gum tragacanth, gum guar, larch arabinogalactan, alginate, and laminarin. Some plant polysaccharides such as gum arabic, gum karaya, gum ghatti and fucoidan, were not utilized by any of the strains tested. The ability to utilize mucins and plant polysaccharides varied considerably among the Bacteroides species tested. PMID:848954

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.

PubMed

Lange, Anna; Beier, Sina; Steimle, Alex; Autenrieth, Ingo B; Huson, Daniel H; Frick, Julia-Stefanie

2016-04-25

Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics.

PubMed

Stentz, Régis; Horn, Nikki; Cross, Kathryn; Salt, Louise; Brearley, Charles; Livermore, David M; Carding, Simon R

2015-03-01

To identify β-lactamase genes in gut commensal Bacteroides species and to assess the impact of these enzymes, when carried by outer membrane vesicles (OMVs), in protecting enteric pathogens and commensals. A deletion mutant of the putative class A β-lactamase gene (locus tag BT_4507) found in the genome of the human commensal Bacteroides thetaiotaomicron was constructed and a phenotypic analysis performed. A phylogenetic tree was built from an alignment of nine Bacteroides cephalosporinase protein sequences, using the maximum likelihood method. The rate of cefotaxime degradation after incubation with OMVs produced by different Bacteroides species was quantified using a disc susceptibility test. The resistance of Salmonella Typhimurium and Bifidobacterium breve to cefotaxime in liquid culture in the presence of B. thetaiotaomicron OMVs was evaluated by measuring bacterial growth. The B. thetaiotaomicron BT_4507 gene encodes a β-lactamase related to the CepA cephalosporinase of Bacteroides fragilis. OMVs produced by B. thetaiotaomicron and several other Bacteroides species, except Bacteroides ovatus, carried surface-associated β-lactamases that could degrade cefotaxime. β-Lactamase-harbouring OMVs from B. thetaiotaomicron protected Salmonella Typhimurium and B. breve from an otherwise lethal dose of cefotaxime. The production of membrane vesicles carrying surface-associated β-lactamases by Bacteroides species, which constitute a major part of the human colonic microbiota, may protect commensal bacteria and enteric pathogens, such as Salmonella Typhimurium, against β-lactam antibiotics. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain HJ

PubMed Central

Kiseleva, Larisa; Garushyants, Sofya K.; Briliute, Justina; Simpson, David J. W.; Goryanin, Igor

2015-01-01

We present the draft genome of the petroleum-degrading Thalassospira sp. strain HJ, isolated from tidal marine sediment. Knowledge of this genomic information will inform studies on electrogenesis and means to degrade environmental organic contaminants, including compounds found in petroleum. PMID:25977412

Complete Genome Sequence of Bacteroides ovatus V975.

PubMed

Wegmann, Udo; Goesmann, Alexander; Carding, Simon R

2016-12-01

The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of a single circular chromosome of 6,475,296 bp containing five rRNA operons, 68 tRNA genes, and 4,959 coding genes. Copyright © 2016 Wegmann et al.

Products of Dark CO2 Fixation in Pea Root Nodules Support Bacteroid Metabolism 1

PubMed Central

Rosendahl, Lis; Vance, Carroll P.; Pedersen, Walther B.

1990-01-01

Products of the nodule cytosol in vivo dark [14C]CO2 fixation were detected in the plant cytosol as well as in the bacteroids of pea (Pisum sativum L. cv “Bodil”) nodules. The distribution of the metabolites of the dark CO2 fixation products was compared in effective (fix+) nodules infected by a wild-type Rhizobium leguminosarum (MNF 300), and ineffective (fix−) nodules of the R. leguminosarum mutant MNF 3080. The latter has a defect in the dicarboxylic acid transport system of the bacterial membrane. The 14C incorporation from [14C]CO2 was about threefold greater in the wild-type nodules than in the mutant nodules. Similarly, in wild-type nodules the in vitro phosphoenolpyruvate carboxylase activity was substantially greater than that of the mutant. Almost 90% of the 14C label in the cytosol was found in organic acids in both symbioses. Malate comprised about half of the total cytosol organic acid content on a molar basis, and more than 70% of the cytosol radioactivity in the organic acid fraction was detected in malate in both symbioses. Most of the remaining 14C was contained in the amino acid fraction of the cytosol in both symbioses. More than 70% of the 14C label found in the amino acids of the cytosol was incorporated in aspartate, which on a molar basis comprised only about 1% of the total amino acid pool in the cytosol. The extensive 14C labeling of malate and aspartate from nodule dark [14C]CO2 fixation is consistent with the role of phosphoenolpyruvate carboxlase in nodule dark CO2 fixation. Bacteroids from the effective wild-type symbiosis accumulated sevenfold more 14C than did the dicarboxylic acid transport defective bacteroids. The bacteroids of the effective MNF 300 symbiosis contained the largest proportion of the incorporated 14C in the organic acids, whereas ineffective MNF 3080 bacteroids mainly contained 14C in the amino acid fraction. In both symbioses a larger proportion of the bacteroid 14C label was detected in malate and aspartate

Complete genome sequence of Bacteroides salanitronis type strain (BL78T)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gronow, Sabine; Held, Brittany; Lucas, Susan

2011-01-01

Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. The species is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microflora of the cecum is of benefit for the host and may impact poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and 101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.

PubMed

Luis, Ana S; Briggs, Jonathon; Zhang, Xiaoyang; Farnell, Benjamin; Ndeh, Didier; Labourel, Aurore; Baslé, Arnaud; Cartmell, Alan; Terrapon, Nicolas; Stott, Katherine; Lowe, Elisabeth C; McLean, Richard; Shearer, Kaitlyn; Schückel, Julia; Venditto, Immacolata; Ralet, Marie-Christine; Henrissat, Bernard; Martens, Eric C; Mosimann, Steven C; Abbott, D Wade; Gilbert, Harry J

2018-02-01

The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.

Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community.

PubMed

Robert, Céline; Chassard, Christophe; Lawson, Paul A; Bernalier-Donadille, Annick

2007-07-01

A strictly anaerobic cellulolytic bacterium, strain CRE21(T), was isolated from a human faecal sample. Cells were Gram-negative non-motile rods that were about 1.7 microm in length and 0.9 microm in width. Strain CRE21(T) degraded different types of cellulose and was able to grow on a variety of carbohydrates. Cellulose and sugars were mainly converted to acetate, propionate and succinate. The G+C content of the DNA was 41.1 mol%. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacteroides with highest sequence similarity to the type strain of Bacteroides intestinalis (98 %). DNA-DNA hybridization results revealed that strain CRE21(T) was distinct from B. intestinalis (40 % DNA-DNA relatedness). Strain CRE21(T) also showed several characteristics distinct from B. intestinalis. In particular, it exhibited different capacity to degrade polysaccharides such as cellulose. On the basis of phylogenetic analysis and the morphological, physiological and biochemical data presented in this study, strain CRE21(T) can be readily differentiated from recognized species of the genus Bacteroides. The name Bacteroides cellulosilyticus sp. nov. is proposed to accommodate this organism. The type strain is CRE21(T) (=DSM 14838(T)=CCUG 44979(T)).

Validity of the Omron HJ-112 pedometer during treadmill walking.

PubMed

Hasson, Rebecca E; Haller, Jeannie; Pober, David M; Staudenmayer, John; Freedson, Patty S

2009-04-01

The purpose of this investigation was to examine the validity of step counts measured with the Omron HJ-112 pedometer and to assess the effect of pedometer placement. Ninety-two subjects (44 males and 48 females; 71 with body mass index [BMI] <30 kg.m and 21 with BMI >or=30 kg.m) completed three, 12-min bouts of treadmill walking at speeds of 1.12, 1.34, and 1.56 mxs. A subset (21 males and 23 females; 38 BMI <30 kg.m and 6 BMI >or=30 kg.m) completed a variable walking condition. For all conditions, participants wore an Omron HJ-112 pedometer on the hip, in the pants pocket, in the chest shirt pocket, and around the neck. Hip pedometer placement was alternated between right and left sides with the Yamax Digiwalker SW-701. During each walk, an investigator recorded actual steps with a manual hand counter. There was no substantial bias with the Omron in any speed condition (-0.1% to 0.5%). Bias was larger with the Yamax (-3.6% to 2.0%). The largest random error for the Omron was 3.7% in the variable-speed condition for the BMI <30 kg.m group, whereas random errors for the Yamax were larger and up to 20%. None of the Omron placement positions produced statistically significant bias. Hip mounting produced the smallest random error (1.2%), followed by shirt pocket (1.7%), neck (2.2%), and pants pocket (5.8%). The Omron HJ-112 pedometer validly assesses steps in different BMI groups during constant- and variable-speed walking; other than that in the pants pocket, placement of the pedometer has little effect on validity.

[Effect of indolylacetic acid on formation of bacteroid forms of Rhizobium leguminosarum].

PubMed

Lobanok, E V; Bakanchikova, T I

1979-01-01

The purpose of this work was to study the effect of indolylacetic acid (IAA) on the strains of Rhizobium leguminosarum, effective and noneffective with respect to symbiotic nitrogen fixation (L4 and 245a, and 14--73, respectively). IAA at a concentration of 50 mcg/ml and higher inhibited the growth of the bacterium, temporarily delayed celular division, and induced intensive formation of elongated bacteroid-like cells, predominantly Y-shaped or having a clavate shape. Many bacteroid-like cells were capable of division after a certain delay.

Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions.

PubMed

Kim, Young-Min; Yamamoto, Eiji; Kang, Min-Sun; Nakai, Hiroyuki; Saburi, Wataru; Okuyama, Masayuki; Mori, Haruhide; Funane, Kazumi; Momma, Mitsuru; Fujimoto, Zui; Kobayashi, Mikihiko; Kim, Doman; Kimura, Atsuo

2012-09-01

Bacteroides thetaiotaomicron VPI-5482 harbors a gene encoding a putative cycloisomaltooligosaccharide glucanotransferase (BT3087) belonging to glycoside hydrolase family 66. The goal of the present study was to characterize the catalytic properties of this enzyme. Therefore, we expressed BT3087 (recombinant endo-dextranase from Bacteroides thetaiotaomicron VPI-5482) in Escherichia coli and determined that recombinant endo-dextranase from Bacteroides thetaiotaomicron VPI-5482 preferentially synthesized isomaltotetraose and isomaltooligosaccharides (degree of polymerization > 4) from dextran. The enzyme also generated large cyclic isomaltooligosaccharides early in the reaction. We conclude that members of the glycoside hydrolase 66 family may be classified into three types: (a) endo-dextranases, (b) dextranases possessing weak cycloisomaltooligosaccharide glucanotransferase activity, and (c) cycloisomaltooligosaccharide glucanotransferases. © 2012 The Authors Journal compilation © 2012 FEBS.

Marsh soils as potential sinks for Bacteroides fecal indicator bacteria, Waccamaw National Wildlife Refuge, Georgetown, SC, USA

USGS Publications Warehouse

Drexler, Judith Z.; Johnson, Heather E.; Duris, Joseph W.; Krauss, Ken W.

2014-01-01

A soil core collected in a tidal freshwater marsh in the Waccamaw National Wildlife Refuge (Georgetown, SC) exuded a particularly strong odor of cow manure upon extrusion. In order to test for manure and determine its provenance, we carried out microbial source tracking using DNA markers for Bacteroides, a noncoliform, anaerobic bacterial group that represents a broad group of the fecal population. Three core sections from 0-3 cm, 9-12 cm and 30-33 were analyzed for the presence of Bacteroides. The ages of core sediments were estimated using 210Pb and 137Cs dating. All three core sections tested positive for Bacteroides DNA markers related to cow or deer feces. Because cow manure is stockpiled, used as fertilizer, and a source of direct contamination in the Great Pee Dee River/Winyah Bay watershed, it is very likely the source of the Bacteroides that was deposited on the marsh. The mid-points of the core sections were dated as follows: 0-3 cm: 2009; 9-12 cm: 1999, and 30-33 cm: 1961. The presence of Bacteroides at different depths/ages in the soil profile indicates that soils in tidal freshwater marshes are, at the least, capable of being short-term sinks for Bacteroides and, may have the potential to be long-term sinks of stable, naturalized populations.

Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain HJ.

PubMed

Kiseleva, Larisa; Garushyants, Sofya K; Briliute, Justina; Simpson, David J W; Cohen, Michael F; Goryanin, Igor

2015-05-14

We present the draft genome of the petroleum-degrading Thalassospira sp. strain HJ, isolated from tidal marine sediment. Knowledge of this genomic information will inform studies on electrogenesis and means to degrade environmental organic contaminants, including compounds found in petroleum. Copyright © 2015 Kiseleva et al.

Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation

PubMed Central

Kuwahara, Tomomi; Yamashita, Atsushi; Hirakawa, Hideki; Nakayama, Haruyuki; Toh, Hidehiro; Okada, Natsumi; Kuhara, Satoru; Hattori, Masahira; Hayashi, Tetsuya; Ohnishi, Yoshinari

2004-01-01

Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major species, Bacteroides thetaiotaomicron (BT), concentrates within the colon. We find corresponding differences in their genomes, based on determination of the genome sequence of BF and comparative analysis with BT. Both species have acquired two mechanisms that contribute to their dominance among the colonic microbiota: an exceptional capability to use a wide range of dietary polysaccharides by gene amplification and the capacity to create variable surface antigenicities by multiple DNA inversion systems. However, the gene amplification for polysaccharide assimilation is more developed in BT, in keeping with its internal localization. In contrast, external antigenic structures can be changed more systematically in BF. Thereby, at the mucosal surface, where microbes encounter continuous attack by host defenses, BF evasion of the immune system is favored, and its colonization and infectious potential are increased. PMID:15466707

Radiometric Cross-Calibration of the HJ-1B IRS in the Thermal Infrared Spectral Band

NASA Astrophysics Data System (ADS)

Sun, K.

2012-12-01

The natural calamities occur continually, environment pollution and destruction in a severe position on the earth presently, which restricts societal and economic development. The satellite remote sensing technology has an important effect on improving surveillance ability of environment pollution and natural calamities. The radiometric calibration is precondition of quantitative remote sensing; which accuracy decides quality of the retrieval parameters. Since the China Environment Satellite (HJ-1A/B) has been launched successfully on September 6th, 2008, it has made an important role in the economic development of China. The satellite has four infrared bands; and one of it is thermal infrared. With application fields of quantitative remote sensing in china, finding appropriate calibration method becomes more and more important. Many kinds of independent methods can be used to do the absolute radiometric calibration. In this paper, according to the characteristic of thermal infrared channel of HJ-1B thermal infrared multi-spectral camera, the thermal infrared spectral band of HJ-1B IRS was calibrated using cross-calibration methods based on MODIS data. Firstly, the corresponding bands of the two sensors were obtained. Secondly, the MONDTRAN was run to analyze the influences of different spectral response, satellite view zenith angle, atmosphere condition and temperature on the match factor. In the end, their band match factor was calculated in different temperature, considering the dissimilar band response of the match bands. Seven images of Lake Qinghai in different time were chosen as the calibration data. On the basis of radiance of MODIS and match factor, the IRS radiance was calculated. And then the calibration coefficients were obtained by linearly regressing the radiance and the DN value. We compared the result of this cross-calibration with that of the onboard blackbody calibration, which consistency was good.The maximum difference of brightness temperature

Suppression of bactericidal activity of human polymorphonuclear leukocytes by Bacteroides gingivalis.

PubMed Central

Yoneda, M; Maeda, K; Aono, M

1990-01-01

The direct effects of the culture supernatant of oral microorganisms on the bactericidal activity of human polymorphonuclear leukocytes (PMNs) were investigated. The bactericidal activity of PMNs, which were preincubated with the supernatant of Bacteroides gingivalis, Bacteroides intermedius, Bacteroides melaninogenicus or phosphate-buffered saline, was examined by counting the surviving bacteria. B. gingivalis-treated PMNs were found to have a diminished ability for killing bacteria in the presence or absence of serum. The chemiluminescence response of PMNs, which were preincubated with the culture supernatant of B. gingivalis, was strikingly reduced compared with that of PMNs preincubated with phosphate-buffered saline or other bacterial culture supernatants. The production of superoxide anion (O2-) by PMNs stimulated with either formyl-methionyl-leucyl-phenylalanine or phorbol myristate acetate was reduced in both cases after the PMNs were preincubated with the culture supernatant of B. gingivalis. However, it was observed that there was more reduction in superoxide anion (O2-) production stimulated with formyl-methionyl-leucyl-phenylalanine compared with that stimulated with phorbol myristate acetate. These results suggest that B. gingivalis releases a factor which interferes with the bactericidal activity of PMNs by modulating the generation of reactive oxygen species. These suppressive effects on bactericidal activity may be important in the pathogenesis of this microorganism. PMID:2153632

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns.

PubMed

De Filippis, Francesca; Pellegrini, Nicoletta; Laghi, Luca; Gobbetti, Marco; Ercolini, Danilo

2016-10-21

Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations. Here, we used oligotyping of 16S rRNA gene sequencing data to exploit the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore and non-omnivore subjects from a previously studied cohort. A great heterogeneity was found in oligotype composition. Nevertheless, different oligotypes within the same genus showed distinctive correlation patterns with dietary components and metabolome. We found that some Prevotella oligotypes are significantly associated with the plant-based diet but some are associated with animal-based nutrients, and the same applies to Bacteroides. Therefore, an indiscriminate association of Bacteroidetes genera with specific dietary patterns may lead to an oversimplified vision that does not take into account sub-genus diversity and the different possible responses to dietary components. We demonstrated that Prevotella and Bacteroides oligotypes show distinctive correlation patterns with dietary components and metabolome. These results substantiate a current oversimplification of diet-dependent microbe-host associations and highlighted that sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits.

[A snow depth inversion method for the HJ-1B satellite data].

PubMed

Dong, Ting-Xu; Jiang, Hong-Bo; Chen, Chao; Qin, Qi-Ming

2011-10-01

The importance of the snow is self-evident, while the harms caused by the snow have also received more and more attention. At present, the retrieval of snow depth mainly focused on the use of microwave remote sensing data or a small amount of optical remote sensing data, such as the meteorological data or the MODIS data. The small satellites for environment and disaster monitoring of China are quite different form the meteorological data and MODIS data, both in the spectral resolution or spatial resolution. In this paper, aimed at the HJ-1B data, snow spectral of different underlying surfaces and depths were surveyed. The correlation between snow cover index and snow depth was also analyzed to establish the model for the snow depth retrieval using the HJ-1B data. The validation results showed that it can meet the requirements of real-time monitoring the snow depth on the condition of conventional snow depth.

In Vitro Evaluation of the Activity of Imipenem-Relebactam against 451 Recent Clinical Isolates of Bacteroides Group and Related Species

PubMed Central

Jacobus, Nilda V.; McDermott, Laura A.

2016-01-01

We evaluated the in vitro activity of imipenem-relebactam (imipenem-MK7655) against 451 recent clinical isolates within the Bacteroides group and related species. Relebactam did not enhance or inhibit the activity of imipenem against Bacteroides fragilis or other Bacteroides species. No synergistic or antagonistic effect was observed. The MICs of imipenem-relebactam were equal to or within one dilution of the MICs of these isolates to imipenem. PMID:27480858

Induction of vascular endothelial growth factor expression in human pulp fibroblasts stimulated with black-pigmented Bacteroides.

PubMed

Yang, L-C; Tsai, C-H; Huang, F-M; Su, Y-F; Lai, C-C; Liu, C-M; Chang, Y-C

2004-09-01

To investigate the effect of black-pigmented Bacteroides on the expression of vascular endothelial growth factor (VEGF) gene in human pulp fibroblasts. The supernatants of Porphyromonas endodontalis, Porphyromonas gingivalis and Prevotella intermedia were used to evaluate VEGF gene expression in human pulp fibroblasts. The levels of mRNAs were measured by the quantitative reverse-transcriptase polymerase chain reaction analysis. Black-pigmented Bacteroides induced significantly high levels of VEGF mRNA gene expression in human pulp fibroblasts (P < 0.05). In addition, the expression of VEGF depended on the bacteria tested. Black-pigmented Bacteroides may be involved in developing pulpal disease through the stimulation of VEGF production that would lead to the expansion of the vascular network coincident to progression of the inflammation.

Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters.

PubMed

Converse, Reagan R; Blackwood, A Denene; Kirs, Marek; Griffith, John F; Noble, Rachel T

2009-11-01

Concentrations of fecal indicator bacteria (FIB; e.g. Escherichia coli, and Enterococcus sp.) can only be used in limited ways for determining the source of fecal contamination in recreational waters because they cannot distinguish human from non-human fecal contamination. Several Bacteroides spp. have been suggested as potential alternative indicators. We have developed a rapid, culture-independent method for quantifying fecal Bacteroides spp. using quantitative PCR (QPCR) targeting the 16S rRNA gene. The assay specifically targets and quantifies the most common human Bacteroides spp. The details of the method are presented, including analyses of a wide range of fecal samples from different organisms. Specificity and performance of the QPCR assay were also tested via a laboratory experiment where human sewage and gull guano were inoculated into a range of environmental water samples. Concentrations of fecal Bacteroides spp., total Enterococcus sp., Enterococcus faecium, Enterococcus faecalis, and Enterococcus casseliflavus were measured using QPCR, and total Enterococcus sp. and E. coli were quantified by membrane filtration (MF). Samples spiked with gull guano were highly concentrated with total Enterococcus sp., E. coli, E. faecalis, and E. casseliflavus, demonstrating that these indicators are prominent in animal feces. On the other hand, fecal Bacteroides spp. concentrations were high in samples containing sewage and were relatively low in samples spiked with gull guano. Sensitivity and specificity results suggest that the rapid fecal Bacteroides spp. QPCR assay may be a useful tool to effectively predict the presence and concentration of human-specific fecal pollution.

Differential Decay of Human Faecal Bacteroides in Marine and Freshwater

EPA Science Inventory

Gene sequences from Bacteroides and relatives are being considered for the enumeration of aquatic fecal contamination and estimation of public health risk. To interpret these data, it is necessary to understand the decay of molecular and cultivated indicators and pathogens in en...

Isolation and characterization of Bacteroides host strain HB-73 used to detect sewage specific phages in Hawaii.

PubMed

Vijayavel, Kannappan; Fujioka, Roger; Ebdon, James; Taylor, Huw

2010-06-01

Previous studies have shown that Escherichia coli and enterococci are unreliable indicators of fecal contamination in Hawaii because of their ability to multiply in environmental soils. In this study, the method of detecting Bacteroides phages as specific markers of sewage contamination in Hawaii's recreational waters was evaluated because these sewage specific phages cannot multiply under environmental conditions. Bacteroides hosts (GB-124, GA-17), were recovered from sewage samples in Europe and were reported to be effective in detecting phages from sewage samples obtained in certain geographical areas. However, GB-124 and GA-17 hosts were ineffective in detecting phages from sewage samples obtained in Hawaii. Bacteroides host HB-73 was isolated from a sewage sample in Hawaii, confirmed as a Bacteroides sp. and shown to recover phages from multiple sources of sewage produced in Hawaii at high concentrations (5.2-7.3 x 10(5) PFU/100 mL). These Bacteroides phages were considered as potential markers of sewage because they also survived for three days in fresh stream water and two days in marine water. Water samples from Hawaii's coastal swimming beaches and harbors, which were known to be contaminated with discharges from streams, were shown to contain moderate (20-187 CFU/100 mL) to elevated (173-816 CFU/100 mL) concentrations of enterococci. These same samples contained undetectable levels (<10 PFU/100 mL) of F+ coliphage and Bacteroides phages and provided evidence to suggest that these enterococci may not necessarily be associated with the presence of raw sewage. These results support previous conclusions that discharges from streams are the major sources of enterococci in coastal waters of Hawaii and the most likely source of these enterococci is from environmental soil rather than from sewage. 2010 Elsevier Ltd. All rights reserved.

Bacteroides (Parabacteroides) distasonis splenic abscess in a sickle cell patient.

PubMed

Al-Tawfiq, Jaffar A

2008-01-01

Splenic abscess is not an uncommon complication of patients with sickle-cell disease. Here we describe an 18 year-old boy with sickle cell disease and left upper quadrant abdominal pain. Computerized axial tomography revealed left sided free flowing pleural effusion and splenomegaly with liquefaction and possible gas formation. The splenic fluid grew an unusual organism known as Bacteroides distasonis. The patient received antimicrobial therapy and underwent a splenectomy with full recovery. The spleen was cystically infarcted and measured 22 x 16 x 5 cm. The capsule was thickened and covered by fibrinous exudate. Histopathologic examination of the spleen showed complete necrosis with reparative fibrosis. This case presents an unusual cause of splenic abscess due to Bacteroides distasonis with a subacute to chronic course. The presence of fever and left sided pleuritic chest pain in patients with sickle cell disease should raise the suspicion of splenic abscess.

In Vitro Evaluation of the Activity of Imipenem-Relebactam against 451 Recent Clinical Isolates of Bacteroides Group and Related Species.

PubMed

Snydman, David R; Jacobus, Nilda V; McDermott, Laura A

2016-10-01

We evaluated the in vitro activity of imipenem-relebactam (imipenem-MK7655) against 451 recent clinical isolates within the Bacteroides group and related species. Relebactam did not enhance or inhibit the activity of imipenem against Bacteroides fragilis or other Bacteroides species. No synergistic or antagonistic effect was observed. The MICs of imipenem-relebactam were equal to or within one dilution of the MICs of these isolates to imipenem. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Evaluation of the Omron HJ-720ITC pedometer under free-living conditions.

PubMed

Silcott, Nathan A; Bassett, David R; Thompson, Dixie L; Fitzhugh, Eugene C; Steeves, Jeremy A

2011-09-01

The primary purpose of this study was to examine the accuracy of the Omron HJ-720ITC piezoelectric pedometer in a free-living environment during a 24-h period. A secondary purpose was to compare the accuracy the Omron to that of a spring-levered pedometer. A total of 62 adult volunteers were classified according to body mass index (BMI) category: normal weight (n = 19), overweight (n = 23), and obese (n = 20). Subjects wore five devices during a 24-h period except when bathing or sleeping. The criterion pedometer (StepWatch-3) was worn on the lateral side of the right ankle. Omron HJ-720ITC pedometers were worn in three locations: (a) on the belt, (b) in the pants pocket, and (c) on a lanyard around the neck. A comparison pedometer (Yamax SW-200) was worn on the belt. The Omron HJ-720ITC underestimated the steps per day in all three BMI categories compared with the criterion measure (P < 0.05). The Omron was most accurate in the pocket location, recording 68%, 70%, and 65% of steps in the normal, overweight, and obese BMI categories, respectively. In the obese group, the Omron was more accurate than the Yamax pedometer, but in the normal and overweight groups, it was less accurate than the Yamax. Results from our study show that the Omron significantly underestimates steps per day under free-living conditions. This is due, in part, to the presence of a 4-s step filter that contributes to an underestimation of steps accumulated during intermittent activities. In the pocket, the Omron accuracy was similar for lean, overweight, and obese individuals. In contrast, the accuracy of the Yamax pedometer declined with increasing BMI categories.

The relationship between nitrogen fixation and the production of HD from D2 by cell-free extracts of soya-bean nodule bacteroids

PubMed Central

Turner, G. L.; Bergersen, F. J.

1969-01-01

1. Cell-free extracts prepared from soya-bean nodule bacteroids produced HD from D2 in the presence of dithionite, an ATP-generating system and nitrogen. 2. Crude extracts of bacteroids or of Azotobacter vinelandii showed some background D2 exchange when any one of these was omitted. 3. Partial purification of bacteroid extracts diminished this background activity and gave increased D2 exchange and nitrogen fixation. 4. Although increasing pN2 stimulated both reactions, the apparent Km (N2) for nitrogen fixation was much higher than the apparent Km (N2) for D2 exchange when partially purified bacteroid extracts were used. 5. Carbon monoxide was a competitive inhibitor of nitrogen fixation by partially purified bacteroid extracts, but D2 exchange was inhibited in a non-competitive fashion. 6. These results are discussed in relation to the possible existence of enzyme-bound intermediates of nitrogen fixation. PMID:5353527

Research publications of the H.J. Andrews Experimental Forest, Cascade Range, Oregon: 1988 supplement.

Treesearch

T. Blinn; F.J. Swanson; A. McKee

1988-01-01

This bibliography updates the list of publications, abstracts, theses, and unpublished reports included in "Research Publications of the H.J. Andrews Experimental Forest, Cascade Range, Oregon, 1948 to 1986," General Technical Report PNW-GTR-201. Citations are referenced under appropriate keywords.

A Novel Tightly Regulated Gene Expression System for the Human Intestinal Symbiont Bacteroides thetaiotaomicron.

PubMed

Horn, Nikki; Carvalho, Ana L; Overweg, Karin; Wegmann, Udo; Carding, Simon R; Stentz, Régis

2016-01-01

There is considerable interest in studying the function of Bacteroides species resident in the human gastrointestinal (GI)-tract and the contribution they make to host health. Reverse genetics and protein expression techniques, such as those developed for well-characterized Escherichia coli cannot be applied to Bacteroides species as they and other members of the Bacteriodetes phylum have unique promoter structures. The availability of useful Bacteroides-specific genetic tools is therefore limited. Here we describe the development of an effective mannan-controlled gene expression system for Bacteroides thetaiotaomicron containing the mannan-inducible promoter-region of an α-1,2-mannosidase gene (BT_3784), a ribosomal binding site designed to modulate expression, a multiple cloning site to facilitate the cloning of genes of interest, and a transcriptional terminator. Using the Lactobacillus pepI as a reporter gene, mannan induction resulted in an increase of reporter activity in a time- and concentration-dependent manner with a wide range of activity. The endogenous BtcepA cephalosporinase gene was used to demonstrate the suitability of this novel expression system, enabling the isolation of a His-tagged version of BtCepA. We have also shown with experiments performed in mice that the system can be induced in vivo in the presence of an exogenous source of mannan. By enabling the controlled expression of endogenous and exogenous genes in B. thetaiotaomicron this novel inducer-dependent expression system will aid in defining the physiological role of individual genes and the functional analyses of their products.

A Novel Tightly Regulated Gene Expression System for the Human Intestinal Symbiont Bacteroides thetaiotaomicron

PubMed Central

Horn, Nikki; Carvalho, Ana L.; Overweg, Karin; Wegmann, Udo; Carding, Simon R.; Stentz, Régis

2016-01-01

There is considerable interest in studying the function of Bacteroides species resident in the human gastrointestinal (GI)-tract and the contribution they make to host health. Reverse genetics and protein expression techniques, such as those developed for well-characterized Escherichia coli cannot be applied to Bacteroides species as they and other members of the Bacteriodetes phylum have unique promoter structures. The availability of useful Bacteroides-specific genetic tools is therefore limited. Here we describe the development of an effective mannan-controlled gene expression system for Bacteroides thetaiotaomicron containing the mannan-inducible promoter–region of an α-1,2-mannosidase gene (BT_3784), a ribosomal binding site designed to modulate expression, a multiple cloning site to facilitate the cloning of genes of interest, and a transcriptional terminator. Using the Lactobacillus pepI as a reporter gene, mannan induction resulted in an increase of reporter activity in a time- and concentration-dependent manner with a wide range of activity. The endogenous BtcepA cephalosporinase gene was used to demonstrate the suitability of this novel expression system, enabling the isolation of a His-tagged version of BtCepA. We have also shown with experiments performed in mice that the system can be induced in vivo in the presence of an exogenous source of mannan. By enabling the controlled expression of endogenous and exogenous genes in B. thetaiotaomicron this novel inducer-dependent expression system will aid in defining the physiological role of individual genes and the functional analyses of their products. PMID:27468280

Bacteriophages infecting Bacteroides as a marker for microbial source tracking.

PubMed

Jofre, Joan; Blanch, Anicet R; Lucena, Francisco; Muniesa, Maite

2014-05-15

Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Study on forest above-ground biomass synergy inversion from GLAS and HJ-1 data

NASA Astrophysics Data System (ADS)

Fang, Zhou; Cao, Chunxiang; Ji, Wei; Xu, Min; Chen, Wei

2012-10-01

The need exists to develop a systematic approach to inventory and monitor global forests, both for carbon stock evaluation and for land use change analysis. The use of freely available satellite-based data for carbon stock estimation mitigates both the cost and the spatial limitations of field-based techniques. Spaceborne lidar data have been demonstrated as useful for forest aboveground biomass (AGB) estimation over a wide range of biomass values and forest types. However, the application of these data is limited because of their spatially discrete nature. Spaceborne multispectral sensors have been used extensively to estimate AGB, but these methods have been demonstrated as inappropriate for forest structure characterization in high-biomass mature forests. This study uses an integration of ICESat Geospatial Laser Altimeter System (GLAS) lidar and HJ-1 satellites data to develop methods to estimate AGB in an area of Qilian Mountains, Northwest China. Considering the study area belongs to mountainous terrain, the difficulties of this article are how to extract canopy height from GLAS waveform metrics. Combining with HJ-1 data and ground survey data of the study area, we establish forest biomass estimation model for the GLAS data based on BP neural network model. In order to estimate AGB, the training sample data includes the canopy height extracted from GLAS, LAI, vegetation coverage and several kinds of vegetation indices from HJ-1 data. The results of forest aboveground biomass are very close to the fields measured results, and are consistent with land cover data in the spatial distribution.

Carriers in electron transport from molecular hydrogen to oxygen in Rhizobium japonicum bacteroids.

PubMed Central

Eisbrenner, G; Evans, H J

1982-01-01

An investigation has been conducted to identify electron transport carriers that participate in the oxidation of H2 by H2 uptake-positive strains of Rhizobium japonicum bacteroids. We have observed that the reduced form of dibromothymoquinone at a concentration of 0.2 mM strongly inhibited H2 uptake, endogenous respiration, and C2H2 reduction by bacteroid suspensions. Reduced dibromothymoquinone, however, failed to inhibit the transfer of electrons from H2 to methylene blue under anaerobic conditions, indicating that the hydrogenase per se is insensitive to this inhibitor. Metronidazole, at 1 mM, affected rates of H2 uptake and endogenous respiration only slightly, but strongly inhibited C2H2 reduction. Evidence for H2-dependent cytochrome reduction in an H2 uptake-positive strain of R. japonicum bacteroids is presented. In kinetic studies, the rates of reduction of the type b and c cytochromes in the presence of H2 were shown to be severalfold higher than the rates due to endogenous respiration alone. With hydrogenase-deficient mutants of R. japonicum, no measurable effect of H2 on cytochrome reduction was observed. Our results indicate that ubiquinone and cytochromes of types b and c are involved in the oxyhydrogen reaction in R. japonicum. PMID:6277845

Direct Ethanol Production from Lignocellulosic Sugars and Sugarcane Bagasse by a Recombinant Trichoderma reesei Strain HJ48

PubMed Central

Huang, Jun; Chen, Dong; Wei, Yutuo; Wang, Qingyan; Li, Zhenchong; Chen, Ying; Huang, Ribo

2014-01-01

Trichoderma reesei can be considered as a candidate for consolidated bioprocessing (CBP) microorganism. However, its ethanol yield needs to be improved significantly. Here the ethanol production of T. reesei CICC 40360 was improved by genome shuffling while simultaneously enhancing the ethanol resistance. The initial mutant population was generated by nitrosoguanidine treatment of the spores, and an improved population producing more than fivefold ethanol than wild type was obtained by genome shuffling. The results show that the shuffled strain HJ48 can efficiently convert lignocellulosic sugars to ethanol under aerobic conditions. Furthermore, it was able to produce ethanol directly from sugarcane bagasse, demonstrating that the shuffled strain HJ48 is a suitable microorganism for consolidated bioprocessing. PMID:24995362

Direct ethanol production from lignocellulosic sugars and sugarcane bagasse by a recombinant Trichoderma reesei strain HJ48.

PubMed

Huang, Jun; Chen, Dong; Wei, Yutuo; Wang, Qingyan; Li, Zhenchong; Chen, Ying; Huang, Ribo

2014-01-01

Trichoderma reesei can be considered as a candidate for consolidated bioprocessing (CBP) microorganism. However, its ethanol yield needs to be improved significantly. Here the ethanol production of T. reesei CICC 40360 was improved by genome shuffling while simultaneously enhancing the ethanol resistance. The initial mutant population was generated by nitrosoguanidine treatment of the spores, and an improved population producing more than fivefold ethanol than wild type was obtained by genome shuffling. The results show that the shuffled strain HJ48 can efficiently convert lignocellulosic sugars to ethanol under aerobic conditions. Furthermore, it was able to produce ethanol directly from sugarcane bagasse, demonstrating that the shuffled strain HJ48 is a suitable microorganism for consolidated bioprocessing.

[NDVI difference rate recognition model of deciduous broad-leaved forest based on HJ-CCD remote sensing data].

PubMed

Wang, Yan; Tian, Qing-Jiu; Huang, Yan; Wei, Hong-Wei

2013-04-01

The present paper takes Chuzhou in Anhui Province as the research area, and deciduous broad-leaved forest as the research object. Then it constructs the recognition model about deciduous broad-leaved forest was constructed using NDVI difference rate between leaf expansion and flowering and fruit-bearing, and the model was applied to HJ-CCD remote sensing image on April 1, 2012 and May 4, 2012. At last, the spatial distribution map of deciduous broad-leaved forest was extracted effectively, and the results of extraction were verified and evaluated. The result shows the validity of NDVI difference rate extraction method proposed in this paper and also verifies the applicability of using HJ-CCD data for vegetation classification and recognition.

Long-term experiments on log decomposition at the H.J. Andrews Experimental Forest.

Treesearch

M.E. Harmon

1992-01-01

A long-term decomposition experiment was established at the H.J. Andrews Experimental Forest, Oregon, during 1985to test the importance of substrate heterogeneity, colonization patterns, and invertebrates on the decomposition of logs. The duration of the study is anticipated to be 200 years. A total of 530 logs (50 centimeters in diameter and 5.5 meters long) were...

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota.

PubMed

Chen, Tingting; Long, Wenmin; Zhang, Chenhong; Liu, Shuang; Zhao, Liping; Hamaker, Bruce R

2017-06-01

The gut microbiota of individuals are dominated by different fiber-utilizing bacteria, which ferment dietary fiber into short chain fatty acids (SCFAs) known to be important for human health. Here, we show that the dominance of Prevotella versus Bacteroides in fecal innocula, identified into two different enterotypes, differentially impacts in vitro fermentation profiles of SCFAs from fibers with different chemical structures. In a microbiome of the Prevotella enterotype, fructooligosaccharides, and sorghum and corn arabinoxylans significantly promoted one single Prevotella OTU with equally high production of total SCFAs with propionate as the major product. Conversely, in the Bacteroides-dominated microbiota, the three fibers enriched different OTUs leading to different levels and ratios of SCFAs. This is the first report showing how individual differences in two enterotypes cause distinctly different responses to dietary fiber. Microbiota dominated by different fiber-utilizing bacteria may impact host health by way of producing different amounts and profiles of SCFAs from the same carbohydrate substrates.

Combining HJ CCD, GF-1 WFV and MODIS Data to Generate Daily High Spatial Resolution Synthetic Data for Environmental Process Monitoring.

PubMed

Wu, Mingquan; Huang, Wenjiang; Niu, Zheng; Wang, Changyao

2015-08-20

The limitations of satellite data acquisition mean that there is a lack of satellite data with high spatial and temporal resolutions for environmental process monitoring. In this study, we address this problem by applying the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM) and the Spatial and Temporal Data Fusion Approach (STDFA) to combine Huanjing satellite charge coupled device (HJ CCD), Gaofen satellite no. 1 wide field of view camera (GF-1 WFV) and Moderate Resolution Imaging Spectroradiometer (MODIS) data to generate daily high spatial resolution synthetic data for land surface process monitoring. Actual HJ CCD and GF-1 WFV data were used to evaluate the precision of the synthetic images using the correlation analysis method. Our method was tested and validated for two study areas in Xinjiang Province, China. The results show that both the ESTARFM and STDFA can be applied to combine HJ CCD and MODIS reflectance data, and GF-1 WFV and MODIS reflectance data, to generate synthetic HJ CCD data and synthetic GF-1 WFV data that closely match actual data with correlation coefficients (r) greater than 0.8989 and 0.8643, respectively. Synthetic red- and near infrared (NIR)-band data generated by ESTARFM are more suitable for the calculation of Normalized Different Vegetation Index (NDVI) than the data generated by STDFA.

Combining HJ CCD, GF-1 WFV and MODIS Data to Generate Daily High Spatial Resolution Synthetic Data for Environmental Process Monitoring

PubMed Central

Wu, Mingquan; Huang, Wenjiang; Niu, Zheng; Wang, Changyao

2015-01-01

The limitations of satellite data acquisition mean that there is a lack of satellite data with high spatial and temporal resolutions for environmental process monitoring. In this study, we address this problem by applying the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM) and the Spatial and Temporal Data Fusion Approach (STDFA) to combine Huanjing satellite charge coupled device (HJ CCD), Gaofen satellite no. 1 wide field of view camera (GF-1 WFV) and Moderate Resolution Imaging Spectroradiometer (MODIS) data to generate daily high spatial resolution synthetic data for land surface process monitoring. Actual HJ CCD and GF-1 WFV data were used to evaluate the precision of the synthetic images using the correlation analysis method. Our method was tested and validated for two study areas in Xinjiang Province, China. The results show that both the ESTARFM and STDFA can be applied to combine HJ CCD and MODIS reflectance data, and GF-1 WFV and MODIS reflectance data, to generate synthetic HJ CCD data and synthetic GF-1 WFV data that closely match actual data with correlation coefficients (r) greater than 0.8989 and 0.8643, respectively. Synthetic red- and near infrared (NIR)-band data generated by ESTARFM are more suitable for the calculation of Normalized Different Vegetation Index (NDVI) than the data generated by STDFA. PMID:26308017

A new chromogenic medium for isolation of Bacteroides fragilis suitable for screening for strains with antimicrobial resistance.

PubMed

Tierney, Daniel; Copsey, Sarah D; Morris, Trefor; Perry, John D

2016-06-01

There have been an increasing number of reports describing the acquisition of antimicrobial resistance by Bacteroides fragilis including the occurrence of strains with resistance to multiple antimicrobials that are relied upon for treatment of infections. The aim of this study was to design a chromogenic selective medium for isolation of B. fragilis that could be adapted for specific isolation of antimicrobial-resistant strains. Bacteroides chromogenic agar (BCA) was the result of this endeavour and allowed growth of Bacteroides spp. as black colonies and the efficient inhibition of almost all other genera tested. The medium also allowed some differentiation of B. fragilis from other members of the B. fragilis group. When compared with an adaptation of Bacteroides bile-esculin agar (BBE) for the isolation of B. fragilis from 100 stool samples, 30 isolates of B. fragilis were recovered on BCA compared with 19 isolates recovered on BBE (P = 0.022). When supplemented with meropenem (4 μg/ml) or metronidazole (2 μg/ml), BCA could be used to select for the growth of B. fragilis isolates with resistance to these agents. We conclude that BCA is a useful research tool for surveillance studies to assess the prevalence of B. fragilis and, in particular, the occurrence of antimicrobial-resistant strains. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of bacteroides-prevotella 16S rRNA genetic markers for fecal samples from different animal species.

PubMed

Fogarty, Lisa R; Voytek, Mary A

2005-10-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species

PubMed Central

Fogarty, Lisa R.; Voytek, Mary A.

2005-01-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment. PMID:16204514

Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

USGS Publications Warehouse

Fogarty, L.R.; Voytek, M.A.

2005-01-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome.

PubMed

Tajkarimi, Mehrdad; Wexler, Hannah M

2017-01-01

Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis ( n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains

CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome

PubMed Central

Tajkarimi, Mehrdad; Wexler, Hannah M.

2017-01-01

Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis (n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains

Estimation of the Relative Abundance of Different Bacteroides and Prevotella Ribotypes in Gut Samples by Restriction Enzyme Profiling of PCR-Amplified 16S rRNA Gene Sequences

PubMed Central

Wood, Jacqueline; Scott, Karen P.; Avguštin, Gorazd; Newbold, C. James; Flint, Harry J.

1998-01-01

We describe an approach for determining the genetic composition of Bacteroides and Prevotella populations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides and Prevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution of Bacteroides and Prevotella sequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA. Bacteroides and Prevotella 16S rDNA accounted for between 12 and 62% of total eubacterial 16S rDNA in samples of ruminal contents from six sheep and a cow. Ribotypes 4, 5, 6, and 7, which include most cultivated rumen Prevotella strains, together accounted for between 20 and 86% of the total amplified Bacteroides and Prevotella rDNA in these samples. The most abundant Bacteroides or Prevotella ribotype in four animals, however, was ribotype 8, for which there is only one known cultured isolate, while ribotypes 1 and 2, which include many colonic Bacteroides spp., were the most abundant in two animals. This indicates that some abundant Bacteroides and Prevotella groups in the rumen are underrepresented among cultured rumen Prevotella isolates. The approach described here provides a rapid, convenient, and widely applicable method for comparing the genotypic composition of bacterial populations in gut samples. PMID:9758785

Research publications of the H.J. Andrews Experimental Forest, Cascade Range, Oregon: 1948 to 1986.

Treesearch

A. McKee; G.M. Stonedahl; J.F. Franklin; F.J. Swanson

1987-01-01

A list of publications resulting from research at th H.J. Andrews Experimental Forest, Willamette National Forest, Oregon, from 1948 to 1986 is presented. Nearly 600 publications are listed, including papers, theses, and abstracts. An index is provided that cross-references the listings under appropriate keywords.

[The effect of oxygen on endotoxin production in bacteria of the Bacteroides fragilis group isolated from patients with colorectal carcinoma].

PubMed

Chmelař, D; Hájek, M; Janečková, J; Vobejdová, J; Martineková, P; Kašíková, A

The aim of the study was to draw attention to the risk posed by anaerobic bacteria of the Bacteroides fragilis (BAFR) group, isolated particularly from abdominal lesions, and to assess the possible role of these species in colorectal cancer. A correlation has previously been suggested between the detection of the bacteria of the genus Bacteroides in patients on a meat-based diet and intestinal and, in particular, colorectal cancer. Given that the species of the BAFR group are major producers of endotoxins, measurements and statistical analysis of endotoxin production were used to compare the Bacteroides strains isolated from clinical specimens of patients with colon cancer, rectal cancer, and other abdominal lesions. Endotoxin production was detected in bacterial strains of the BAFR group (B. fragilis, B. thetaiotaomicron, B. distasonis, and B. vulgatus) isolated from clinical specimens of patients with rectal cancer, colon cancer, and intestinal cancer and was compared with that in strains from samples of patients with inflammatory conditions (anal abscess, appendicitis, skin abscess, etc.) under anaerobic and microaerophilic (with 5% of oxygen) culture conditions. The production of endotoxins was detected quantitatively using the Pyrosate LAL assay kit (Limulus Amoebocyte Lysate Test, BIOGENIX, CR) in four species of the BAFR group after anaerobic and microaerophilic culture. Five strains of each isolated Bacteroides species from each type of specimens were tested (in total 140 BAFR strains). The amount of endotoxin was given in endotoxin units per ml (EU/ml). Endotoxin production by bacteria under microaerophilic culture conditions was several times higher in comparison with strictly anaerobic culture.The difference was statistically significant (F1.269 = 160, p <0.0001). As regards the effect of oxygen on endotoxin production, the amount of endotoxins produced under microaerophilic culture conditions (average 889.1 EU/ml) was 2.5 times as high as that observed

[Atmospheric correction of HJ-1 CCD data for water imagery based on dark object model].

PubMed

Zhou, Li-Guo; Ma, Wei-Chun; Gu, Wan-Hua; Huai, Hong-Yan

2011-08-01

The CCD multi-band data of HJ-1A has great potential in inland water quality monitoring, but the precision of atmospheric correction is a premise and necessary procedure for its application. In this paper, a method based on dark pixel for water-leaving radiance retrieving is proposed. Beside the Rayleigh scattering, the aerosol scattering is important to atmospheric correction, the water quality of inland lakes always are case II water and the value of water leaving radiance is not zero. So the synchronous MODIS shortwave infrared data was used to obtain the aerosol parameters, and in virtue of the characteristic that aerosol scattering is relative stabilized in 560 nm, the water-leaving radiance for each visible and near infrared band were retrieved and normalized, accordingly the remotely sensed reflectance of water was computed. The results show that the atmospheric correction method based on the imagery itself is more effective for the retrieval of water parameters for HJ-1A CCD data.

Bacteroides induce higher IgA production than Lactobacillus by increasing activation-induced cytidine deaminase expression in B cells in murine Peyer's patches.

PubMed

Yanagibashi, Tsutomu; Hosono, Akira; Oyama, Akihito; Tsuda, Masato; Hachimura, Satoshi; Takahashi, Yoshimasa; Itoh, Kikuji; Hirayama, Kazuhiro; Takahashi, Kyoko; Kaminogawa, Shuichi

2009-02-01

The gut mucosal immune system is crucial in host defense against infection by pathogenic microbacteria and viruses via the production of IgA. Previous studies have shown that intestinal commensal bacteria enhance mucosal IgA production. However, it is poorly understood how these bacteria induce IgA production and which genera of intestinal commensal bacteria induce IgA production effectively. In this study, we compared the immunomodulatory effects of Bacteroides and Lactobacillus on IgA production by Peyer's patches lymphocytes. IgA production by Peyer's patches lymphocytes co-cultured with Bacteroides was higher than with Lactobacillus. In addition, the expression of activation-induced cytidine deaminase increased in co-culture with Bacteroides but not with Lactobacillus. We found that intestinal commensal bacteria elicited IgA production. In particular, Bacteroides induced the differentiation of Peyer's patches B cell into IgA(+) B cells by increasing activation-induced cytidine deaminase expression.

The Bacteroides fragilis cell envelope: quarterback, linebacker, coach-or all three?

PubMed

Pumbwe, Lilian; Skilbeck, Christopher A; Wexler, Hannah M

2006-01-01

Bacteroides fragilis is an anaerobic commensal constituting only 1-2% of the micro-flora of the human gastrointestinal tract, yet it is the predominant anaerobic isolate in cases of intraabdominal sepsis and bacteremia. B. fragilis can play two roles in the host: in its role as friendly commensal, it must be able to establish itself in the host intestinal mucosa, to utilize and process polysaccharides for use by the host, and to resist the noxious effects of bile salts. In its role as pathogen, it must be able to attach itself to the site of infection, evade killing mechanisms by host defense, withstand antimicrobial treatment and produce factors that damage host tissue. The cell envelope of B. fragilis, likewise, must be able to function in the roles of aggressor, defender and strategist in allowing the organism to establish itself in the host--whether as friend or foe. Recent studies of the genomes and proteomes of the genus Bacteroides suggest that these organisms have evolved strategies to survive and dominate in the overcrowded gastrointestinal neighborhood. Analysis of the proteomes of B. fragilis and Bacteroides thetaiotaomicron demonstrates both a tremendous capacity to use a wide range of dietary polysaccharides, and the capacity to create variable surface antigenicities by multiple DNA inversion systems. The latter characteristic is particularly pronounced in the species B. fragilis, which is more frequently found at the mucosal surface (i.e., often the site of attack by host defenses). The B. fragilis cell envelope undergoes major protein expression and ultrastructural changes in response to stressors such as bile or antimicrobial agents. These agents may also act as signals for attachment and colonization. Thus the bacterium manages its surface characteristics to enable it to bind to its target, to use the available nutrients, and to avoid or evade hostile forces (host-derived or external) in its multiple roles.

Cross-inhibition between black-pigmented Bacteroides species.

PubMed

Van Winkelhoff, A J; Kippuw, N; De Graaff, J

1987-11-01

Cross-inhibition within the group of black-pigmented Bacteroides, including both oral and non-oral strains, was studied by means of a membrane filter technique. It was found that B. gingivalis possessed the most extended inhibitory capacity among all species tested. B. gingivalis showed inhibitory activity against B. intermedius, B. endodontalis, B. loescheii, and B. melaninogenicus. B. endodontalis was active against some B. intermedius strains. Among the saccharolytic species, some B. melaninogenicus strains were inhibitory for some B. endodontalis strains, some B. gingivalis strains, and some B. intermedius strains. These inhibitory activities observed in vitro may play a role in the colonization of the periodontal pocket.

Specificity of a Bacteroides thetaiotaomicron marker for human feces

USGS Publications Warehouse

Carson, C.A.; Christiansen, J.M.; Yampara-Iquise, H.; Benson, V.W.; Baffaut, C.; Davis, J.V.; Broz, R.R.; Kurtz, W.B.; Rogers, W.M.; Fales, W.H.

2005-01-01

A bacterial primer set, known to produce a 542-bp amplicon specific for Bacteroides thetaiotaomicron, generated this product in PCR with 1 ng of extracted DNA from 92% of 25 human fecal samples, 100% of 20 sewage samples, and 16% of 31 dog fecal samples. The marker was not detected in 1 ng of fecal DNA from 61 cows, 35 horses, 44 pigs, 24 chickens, 29 turkeys, and 17 geese. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.

Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways.

PubMed

Marcobal, Angela; Barboza, Mariana; Sonnenburg, Erica D; Pudlo, Nicholas; Martens, Eric C; Desai, Prerak; Lebrilla, Carlito B; Weimer, Bart C; Mills, David A; German, J Bruce; Sonnenburg, Justin L

2011-11-17

Newborns are colonized with an intestinal microbiota shortly after birth, but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut, where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-N-neotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when biassociated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucus-adapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion. Copyright © 2011 Elsevier Inc. All rights reserved.

Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

PubMed Central

Marcobal, A.; Barboza, M.; Sonnenburg, E.D.; Pudlo, N.; Martens, E.C.; Desai, P.; Lebrilla, C.B.; Weimer, B.C.; Mills, D.A.; German, J.B.; Sonnenburg, J.L.

2011-01-01

Summary Newborns are colonized with an intestinal microbiota shortly after birth but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-N-neotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when bi-associated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucus-adapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion. PMID:22036470

Short communication: identification of a novel HIV type 1 subtype H/J recombinant in Canada with discordant HIV viral load (RNA) values in three different commercial assays.

PubMed

Kim, John E; Beckthold, Brenda; Chen, Zhaoxia; Mihowich, Jennifer; Malloch, Laurie; Gill, Michael John

2007-11-01

The presence of HIV-1 non-B subtypes is increasing worldwide. This poses challenges to commercial diagnostic and viral load (RNA) monitoring tests that are predominantly based on HIV-1 subtype B strains. Based on phylogenetic analysis of the gag, pol, and env gene regions, we describe the first HIV-1 H/J recombinant in Canada that presented divergent viral load values. DNA sequence analysis of the gag gene region further revealed that genetic diversity between this H/J recombinant and the primers and probes used in the bio-Merieux Nuclisens HIV-1 QT (Nuclisens) and Roche Amplicor Monitor HIV-1, v1.5 (Monitor) viral RNA assays can erroneously lead to undetectable viral load values. This observation appears to be more problematic in the Nuclisens assay. In light of increasing genetic diversity in HIV worldwide we recommend that DNA sequencing of HIV, especially in the gag gene region targeted by primers and probes used in molecular diagnostic and viral load tests, be incorporated into clinical monitoring practices.

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

PubMed Central

Wu, Meng; McNulty, Nathan P.; Rodionov, Dmitry A.; Khoroshkin, Matvei S.; Griffin, Nicholas W.; Cheng, Jiye; Latreille, Phil; Kerstetter, Randall A.; Terrapon, Nicolas; Henrissat, Bernard; Osterman, Andrei L.; Gordon, Jeffrey I.

2015-01-01

Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in ordered sequence. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability and resilience, and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. PMID:26430127

Validity and reliability of the Omron HJ-303 tri-axial accelerometer-based pedometer.

PubMed

Steeves, Jeremy A; Tyo, Brian M; Connolly, Christopher P; Gregory, Douglas A; Stark, Nyle A; Bassett, David R

2011-09-01

This study compared the validity of a new Omron HJ-303 piezoelectric pedometer and 2 other pedometers (Sportline Traq and Yamax SW200). To examine the effect of speed, 60 subjects walked on a treadmill at 2, 3, and 4 mph. Twenty subjects also ran at 6, 7, and 8 mph. To test lifestyle activities, 60 subjects performed front-back-side-side stepping, elliptical machine and stair climbing/descending. Twenty others performed ballroom dancing. Sixty participants completed 5 100-step trials while wearing 5 different sets of the devices tested device reliability. Actual steps were determined using a hand tally counter. Significant differences existed among pedometers (P < .05). For walking, the Omron pedometers were the most valid. The Sportline overestimated and the Yamax underestimated steps (P < .05). Worn on the waist or in the backpack, the Omron device and Sportline were valid for running. The Omron was valid for 3 activities (elliptical machine, ascending and descending stairs). The Sportline overestimated all of these activities, and Yamax was only valid for descending stairs. The Omron andYamax were both valid and reliable in the 100-step trials. The Omron HJ-303, worn on the waist, appeared to be the most valid of the 3 pedometers.

Assessing the effects of land use spatial structure on urban heat islands using HJ-1B remote sensing imagery in Wuhan, China

NASA Astrophysics Data System (ADS)

Wu, Hao; Ye, Lu-Ping; Shi, Wen-Zhong; Clarke, Keith C.

2014-10-01

Urban heat islands (UHIs) have attracted attention around the world because they profoundly affect biological diversity and human life. Assessing the effects of the spatial structure of land use on UHIs is essential to better understanding and improving the ecological consequences of urbanization. This paper presents the radius fractal dimension to quantify the spatial variation of different land use types around the hot centers. By integrating remote sensing images from the newly launched HJ-1B satellite system, vegetation indexes, landscape metrics and fractal dimension, the effects of land use patterns on the urban thermal environment in Wuhan were comprehensively explored. The vegetation indexes and landscape metrics of the HJ-1B and other remote sensing satellites were compared and analyzed to validate the performance of the HJ-1B. The results have showed that land surface temperature (LST) is negatively related to only positive normalized difference vegetation index (NDVI) but to Fv across the entire range of values, which indicates that fractional vegetation (Fv) is an appropriate predictor of LST more than NDVI in forest areas. Furthermore, the mean LST is highly correlated with four class-based metrics and three landscape-based metrics, which suggests that the landscape composition and the spatial configuration both influence UHIs. All of them demonstrate that the HJ-1B satellite has a comparable capacity for UHI studies as other commonly used remote sensing satellites. The results of the fractal analysis show that the density of built-up areas sharply decreases from the hot centers to the edges of these areas, while the densities of water, forest and cropland increase. These relationships reveal that water, like forest and cropland, has a significant effect in mitigating UHIs in Wuhan due to its large spatial extent and homogeneous spatial distribution. These findings not only confirm the applicability and effectiveness of the HJ-1B satellite system for

Morphology and formation mechanism in precipitation of calcite induced by Curvibacter lanceolatus strain HJ-1

NASA Astrophysics Data System (ADS)

Zhang, Chonghong; Li, Fuchun; Lv, Jiejie

2017-11-01

Precipitation of calcium carbobate induced by microbial activities is common occurrence in controlled solution, but the formation mechanism and morphology in precipitation of calcite in solution systems is unclear, and the role of microbes is disputed. Here, culture experiment was performed for 50 days using the Curvibacter lanceolatus strain HJ-1 in a M2 culture medium, and the phase composition and morphology of the precipitates were characterized by the X-ray diffraction (XRD), Fourier transform infrared (FT-IR), and scanning electron microscopy (SEM) techniques. We show that the precipitation processes in our experiment lead to unusual morphologies of crystals corresponding to different growth stages, and the morphologies of the precipitated crystal aggregates ranging from the main rod-, cross-, star-, cauliflower-like morphologies to spherulitic structure. The complex and unusual morphologies of the precipitated calcite by strain HJ-1 may provide a reference point for better understanding the biomineralization mechanism of calcite, moreover, morphological transition of minerals revealed that the multi-ply crystals-aggregation mechanism for calcite growth in crystallisation media.

15. 'Concrete Bridge Over Salt River, Port Kenyon, Humboldt County, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. 'Concrete Bridge Over Salt River, Port Kenyon, Humboldt County, California, A.J. Logan, County Surveyor, H.J. Brunnier, Consulting Engineer, March 7, 1919,' showing general plan, plan of top chord, elevation of main girder, transverse section, plan section at deck level. - Salt River Bridge, Spanning Salt River at Dillon Road, Ferndale, Humboldt County, CA

Persistence of Bacteroides ovatus under simulated sunlight irradiation

PubMed Central

2014-01-01

Background Bacteroides ovatus, a member of the genus Bacteroides, is considered for use in molecular-based methods as a general fecal indicator. However, knowledge on its fate and persistence after a fecal contamination event remains limited. In this study, the persistence of B. ovatus was evaluated under simulated sunlight exposure and in conditions similar to freshwater and seawater. By combining propidium monoazide (PMA) treatment and quantitative polymerase chain reaction (qPCR) detection, the decay rates of B. ovatus were determined in the presence and absence of exogenous photosensitizers and in salinity up to 39.5 parts per thousand at 27°C. Results UVB was found to be important for B. ovatus decay, averaging a 4 log10 of decay over 6 h of exposure without the presence of extracellular photosensitizers. The addition of NaNO2, an exogenous sensitizer producing hydroxyl radicals, did not significantly change the decay rate of B. ovatus in both low and high salinity water, while the exogenous sensitizer algae organic matter (AOM) slowed down the decay of B. ovatus in low salinity water. At seawater salinity, the decay rate of B. ovatus was slower than that in low salinity water, except when both NaNO2 and AOM were present. Conclusion The results of laboratory experiments suggest that if B. ovatus is released into either freshwater or seawater environment in the evening, 50% of it may be intact by the next morning; if it is released at noon, only 50% may be intact after a mere 5 min of full spectrum irradiation on a clear day. This study provides a mechanistic understanding to some of the important environmental relevant factors that influenced the inactivation kinetics of B. ovatus in the presence of sunlight irradiation, and would facilitate the use of B. ovatus to indicate the occurrence of fecal contamination. PMID:24993443

Invertebrates of The H.J. Andrews Experimental Forest, Western Cascades, Oregon: III. The Orthoptera (Grasshoppers and Crickets).

Treesearch

David C. Lightfoot

1986-01-01

An inventory of Orthoptera (grasshoppers and crickets) at the H.J. Andrews Experimental Forest, near Blue River, Oregon, was conducted to determine the species present and ecological relationships. A key for identification and an annotated list are presented. From qualitative assessments of successional habitat relationships, generalized species associations of forest...

Near-complete genome sequence of the cellulolytic Bacterium Bacteroides ( Pseudobacteroides) cellulosolvens ATCC 35603

DOE PAGES

Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; ...

2015-09-24

We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

Morphology, antigenicity, and nucleic acid content of the Bacteroides sp. used in the culture of Entamoeba histolytica.

PubMed

Albach, R A; Shaffer, J G; Watson, R H

1965-10-01

Albach, Richard A. (Lutheran General Hospital, Park Ridge, Ill.), James G. Shaffer, and Robert H. Watson. Morphology, antigenicity, and nucleic acid content of the Bacteroides sp. used in the culture of Entamoeba histolytica. J. Bacteriol. 90:1045-1053. 1965.-Certain changes in morphology, antigenicity, and nucleic acid content that occur in a culture of Bacteroides sp. in the presence of penicillin G in CLG medium are described. This "variant" is one of seven recovered in several laboratories, all of which are descendants of the original Bacteroides isolated by Shaffer and Frye. Penicillin-inhibited cells of this culture are currently being used in the routine propagation of Entamoeba histolytica in CLG medium. Evidence is presented for the loss of ability to react with antibody in these penicillin-inhibited bacteria in CLG medium, when studied by fluorescent-antibody techniques. The implications of the antigenic changes observed as they pertain to similar antigenic studies of the amoebas are discussed. A pronounced reduction in the ribonucleic acid (RNA) content of such penicillin-inhibited cells was also observed. The potential importance of the changes that occur in the RNA of these cells with respect to considerations of the growth requirements of the amoebas is also discussed.

Feeding the masses: H.J. Heinz and the creation of industrial food.

PubMed

Petrick, Gabriella M

2009-03-01

The H.J. Heinz Company's commitment to the purity and quality of its products in the late nineteenth and early twentieth century helped usher in an era of industrial food. While canning had been around for decades, it was not until both scientist and technologists innovations solved problems like bacterial contamination and mass-produced cans that Americans began to eat canned food on a regular basis. In addition to money-back guarantees, Heinz pioneered product tastings as a marketing tool in an attempt to convince skeptical housewives that his products were not only delicious, but were also safe to eat.

High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

DOE PAGES

Sakamoto, Mitsuo; Lapidus, Alla L.; Han, James; ...

2015-08-02

Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2T is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. We report that the 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakamoto, Mitsuo; Lapidus, Alla L.; Han, James

Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2T is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. We report that the 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Influence of Environmental and Genetic Factors Linked to Celiac Disease Risk on Infant Gut Colonization by Bacteroides Species▿

PubMed Central

Sánchez, Ester; De Palma, Giada; Capilla, Amalia; Nova, Esther; Pozo, Tamara; Castillejo, Gemma; Varea, Vicente; Marcos, Ascensión; Garrote, José Antonio; Polanco, Isabel; López, Ana; Ribes-Koninckx, Carmen; García-Novo, Maria Dolores; Calvo, Carmen; Ortigosa, Luis; Palau, Francesc; Sanz, Yolanda

2011-01-01

Celiac disease (CD) is an immune-mediated enteropathy involving genetic and environmental factors whose interaction might influence disease risk. The aim of this study was to determine the effects of milk-feeding practices and the HLA-DQ genotype on intestinal colonization of Bacteroides species in infants at risk of CD development. This study included 75 full-term newborns with at least one first-degree relative suffering from CD. Infants were classified according to milk-feeding practice (breast-feeding or formula feeding) and HLA-DQ genotype (high or low genetic risk). Stools were analyzed at 7 days, 1 month, and 4 months by PCR and denaturing gradient gel electrophoresis (DGGE). The Bacteroides species diversity index was higher in formula-fed infants than in breast-fed infants. Breast-fed infants showed a higher prevalence of Bacteroides uniformis at 1 and 4 months of age, while formula-fed infants had a higher prevalence of B. intestinalis at all sampling times, of B. caccae at 7 days and 4 months, and of B. plebeius at 4 months. Infants with high genetic risk showed a higher prevalence of B. vulgatus, while those with low genetic risk showed a higher prevalence of B. ovatus, B. plebeius, and B. uniformis. Among breast-fed infants, the prevalence of B. uniformis was higher in those with low genetic risk than in those with high genetic risk. Among formula-fed infants, the prevalence of B. ovatus and B. plebeius was increased in those with low genetic risk, while the prevalence of B. vulgatus was higher in those with high genetic risk. The results indicate that both the type of milk feeding and the HLA-DQ genotype influence the colonization process of Bacteroides species, and possibly the disease risk. PMID:21642397

DESIGN AND EVALUATION OF BACTEROIDES DNA PROBES FOR THE SPECIFIC DETECTION OF HUMAN FECAL POLLUTION

EPA Science Inventory

Because Bacteroides spp. are obligate anaerobes that dominate the human fecal flora, and because some species may live only in the human intestine, these bacteria might be useful to distinguish human from nonhuman sources of fecal pollution. To test this hypothesis, PCR primers s...

Porphyromonas (Bacteroides) endodontalis: its role in endodontal infections.

PubMed

van Winkelhoff, A J; van Steenbergen, T J; de Graaff, J

1992-09-01

Porphyromonas endodontalis (formerly Bacteroides endodontalis) is a black-pigmented anaerobic Gram-negative rod which is associated with endodontal infections. It has been isolated from infected dental root canals and submucous abscesses of endodontal origin. The presence of P. endodontalis in infected dental root canals has been correlated with symptoms of an acute infection. It is occasionally found on oral mucous membranes and periodontal pockets. P. endodontalis has shown relatively low virulence in experimental monoinfections. In anaerobic mixed infections it can play an essential role. Differences in virulence between strains have been related to capsular material. On the basis of different types of capsules, three serotypes have been described. P. endodontalis is sensitive to a wide range of antibiotics, including the penicillins, the tetracyclines, and metronidazole.

USE OF BACTEROIDES PCR-BASED METHODS TO EXAMINE FECAL CONTAMINATION SOURCES IN TROPICAL COASTAL WATERS

EPA Science Inventory

Several library independent Microbial Source Tracking methods have been developed to rapidly determine the source of fecal contamination. Thus far, none of these methods have been tested in tropical marine waters. In this study, we used a Bacteroides 16S rDNA PCR-based...

Vertebral osteomyelitis caused by Prevotella (Bacteroides) melaninogenicus.

PubMed

Mukhopadhyay, Surabhi; Rose, Fredrick; Frechette, Vincent

2005-02-01

A 35-year-old, previously healthy female presented with severe low back pain, fever, and a high erythrocyte sedimentation rate 1 week after a routine dental cleaning. Technetium-labeled leukocyte scanning and magnetic resonance imaging scan of the spine were negative for osteomyelitis. The patient underwent biopsy, cultures from which grew Prevotella (Bacteroides) melaninogenicus. Appropriate antibiotic therapy resulted in resolution of symptoms. P. melaninogenicus is a gram-negative anaerobic bacillus that is part of the indigenous oral flora. It may cause dental, sinus, skin, and soft tissue infections. Infection of bone is rare. Only three cases of vertebral osteomyelitis due to P. melaninogenicus have been reported in the literature. The early diagnosis of vertebral osteomyelitis requires a high index of clinical suspicion and cannot be excluded by negative imaging tests alone. The recovery of this unusual organism highlights the importance of requesting anaerobic cultures of biopsy specimens.

Degradation of paracetamol by Pseudomonas aeruginosa strain HJ1012.

PubMed

Hu, Jun; Zhang, Li L; Chen, Jian M; Liu, Yu

2013-01-01

Pseudomonas aeruginosa strain HJ1012 was isolated on paracetamol as a sole carbon and energy source. This organism could completely degrade paracetamol as high as 2200 mg/L. Following paracetamol consumption, a CO₂ yield rate up to 71.4% proved that the loss of paracetamol was mainly via mineralization. Haldane's equation adequately described the relationship between the specific growth rate and substrate concentration. The maximum specific growth rate and yield coefficient were 0.201 g-Paracetamol/g-VSS·h and 0.101 mg of biomass yield/mg of paracetamol consumed, respectively. A total of 8 metabolic intermediates was identified and classified into aromatic compounds, carboxylic acids, and inorganic species (nitrite and nitrate ions). P-aminophenol and hydroquinone are the two key metabolites of the initial steps in the paracetamol catabolic pathway. Paracetamol is degraded predominantly via p-aminophenol to hydroquinone with subsequent ring fission, suggesting partially new pathways for paracetamol-degrading bacteria.

Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron.

PubMed

Schwalm, Nathan D; Townsend, Guy E; Groisman, Eduardo A

2016-10-11

The utilization of simple sugars is widespread across all domains of life. In contrast, the breakdown of complex carbohydrates is restricted to a subset of organisms. A regulatory paradigm for integration of complex polysaccharide breakdown with simple sugar utilization was established in the mammalian gut symbiont Bacteroides thetaiotaomicron, whereby sensing of monomeric fructose regulates catabolism of both fructose and polymeric fructans. We now report that a different regulatory paradigm governs utilization of monomeric arabinose and the arabinose polymer arabinan. We establish that (i) arabinan utilization genes are controlled by a transcriptional activator that responds to arabinan and by a transcriptional repressor that responds to arabinose, (ii) arabinose utilization genes are regulated directly by the arabinose-responding repressor but indirectly by the arabinan-responding activator, and (iii) activation of both arabinan and arabinose utilization genes requires a pleiotropic transcriptional regulator necessary for survival in the mammalian gut. Genomic analysis predicts that this paradigm is broadly applicable to the breakdown of other polysaccharides in both B. thetaiotaomicron and other gut Bacteroides spp. The uncovered mechanism enables regulation of polysaccharide utilization genes in response to both the polysaccharide and its breakdown products. Breakdown of complex polysaccharides derived from "dietary fiber" is achieved by the mammalian gut microbiota. This breakdown creates a critical nutrient source for both the microbiota and its mammalian host. Because the availability of individual polysaccharides fluctuates with variations in the host diet, members of the microbiota strictly control expression of polysaccharide utilization genes. Our findings define a regulatory architecture that controls the breakdown of a polysaccharide by a gut bacterium in response to three distinct signals. This architecture integrates perception of a complex

Clustering Disjoint HJ-Biplot: A new tool for identifying pollution patterns in geochemical studies.

PubMed

Nieto-Librero, A B; Sierra, C; Vicente-Galindo, M P; Ruíz-Barzola, O; Galindo-Villardón, M P

2017-06-01

This paper introduces a new mathematical algorithm termed Clustering Disjoint HJ-Biplot (CDBiplot), which searches for the underlying data structure in order to find the best classification of the object groups in a reduced space. To this end, disjoint factorial axes are generated, in which each variable only contributes to the formation of one factorial axis. A graphical representation of the individuals and variables is performed using the HJ-Biplot method. In order to facilitate the use of this new method within any practical context, a function in the language R has been developed. This work applies the CDBiplot to study an environmental geochemistry case involving environmental pollution in river surface sediments. The study focuses on an area close to an important mining and metallurgical site, where sediments share a similar geological origin and chemical composition. The algorithm permitted a detailed study of the geochemical interactions and performed an excellent separation of the samples. Thus, the groups obtained were formed according to a similar geological origin, location, and nature of the anthropogenic inputs based only on chemical composition data. These results allowed clear identification of the sources of pollution and the delimitation of the polluted zones. All things considered, we conclude that the proposed algorithm is a powerful tool for studying environmental geochemistry data sets, and suggest that the application of this methodology be extended to other research fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides

PubMed Central

Benítez-Páez, Alfonso; Gómez del Pulgar, Eva M.; Sanz, Yolanda

2017-01-01

Bacteroides spp. are dominant components of the phylum Bacteroidetes in the gut microbiota and prosper in glycan enriched environments. However, knowledge of the machinery of specific species isolated from humans (like Bacteroides uniformis) contributing to the utilization of dietary and endogenous sources of glycans and their byproducts is limited. We have used the cutting-edge nanopore-based technology to sequence the genome of B. uniformis CECT 7771, a human symbiont with a proven pre-clinical efficacy on metabolic and immune dysfunctions in obesity animal models. We have also used massive sequencing approaches to distinguish the genome expression patterns in response to carbon sources of different complexity during growth. At genome-wide level, our analyses globally demonstrate that B. uniformis strains exhibit an expanded glycolytic capability when compared with other Bacteroides species. Moreover, by studying the growth and whole-genome expression of B. uniformis CECT 7771 in response to different carbon sources, we detected a differential growth fitness and expression patterns across the genome depending on the carbon source of the culture media. The dietary fibers used exerted different effects on B. uniformis CECT 7771 activating different molecular pathways and, therefore, allowing the production of different metabolite types with potential impact on gut health. The genome and transcriptome analysis of B. uniformis CECT 7771, in response to different carbon sources, shows its high versatility to utilize both dietary and endogenous glycans along with the production of potentially beneficial end products for both the bacterium and the host, pointing to a mechanistic basis of a mutualistic relationship. PMID:28971068

Characterization of saccharolytic Bacteroides and Prevotella isolates from infected dog and cat bite wounds in humans.

PubMed Central

Alexander, C J; Citron, D M; Hunt Gerardo, S; Claros, M C; Talan, D; Goldstein, E J

1997-01-01

Saccharolytic, nonpigmented, anaerobic gram-negative rods isolated from infected dog and cat bite wounds in humans have been poorly characterized, and most are not included in the databases of kits used for anaerobic identification; thus, they are problematic for clinical laboratories to identify. Fifty strains isolated from such wounds were characterized with commercial kits for preformed-enzyme detection, carbohydrate fermentation, and other biochemical tests. PCR fingerprinting was performed on these strains to further characterize subgroups within these species. Bacteroides tectum is a frequent isolate in bite wounds and resembles Prevotella bivia in colony morphology and saccharolytic activity, except that it grows in 20% bile and hydrolyzes esculin. Profile numbers generated by various kits associate B. tectum with P. bivia, Prevotella oralis group, or Prevotella melaninogenica. PCR fingerprinting identified at least four subgroups and confirmed the heterogeneous nature of this species. Prevotella heparinolytica was also frequently isolated from these bite wounds. It produces indole and generates a profile number in preformed-enzyme kits that is usually associated with Bacteroides uniformis. However, it is bile sensitive and quite distinct from the Bacteroides fragilis group of anaerobes. The PCR fingerprint profiles generated by strains of P. heparinolytica were very similar to that of the type strain and to each other. Prevotella zoogleoformans, occasionally isolated from dog and cat bite wounds in humans, resembles P. heparinolytica except for a negative indole test. Clinical laboratories should be aware of the characteristics of these animal species when identifying isolates from animal bite wounds in humans. PMID:9003606

Characterization of saccharolytic Bacteroides and Prevotella isolates from infected dog and cat bite wounds in humans.

PubMed

Alexander, C J; Citron, D M; Hunt Gerardo, S; Claros, M C; Talan, D; Goldstein, E J

1997-02-01

Saccharolytic, nonpigmented, anaerobic gram-negative rods isolated from infected dog and cat bite wounds in humans have been poorly characterized, and most are not included in the databases of kits used for anaerobic identification; thus, they are problematic for clinical laboratories to identify. Fifty strains isolated from such wounds were characterized with commercial kits for preformed-enzyme detection, carbohydrate fermentation, and other biochemical tests. PCR fingerprinting was performed on these strains to further characterize subgroups within these species. Bacteroides tectum is a frequent isolate in bite wounds and resembles Prevotella bivia in colony morphology and saccharolytic activity, except that it grows in 20% bile and hydrolyzes esculin. Profile numbers generated by various kits associate B. tectum with P. bivia, Prevotella oralis group, or Prevotella melaninogenica. PCR fingerprinting identified at least four subgroups and confirmed the heterogeneous nature of this species. Prevotella heparinolytica was also frequently isolated from these bite wounds. It produces indole and generates a profile number in preformed-enzyme kits that is usually associated with Bacteroides uniformis. However, it is bile sensitive and quite distinct from the Bacteroides fragilis group of anaerobes. The PCR fingerprint profiles generated by strains of P. heparinolytica were very similar to that of the type strain and to each other. Prevotella zoogleoformans, occasionally isolated from dog and cat bite wounds in humans, resembles P. heparinolytica except for a negative indole test. Clinical laboratories should be aware of the characteristics of these animal species when identifying isolates from animal bite wounds in humans.

Necessary work: discovering old forests, new outlooks, and community on the H.J. Andrews Experimental Forest, 1948-2000.

Treesearch

Max G. Geier

2007-01-01

The H.J. Andrews Experimental Forest (Andrews Forest) is both an idea and a particular place. It is an experimental landscape, a natural resource, and an ecosystem that has long inspired many people. On the landscape of the Andrews Forest, some of those people built the foundation for a collaborative community that fosters closer communication among the scientists and...

Invertebrates of the H.J. Andrews Experimental Forest, western Cascades, Oregon II. an annotated checklist of caddisflies (Trichoptera)

Treesearch

N.H. Anderson; G.M. Cooper; D.G Denning

1982-01-01

At least 99 species, representing 14 families of Trichoptera, are recorded from the H.J. Andrews Experimental Forest, near Blue River, Oregon. The collecting sites include a wide diversity of environmental conditions in a 6000-hectare watershed of the western Cascade Range (from 400 to 1 630 meters in altitude and from 1st- to 7th-order streams).

Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States

EPA Science Inventory

Phages infecting human-associated Bacteroides fragilis (GB-124 phages) have been employed in the European Union (EU) to identify human fecal pollution, but their utility for U.S. was unclear. Primary sewage effluent samples were collected seasonally from seven wastewater treatme...

Measurement of the Position Angle and Separation of HJ 1924

NASA Astrophysics Data System (ADS)

Badami, Umar Ahmed; Tock, Kalée.; Carpenter, Steve; Kruger, Kurt; Freed, Rachel; Genet, Russell

2018-01-01

The position angle and separation of the binary HJ 1924 have been measured and noted in 10 publications since John Herschel's initial observation in 1828. Measurement techniques have improved in both precision and accuracy since that time. Although Herschel's initial measurement was slightly different, the position angle and separation of these stars have remained relatively constant for the past 122 years. The system was observed using the Skynet Robotic Telescope Network. AstroImageJ software was used to contribute a new data point. Our measurement of 8.12" ± 0.0127 (1 ± SEM), 225.1o ± 0.0298 (1 ± SEM),was in agreement with the 10 most recent published measurements, but not the initial one, implying that Herschel's measurement may have been inaccurate. While these stars appear to exhibit similar proper motion, and may therefore share a common origin, they are unlikely to be gravitationally bound.

Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

DOE PAGES

Natarajan, Padmaja; Punta, Marco; Kumar, Abhinav; ...

2015-01-16

N-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family can be found in most Bacteroides species and, in large numbers, in all human gut microbiome samples. Both BVU_4064 and BF1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. The C-terminal half of BVU_4064 is assigned to protein family PF12986 (DUF3870); the equivalent part of BF1687 was unclassified.

Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

USGS Publications Warehouse

Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

2013-01-01

Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

Use of abundance ratios of somatic coliphages and bacteriophages of Bacteroides thetaiotaomicron GA17 for microbial source identification.

PubMed

Muniesa, Maite; Lucena, Francisco; Blanch, Anicet R; Payán, Andrey; Jofre, Juan

2012-12-01

Water contaminated with human faeces is a risk to human health and management of water bodies can be improved by determining the sources of faecal pollution. Field studies show that existing methods are insufficient and that different markers are required. This study proposes the combined use of two microbial indicators, the concentrations of which are presented as ratios. This provides a more reliable approach to identifying faecal sources as it avoids variation due to treatment or ageing of the contamination. Among other indicators, bacteriophages have been proposed as rapid and cheap indicators of faecal pollution. Samples analysed in this study were derived from wastewater treatment plants (raw sewage, secondary and tertiary effluents and raw sewage sludge) river water, seawater and animal related wastewater. The abundance ratios of faecal coliforms and Bacteroides phages, either strain RYC2056 (non-specific for faecal origin) or strain GA17 (specific for human pollution), and among somatic coliphages and phages infecting both Bacteroides strains, were evaluated. The results indicate that the ratio of somatic coliphages and phages infecting Bacteroides strain GA17, which is specific to human faecal sources, provides a robust method for discriminating samples, even those presenting different levels and ages of pollution, and allows samples polluted with human faeces to be distinguished from those containing animal faecal pollution. This method allows the generation of numerical data that can be further applied to numerical methods for faecal pollution discrimination. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison of randomly cloned and whole genomic DNA probes for the detection of Porphyromonas gingivalis and Bacteroides forsythus

PubMed Central

Wong, M.; DiRienzo, J.M.; Lai, C.-H.; Listgarten, M. A.

2012-01-01

Whole genomic and randomly-cloned DNA probes for two fastidious periodontal pathogens, Porphyromonas gingivalis and Bacteroides forsythus were labeled with digoxigenin and detected by a colorimetric method. The specificity and sensitivity of the whole genomic and cloned probes were compared. The cloned probes were highly specific compared to the whole genomic probes. A significant degree of cross-reactivity with Bacteroides species. Capnocytophaga sp. and Prevotella sp. was observed with the whole genomic probes. The cloned probes were less sensitive than the whole genomic probes and required at least 106 target cells or a minimum of 10 ng of target DNA to be detected during hybridization. Although a ten-fold increase in sensitivity was obtained with the whole genomic probes, cross-hybridization to closely related species limits their reliability in identifying target bacteria in subgingival plaque samples. PMID:8636873

Improved HF183 reverse primer and probe for greater analytical sensitivity of human Bacteroides in the environment

EPA Science Inventory

Background: Numerous indicators have been used to assess the presence of fecal pollution, many relying on molecular methods such as qPCR. One of the targets frequently used, the human-associated Bacteroides 16s rRNA region, has several assays in current usage. These assays vary...

Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks

USGS Publications Warehouse

McGinnis, Shannon; Spencer, Susan K.; Firnstahl, Aaron; Stokdyk, Joel; Borchardt, Mark A.; McCarthy, David; Murphy, Heather

2018-01-01

Combined sewer overflows (CSOs) are a known source of human fecal pollution and human pathogens in urban water bodies, which may present a significant public health threat. To monitor human fecal contamination in water, bacterial fecal indicator organisms (FIOs) are traditionally used. However, because FIOs are not specific to human sources and do not correlate with human pathogens, alternative fecal indicators detected using qPCR are becoming of interest to policymakers. For this reason, this study measured correlations between the number and duration of CSOs and mm of rainfall, concentrations of traditional FIOs and alternative indicators, and the presence of human pathogens in two urban creeks. Samples were collected May–July 2016 and analyzed for concentrations of FIOs (total coliforms and E. coli) using membrane filtration as well as for three alternative fecal indicators (human Bacteroides HF183 marker, human polyomavirus (HPoV), pepper mild mottle virus (PMMoV)) and nine human pathogens using qPCR. Four of the nine pathogens analyzed were detected at these sites including adenovirus, Enterohemorrhagic E. coli, norovirus, and Salmonella. Among all indicators studied, human Bacteroides and total coliforms were significantly correlated with recent CSO and rainfall events, while E. coli, PMMoV, and HPoV did not show consistent significant correlations. Further, human Bacteroides were a more specific indicator, while total coliforms were a more sensitive indicator of CSO and rainfall events. Results may have implications for the use and interpretation of these indicators in future policy or monitoring programs.

Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks.

PubMed

McGinnis, Shannon; Spencer, Susan; Firnstahl, Aaron; Stokdyk, Joel; Borchardt, Mark; McCarthy, David T; Murphy, Heather M

2018-07-15

Combined sewer overflows (CSOs) are a known source of human fecal pollution and human pathogens in urban water bodies, which may present a significant public health threat. To monitor human fecal contamination in water, bacterial fecal indicator organisms (FIOs) are traditionally used. However, because FIOs are not specific to human sources and do not correlate with human pathogens, alternative fecal indicators detected using qPCR are becoming of interest to policymakers. For this reason, this study measured correlations between the number and duration of CSOs and mm of rainfall, concentrations of traditional FIOs and alternative indicators, and the presence of human pathogens in two urban creeks. Samples were collected May-July 2016 and analyzed for concentrations of FIOs (total coliforms and E. coli) using membrane filtration as well as for three alternative fecal indicators (human Bacteroides HF183 marker, human polyomavirus (HPoV), pepper mild mottle virus (PMMoV)) and nine human pathogens using qPCR. Four of the nine pathogens analyzed were detected at these sites including adenovirus, Enterohemorrhagic E. coli, norovirus, and Salmonella. Among all indicators studied, human Bacteroides and total coliforms were significantly correlated with recent CSO and rainfall events, while E. coli, PMMoV, and HPoV did not show consistent significant correlations. Further, human Bacteroides were a more specific indicator, while total coliforms were a more sensitive indicator of CSO and rainfall events. Results may have implications for the use and interpretation of these indicators in future policy or monitoring programs. Copyright © 2018 Elsevier B.V. All rights reserved.

Identification and Use of the Putative Bacteroides ovatus Xylanase Promoter for the Inducible Production of Recombinant Human Proteins

USDA-ARS?s Scientific Manuscript database

The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ov...

Observation of sand waves in the Taiwan Banks using HJ-1A/1B sun glitter imagery

NASA Astrophysics Data System (ADS)

Zhang, Hua-guo; Lou, Xiu-lin; Shi, Ai-qin; He, Xie-kai; Guan, Wei-bing; Li, Dong-ling

2014-01-01

This study focuses on the large sand waves in the Taiwan Banks. Our goals are to observe the sand waves as completely as possible, to obtain their direction, wavelength, density, and ridge length, to analyze their spatial distributions, and to understand the effects of the current field and water depth on the sand waves. This study demonstrates the possibility of using HJ-1A/1B sun glitter imagery with a large swath width and rapid coverage in studying sand waves. Six cloud-free HJ-1A/1B optical images with sun glitter signals received during 2009 to 2011 were processed. The sand waves were mapped based on their features in the images; their direction, wavelength, density, and ridge length were measured and analyzed. We identified 4604 sand waves distributed in an area of 16,400 km2. The distributions of sand waves and their characteristics were analyzed, and the differences of sand waves between the northwestern subregion and the southeastern subregion are reported. Further analysis and discussion of the relationships between spatial distribution of the sand waves and both the tidal current field from a numerical simulation and water depth led to some interesting conclusions. The current field determines the orientation of the sand wave, while the hydrodynamic conditions and water depth influence the shape, size, and density of sand waves to a certain degree.

Growth yields and fermentation balance of Bacteroides fragilis cultured in glucose-enriched medium.

PubMed

Frantz, J C; McCallum, R E

1979-03-01

Bacteroides fragilis is an obligate anaerobic bacterium classified with the gram-negative, non-sporeforming bacilli and is the Bacteroides species most frequently isolated from human infections. In the present study, experiments were designed to investigate growth characteristics of B. fragilis in a complex medium. In a minimal defined medium, which was employed for comparison purposes, B. fragilis grew with a generation time of 2 h. Growth of the organism in glucose-enriched medium used in the present study was superior. Maximum generation time was 60 min. Total and viable cells (colony-forming units) were 8.9 x 10(9) and 2.1 x 10(9), respectively, at maximum measurable growth. The molar growth yield (Ym) was 51.5. Growth yields were found to reach a maximum 2 to 3 h before maximum growth and to vary with respect to the phase of growth. Estimates of the fermentation products indicated that glucose was the sole energy substrate. Major products included acetic acid, propionic acid, lactic acid, and succinic acid. Other products included ethyl alcohol, pyruvic acid, and fumaric acid. No attempt was made to recover CO2 or formic acid. The OR balances from two experiments were 0.013 and -0.093 and the respective carbon recoveries were 6.268 and 6.241. The results of the present study show that B. fragilis is capable of rapid rates of growth in vitro by using glucose as the sole energy source.

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

USDA-ARS?s Scientific Manuscript database

Bacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host-derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, in...

Two Multidrug-Resistant Clinical Isolates of Bacteroides fragilis Carry a Novel Metronidazole Resistance nim Gene (nimJ)

PubMed Central

Veeranagouda, Yaligara; Hsi, Justin; Meggersee, Rosemary; Abratt, Valerie; Wexler, Hannah M.

2013-01-01

Two multidrug-resistant Bacteroides fragilis clinical isolates contain and express a novel nim gene, nimJ, that is not recognized by the “universal” nim primers and can confer increased resistance to metronidazole when introduced into a susceptible strain on a multicopy plasmid. HMW615, an appendiceal isolate, contains at least two copies of nimJ on its genome, while HMW616, an isolate from a patient with sepsis, contains one genomic copy of nimJ. B. fragilis NimJ is phylogenetically closer to Prevotella baroniae NimI and Clostridium botulinum NimA than to the other known Bacteroides Nim proteins. The predicted protein structure of NimJ, based on fold recognition analysis, is consistent with the crystal structures derived for known Nim proteins, and specific amino acid residues important for substrate binding in the active site are conserved. This study demonstrates that the “universal” nim primers will not detect all nim genes with the ability to confer metronidazole resistance, but nimJ alone cannot account for the very high metronidazole MICs of these resistant clinical isolates. PMID:23716049

Invertebrates of The H.J. Andrews Experimental Forest, Western Cascade Range, Oregon. V: An Annotated List of Insects and Other Arthropods

Treesearch

Gary L. Parson; Gerasimos Cassis; Andrew R. Moldenke; John D. Lattin; Norman H. Anderson; Jeffrey C Miller; Paul Hammond; Timothy D. Schowalter

1991-01-01

An annotated list of species of insects and other arthropods that have been collected and studies on the H.J. Andrews Experimental forest, western Cascade Range, Oregon. The list includes 459 families, 2,096 genera, and 3,402 species. All species have been authoritatively identified by more than 100 specialists. Information is included on habitat type, functional group...

Invertebrates of The H.J. Andrews Experimental Forest, western Cascade Range, Oregon. V: An annotated list of insects and other arthropods.

Treesearch

Gary L. Parson; Gerasimos Cassis; Andrew R. Moldenke; John D. Lattin; Norman H. Anderson; Jeffrey C Miller; Paul Hammond; Timothy D. Schowalter

1991-01-01

An annotated list of species of insects and other arthropods that have been collected and studies on the H.J. Andrews Experimental forest, western Cascade Range, Oregon. The list includes 459 families, 2,096 genera, and 3,402 species. All species have been authoritatively identified by more than 100 specialists. Information is included on habitat type, functional group...

Interaction of metronidazole with resistant and susceptible Bacteroides fragilis.

PubMed Central

McLafferty, M A; Koch, R L; Goldman, P

1982-01-01

The kinetics of the lethal action of metronidazole and the formation of acetamide have been studied in a strain of Bacteroides fragilis which is relatively resistant to metronidazole. As with a susceptible strain of B. fragilis, the data are consistent with a model in which a labile intermediate in metronidazole metabolism interacts either with water to form acetamide or with a bacterium to cause its death. Although the relatively resistant strain grows more slowly than the susceptible one and is killed less rapidly by metronidazole, the resistant strain displays the same relationship between the lethal action of metronidazole and metronidazole metabolism to acetamide. The relatively resistant strain, like the susceptible one, has an enhanced lethal response to metronidazole in the presence of a strain of Escherichia coli. The results suggest that the proposed labile reactive intermediate of metronidazole forms more slowly in the resistant strains. PMID:7081970

Suppurative otitis and ascending meningoencephalitis associated with Bacteroides tectus and Porphyromonas gulae in a captive Parma wallaby (Macropus parma) with toxoplasmosis.

PubMed

Giannitti, Federico; Schapira, Andrea; Anderson, Mark; Clothier, Kristin

2014-09-01

A 6-year-old female Parma wallaby (Macropus parma) at a zoo in California developed acute ataxia and left-sided circling. Despite intensive care, clinical signs progressed to incoordination and prostration, and the animal was euthanized. At necropsy, the left tympanic cavity was filled with homogeneous suppurative exudate that extended into the cranium expanding the meninges and neuroparenchyma in the lateral and ventral aspect of the caudal ipsilateral brainstem and medulla oblongata. Microscopically, the brainstem showed regional severe suppurative meningoencephalitis with large numbers of neutrophils, fewer macrophages, and lymphocytes admixed with fibrin, necrotic cellular debris, hemorrhage, and mineralization, with numerous intralesional Gram-negative bacilli. Bacteroides spp. and Porphyromonas spp. were isolated on anaerobic culture from the meninges, and the bacteria were further characterized by partial 16S ribosomal RNA gene sequencing as Bacteroides tectus and Porphyromonas gulae. Bacterial aerobic culture from the meninges yielded very low numbers of mixed flora and Proteus spp., which were considered contaminants. Culture of Mycoplasma spp. from middle ear and meninges was negative. Additionally, Toxoplasma gondii cysts were detected by immunohistochemistry in the heart and brain, and anti-Toxoplasma antibodies were detected in serum. The genera Bacteroides and Porphyromonas have been associated with oral disease in marsupials; but not with otitis and meningoencephalitis. The results of the present work highlight the importance of performing anaerobic cultures in the diagnostic investigation of cases of suppurative otitis and meningoencephalitis in macropods. © 2014 The Author(s).

Medicago truncatula DNF2 is a PI-PLC-XD-containing protein required for bacteroid persistence and prevention of nodule early senescence and defense-like reactions.

PubMed

Bourcy, Marie; Brocard, Lysiane; Pislariu, Catalina I; Cosson, Viviane; Mergaert, Peter; Tadege, Millon; Mysore, Kirankumar S; Udvardi, Michael K; Gourion, Benjamin; Ratet, Pascal

2013-03-01

Medicago truncatula and Sinorhizobium meliloti form a symbiotic association resulting in the formation of nitrogen-fixing nodules. Nodule cells contain large numbers of bacteroids which are differentiated, nitrogen-fixing forms of the symbiotic bacteria. In the nodules, symbiotic plant cells home and maintain hundreds of viable bacteria. In order to better understand the molecular mechanism sustaining the phenomenon, we searched for new plant genes required for effective symbiosis. We used a combination of forward and reverse genetics approaches to identify a gene required for nitrogen fixation, and we used cell and molecular biology to characterize the mutant phenotype and to gain an insight into gene function. The symbiotic gene DNF2 encodes a putative phosphatidylinositol phospholipase C-like protein. Nodules formed by the mutant contain a zone of infected cells reduced to a few cell layers. In this zone, bacteria do not differentiate properly into bacteroids. Furthermore, mutant nodules senesce rapidly and exhibit defense-like reactions. This atypical phenotype amongst Fix(-) mutants unravels dnf2 as a new actor of bacteroid persistence inside symbiotic plant cells. © 2012 CNRS. New Phytologist © 2012 New Phytologist Trust.

Products of dark CO sub 2 fixation in pea root nodules support bacteroid metabolism. [Pisum sativum L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosendahl, L.; Pedersen, W.B.; Vance, C.P.

1990-05-01

Products of the nodule cytosol in vivo dark ({sup 14}C)CO{sub 2} fixation were detected in the plant cytosol as well as in the bacteroids of pea (Pisum sativum L. cv Bodil) nodules. The distribution of the metabolites of the dark CO{sub 2} fixation products was compared in effective (fix{sup +}) nodules infected by a wild-type Rhizobium leguminosarum (MNF 300), and ineffective (fix{sup {minus}}) nodules of the R. leguminosarum mutant MNF 3080. The latter has a defect in the dicarboxylic acid transport system of the bacterial membrane. The {sup 14}C incorporation from ({sup 14}C)CO{sub 2} was about threefold greater in themore » wild-type nodules than in the mutant nodules. Similarly, in wild-type nodules the in vitro phosphoenolpyruvate carboxylase activity was substantially greater than that of the mutant. Almost 90% of the {sup 14}C label in the cytosol was found in organic acids in both symbioses. The results indicate a central role for nodule cytosol dark CO{sub 2} fixation in the supply of the bacteroids with dicarboxylic acids.« less

Cross calibration of GF-1 satellite wide field of view sensor with Landsat 8 OLI and HJ-1A HSI

NASA Astrophysics Data System (ADS)

Liu, Li; Gao, Hailiang; Pan, Zhiqiang; Gu, Xingfa; Han, Qijin; Zhang, Xuewen

2018-01-01

This paper focuses on cross calibrating the GaoFen (GF-1) satellite wide field of view (WFV) sensor using the Landsat 8 Operational Land Imager (OLI) and HuanJing-1A (HJ-1A) hyperspectral imager (HSI) as reference sensors. Two methods are proposed to calculate the spectral band adjustment factor (SBAF). One is based on the HJ-1A HSI image and the other is based on ground-measured reflectance. However, the HSI image and ground-measured reflectance were measured at different dates, as the WFV and OLI imagers passed overhead. Three groups of regions of interest (ROIs) were chosen for cross calibration, based on different selection criteria. Cross-calibration gains with nonzero and zero offsets were both calculated. The results confirmed that the gains with zero offset were better, as they were more consistent over different groups of ROIs and SBAF calculation methods. The uncertainty of this cross calibration was analyzed, and the influence of SBAF was calculated based on different HSI images and ground reflectance spectra. The results showed that the uncertainty of SBAF was <3% for bands 1 to 3. Two other large uncertainties in this cross calibration were variation of atmosphere and low ground reflectance.

Xylan-regulated Delivery of Human Keratinocyte Growth Factor-2 to the Inflamed Colon by the Human Anaerobic Commensal Bacterium Bacteroides ovatus

USDA-ARS?s Scientific Manuscript database

The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ov...

A mitochondrial-like aconitase in the bacterium Bacteroides fragilis: implications for the evolution of the mitochondrial Krebs cycle.

PubMed

Baughn, Anthony D; Malamy, Michael H

2002-04-02

Aconitase and isocitrate dehydrogenase (IDH) enzyme activities were detected in anaerobically prepared cell extracts of the obligate anaerobe Bacteroides fragilis. The aconitase gene was located upstream of the genes encoding the other two components of the oxidative branch of the Krebs cycle, IDH and citrate synthase. Mutational analysis indicates that these genes are cotranscribed. A nonpolar in-frame deletion of the acnA gene that encodes the aconitase prevented growth in glucose minimal medium unless heme or succinate was added to the medium. These results imply that B. fragilis has two pathways for alpha-ketoglutarate biosynthesis-one from isocitrate and the other from succinate. Homology searches indicated that the B. fragilis aconitase is most closely related to aconitases of two other Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria, Cytophaga hutchinsonii and Fibrobacter succinogenes. Phylogenetic analysis indicates that the CFB group aconitases are most closely related to mitochondrial aconitases. In addition, the IDH of C. hutchinsonii was found to be most closely related to the mitochondrial/cytosolic IDH-2 group of eukaryotic organisms. These data suggest a common origin for these Krebs cycle enzymes in mitochondria and CFB group bacteria.

Activation of Bacteroides fragilis toxin by a novel bacterial protease contributes to anaerobic sepsis in mice.

PubMed

Choi, Vivian M; Herrou, Julien; Hecht, Aaron L; Teoh, Wei Ping; Turner, Jerrold R; Crosson, Sean; Bubeck Wardenburg, Juliane

2016-05-01

Bacteroides fragilis is the leading cause of anaerobic bacteremia and sepsis. Enterotoxigenic strains that produce B. fragilis toxin (BFT, fragilysin) contribute to colitis and intestinal malignancy, yet are also isolated in bloodstream infection. It is not known whether these strains harbor unique genetic determinants that confer virulence in extra-intestinal disease. We demonstrate that BFT contributes to sepsis in mice, and we identify a B. fragilis protease called fragipain (Fpn) that is required for the endogenous activation of BFT through the removal of its auto-inhibitory prodomain. Structural analysis of Fpn reveals a His-Cys catalytic dyad that is characteristic of C11-family cysteine proteases that are conserved in multiple pathogenic Bacteroides spp. and Clostridium spp. Fpn-deficient, enterotoxigenic B. fragilis has an attenuated ability to induce sepsis in mice; however, Fpn is dispensable in B. fragilis colitis, wherein host proteases mediate BFT activation. Our findings define a role for B. fragilis enterotoxin and its activating protease in the pathogenesis of bloodstream infection, which indicates a greater complexity of cellular targeting and activity of BFT than previously recognized. The expression of fpn by both toxigenic and nontoxigenic strains suggests that this protease may contribute to anaerobic sepsis in ways that extend beyond its role in toxin activation. It could thus potentially serve as a target for disease modification.

Brain abscess due to Aggregatibacter aphrophilus and Bacteroides uniformis.

PubMed

Bogdan, Maja; Zujić Atalić, Vlasta; Hećimović, Ivan; Vuković, Dubravka

2015-01-01

The aim of this report was to describe the occurrence of a bacterial brain abscess in a healthy individual, without any predisposing condition. A thirteen-year old boy was admitted to the Department of Neurosurgery after the onset of vomiting, headache and dizziness. A neurological deficit was detected during the physical examination so urgent magnetic resonance imaging of the brain was performed, revealing an intrahemispheric, right positioned solitary expansive mass with ring enhancement. Purulent material was obtained during osteoplastic craniotomy with total extirpation of the brain abscess. Aggregatibacter aphrophilus and Bacteroides uniformis were isolated. The patient's general condition improved and the neurological deficit subsided as a result of the prompt recognition and treatment of this life threatening condition. To achieve a favourable clinical outcome, prompt recognition and surgical treatment of a brain abscess are of primary importance,followed by administration of appropriate antimicrobial therapy. To our best knowledge, this is the first report of this combination of microorganisms as the cause of a brain abscess. Copyright © 2015 by Academy of Sciences and Arts of Bosnia and Herzegovina.

Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia.

PubMed

Lu, Haifeng; Qian, Guirong; Ren, Zhigang; Zhang, Chunxia; Zhang, Hua; Xu, Wei; Ye, Ping; Yang, Yunmei; Li, Lanjuan

2015-06-23

The microbiomes of humans are associated with liver and lung inflammation. We identified and verified alterations of the oropharyngeal microbiome and assessed their association with cirrhosis and pneumonia. Study components were as follows: (1) determination of the temporal stability of the oropharyngeal microbiome; (2) identification of oropharyngeal microbial variation in 90 subjects; (3) quantitative identification of disease-associated bacteria. DNAs enriched in bacterial sequences were produced from low-biomass oropharyngeal swabs using whole genome amplification and were analyzed using denaturing gradient gel electrophoresis analysis. Whole genome amplification combined with denaturing gradient gel electrophoresis analysis monitored successfully oropharyngeal microbial variations and showed that the composition of each subject's oropharyngeal microbiome remained relatively stable during the follow-up. The microbial composition of cirrhotic patients with pneumonia differed from those of others and clustered together in subgroup analysis. Further, species richness and the value of Shannon's diversity and evenness index increased significantly in patients with cirrhosis and pneumonia versus others (p < 0.001, versus healthy controls; p < 0.01, versus cirrhotic patients without pneumonia). Moreover, we identified variants of Bacteroides, Eubacterium, Lachnospiraceae, Neisseria, Actinomyces, and Streptococcus through phylogenetic analysis. Quantitative polymerase chain reaction assays revealed that the populations of Bacteroides, Neisseria, and Actinomycetes increased, while that of Streptococcus decreased in cirrhotic patients with pneumonia versus others (p < 0.001, versus Healthy controls; p < 0.01, versus cirrhotic patients without pneumonia). Alterations of Bacteroides, Neisseria, Actinomyces, and Streptococcus populations in the oropharyngeal microbiome were associated with liver cirrhosis and pneumonia.

Bacteroides gingivalis-Actinomyces viscosus cohesive interactions as measured by a quantitative binding assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwarz, S.; Ellen, R.P.; Grove, D.A.

1987-10-01

There is limited evidence, mostly indirect, to suggest that the adherence of Bacteroides gingivalis to teeth may be enhanced by the presence of gram-positive dental plaque bacteria like Actinomyces viscosus. The purpose of this study was to carry out direct quantitative assessments of the cohesion of B gingivalis and A. viscosus by using an in vitro assay modeled on the natural sequence in which these two species colonize the teeth. The assay allowed comparisons to be made of the adherence of /sup 3/H-labeled B. gingivalis 2561 and 381 to saliva-coated hydroxyapatite beads (S-HA) and A. viscosus WVU627- or T14V-coated S-HAmore » (actinobeads) in equilibrium and kinetics binding studies. A series of preliminary binding studies with 3H-labeled A. viscosus and parallel studies by scanning electron microscopy with unlabeled A. viscosus were conducted to establish a protocol by which actinobeads suitable for subsequent Bacteroides adherence experiments could be prepared. By scanning electron microscopy, the actinobeads had only small gaps of exposed S-HA between essentially irreversibly bound A. viscosus cells. Furthermore, B. gingivalis cells appeared to bind preferentially to the Actinomyces cells instead of the exposed S-HA. B. gingivalis binding to both S-HA and actinobeads was saturable with at least 2 X 10(9) to 3 X 10(9) cells per ml, and equilibrium with saturating concentrations was reached within 10 to 20 min. B. gingivalis always bound in greater numbers to the actinobeads than to S-HA. These findings provide direct measurements supporting the concept that cohesion with dental plaque bacteria like A. viscosus may foster the establishment of B. gingivalis on teeth by enhancing its adherence.« less

Atmospheric correction of HJ-1 CCD imagery over turbid lake waters.

PubMed

Zhang, Minwei; Tang, Junwu; Dong, Qing; Duan, Hongtao; Shen, Qian

2014-04-07

We have presented an atmospheric correction algorithm for HJ-1 CCD imagery over Lakes Taihu and Chaohu with highly turbid waters. The Rayleigh scattering radiance (Lr) is calculated using the hyperspectral Lr with a wavelength interval 1nm. The hyperspectral Lr is interpolated from Lr in the central wavelengths of MODIS bands, which are converted from the band response-averaged Lr calculated using the Rayleigh look up tables (LUTs) in SeaDAS6.1. The scattering radiance due to aerosol (La) is interpolated from La at MODIS band 869nm, which is derived from MODIS imagery using a shortwave infrared atmospheric correction scheme. The accuracy of the atmospheric correction algorithm is firstly evaluated by comparing the CCD measured remote sensing reflectance (Rrs) with MODIS measurements, which are validated by the in situ data. The CCD measured Rrs is further validated by the in situ data for a total of 30 observation stations within ± 1h time window of satellite overpass and field measurements. The validation shows the mean relative errors about 0.341, 0.259, 0.293 and 0.803 at blue, green, red and near infrared bands.

Incorporation of leucine into phospholipids of Bacteroides thetaiotaomicron.

PubMed Central

Smith, R D; Salyers, A A

1981-01-01

L-[4,5-3H]- or L-[U-14C]leucine was incorporated by Bacteroides thetaiotaomicron into acid-precipitable material even when the bacteria were treated with concentrations of tetracycline high enough to prevent growth. Similar results were obtained when L-[2,3,4-3H]valine or L-[4,5-3H]isoleucine was used instead of leucine. In bacteria which had been treated with tetracycline, the acid-precipitable label was not solubilized by treatment with protease, lysozyme, or deoxyribonuclease. However, virtually all of the label was extractable with chloroform-methanol, indicating that the label had been incorporated into membrane lipids. Since L-[1-14C]leucine was not incorporated into lipids, leucine was probably decarboxylated before incorporation. When a chloroform extract from bacteria which had been labeled with both [32P]phosphate and [3H]leucine was resolved into component phospholipids by two-dimensional thin-layer chromatography, 3H was incorporated into all of the phospholipids. When these phospholipids were deacylated, the 3H from leucine was associated with released fatty acids rather than with the head groups. Thus, it appears that B. thetaiotaomicron can utilize leucine and similar amino acids not only by incorporating them into protein but also by incorporating portions of these amino acids into membrane phospholipids. PMID:7462155

Monoclonal antibody against a serotype antigen of Porphyromonas (Bacteroides) endodontalis and characteristics of the antigen.

PubMed Central

Hanazawa, S; Sagiya, T; Amano, S; Nishikawa, H; Kitano, S

1990-01-01

Recent studies have demonstrated the presence of three serotypes (O1K1, O1K2, and O1K-) of Porphyromonas (Bacteroides) endodontalis. In the present study, a hybridoma cell line producing monoclonal antibody (BEE11) specific for serotype O1K1 of P. endodontalis was established. The specificity of the antibody was evaluated by enzyme-linked immunosorbent assay and immunoslot blot analysis. BEE11 antibody reacted with strains ATCC 35406, HG 400, and HG 421 of the bacterium. However, it did not react with HG 422 or HG 948. Also, the antibody did not react with any of the black-pigmented Bacteroides strains tested. Although the antibody reacted with total cell envelope and capsule materials, it did not do so with lipopolysaccharide. The antibody reacted with antigen material having a molecular mass of 110 kilodaltons (kDa), as judged from fractionation by Superose 12 prep gel chromatography. When the peak fraction from the Superose 12 column was subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analysis, the reactivity was detected as a single band at an apparent molecular mass of about 52 kDa. The antigen material purified partially by high-performance liquid chromatography was sensitive to trypsin, V8 protease, and heating to 80 degrees C but not to neuraminidase. Therefore, the present study shows that BEE11 antibody recognizes a serotype antigen of P. endodontalis which may be a dimer consisting of monomers having molecular masses of approximately 52 kDa and sensitivity to proteases and heat. Images PMID:2370106

Generation and purification of recombinant fimbrillin from Porphyromonas (Bacteroides) gingivalis 381.

PubMed Central

Washington, O R; Deslauriers, M; Stevens, D P; Lyford, L K; Haque, S; Yan, Y; Flood, P M

1993-01-01

Fimbrillin is the major subunit protein of fimbriae from the human periodontal pathogen Porphyromonas (Bacteroides) gingivalis. We describe here the generation and initial characterization of recombinant fimbrillin (r-fimbrillin) isolated from P. gingivalis 381. A fragment of DNA encoding the gene for fimbrillin was generated by polymerase chain reaction and cloned into the expression vector pET11b. Plasmids containing the recombinant gene were transfected into Escherichia coli. Clones were selected on plates for ampicillin resistance and individually screened by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for protein production after activation with IPTG (isopropyl-beta-D- thiogalactopyranoside). One clone, OW0.2, produced significant amounts of a 42-kDa protein after induction with IPTG. This clone contained the pET11b plasmid with a 1-kb insert that had sequence homology to the gene encoding fimbrillin. The majority of recombinant protein from clone OW0.2 was found in the cytoplasm within inclusion bodies. Protein aggregates were solubilized in 8 M urea, and SDS-PAGE analysis showed two major protein bands, one at 42 kDa and the other at 17 kDa. These two proteins coeluted from a DEAE-Sepharose column at 0.15 M NaCl and were reactive to rabbit antiserum to fimbrillin in a Western blot (immunoblot). A preparation giving a single protein band at 42 kDa in SDS-PAGE was obtained by size fractionation by using continuous-elution electrophoresis. Lymph node cells from animals immunized with either fimbrillin from P. gingivalis or r-fimbrillin showed antigen-specific proliferation to both P. gingivalis fimbrillin and r-fimbrillin in an in vitro recall assay. Therefore, it appears that r-fimbrillin is chemically, antigenically, and serologically identical to fimbrillin isolated from P. gingivalis 381. Images PMID:8094377

Multiple mobile promoter regions for the rare carbapenem resistance gene of Bacteroides fragilis.

PubMed

Podglajen, I; Breuil, J; Rohaut, A; Monsempes, C; Collatz, E

2001-06-01

Two novel insertion sequences (IS), IS1187 and IS1188, are described upstream from the carbapenem resistance gene cfiA in strains of Bacteroides fragilis. Mapping, with the RACE procedure, of transcription start sites of cfiA in these and two other previously reported IS showed that transcription of this rarely encountered gene is initiated close to a variety of B. fragilis consensus promoter sequences, as recently defined (D. P. Bayley, E. R. Rocha, and C. J. Smith, FEMS Microbiol. Lett. 193:149-154, 2000). In the cases of IS1186 and IS1188, these sequences overlap with putative Esigma(70) promoter sequences, while in IS942 and IS1187 such sequences can be observed either upstream or downstream of the B. fragilis promoters.

Formation of glycosidases in batch and continuous culture of Bacteroides fragilis.

PubMed Central

Berg, J O; Nord, C E; Wadström, T

1978-01-01

Nine strains of bacteroides fragilis were cultivated in stirred fermentors and tested for their ability to produce glycosidases. B. fragilis subsp. vulgatus B70 was used for optimizing the production of glycosidases. The highest bacterial yield was obtained in proteose peptone-yeast extract medium. The optimum pH for maximal bacterial yield was 7.0, and the optimum temperature for growth was 37 degrees C. The formation of glycosidases was optimal between pH 6.5 and 7.5, and the optimum temperature for synthesis of glycosidases was between 33 and 37 degrees C. Culture under controlled conditions in fermentors gave more reproducible production of glycosidases than static cultures in bottles. The strain was also grown in continuous culture at a dilution rate of 0.1 liter/h at pH 7.0 and 37 degrees C with a yield of 2.0 mg of dry weight per ml in the complex medium. The formation of glycosidases remained constant during the entire continuous process. PMID:25044

The capability of non-native strains of Bacteroides bacteria to detect bacteriophages as faecal indicators in a tropical area.

PubMed

Sirikanchana, K; Wangkahad, B; Mongkolsuk, S

2014-12-01

To evaluate the use of nonlocal, already-available strains of phages to indicate faecal contamination in Thailand waters. Phages of Bacteroides fragilis strains ATCC 700786 (RYC2056PH) and ATCC 51477 (HSP40PH) were measured in 71 human and animal wastewater samples in Thailand using a double-layer agar assay. Bacteriophage RYC2056PH was detected at concentrations comparable to representative human and animal wastewater samples from European and Mediterranean countries, with 61·7 and 33·3% above the threshold value of 100 PFU 100 ml(-1) in wastewater samples of human and animal origins, respectively. On the other hand, HSP40PH was detected at low concentrations in both human- and animal-polluted wastewaters. Moreover, RYC2056PH was found in 12 canal waters with human-influenced pollution and was not detected in 6 nonpolluted river waters being tested in this study. The presence of RYC2056PH could indicate nonsource-specific faecal contamination in Thailand. This study provided the first evidence that bacteriophages of the European-isolated B. fragilis strain RYC2056 could be used as nonsource-specific faecal indicators in the Southeast Asian region. The results of this study support the worldwide use of Bacteroides phages as faecal indicators. © 2014 The Society for Applied Microbiology.

Isolation and reconstitution of iron- and manganese-containing superoxide dismutases from Bacteroides thetaiotaomicron.

PubMed Central

Pennington, C D; Gregory, E M

1986-01-01

Superoxide dismutase (SOD) from extracts of anaerobically maintained Bacteroides thetaiotaomicron was a dimer of equally sized 23,000-molecular-weight monomers joined noncovalently. A preparation with a specific activity of 1,200 U/mg contained 1.1 g-atom of Fe, 0.6 g-atom of Zn, and less than 0.05 g-atom of Mn per mol of dimer. The apoprotein, prepared by dialysis of iron-SOD in 5 M guanidinium chloride-20 mM 8-hydroxyquinoline, had no superoxide-scavenging activity when renatured without exogenous metal. Enzymatic activity was restored to the denatured apoprotein by dialysis against either 1 mM Fe(NH4)2 or 1 mM MnCl2 in 20 mM Tris (pH 7.0). The Fe-reconstituted enzyme and the native enzyme were inhibited approximately 50% by 0.2 mM NaN3, whereas the Mn-reconstituted enzyme was inhibited 60% by 10 mM NaN3. Aeration of the anaerobic cells resulted in a fourfold induction of an azide-resistant SOD. The enzyme (43,000 molecular weight) isolated from aerated cells was a dimer of equally sized subunits. The metal content was 1.0 g-atom of Mn, 0.55 g-atom of Fe, and 0.3 g-atom of Zn per mol of dimer. Enzymatic activity of the denatured apoprotein from this enzyme was also restored on addition of either iron or manganese. The constitutive Fe-SOD and the O2-induced Mn-SOD, tested alone and in combination, migrated identically on acrylamide gels, had similar amino acid compositions, and had alanine as the sole N-terminal amino acid. These data are consistent with the synthesis of a single apoprotein in either anaerobically maintained or oxygenated cells. We have observed a similar phenomenon with SOD from Bacteroides fragilis (E. M. Gregory, Arch. Biochem. Biophys. 238:83-89, 1985). PMID:3700336

Pirin-like proteins are regulated by oxidative stress and iron in bacteroides fragilis and involved in the modulation of central energy metabolism and metronidazole susceptibility

USDA-ARS?s Scientific Manuscript database

Bacteroides fragilis is the most frequent anaerobe isolated from human infections. Clinical isolates of B. fragilis are among the highest aerotolerant anaerobic bacteria. The oxidative stress response (OSR) in B. fragilis induces an array of genes enabling them to survive prolonged oxygen exposure i...

[Spectrum similarities-based analysis of spatial difference of snow cover for multi-scale satellite data-a case study of MODIS and HJ-1B data].

PubMed

Liu, Yan; Li, Yang; Yang, Yun; Jian, Ji

2014-05-01

Vegetation and bare soil were collected in the areas of Miyaluo district in northwest of Sichuan province, the Qilian Mountains in Qinghai province and northern areas of Xinjiang during the years of 2007 and 2013. Then these data were converted to spectral reflectance by applying sensor response function of MODIS and HJ-1B respectively within the range of visible light, near-infrared and shortwave infrared. Comprehensive analysis was made on spectral characteristics and reflectivity similarities and differences of different sensors between old and new snowmelt, under the condition of different snow depth and different snow cover. The conclusions can be drawn That is, there exists high consistency of spectral response between new snow and dirty snow for each sensor in the visible wavelength range, also it is true for bare soil and low vegetation. However, low consistency happens to other types of snow; especially snowmelt and frozen snow. The range of NDSI is relatively stable under the condition of different snow depth for full snow cover and the trend of NDSI shows great consistency for different sensors; NDSI threshold method for monitoring snow by using MODIS and HJ-1B data showed very obvious difference in spatial scales, which is a reasonable explanation of the existence of mixed pixels.

Amino Acid and Vitamin Requirements of Several Bacteroides Strains

PubMed Central

Quinto, Grace

1966-01-01

Nutritional studies were performed on nine Bacteroides strains, by use of the methodology and media of anaerobic rumen microbiology. Ristella perfoetens CCI required l-arginine hydrochloride, l-tryptophan, l-leucine, l-histidine hydrochloride, l-cysteine hydrochloride, dl-valine, dl-tyrosine, and the vitamin calcium-d-pantothenate, since scant turbidity developed in media without these nutrients. R. perfoetens was stimulated by glycine, dl-lysine hydrochloride, dl-isoleucine, l-proline, l-glutamic acid, dl-alanine, dl-phenylalanine, dl-methionine, and the vitamins nicotinamide and p-aminobenzoic acid, since maximal turbidity developed more slowly in media without these nutrients than in complete medium. Medium A-23, which was devised for R. perfoetens, contained salts, 0.0002% nicotinamide and calcium d-pantothenate, 0.00001% p-aminobenzoic acid, 0.044% l-tryptophan, 0.09% l-glutamic acid, and 0.1% of the other 13 amino acids listed above. Zuberella clostridiformis and seven strains of R. pseudoinsolita did not require vitamins, and showed no absolute requirement for any one amino acid. Various strains produced maximal turbidity more slowly in media deficient in l-proline, glycine, l-glutamic acid, dl-serine, l-histidine hydrochloride, dl-alanine, or l-cysteine hydrochloride, than in complete medium. These eight strains grew optimally in medium A-23 plus 0.1% dl-serine but without vitamins. PMID:16349673

Stimulation of matrix metalloproteinases by black-pigmented Bacteroides in human pulp and periodontal ligament cell cultures.

PubMed

Chang, Yu-Chao; Lai, Chung-Chih; Yang, Shun-Fa; Chan, You; Hsieh, Yih-Shou

2002-02-01

Matrix metalloproteinases (MMPs) are a group of proteolytic enzymes capable of degrading most components of the extracellular matrix. Recently, evidence has shown that MMPs may play a role in tissue degradation in inflamed dental pulp. To date very little is known regarding the mechanism of extracellular matrix destruction at the site of bacterial infection. The purpose of this study was to determine the effects of the supernatants from Porphyromonas endodontalis and Porphyromonas gingivalis on the production and secretion of MMPs by primary human pulp and periodontal ligament (PDL) cell cultures in vitro. The results were evaluated by substrate gel zymography from long-term cultures. The main gelatinase secreted by human pulp and PDL cells migrated at 72 kDa and represented MMP-2. Minor gelatinolytic bands were also observed at 92 kDa regions that correspond to MMP-9. After an 8-day culture period, P. endodontalis and P. gingivalis were found to elevate MMP-2 production both in human pulp and PDL cell cultures. In addition, the stimulation was in a dose- and time-dependent manner. Both human pulp and PDL cells, however, treated with either P. endodontalis or P. gingivalis had no effect on the pattern of MMP-9 produced or secreted in either cell extracts or conditioned medium fractions. These results indicate that black-pigmented Bacteroides species play an important role in tissue destruction and disintegration of extracellular matrix in pulpal and periapical diseases. Thus, activation of MMPs may be one of the distinct host degradative pathways in the pathogenesis of microbial-induced pulpal and periapical lesion. An understanding of the actions of these black-pigmented Bacteroides species on pulp and PDL cells may result in new therapies to augment current treatment of pulpal and periapical lesions.

Bacteroides fragilis RecA protein overexpression causes resistance to metronidazole

PubMed Central

Steffens, Laura S.; Nicholson, Samantha; Paul, Lynthia V.; Nord, Carl Erik; Patrick, Sheila; Abratt, Valerie R.

2010-01-01

Bacteroides fragilis is a human gut commensal and an opportunistic pathogen causing anaerobic abscesses and bacteraemias which are treated with metronidazole (Mtz), a DNA damaging agent. This study examined the role of the DNA repair protein, RecA, in maintaining endogenous DNA stability and its contribution to resistance to Mtz and other DNA damaging agents. RT-PCR of B. fragilis genomic DNA showed that the recA gene was co-transcribed as an operon together with two upstream genes, putatively involved in repairing oxygen damage. A B. fragilis recA mutant was generated using targeted gene inactivation. Fluorescence microscopy using DAPI staining revealed increased numbers of mutant cells with reduced intact double-stranded DNA. Alkaline gel electrophoresis of the recA mutant DNA showed increased amounts of strand breaks under normal growth conditions, and the recA mutant also showed less spontaneous mutagenesis relative to the wild type strain. The recA mutant was sensitive to Mtz, ultraviolet light and hydrogen peroxide. A B. fragilis strain overexpressing the RecA protein exhibited increased resistance to Mtz compared to the wild type. This is the first study to show that overexpression of a DNA repair protein in B. fragilis increases Mtz resistance. This represents a novel drug resistance mechanism in this bacterium. PMID:20435137

Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism*

PubMed Central

Cameron, Elizabeth A.; Maynard, Mallory A.; Smith, Christopher J.; Smith, Thomas J.; Koropatkin, Nicole M.; Martens, Eric C.

2012-01-01

Human colonic bacteria are necessary for the digestion of many dietary polysaccharides. The intestinal symbiont Bacteroides thetaiotaomicron uses five outer membrane proteins to bind and degrade starch. Here, we report the x-ray crystallographic structures of SusE and SusF, two outer membrane proteins composed of tandem starch specific carbohydrate-binding modules (CBMs) with no enzymatic activity. Examination of the two CBMs in SusE and three CBMs in SusF reveals subtle differences in the way each binds starch and is reflected in their Kd values for both high molecular weight starch and small maltooligosaccharides. Thus, each site seems to have a unique starch preference that may enable these proteins to interact with different regions of starch or its breakdown products. Proteins similar to SusE and SusF are encoded in many other polysaccharide utilization loci that are possessed by human gut bacteria in the phylum Bacteroidetes. Thus, these proteins are likely to play an important role in carbohydrate metabolism in these abundant symbiotic species. Understanding structural changes that diversify and adapt related proteins in the human gut microbial community will be critical to understanding the detailed mechanistic roles that they perform in the complex digestive ecosystem. PMID:22910908

Generation of a rabbit single-chain fragment variable (scFv) antibody for specific detection of Bradyrhizobium sp. DOA9 in both free-living and bacteroid forms

PubMed Central

Srila, Witsanu; Yuttavanichakul, Watcharin; Teamtisong, Kamonluck; Teaumroong, Neung; Boonkerd, Nantakorn; Tittabutr, Panlada

2017-01-01

A simple and reliable method for the detection of specific nitrogen-fixing bacteria in both free-living and bacteroid forms is essential for the development and application of biofertilizer. Traditionally, a polyclonal antibody generated from an immunized rabbit was used for detection. However, the disadvantages of using a polyclonal antibody include limited supply and cross-reactivity to related bacterial strains. This is the first report on the application of phage display technology for the generation of a rabbit recombinant monoclonal antibody for specific detection and monitoring of nitrogen-fixing bacteria in both free-living form and in plant nodules. Bradyrhizobium sp. DOA9, a broad host range soil bacteria, originally isolated from the root nodules of Aeschynomene americana in Thailand was used as a model in this study. A recombinant single-chain fragment variable (scFv) antibody library was constructed from the spleen of a rabbit immunized with DOA9. After three rounds of biopanning, one specific phage-displayed scFv antibody, designated bDOA9rb8, was identified. Specific binding of this antibody was confirmed by phage enzyme-linked immunosorbent assay (phage ELISA). The phage antibody could bind specifically to DOA9 in both free-living cells (pure culture) and bacteroids inside plant nodules. In addition to phage ELISA, specific and robust immunofluorescence staining of both free-living and bacteroid forms could also be observed by confocal-immunofluorescence imaging, without cross-reactivity with other tested bradyrhizobial strains. Moreover, specific binding of free scFv to DOA9 was also demonstrated by ELISA. This recombinant antibody can also be used for the study of the molecular mechanism of plant–microbe interactions in the future. PMID:28654662

Generation of a rabbit single-chain fragment variable (scFv) antibody for specific detection of Bradyrhizobium sp. DOA9 in both free-living and bacteroid forms.

PubMed

Vu, Nguyen Xuan; Pruksametanan, Natcha; Srila, Witsanu; Yuttavanichakul, Watcharin; Teamtisong, Kamonluck; Teaumroong, Neung; Boonkerd, Nantakorn; Tittabutr, Panlada; Yamabhai, Montarop

2017-01-01

A simple and reliable method for the detection of specific nitrogen-fixing bacteria in both free-living and bacteroid forms is essential for the development and application of biofertilizer. Traditionally, a polyclonal antibody generated from an immunized rabbit was used for detection. However, the disadvantages of using a polyclonal antibody include limited supply and cross-reactivity to related bacterial strains. This is the first report on the application of phage display technology for the generation of a rabbit recombinant monoclonal antibody for specific detection and monitoring of nitrogen-fixing bacteria in both free-living form and in plant nodules. Bradyrhizobium sp. DOA9, a broad host range soil bacteria, originally isolated from the root nodules of Aeschynomene americana in Thailand was used as a model in this study. A recombinant single-chain fragment variable (scFv) antibody library was constructed from the spleen of a rabbit immunized with DOA9. After three rounds of biopanning, one specific phage-displayed scFv antibody, designated bDOA9rb8, was identified. Specific binding of this antibody was confirmed by phage enzyme-linked immunosorbent assay (phage ELISA). The phage antibody could bind specifically to DOA9 in both free-living cells (pure culture) and bacteroids inside plant nodules. In addition to phage ELISA, specific and robust immunofluorescence staining of both free-living and bacteroid forms could also be observed by confocal-immunofluorescence imaging, without cross-reactivity with other tested bradyrhizobial strains. Moreover, specific binding of free scFv to DOA9 was also demonstrated by ELISA. This recombinant antibody can also be used for the study of the molecular mechanism of plant-microbe interactions in the future.

Fish meal extract bile esculin agar (FMBE) a selective medium for Bacteroides fragilis group.

PubMed

Beena, V K; Rao, S; Kotian, M; Shivananda, P G

1997-07-01

Fish meal extract bile esculin agar (FMBE) is prepared using Fish meal extract concentrate as the basal substance, for the selective isolation and presumptive identification of B.fragilis group. The efficiency of the medium was evaluated by growing stock cultures of B.fragilis groups as well as inoculating clinical specimens and comparing the results with Bacteroides bile esculin agar (BBE). All the 87 stock cultures of B.fragilis grew on FMBE and BBE. No other anaerobes tested grew on the medium. However 7 out of 65 neomycin resistant aerobes grew on the FMBE. From the 100 clinical samples, 62 strains of B. Fragilis group were recovered on FMBE and BBE, and 53 strains on supplemented BHIBA. The cost effectiveness, selectivity and the ability to detect esculin hydrolysis will enable FMBE as a suitable medium as comparable to that of BBE, if not superior.

Bacteroides fragilis mobilizable transposon Tn5520 requires a 71 base pair origin of transfer sequence and a single mobilization protein for relaxosome formation during conjugation.

PubMed

Vedantam, Gayatri; Knopf, Sarah; Hecht, David W

2006-01-01

Tn5520 is the smallest known bacterial mobilizable transposon and was isolated from an antibiotic resistant Bacteroides fragilis clinical isolate. When a conjugation apparatus is provided in trans, Tn5520 is mobilized (transferred) efficiently within, and from, both Bacteroides spp. and Escherichia coli. Only two genes are present on Tn5520; one encodes an integrase, and the other a multifunctional mobilization (Mob) protein BmpH. BmpH is essential for Tn5520 mobility. The focus of this study was to identify the Tn5520 origin of conjugative transfer (oriT) and to study BmpH-oriT binding. We delimited the functional Tn5520 oriT to a 71 bp sequence upstream of the bmpH gene. A plasmid vector harbouring this minimal 71 bp oriT was mobilized at the same frequency as that of intact Tn5520. The minimal oriT contains one 17 bp inverted repeat (IR) sequence. We constructed and tested multiple IR mutants and showed that the IR was essential in its entirety for mobilization. A nick site sequence (5'-GCTAC-3') was also identified within the minimal oriT; this sequence resembled nick sites found in plasmids of Gram positive origin. We further showed that mutation of a highly conserved GC dinucleotide in the nick site sequence completely abolished mobilization. We also purified BmpH and showed that it specifically bound a Tn5520 oriT fragment in electrophoretic mobility shift assays. We also identified non-nick site sequences within the minimal oriT that were essential for mobilization. We hypothesize that transposon-based single Mob protein systems may contribute to efficient gene dissemination from Bacteroides spp., because fewer DNA processing proteins are required for relaxosome formation.

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome.

PubMed

Lam, Kathy N; Martens, Eric C; Charles, Trevor C

2018-01-01

Functional metagenomics is a powerful method that allows the isolation of genes whose role may not have been predicted from DNA sequence. In this approach, first, environmental DNA is cloned to generate metagenomic libraries that are maintained in Escherichia coli, and second, the cloned DNA is screened for activities of interest. Typically, functional screens are carried out using E. coli as a surrogate host, although there likely exist barriers to gene expression, such as lack of recognition of native promoters. Here, we describe efforts to develop Bacteroides thetaiotaomicron as a surrogate host for screening metagenomic DNA from the human gut. We construct a B. thetaiotaomicron-compatible fosmid cloning vector, generate a fosmid clone library using DNA from the human gut, and show successful functional complementation of a B. thetaiotaomicron glycan utilization mutant. Though we were unable to retrieve the physical fosmid after complementation, we used genome sequencing to identify the complementing genes derived from the human gut microbiome. Our results demonstrate that the use of B. thetaiotaomicron to express metagenomic DNA is promising, but they also exemplify the challenges that can be encountered in the development of new surrogate hosts for functional screening. IMPORTANCE Human gut microbiome research has been supported by advances in DNA sequencing that make it possible to obtain gigabases of sequence data from metagenomes but is limited by a lack of knowledge of gene function that leads to incomplete annotation of these data sets. There is a need for the development of methods that can provide experimental data regarding microbial gene function. Functional metagenomics is one such method, but functional screens are often carried out using hosts that may not be able to express the bulk of the environmental DNA being screened. We expand the range of current screening hosts and demonstrate that human gut-derived metagenomic libraries can be

Studying the Pair WDS 01487+7528 = HJ 2075 AB Using the GAIA-DR1 Data

NASA Astrophysics Data System (ADS)

Romero, Francisco Rica

2018-01-01

In September 2016, the European Space Agency (ESA) released GAIA-DR1. ESA also published TGAS, a subset of Gaia source comprising those stars in the Hipparcos and Tycho-2 catalogs for which a full 5-parameters astrometric solution have been achieved. After publication of TGAS, the author decided to use the parallaxes and proper motions to review the double stars studied by LIADA’s Double Star Section during 2003. This year LIADA measured and studied 103 pairs of which only 10 have both stellar components listed in TGAS. Of those 10 pairs, 80% (8 double stars) are optical and only 2 are physical (with common parallaxes and proper motions).The main object of this work is a new study of HJ 2075 AB (WDS 01487+7528), located at 60 pc and composed of stars of 10.0 and 11.3 magnitudes with spectral types G8V and K4V separated by 31". This is a physical pair according to TGAS data (common parallaxes and proper motions).

Characterization of Glycosaminoglycan (GAG) Sulfatases from the Human Gut Symbiont Bacteroides thetaiotaomicron Reveals the First GAG-specific Bacterial Endosulfatase*

PubMed Central

Ulmer, Jonathan E.; Vilén, Eric Morssing; Namburi, Ramesh Babu; Benjdia, Alhosna; Beneteau, Julie; Malleron, Annie; Bonnaffé, David; Driguez, Pierre-Alexandre; Descroix, Karine; Lassalle, Gilbert; Le Narvor, Christine; Sandström, Corine; Spillmann, Dorothe; Berteau, Olivier

2014-01-01

Despite the importance of the microbiota in human physiology, the molecular bases that govern the interactions between these commensal bacteria and their host remain poorly understood. We recently reported that sulfatases play a key role in the adaptation of a major human commensal bacterium, Bacteroides thetaiotaomicron, to its host (Benjdia, A., Martens, E. C., Gordon, J. I., and Berteau, O. (2011) J. Biol. Chem. 286, 25973–25982). We hypothesized that sulfatases are instrumental for this bacterium, and related Bacteroides species, to metabolize highly sulfated glycans (i.e. mucins and glycosaminoglycans (GAGs)) and to colonize the intestinal mucosal layer. Based on our previous study, we investigated 10 sulfatase genes induced in the presence of host glycans. Biochemical characterization of these potential sulfatases allowed the identification of GAG-specific sulfatases selective for the type of saccharide residue and the attachment position of the sulfate group. Although some GAG-specific bacterial sulfatase activities have been described in the literature, we report here for the first time the identity and the biochemical characterization of four GAG-specific sulfatases. Furthermore, contrary to the current paradigm, we discovered that B. thetaiotaomicron possesses an authentic GAG endosulfatase that is active at the polymer level. This type of sulfatase is the first one to be identified in a bacterium. Our study thus demonstrates that bacteria have evolved more sophisticated and diverse GAG sulfatases than anticipated and establishes how B. thetaiotaomicron, and other major human commensal bacteria, can metabolize and potentially tailor complex host glycans. PMID:25002587

Safety Evaluation of a Novel Strain of Bacteroides fragilis.

PubMed

Wang, Ye; Deng, Huimin; Li, Zhengchao; Tan, Yafang; Han, Yanping; Wang, Xiaoyi; Du, Zongmin; Liu, Yangyang; Yang, Ruifu; Bai, Yang; Bi, Yujing; Zhi, Fachao

2017-01-01

Commensal non-toxigenic Bacteroides fragilis confers powerful health benefits to the host, and has recently been identified as a promising probiotic candidate. We previously isolated B. fragilis strain ZY-312 and identified it as a novel strain based on 16S rRNA sequencing and morphological analyses. We also determined that ZY-312 displayed desirable probiotic properties, including tolerance to simulated digestive fluid, adherence, and in vitro safety. In this study, we aim to investigate whether ZY-312 meets the safety criteria required for probiotic bacteria through comprehensive and systematic evaluation. Consequently, the fatty acid profile, metabolite production, and biochemical activity of strain ZY-312 were found to closely resemble descriptions of B. fragilis in Bergey's manual. Taxonomic identification of strain ZY-312 based on whole genome sequencing indicated that ZY-312 and ATCC 25285 showed 99.99% similarity. The 33 putative virulence-associated factors identified in ZY-312 mainly encoded structural proteins and proteins with physiological activity, while the lack of bft indicated that ZY-312 was non-toxigenic. In vivo safety was proven in both normal and immune-deficient mice. The 11 identified antibiotic resistance genes were located on the chromosome rather than on a plasmid, ruling out the risk of plasmid-mediated transfer of antibiotic resistance. In vitro , ZY-312 showed resistance to cefepime, kanamycin, and streptomycin. Finally, and notably, ZY-312 exhibited high genetic stability after 100 passages in vitro . This study supplements the foundation work on the safety evaluation of ZY-312, and contributes to the development of the first probiotic representative from the dominant Bacteroidetes phylum.

Dynamic monitoring of water petroleum substance using HJ-1/CCD remote sensing data

NASA Astrophysics Data System (ADS)

Huang, Miaofen; Xing, Xufeng; Zhao, Zulong; Li, Zhanqiang

2014-03-01

The experiment data used in this paper include CDOM(Chromophoric dissolved organic matter) absorption coefficient, water apparent optical properties and petroleum pollution concentration, which were obtained in May 2008, August 2009 and June 2010 respectively at Liaohe Oilfield in Panjin city, Liaoning province of China. A model between CDOM absorption coefficient and petroleum pollution concentration was developed, and then was applied to eight HJ-1CCD remote sense images obtained from 2009 to 2011, to produce multi-period temporal and spatial distribution maps of petroleum concentration in costal waters. Based on these thematic maps, the dynamic monitoring of petroleum pollution concentration distribution was done. The results showed that (1)There was a decreasing trend of petroleum concentration from costal waters to open sea, which manifest itself as an approximately zonal distribution;(2) due to low precipitation in May and June every year, the concentration of petroleum keeps in a relatively high value state; (3) in September, the concentration of petroleum decreases dramatically as pre increases, most of the area below 0.29 mg/L; (4) compared with that in the same period, the concentration of petroleum in April 2010 is apparently higher than in April 2011, and among the images in September from 2009 to 2011,the highest concentration of petroleum appears in 2010, and the lowest in 2009.

Bacteroides fragilis induce necrosis on mice peritoneal macrophages: In vitro and in vivo assays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vieira, J.M.B.D., E-mail: jmanya@terra.com.br; Laboratorio de Biologia de Anaerobios, IMPPG, UFRJ, Rio de Janeiro; Seabra, S.H.

Bacteroides fragilis is an anaerobic bacteria component of human intestinal microbiota and agent of infections. In the host B. fragilis interacts with macrophages, which produces toxic radicals like NO. The interaction of activated mice peritoneal macrophages with four strains of B. fragilis was evaluated on this study. Previously was shown that such strains could cause metabolic and morphologic alterations related to macrophage death. In this work propidium iodide staining showed the strains inducing macrophage necrosis in that the labeling was evident. Besides nitroblue tetrazolium test showed that B. fragilis stimulates macrophage to produce oxygen radicals. In vivo assays performed inmore » BalbC mice have results similar to those for in vitro tests as well as scanning electron microscopy, which showed the same surface pore-like structures observed in vitro before. The results revealed that B. fragilis strains studied lead to macrophage death by a process similar to necrosis.« less

Bioluminescence Imaging to Track Bacteroides fragilis Inhibition of Vibrio parahaemolyticus Infection in Mice.

PubMed

Li, Zhengchao; Deng, Huimin; Zhou, Yazhou; Tan, Yafang; Wang, Xiaoyi; Han, Yanping; Liu, Yangyang; Wang, Ye; Yang, Ruifu; Bi, Yujing; Zhi, Fachao

2017-01-01

Bacteroides fragilis is an anaerobic, Gram-negative, commensal bacterium of the human gut. It plays an important role in promoting the maturation of the immune system, as well as suppressing abnormal inflammation. Many recent studies have focused on the relationship between B. fragilis and human immunity, and indicate that B. fragilis has many useful probiotic effects. As inhibition of intestinal pathogens is an important characteristic of probiotic strains, this study examined whether B. fragilis could inhibit pathogenic bacteria. Results showed that Vibrio parahaemolyticus was inhibited by B. fragilis in vitro , and that B. fragilis could protect both RAW 264.7 and LoVo cells from damage caused by V. parahaemolyticus . Using in vivo imaging, we constructed a light-emitting V. parahaemolyticus strain and showed that B. fragilis might shorten the colonization time and reduce the number of lux -expressing bacteria in a mouse model. These results provide useful information for developing B. fragilis into a probiotic product, and also indicate that this commensal bacterium might aid in the clinical treatment of gastroenteritis caused by V. parahaemolyticus .

Bioluminescence Imaging to Track Bacteroides fragilis Inhibition of Vibrio parahaemolyticus Infection in Mice

PubMed Central

Li, Zhengchao; Deng, Huimin; Zhou, Yazhou; Tan, Yafang; Wang, Xiaoyi; Han, Yanping; Liu, Yangyang; Wang, Ye; Yang, Ruifu; Bi, Yujing; Zhi, Fachao

2017-01-01

Bacteroides fragilis is an anaerobic, Gram-negative, commensal bacterium of the human gut. It plays an important role in promoting the maturation of the immune system, as well as suppressing abnormal inflammation. Many recent studies have focused on the relationship between B. fragilis and human immunity, and indicate that B. fragilis has many useful probiotic effects. As inhibition of intestinal pathogens is an important characteristic of probiotic strains, this study examined whether B. fragilis could inhibit pathogenic bacteria. Results showed that Vibrio parahaemolyticus was inhibited by B. fragilis in vitro, and that B. fragilis could protect both RAW 264.7 and LoVo cells from damage caused by V. parahaemolyticus. Using in vivo imaging, we constructed a light-emitting V. parahaemolyticus strain and showed that B. fragilis might shorten the colonization time and reduce the number of lux-expressing bacteria in a mouse model. These results provide useful information for developing B. fragilis into a probiotic product, and also indicate that this commensal bacterium might aid in the clinical treatment of gastroenteritis caused by V. parahaemolyticus. PMID:28553617

The forgotten dispute: A.I. Oparin and H.J. Muller on the origin of life.

PubMed

Falk, Raphael; Lazcano, Antonio

2012-01-01

The debate between A.I. Oparin's heterotrophic proposal of the origin of life and H.J. Muller's suggestion that what may be considered a posteriori the beginning of life, was an autocatalytic, replicative gene, is analyzed. Although both recognized that what was needed was an interacting system contiguous in space and time, it is now rarely mentioned that this scientific confrontation went on for several decades against the background of intense ideological issues, political tensions, and scientific developments that include the rise and demise of Lysenkoism, on the one hand, and, on the other, the establishment of neoDarwinism and the birth of molecular biology. Whereas for Oparin life was the outcome of the step-wise slow process of precellular evolution in which membrane-bounded polymolecular systems played a key role, Muller argued that life started with the appearance of the first nucleic-acid (DNA) molecule in the primitive oceans. Oparin and Muller came from different scientific backgrounds and almost opposite intellectual traditions, so their common interest in the origin of life did nothing to assuage their opposing views, which as argued soon became part of the debates that took place within the framework of intense ideological confrontations.

Classification mapping and species identification of salt marshes based on a short-time interval NDVI time-series from HJ-1 optical imagery

NASA Astrophysics Data System (ADS)

Sun, Chao; Liu, Yongxue; Zhao, Saishuai; Zhou, Minxi; Yang, Yuhao; Li, Feixue

2016-03-01

Salt marshes are seen as the most dynamic and valuable ecosystems in coastal zones, and in these areas, it is crucial to obtain accurate remote sensing information on the spatial distributions of species over time. However, discriminating various types of salt marsh is rather difficult because of their strong spectral similarities. Previous salt marsh mapping studies have focused mainly on high spatial and spectral (i.e., hyperspectral) resolution images combined with auxiliary information; however, the results are often limited to small regions. With a high temporal and moderate spatial resolution, the Chinese HuanJing-1 (HJ-1) satellite optical imagery can be used not only to monitor phenological changes of salt marsh vegetation over short-time intervals, but also to obtain coverage of large areas. Here, we apply HJ-1 satellite imagery to the middle coast of Jiangsu in east China to monitor changes in saltmarsh vegetation cover. First, we constructed a monthly NDVI time-series to classify various types of salt marsh and then we tested the possibility of using compressed time-series continuously, to broaden the applicability of this particular approach. Our principal findings are as follows: (1) the overall accuracy of salt marsh mapping based on the monthly NDVI time-series was 90.3%, which was ∼16.0% higher than the single-phase classification strategy; (2) a compressed time-series, including NDVI from six key months (April, June-September, and November), demonstrated very little reduction (2.3%) in overall accuracy but led to obvious improvements in unstable regions; and (3) a simple rule for Spartina alterniflora identification was established using a scene solely from November, which may provide an effective way for regularly monitoring its distribution.

The Correlation Between Cognitive and Movement Shifting and Brain Activity in Children With ADHD.

PubMed

Kang, Kyoung Doo; Han, Doug Hyun; Kim, Sun Mi; Bae, Sujin; Renshaw, Perry F

2018-05-01

We assessed the correlation between the deficits of cognition, movement, and brain activity in children with Attention Deficit Hyperactvity Disorder (ADHD). We recruited 15 children with ADHD and 15 age- and sex-matched healthy control participants. Clinical symptoms, cognitive shifting, movement shifting, and brain activity were assessed using the Korean ADHD Rating Scale, the Wisconsin Card Sorting Test (WCST), the 7- and 14-ring drill test with hop jumps (7 HJ and 14 HJ), and 3.0 Tesla functional magnetic resonance imaging scanner, respectively. ADHD children showed an increased distance traveled and decreased speed on the 14 HJ task. In response to the WCST task, ADHD children showed decreased activation within right gyrus. Total distance on the 14 HJ task was negatively correlated with the mean β value of Cluster 2 in ADHD children. These results suggested that children with ADHD showed difficulty with attention shifting as well as with movement shifting.

Analysis of Poly-β-Hydroxybutyrate in Rhizobium japonicum Bacteroids by Ion-Exclusion High-Pressure Liquid Chromatography and UV Detection †

PubMed Central

Karr, Dale B.; Waters, James K.; Emerich, David W.

1983-01-01

Ion-exclusion high-pressure liquid chromatography (HPLC) was used to measure poly-β-hydroxybutyrate (PHB) in Rhizobium japonicum bacteroids. The products in the acid digest of PHB-containing material were fractionated by HPLC on Aminex HPX-87H ion-exclusion resin for organic acid analysis. Crotonic acid formed from PHB during acid digestion was detected by its intense absorbance at 210 nm. The Aminex-HPLC method provides a rapid and simple chromatographic technique for routine analysis of organic acids. Results of PHB analysis by Aminex-HPLC were confirmed by gas chromatography and spectrophotometric analysis. PMID:16346443

Analysis of Gut Microbiota in Patients with Parkinson's Disease.

PubMed

Petrov, V A; Saltykova, I V; Zhukova, I A; Alifirova, V M; Zhukova, N G; Dorofeeva, Yu B; Tyakht, A V; Kovarsky, B A; Alekseev, D G; Kostryukova, E S; Mironova, Yu S; Izhboldina, O P; Nikitina, M A; Perevozchikova, T V; Fait, E A; Babenko, V V; Vakhitova, M T; Govorun, V M; Sazonov, A E

2017-04-01

Gut microbiota of patients with Parkinson's disease and healthy volunteers was analyzed by the method of high throughput 16S rRNA sequencing of bacterial genomes. In patients with Parkinson's diseases, changes in the content of 9 genera and 15 species of microorganisms were revealed: reduced content of Dorea, Bacteroides, Prevotella, Faecalibacterium, Bacteroides massiliensis, Stoquefichus massiliensis, Bacteroides coprocola, Blautia glucerasea, Dorea longicatena, Bacteroides dorei, Bacteroides plebeus, Prevotella copri, Coprococcus eutactus, and Ruminococcus callidus, and increased content of Christensenella, Catabacter, Lactobacillus, Oscillospira, Bifidobacterium, Christensenella minuta, Catabacter hongkongensis, Lactobacillus mucosae, Ruminococcus bromii, and Papillibacter cinnamivorans. This microbiological pattern of gut microflora can trigger local inflammation followed by aggregation of α-synuclein and generation of Lewy bodies.

Safety Evaluation of a Novel Strain of Bacteroides fragilis

PubMed Central

Deng, Huimin; Li, Zhengchao; Tan, Yafang; Han, Yanping; Wang, Xiaoyi; Du, Zongmin; Liu, Yangyang; Yang, Ruifu; Bai, Yang; Bi, Yujing; Zhi, Fachao

2017-01-01

Commensal non-toxigenic Bacteroides fragilis confers powerful health benefits to the host, and has recently been identified as a promising probiotic candidate. We previously isolated B. fragilis strain ZY-312 and identified it as a novel strain based on 16S rRNA sequencing and morphological analyses. We also determined that ZY-312 displayed desirable probiotic properties, including tolerance to simulated digestive fluid, adherence, and in vitro safety. In this study, we aim to investigate whether ZY-312 meets the safety criteria required for probiotic bacteria through comprehensive and systematic evaluation. Consequently, the fatty acid profile, metabolite production, and biochemical activity of strain ZY-312 were found to closely resemble descriptions of B. fragilis in Bergey’s manual. Taxonomic identification of strain ZY-312 based on whole genome sequencing indicated that ZY-312 and ATCC 25285 showed 99.99% similarity. The 33 putative virulence-associated factors identified in ZY-312 mainly encoded structural proteins and proteins with physiological activity, while the lack of bft indicated that ZY-312 was non-toxigenic. In vivo safety was proven in both normal and immune-deficient mice. The 11 identified antibiotic resistance genes were located on the chromosome rather than on a plasmid, ruling out the risk of plasmid-mediated transfer of antibiotic resistance. In vitro, ZY-312 showed resistance to cefepime, kanamycin, and streptomycin. Finally, and notably, ZY-312 exhibited high genetic stability after 100 passages in vitro. This study supplements the foundation work on the safety evaluation of ZY-312, and contributes to the development of the first probiotic representative from the dominant Bacteroidetes phylum. PMID:28367145

Characterizing the Interactions between a Naturally Primed Immunoglobulin A and Its Conserved Bacteroides thetaiotaomicron Species-specific Epitope in Gnotobiotic Mice*

PubMed Central

Peterson, Daniel A.; Planer, Joseph D.; Guruge, Janaki L.; Xue, Lai; Downey-Virgin, Whitt; Goodman, Andrew L.; Seedorf, Henning; Gordon, Jeffrey I.

2015-01-01

The adaptive immune response to the human gut microbiota consists of a complex repertoire of antibodies interacting with a broad range of taxa. Fusing intestinal lamina propria lymphocytes from mice monocolonized with Bacteroides thetaiotaomicron to a myeloma fusion partner allowed us to recover hybridomas that captured naturally primed, antigen-specific antibody responses representing multiple isotypes, including IgA. One of these hybridomas, 260.8, produced a monoclonal antibody that recognizes an epitope specific for B. thetaiotaomicron isolates in a large panel of hospital- and community-acquired Bacteroides. Whole genome transposon mutagenesis revealed a 19-gene locus, involved in LPS O-antigen polysaccharide synthesis and conserved among multiple B. thetaiotaomicron isolates, that is required for 260.8 epitope expression. Mutants in this locus exhibited marked fitness defects in vitro during growth in rich medium and in gnotobiotic mice colonized with defined communities of human gut symbionts. Expression of the 260.8 epitope was sustained during 10 months of daily passage in vitro and during 14 months of monocolonization of gnotobiotic wild-type, Rag1−/−, or Myd88−/− mice. Comparison of gnotobiotic Rag1−/− mice with and without subcutaneous 260.8 hybridomas disclosed that this IgA did not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but did affect bacterial gene expression in ways emblematic of a diminished host innate immune response. Our study illustrates an approach for (i) generating diagnostic antibodies, (ii) characterizing IgA responses along a continuum of specificity/degeneracy that defines the IgA repertoire to gut symbionts, and (iii) identifying immunogenic epitopes that affect competitiveness and help maintain host-microbe mutualism. PMID:25795776

Comparison of lipopolysaccharides from Bacteroides, Porphyromonas, Prevotella, Campylobacter and Wolinella spp. by tricine-SDS-PAGE.

PubMed

Firoozkoohi, J; Zandi, H; Olsen, I

1997-02-01

Lipopolysaccharides (LPSs) of 11 bacterial strains from the type species of the genera Bacteroides (B. fragilis), Prevotella (Pr. melaninogenica), Porphyromonas (Po. gingivalis), Campylobacter (C. fetus subsp. fetus), and Wolinella (W. succinogenes), and from the type strains of B. distasonis, B. forsythus, B. ureolyticus, Po. levii, Po. macacae, and C. gracilis, were extracted with hot water-phenol (Westphal method). S-form LPSs, obtained from all organisms, were well resolved with tricine-sodium-dodecyl-sulphate polyacrylamide gel electrophoresis and visualized by silver staining. Lipid A was not stained. Also profiles from LPS of Escherichia coli, serotypes 0111:B4 and 055:B5, could be distinguished. While W. succinogenes showed a relatively short S-form LPS on electrophoregrams, the other bacteria, including B. fragilis, exhibited long-ladder LPSs. Po. gingivalis displayed the largest number of bands and the longest O-chain. The long O-chain of this bacterium may be important for its virulence.

Intestinal microbiota reduces genotoxic endpoints induced by high-energy protons.

PubMed

Maier, Irene; Berry, David M; Schiestl, Robert H

2014-01-01

Ionizing space radiation causes oxidative DNA damage and triggers oxidative stress responses, and compromised DNA repair mechanisms can lead to increased risk of carcinogenesis. Young adult mice with developed innate and adaptive immune systems that harbored either a conventional intestinal microbiota (CM) or an intestinal microbiota with a restricted microbial composition (RM) were irradiated with a total dose of 1 Gy delivered by high-energy protons (2.5 GeV/n, LET = 0.2-2 keV/μm) or silicon or iron ions (850 MeV/n, LET ≈ 50 keV/μm and 1 GeV/n, LET = 150 keV/μm, respectively). Six hours after whole-body irradiation, acute chromosomal DNA lesions were observed for RM mice but not CM mice. High-throughput rRNA gene sequencing of intestinal mucosal bacteria showed that Barnesiella intestinihominis and unclassified Bacterodiales were significantly more abundant in male RM mice than CM mice, and phylotype densities changed in irradiated mice. In addition, Helicobacter hepaticus and Bacteroides stercoris were higher in CM than RM mice. Elevated levels of persistently phosphorylated γ-H2AX were observed in RM mice exposed to high-energy protons compared to nonirradiated RM mice, and they also were associated with a decrease of the antioxidant glutathione in peripheral blood measured at four weeks after irradiation. After radiation exposure, CM mice showed lower levels of γ-H2AX phosphorylation than RM mice and an increase in specific RM-associated phylotypes, indicating a down-regulating force on DNA repair by differentially abundant phylotypes in RM versus a radiation-sensitive complex CM.

The Compositional HJ-Biplot—A New Approach to Identifying the Links among Bioactive Compounds of Tomatoes

PubMed Central

Hernández Suárez, Marcos; Molina Pérez, Daniel; Rodríguez-Rodríguez, Elena M.; Díaz Romero, Carlos; Espinosa Borreguero, Francisco; Galindo-Villardón, Purificación

2016-01-01

Tomatoes have been described as a functional food because of their particular composition of different bioactive compounds. In this study, the proximate composition, minerals and trace elements, and antioxidant compounds were determined in two tomato cultivars (Mariana and Dunkan) that were grown in Gran Canaria (Spain) either conventionally or hydroponically. Although compositional data of this type require being subjected to the specific statistical techniques of compositional analysis, this approach has not usually been considered in this context. In the present case, a compositional Mann–Whitney U test of the data showed significant differences for each factor (cultivar and cultivation system) in several of the compositional variables studied. For the differences between cultivars, these parameters were the protein, Mg, lycopene, ascorbic acid, citric acid, and fumaric acid contents. For the differences between cultivation systems, they were mainly those of the mineral and trace elements group. Although one-year data are insufficient to make clear relationship among compounds because more repetitions in several localities and years are necessary, the compositional HJ-biplot (in which the links provide estimates of the linear relationship among variables) results agreed with other scientific results about linear relationship among some compounds analyzed. PMID:27827839

Septic abortion presenting as a right lower trapezius abscess secondary to Bacteroides fragilis bacteraemia.

PubMed

Yamanaka, Yusuke; Shimabukuro, Akira

2017-08-21

A 43-year-old Japanese woman was evaluated in the outpatient department for right shoulder pain and fever, which began 5 days earlier. MRI of the right shoulder revealed a high-intensity area deep in the right trapezius muscle. Aspiration revealed purulent fluid, and Gram staining of the fluid showed Gram-negative bacilli. The patient was also found to be profoundly anaemic and to have a positive urine pregnancy test. On admission, we initiated intravenous ampicillin-sulbactam and aztreonam. She underwent dilatation and curettage for septic abortion and surgical drainage of the right shoulder abscess. Bacteroides fragilis was isolated from the blood, uterine aspiration and abscess samples. On hospital day 4, a whole-body CT scan revealed no other abscesses, and ampicillin-sulbactam was continued for 28 days. The patient was discharged on hospital day 29. Gram staining is an important tool for evaluating infectious aetiologies. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The rec A operon: a novel stress response gene cluster in Bacteroides fragilis

PubMed Central

Nicholson, Samantha A; Smalley, Darren; Smith, C. Jeffrey; Abratt, Valerie R

2014-01-01

Bacteroides fragilis, an opportunistic pathogen of humans, is a leading cause of bacteraemias and anaerobic abscesses which are often treated with metronidazole, a drug which damages DNA. This study investigated the responses of the B. fragilis recA three gene operon to the stress experienced during metronidazole treatment and exposure to reactive oxygen species simulating those generated by the host immune system during infection. A transcriptionally regulated response was observed using quantitative RT-PCR after metronidazole and hydrogen peroxide treatment, with all three genes being upregulated under stress conditions. In vivo and in vitro analysis of the functional role of the second gene of the operon was done using heterologous complementation and protein expression (in Escherichia coli), with subsequent biochemical assay. This gene encoded a functional bacterioferritin co-migratory protein (BCP) which was thiol-specific and had antioxidant properties, including protection of the glutamine synthetase III enzyme. This in vitro data supports the hypothesis that the genes of the operon may be involved in protection of the bacteria from the oxidative burst during tissue invasion and may play a significant role in bacterial survival and metronidazole resistance during treatment of B. fragilis infections. PMID:24703997

Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole

PubMed Central

de Freitas, Michele C. R.; Resende, Juliana A.; Ferreira-Machado, Alessandra B.; Saji, Guadalupe D. R. Q.; de Vasconcelos, Ana T. R.; da Silva, Vânia L.; Nicolás, Marisa F.; Diniz, Cláudio G.

2016-01-01

Bacteroides fragilis, member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug. From a wild type B. fragilis ATCC 43859 four derivative strains were selected: first and fourth subcultures under metronidazole exposure and first and fourth subcultures after drug removal. According to global gene expression analysis, 2,146 protein coding genes were identified, of which a total of 1,618 (77%) were assigned to a Gene Ontology term (GO), indicating that most known cellular functions were taken. Among these 2,146 protein coding genes, 377 were shared among all strains, suggesting that they are critical for B. fragilis survival. In order to identify distinct expression patterns, we also performed a K-means clustering analysis set to 15 groups. This analysis allowed us to detect the major activated or repressed genes encoding for enzymes which act in several metabolic pathways involved in metronidazole response such as drug activation, defense mechanisms against superoxide ions, high expression level of multidrug efflux pumps, and DNA repair. The strains collected after metronidazole removal were functionally more similar to those cultured under drug pressure, reinforcing that drug-exposure lead to drastic persistent changes in the B. fragilis gene expression patterns. These results may help to elucidate B. fragilis response during metronidazole exposure, mainly at SIC, contributing with information about bacterial survival strategies under stress conditions in their

Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole.

PubMed

de Freitas, Michele C R; Resende, Juliana A; Ferreira-Machado, Alessandra B; Saji, Guadalupe D R Q; de Vasconcelos, Ana T R; da Silva, Vânia L; Nicolás, Marisa F; Diniz, Cláudio G

2016-01-01

Bacteroides fragilis , member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug. From a wild type B. fragilis ATCC 43859 four derivative strains were selected: first and fourth subcultures under metronidazole exposure and first and fourth subcultures after drug removal. According to global gene expression analysis, 2,146 protein coding genes were identified, of which a total of 1,618 (77%) were assigned to a Gene Ontology term (GO), indicating that most known cellular functions were taken. Among these 2,146 protein coding genes, 377 were shared among all strains, suggesting that they are critical for B. fragilis survival. In order to identify distinct expression patterns, we also performed a K-means clustering analysis set to 15 groups. This analysis allowed us to detect the major activated or repressed genes encoding for enzymes which act in several metabolic pathways involved in metronidazole response such as drug activation, defense mechanisms against superoxide ions, high expression level of multidrug efflux pumps, and DNA repair. The strains collected after metronidazole removal were functionally more similar to those cultured under drug pressure, reinforcing that drug-exposure lead to drastic persistent changes in the B. fragilis gene expression patterns. These results may help to elucidate B. fragilis response during metronidazole exposure, mainly at SIC, contributing with information about bacterial survival strategies under stress conditions in

Characterizing the interactions between a naturally primed immunoglobulin A and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice.

PubMed

Peterson, Daniel A; Planer, Joseph D; Guruge, Janaki L; Xue, Lai; Downey-Virgin, Whitt; Goodman, Andrew L; Seedorf, Henning; Gordon, Jeffrey I

2015-05-15

The adaptive immune response to the human gut microbiota consists of a complex repertoire of antibodies interacting with a broad range of taxa. Fusing intestinal lamina propria lymphocytes from mice monocolonized with Bacteroides thetaiotaomicron to a myeloma fusion partner allowed us to recover hybridomas that captured naturally primed, antigen-specific antibody responses representing multiple isotypes, including IgA. One of these hybridomas, 260.8, produced a monoclonal antibody that recognizes an epitope specific for B. thetaiotaomicron isolates in a large panel of hospital- and community-acquired Bacteroides. Whole genome transposon mutagenesis revealed a 19-gene locus, involved in LPS O-antigen polysaccharide synthesis and conserved among multiple B. thetaiotaomicron isolates, that is required for 260.8 epitope expression. Mutants in this locus exhibited marked fitness defects in vitro during growth in rich medium and in gnotobiotic mice colonized with defined communities of human gut symbionts. Expression of the 260.8 epitope was sustained during 10 months of daily passage in vitro and during 14 months of monocolonization of gnotobiotic wild-type, Rag1-/-, or Myd88-/- mice. Comparison of gnotobiotic Rag1-/- mice with and without subcutaneous 260.8 hybridomas disclosed that this IgA did not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but did affect bacterial gene expression in ways emblematic of a diminished host innate immune response. Our study illustrates an approach for (i) generating diagnostic antibodies, (ii) characterizing IgA responses along a continuum of specificity/degeneracy that defines the IgA repertoire to gut symbionts, and (iii) identifying immunogenic epitopes that affect competitiveness and help maintain host-microbe mutualism. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Luciferase genes cloned from the unculturable luminous bacteroid symbiont of the Caribbean flashlight fish, Kryptophanaron alfredi.

PubMed

Haygood, M G; Cohn, D H

1986-01-01

Light organs of anomalopid (flashlight) fish contain luminous bacteroids that have never been cultured and, consequently, have been difficult to study. We have characterized the luciferase (lux) region of DNA extracted from light organs of the Caribbean flashlight fish Kryptophanaron alfredi by hybridization of cloned Vibrio harveyi lux genes to restriction-endonuclease-digested, light organ DNA. Comparison of the hybridization pattern of light organ DNA with that of DNA of a putative symbiotic isolate provides a method for identifying the authentic luminous symbiont regardless of its luminescence, and was used to reject one such isolate. Light organ DNA was further used to construct a cosmid clone bank and the luciferase genes were isolated. Unlike other bacterial luciferase genes, the genes were not expressed in Escherichia coli. When placed under the control of the E. coli trp promoter, the genes were transcribed but no luciferase was detected, suggesting a posttranscriptional block to expression.

Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level.

PubMed

Despres, Jordane; Forano, Evelyne; Lepercq, Pascale; Comtet-Marre, Sophie; Jubelin, Gregory; Chambon, Christophe; Yeoman, Carl J; Berg Miller, Margaret E; Fields, Christopher J; Martens, Eric; Terrapon, Nicolas; Henrissat, Bernard; White, Bryan A; Mosoni, Pascale

2016-05-04

Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A(T). Transcriptomic analyses of B. xylanisolvens XB1A(T) grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. This study shows that xylan degradation by B. xylanisolvens XB1A(T) is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens

Identification of a collagen type I adhesin of Bacteroides fragilis.

PubMed

Galvão, Bruna P G V; Weber, Brandon W; Rafudeen, Mohamed S; Ferreira, Eliane O; Patrick, Sheila; Abratt, Valerie R

2014-01-01

Bacteroides fragilis is an opportunistic pathogen which can cause life threatening infections in humans and animals. The ability to adhere to components of the extracellular matrix, including collagen, is related to bacterial host colonisation. Collagen Far Western analysis of the B. fragilis outer membrane protein (OMP) fraction revealed the presence two collagen adhesin bands of ∼ 31 and ∼ 34 kDa. The collagen adhesins in the OMP fraction were separated and isolated by two-dimensional SDS-PAGE and also purified by collagen affinity chromatography. The collagen binding proteins isolated by both these independent methods were subjected to tandem mass spectroscopy for peptide identification and matched to a single hypothetical protein encoded by B. fragilis NCTC 9343 (BF0586), conserved in YCH46 (BF0662) and 638R (BF0633) and which is designated in this study as cbp1 (collagen binding protein). Functionality of the protein was confirmed by targeted insertional mutagenesis of the cbp1 gene in B. fragilis GSH18 which resulted in the specific loss of both the ∼ 31 kDa and the ∼ 34 kDa adhesin bands. Purified his-tagged Cbp1, expressed in a B. fragilis wild-type and a glycosylation deficient mutant, confirmed that the cbp1 gene encoded the observed collagen adhesin, and showed that the 34 kDa band represents a glycosylated version of the ∼ 31 kDa protein. Glycosylation did not appear to be required for binding collagen. This study is the first to report the presence of collagen type I adhesin proteins in B. fragilis and to functionally identify a gene encoding a collagen binding protein.

Bacteroides fragilis Lipopolysaccharide and Inflammatory Signaling in Alzheimer’s Disease

PubMed Central

Lukiw, Walter J.

2016-01-01

The human microbiome consists of ~3.8 × 1013 symbiotic microorganisms that form a highly complex and dynamic ecosystem: the gastrointestinal (GI) tract constitutes the largest repository of the human microbiome by far, and its impact on human neurological health and disease is becoming increasingly appreciated. Bacteroidetes, the largest phylum of Gram-negative bacteria in the GI tract microbiome, while generally beneficial to the host when confined to the GI tract, have potential to secrete a remarkably complex array of pro-inflammatory neurotoxins that include surface lipopolysaccharides (LPSs) and toxic proteolytic peptides. The deleterious effects of these bacterial exudates appear to become more important as GI tract and blood-brain barriers alter or increase their permeability with aging and disease. For example, presence of the unique LPSs of the abundant Bacteroidetes species Bacteroides fragilis (BF-LPS) in the serum represents a major contributing factor to systemic inflammation. BF-LPS is further recognized by TLR2, TLR4, and/or CD14 microglial cell receptors as are the pro-inflammatory 42 amino acid amyloid-beta (Aβ42) peptides that characterize Alzheimer’s disease (AD) brain. Here we provide the first evidence that BF-LPS exposure to human primary brain cells is an exceptionally potent inducer of the pro-inflammatory transcription factor NF-kB (p50/p65) complex, a known trigger in the expression of pathogenic pathways involved in inflammatory neurodegeneration. This ‘Perspectives communication’ will in addition highlight work from recent studies that advance novel and emerging concepts on the potential contribution of microbiome-generated factors, such as BF-LPS, in driving pro-inflammatory degenerative neuropathology in the AD brain. PMID:27725817

Identification of a Collagen Type I Adhesin of Bacteroides fragilis

PubMed Central

Galvão, Bruna P. G. V.; Weber, Brandon W.; Rafudeen, Mohamed S.; Ferreira, Eliane O.; Patrick, Sheila; Abratt, Valerie R.

2014-01-01

Bacteroides fragilis is an opportunistic pathogen which can cause life threatening infections in humans and animals. The ability to adhere to components of the extracellular matrix, including collagen, is related to bacterial host colonisation. Collagen Far Western analysis of the B. fragilis outer membrane protein (OMP) fraction revealed the presence two collagen adhesin bands of ∼31 and ∼34 kDa. The collagen adhesins in the OMP fraction were separated and isolated by two-dimensional SDS-PAGE and also purified by collagen affinity chromatography. The collagen binding proteins isolated by both these independent methods were subjected to tandem mass spectroscopy for peptide identification and matched to a single hypothetical protein encoded by B. fragilis NCTC 9343 (BF0586), conserved in YCH46 (BF0662) and 638R (BF0633) and which is designated in this study as cbp1 (collagen binding protein). Functionality of the protein was confirmed by targeted insertional mutagenesis of the cbp1 gene in B. fragilis GSH18 which resulted in the specific loss of both the ∼31 kDa and the ∼34 kDa adhesin bands. Purified his-tagged Cbp1, expressed in a B. fragilis wild-type and a glycosylation deficient mutant, confirmed that the cbp1 gene encoded the observed collagen adhesin, and showed that the 34 kDa band represents a glycosylated version of the ∼31 kDa protein. Glycosylation did not appear to be required for binding collagen. This study is the first to report the presence of collagen type I adhesin proteins in B. fragilis and to functionally identify a gene encoding a collagen binding protein. PMID:24618940

How accurate are Omron X-HJ-304-E and Yamax SW-700/701 pedometers at different speeds and various inclinations?

PubMed

Wallmann-Sperlich, B; Froboese, I; Reed, J L; Mathes, S; Sperlich, B

2015-01-01

The purpose of this study was to investigate step count and energy expenditure accuracy of the piezoelectric Omron (Walking Style X-HJ-304-E) and spring-levered Yamax (Digi-Walker-SW-700/701) pedometers at different speeds and various inclinations. Thirty subjects (15 females, aged: 24 ± 3 years) completed eleven 5-min trials at different treadmill speeds and inclinations (3.24 km∙h⁻¹ [inclination: 0, 9, 20%], 4.68 km∙h⁻¹ [0, 9, 20%], 6.48 km∙h⁻¹ [0, 9%], 9 km∙h⁻¹ [0%], 10.8 km∙h⁻¹ [0%], 12.6 km∙h⁻¹ [0%]). During each trial, an investigator recorded actual steps with a hand tally counter. Actual energy expenditure was measured using a portable indirect calorimeter. The Omron pedometer revealed high step count accuracy for all speeds and inclinations when worn on the hip or a backpack (Mean % of actual steps: 99.6%; Range: 95.8-101.3%). The Yamax pedometer revealed high step count accuracy (Mean % of actual steps: 99.8%; Range: 96.2-103.3%) when worn on the left hip at 6.48-12.6 km∙h⁻¹ (0%), 4.68 km∙h⁻¹ (9%, 20%), 6.48 km∙h⁻¹ (9%) and on the right hip at 10.8 km∙h⁻¹ (0%) and 6.48 km∙h⁻¹ (9%). The accuracy of the Omron and Yamax determined energy expenditure was poor (57.9-59.7%) when compared to indirect calorimetry. The Omron pedometer provides accurate step counts when worn on the hip and backpack at all tested speeds and inclinations. We therefore suggest an accurate application of this device for walking, hiking and running at moderate speeds. Both pedometers underestimated energy expenditure.

Suppression of colorectal tumorigenesis by recombinant Bacteroides fragilis enterotoxin-2 in vivo.

PubMed

Lv, You; Ye, Tao; Wang, Hui-Peng; Zhao, Jia-Ying; Chen, Wen-Jie; Wang, Xin; Shen, Chen-Xia; Wu, Yi-Bin; Cai, Yuan-Kun

2017-01-28

To evaluate the impact of recombinant Bacteroides fragilis enterotoxin-2 (BFT-2, or Fragilysin) on colorectal tumorigenesis in mice induced by azoxymethane/dextran sulfate sodium (AOM/DSS). Recombinant proBFT-2 was expressed in Escherichia coli strain Rosetta (DE3) and BFT-2 was obtained and tested for its biological activity via colorectal adenocarcinoma cell strains SW-480. Seventy C57BL/6J mice were randomly divided into a blank (BC; n = 10), model (AD; n = 20), model + low-dose toxin (ADLT; n = 20, 10 μg), and a model + high-dose toxin (ADHT; n = 20, 20 μg) group. Mice weight, tumor formation and pathology were analyzed. Immunohistochemistry determined Ki-67 and Caspase-3 expression in normal and tumor tissues of colorectal mucosa. Recombinant BFT-2 was successfully obtained, along with its biological activity. The most obvious weight loss occurred in the AD group compared with the ADLT group (21.82 ± 0.68 vs 23.23 ± 0.91, P < 0.05) and the ADHT group (21.82 ± 0.68 vs 23.57 ± 1.06, P < 0.05). More tumors were found in the AD group than in the ADLT and ADHT groups (19.75 ± 3.30 vs 6.50 ± 1.73, P < 0.05; 19.75 ± 3.30 vs 6.00 ± 2.16, P < 0.05). Pathology showed that 12 mice had adenocarcinoma and 6 cases had adenoma in the AD group. Five mice had adenocarcinoma and 15 had adenoma in the ADLT group. Four mice had adenocarcinoma and 16 had adenoma in the ADHT group. The incidence of colorectal adenocarcinoma in both the ADHT group and the ADHT group was reduced compared to that in the AD group ( P < 0.05, P < 0.05). The positive rate of Ki-67 in the ADLT group and the ADHT group was 50% and 40%, respectively, both of which were lower than that found in the AD group (94.44%, P < 0.05, P < 0.05). Caspase-3 expression in the ADLT group and the ADHT group was 45% and 55%, both of which were higher than that found in the BC group (16.67%, P < 0.05, P < 0.05). Oral administration with lower-dose biologically active recombinant BFT-2 inhibited colorectal

Suppression of colorectal tumorigenesis by recombinant Bacteroides fragilis enterotoxin-2 in vivo

PubMed Central

Lv, You; Ye, Tao; Wang, Hui-Peng; Zhao, Jia-Ying; Chen, Wen-Jie; Wang, Xin; Shen, Chen-Xia; Wu, Yi-Bin; Cai, Yuan-Kun

2017-01-01

AIM To evaluate the impact of recombinant Bacteroides fragilis enterotoxin-2 (BFT-2, or Fragilysin) on colorectal tumorigenesis in mice induced by azoxymethane/dextran sulfate sodium (AOM/DSS). METHODS Recombinant proBFT-2 was expressed in Escherichia coli strain Rosetta (DE3) and BFT-2 was obtained and tested for its biological activity via colorectal adenocarcinoma cell strains SW-480. Seventy C57BL/6J mice were randomly divided into a blank (BC; n = 10), model (AD; n = 20), model + low-dose toxin (ADLT; n = 20, 10 μg), and a model + high-dose toxin (ADHT; n = 20, 20 μg) group. Mice weight, tumor formation and pathology were analyzed. Immunohistochemistry determined Ki-67 and Caspase-3 expression in normal and tumor tissues of colorectal mucosa. RESULTS Recombinant BFT-2 was successfully obtained, along with its biological activity. The most obvious weight loss occurred in the AD group compared with the ADLT group (21.82 ± 0.68 vs 23.23 ± 0.91, P < 0.05) and the ADHT group (21.82 ± 0.68 vs 23.57 ± 1.06, P < 0.05). More tumors were found in the AD group than in the ADLT and ADHT groups (19.75 ± 3.30 vs 6.50 ± 1.73, P < 0.05; 19.75 ± 3.30 vs 6.00 ± 2.16, P < 0.05). Pathology showed that 12 mice had adenocarcinoma and 6 cases had adenoma in the AD group. Five mice had adenocarcinoma and 15 had adenoma in the ADLT group. Four mice had adenocarcinoma and 16 had adenoma in the ADHT group. The incidence of colorectal adenocarcinoma in both the ADHT group and the ADHT group was reduced compared to that in the AD group (P < 0.05, P < 0.05). The positive rate of Ki-67 in the ADLT group and the ADHT group was 50% and 40%, respectively, both of which were lower than that found in the AD group (94.44%, P < 0.05, P < 0.05). Caspase-3 expression in the ADLT group and the ADHT group was 45% and 55%, both of which were higher than that found in the BC group (16.67%, P < 0.05, P < 0.05). CONCLUSION Oral administration with lower-dose biologically active recombinant BFT-2

Gas-liquid chromatography for evaluating polysaccharide degradation by Ruminococcus flavefaciens C94 and Bacteroides succinogenes S85.

PubMed

Collings, G F; Yokoyama, M T

1980-03-01

Two predominant rumen cellulolytic bacteria, Ruminococcus flavefaciens C94 and Bacteroides succinogenes S85, were incubated with ground filter paper (Whatman no. 1), cattle manure fiber, wheat straw, Kentucky bluegrass, alfalfa, and corn silage as substrates. Analyses of the initial substrate and the recovered residue after 48 h of static incubation showed that R. flavefaciens C94 was quantitatively more effective than B. succinogenes S85 in degrading total dry matter (32.3% versus 16.1%). However, B. succinogenes S85 demonstrated a qualitative advantage in degrading the hemicellulose and hemicellulosic sugars of particular substrates. R. flavefaciens degraded a mean 29.7% of the cellulose and 35.6% of the hemicellulose in the various substrates, whereas B. succinogenes degraded a mean 17.9 and 31.6% of these fractions, respectively. Gas-liquid chromatography was an important aid in characterizing the polysaccharide-degrading capabilities of these rumen species.

Histological changes and some in vitro biological activities induced by lipopolysaccharide from Bacteroides gingivalis.

PubMed

Isogai, H; Isogai, E; Fujii, N; Oguma, K; Kagota, W; Takano, K

1988-07-01

The biological activities of lipopolysaccharide from Bacteroides gingivalis 381 (B-LPS) were examined in vivo and in vitro. Intra-oral mucosal injection of B-LPS induced an acute inflammation at the injection site. Intravenous injection of B-LPS induced necrotic lesions with many thrombi in the liver and lymphocytic reduction in the spleen. By immunohistochemical examination, B-LPS was detected in macrophages in the liver, spleen and lymph nodes. In vitro analysis showed that B-LPS was a potent activator of both neutrophils and macrophages in luminol-dependent response and IL-1 secretion from macrophages and was mitogenic to the spleen cells not only from BALB/c mice but also from LPS-non-responder C3H/HeJ mice. Interferon production from human peripheral mononuclear leucocytes was induced, in vitro, by stimulation with B-LPS but not with the other enterobacterial LPS. These findings clarified the various biological activities of B-LPS affecting various cells and tissues, especially neutrophils, macrophages and lymphocytes. The potent inflammability of B-LPS shown in the present study indicates that it is one of the effective agents to induce periodontitis.

Extraction of Rice Phenological Differences under Heavy Metal Stress Using EVI Time-Series from HJ-1A/B Data.

PubMed

Liu, Shuyuan; Liu, Xiangnan; Liu, Meiling; Wu, Ling; Ding, Chao; Huang, Zhi

2017-05-30

An effective method to monitor heavy metal stress in crops is of critical importance to assure agricultural production and food security. Phenology, as a sensitive indicator of environmental change, can respond to heavy metal stress in crops and remote sensing is an effective method to detect plant phenological changes. This study focused on identifying the rice phenological differences under varied heavy metal stress using EVI (enhanced vegetation index) time-series, which was obtained from HJ-1A/B CCD images and fitted with asymmetric Gaussian model functions. We extracted three phenological periods using first derivative analysis: the tillering period, heading period, and maturation period; and constructed two kinds of metrics with phenological characteristics: date-intervals and time-integrated EVI, to explore the rice phenological differences under mild and severe stress levels. Results indicated that under severe stress the values of the metrics for presenting rice phenological differences in the experimental areas of heavy metal stress were smaller than the ones under mild stress. This finding represents a new method for monitoring heavy metal contamination through rice phenology.

Islet-reactive CD8+ T cell frequencies in the pancreas, but not in blood, distinguish type 1 diabetic patients from healthy donors.

PubMed

Culina, Slobodan; Lalanne, Ana Ines; Afonso, Georgia; Cerosaletti, Karen; Pinto, Sheena; Sebastiani, Guido; Kuranda, Klaudia; Nigi, Laura; Eugster, Anne; Østerbye, Thomas; Maugein, Alicia; McLaren, James E; Ladell, Kristin; Larger, Etienne; Beressi, Jean-Paul; Lissina, Anna; Appay, Victor; Davidson, Howard W; Buus, Søren; Price, David A; Kuhn, Matthias; Bonifacio, Ezio; Battaglia, Manuela; Caillat-Zucman, Sophie; Dotta, Francesco; Scharfmann, Raphael; Kyewski, Bruno; Mallone, Roberto; Carel, Jean-Claude; Tubiana-Rufi, Nadia; Martinerie, Laetitia; Poidvin, Amélie; JacqzAigrain, Evelyne; Corvez, Laurence; Berruer, Véronique; Gautier, Jean-François; Baz, Baz; Haddadi, Nassima; Andreelli, Fabrizio; Amouyal, Chloé; Jaqueminet, Sophie; Bourron, Olivier; Dasque, Eric; Hartemann, Agnès; Lemoine-Yazigi, Amal; Dubois-Laforgue, Danièle; Travert, Florence; Feron, Marilyne; Rolland, Patrice; Vignali, Valérie; Marre, Michel; Chanson, Philippe; Briet, Claire; Guillausseau, Pierre-Jean; Ait-Bachir, Leila; Collet, Carole; Beziaud, Frédéric; Desforges-Bullet, Virginie; Petit-Aubert, Gwenaelle; Christin-Maitre, Sophie; Fève, Bruno; Vatier, Camille; Bourcigaux, Nathalie; Lautridou, Céline; Lahlou, Najiba; Bakouboula, Prissile; Elie, Caroline; Morel, Hélène; Treluyer, Jean-Marc; Gagnerault, Marie-Claude; Maillard, Claire; Jones, Anna

2018-02-02

The human leukocyte antigen-A2 (HLA-A2)-restricted zinc transporter 8 186-194 (ZnT8 186-194 ) and other islet epitopes elicit interferon-γ secretion by CD8 + T cells preferentially in type 1 diabetes (T1D) patients compared with controls. We show that clonal ZnT8 186-194 -reactive CD8 + T cells express private T cell receptors and display equivalent functional properties in T1D and healthy individuals. Ex vivo analyses further revealed that CD8 + T cells reactive to ZnT8 186-194 and other islet epitopes circulate at similar frequencies and exhibit a predominantly naïve phenotype in age-matched T1D and healthy donors. Higher frequencies of ZnT8 186-194 -reactive CD8 + T cells with a more antigen-experienced phenotype were detected in children versus adults, irrespective of disease status. Moreover, some ZnT8 186-194 -reactive CD8 + T cell clonotypes were found to cross-recognize a Bacteroides stercoris mimotope. Whereas ZnT8 was poorly expressed in thymic medullary epithelial cells, variable thymic expression levels of islet antigens did not modulate the peripheral frequency of their cognate CD8 + T cells. In contrast, ZnT8 186-194 -reactive cells were enriched in the pancreata of T1D patients versus nondiabetic and type 2 diabetic individuals. Thus, islet-reactive CD8 + T cells circulate in most individuals but home to the pancreas preferentially in T1D patients. We conclude that the activation of this common islet-reactive T cell repertoire and progression to T1D likely require defective peripheral immunoregulation and/or a proinflammatory islet microenvironment. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Water Resource Monitoring Based n EO Data: Gained Experience After 10 Years of Dragon Programme over the Yangtze River Reaches: From ERS 1 to Sentinel 1 and from MERIS to HJ1 and Pleiades

NASA Astrophysics Data System (ADS)

Yesou, Herve; Huber, Claire; Huang, Shifeng; Studer, Mathias; Lai, Xijun; Chen, Xiaoling; Daillet, Sylviane

2014-11-01

Water resources monitoring from space is an application of remote sensing under full development, with arriving satellite such as the Sentinels, and of course the development of inland applications of altimetry and the future mission as SWOT. Since 10 years within the framework of the DRAGON ESA MOST programme, a monitoring of Chines major fresh water lakes, Poyang and Dongting lakes on Yangtze reaches, is realized exploiting large source of EO data. Thanks to EO data archive exploitation, the covered period starts in 2000 up to 2014, over these two core lakes, whereas, since a 2012, a similar approach is carried over the small lakes of Anhui Province. A key question is how to access to convenient satellite data with sufficient resource to insure a high temporal frequency, ie ideally with about 10 days of revisit. An opportunistic approach was followed in order to insure this data access thanks to a large ESA support, accessing Envisat and ESA TPM, as well Chinese data. From 2004 to April 2012, ENVISAT Medium resolution products, MERIS and ASAR WSM data, were the core of the monitoring system. Since the lost of Envisat, the data exploited moved from MR to HR (20-30 m), thanks to the access to large volume of HJ1 images in 2012 and 2014, as well as coverage CSK data (30m) thanks agreement with ASI. The assimilation of these data is a fine preparation for the future exploitation of Sentinel1 and 2 dataset. Furthermore a first Sentinel data have been exploited, less than 45 after satellite launch. In addition on most sensitive areas, such as the Poyang Lake natural Reserve (Jiangxi Pr) and Shenjing Lake (Anhui Prov.) a unique set of VHR data, Pleiades, Kompsat, have been exploited. The expect strategy for the coming months and years will be in a first period, the jointly exploitation of Sentinel 1 data if the Chinese areas are rapidly integrated within the Sentinel 1 acquisition scheme, jointly with the Chinese HJ1AB data. In a second time HJ1AB data would be

Water Resource Monitoring Based on EO Data: Gained Experience After 10 Years of Dragon Programme over the Yangtze Middle Reaches: From ERS 1 to Sentinel 1 and from MERIS to HJ1 and Pleiades

NASA Astrophysics Data System (ADS)

Yesou, Herve; Huber, Claire; Huang, Shifeng; Studer, Mathais; Lai, Xijun; Chen, Xiaoling; Daillet, Sylviane

2014-11-01

Water resources monitoring from space is an application of remote sensing under full development, with arriving satellite such as the Sentinels, and of course the development of inland applications of altimetry and the future mission as SWOT. Since 10 years within the framework of the DRAGON ESA MOST programme, a monitoring of Chines major fresh water lakes, Poyang and Dongting lakes on Yangtze reaches, is realized exploiting large source of EO data. Thanks to EO data archive exploitation, the covered period starts in 2000 up to 2014, over these two core lakes, whereas, since a 2012, a similar approach is carried over the small lakes of Anhui Province. A key question is how to access to convenient satellite data with sufficient resource to insure a high temporal frequency, ie ideally with about 10 days of revisit. An opportunistic approach was followed in order to insure this data access thanks to a large ESA support, accessing Envisat and ESA TPM, as well Chinese data. From 2004 to April 2012, ENVISAT Medium resolution products, MERIS and ASAR WSM data, were the core of the monitoring system. Since the lost of Envisat, the data exploited moved from MR to HR (20-30 m), thanks to the access to large volume of HJ1 images in 2012 and 2014, as well as coverage CSK data (30m) thanks agreement with ASI. The assimilation of these data is a fine preparation for the future exploitation of Sentinel1 and 2 dataset. Furthermore a first Sentinel data have been exploited, less than 45 after satellite launch. In addition on most sensitive areas, such as the Poyang Lake natural Reserve (Jiangxi Pr) and Shenjing Lake (Anhui Prov.) a unique set of VHR data, Pleiades, Kompsat, have been exploited. The expect strategy for the coming months and years will be in a first period, the jointly exploitation of Sentinel 1 data if the Chinese areas are rapidly integrated within the Sentinel 1 acquisition scheme, jointly with the Chinese HJ1AB data. In a second time HJ1AB data would be

[Association between Bacteroides forsythus in the infected root canals and clinical symptoms of chronic apical periodontitis].

PubMed

Huang, Ding-ming; Fu, Chun-hua; Zhou, Xue-dong

2005-01-01

To investigate the distribution of Bacteroides forsythus in root canals with chronic apical periodontitis and to determine its associations with clinical symptoms. Thirty-eight tooth root canals from 31 subjects were studied with a 16S rDNA-directed polymerase chain reaction (PCR). These teeth were classified into symptomatic and asymptomatic groups according to the clinical symptoms and signs, including spontaneous pain, percussion pain, sinus tract and swelling, respectively. Ten of the 38 root canal samples were positive for B. forsythus. The prevalence of B. forsythus was 26.3% for 38 root canals, 45.5% for spontaneous pain group, 39.1% for percussion pain group, 29.4% for sinus tract group, 42.9% for swelling group, respectively. Significant positive associations were observed between B. forsythus in infected root canals and the spontaneous pain, percussion pain, and swelling of apical periodontitis, respectively (OR=infinity, 9, 12; P<0.05). There was no significant association between B. forsythus and sinus tract of apical periodontitis (OR=1.33). B. forsythus colonized in the infected root canals. It is the putative pathogen of apical periodontitis.

Single- and double-balloon enteroscopy-assisted endoscopic retrograde cholangiopancreatography in patients with Roux-en-Y plus hepaticojejunostomy anastomosis and Whipple resection.

PubMed

Itokawa, Fumihide; Itoi, Takao; Ishii, Kentaro; Sofuni, Atsushi; Moriyasu, Fuminori

2014-04-01

In patients with Roux-en-Y hepaticojejunostomy (HJ with R-Y) and Whipple resection, endoscopic retrograde cholangiopancreatography (ERCP) can be challenging. We report our experience with ERCP using balloon-assisted enteroscopy (BAE) (BAE-ERCP) in patients with HJ with R-Y, and Whipple resection. BAE-ERCP procedures were carried out in 62 patients (HJ with R-Y:Whipple resection=34:28). Overall, the rates of reaching the anastomosis were 85.3% (29/34) in HJ with R-Y and 96.4% (27/28) in Whipple resection. In terms of HJ with R-Y, insertion success rate by standard single-balloon enteroscopy (SBE) was 89.3% (25/28). Insertion success rate by short BAE, including SBE and double-balloon enteroscopy (DBE), was 50% (3/6). There was a statistically significant difference of insertion success rate between standard long BE and short BE (P=0.021). However, in the Whipple patients, insertion success rate by standard and short SBE was 93.8% (15/16) and 91.7% (11/12), respectively. Initial insertion success rate by short BAE in Whipple patients was significantly higher than in HJ with R-Y (91.7% vs 50%, P=0.045). Therapeutic interventions included dilation of anastomosis stricture, stone extraction, endoscopic mechanical lithotripsy, biliary stent placement, stent extraction, endoscopic nasobiliary drainage, direct cholangioscopy, and electrohydraulic lithotripsy. Our HJ with R-Y series and Whipple series treatment success rate was 90% (18/20) and 95.0% (19/20), respectively. BAE-ERCP enabled ERCP to be carried out in patients with HJ. It is considered safe and feasible. Further experience and device improvement are needed. © 2014 The Authors. Digestive Endoscopy © 2014 Japan Gastroenterological Endoscopy Society.

Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease.

PubMed

Bloom, Seth M; Bijanki, Vinieth N; Nava, Gerardo M; Sun, Lulu; Malvin, Nicole P; Donermeyer, David L; Dunne, W Michael; Allen, Paul M; Stappenbeck, Thaddeus S

2011-05-19

The intestinal microbiota is important for induction of inflammatory bowel disease (IBD). IBD is associated with complex shifts in microbiota composition, but it is unclear whether specific bacterial subsets induce IBD and, if so, whether their proportions in the microbiota are altered during disease. Here, we fulfilled Koch's postulates in host-genotype-specific fashion using a mouse model of IBD with human-relevant disease-susceptibility mutations. From screening experiments we isolated common commensal Bacteroides species, introduced them into antibiotic-pretreated mice, and quantitatively reisolated them in culture. The bacteria colonized IBD-susceptible and -nonsusceptible mice equivalently, but induced disease exclusively in susceptible animals. Conversely, commensal Enterobacteriaceae were >100-fold enriched during spontaneous disease, but an Enterobacteriaceae isolate failed to induce disease in antibiotic-pretreated mice despite robust colonization. We thus demonstrate that IBD-associated microbiota alterations do not necessarily reflect underlying disease etiology. These findings establish important experimental criteria and a conceptual framework for understanding microbial contributions to IBD. Copyright © 2011 Elsevier Inc. All rights reserved.

Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease

PubMed Central

Bloom, Seth M.; Bijanki, Vinieth N.; Nava, Gerardo M.; Sun, Lulu; Malvin, Nicole P.; Donermeyer, David L.; Dunne, W. Michael; Allen, Paul M.; Stappenbeck, Thaddeus S.

2011-01-01

SUMMARY The intestinal microbiota is important for induction of inflammatory bowel disease (IBD). IBD is associated with complex shifts in microbiota composition, but it is unclear whether specific bacterial subsets induce IBD and, if so, whether their proportions in the microbiota are altered during disease. Here we fulfilled Koch’s postulates in host-genotype-specific fashion using a mouse model of IBD with human-relevant disease-susceptibility mutations. From screening experiments we isolated common commensal Bacteroides species, introduced them into antibiotic-pretreated mice, and quantitatively re-isolated them in culture. The bacteria colonized IBD-susceptible and non-susceptible mice equivalently, but induced disease exclusively in susceptible animals. Conversely, commensal Enterobacteriaceae were >100-fold enriched during spontaneous disease but an Enterobacteriaceae isolate failed to induce disease in antibiotic-pretreated mice despite robust colonization. We thus demonstrate that IBD-associated microbiota alterations do not necessarily reflect underlying disease etiology. These findings establish important experimental criteria and a conceptual framework for understanding microbial contributions to IBD. PMID:21575910

The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase.

PubMed

Liu, Na-Nv; Duan, Xiao-Lei; Ai, Xia; Yang, Yan-Tao; Li, Ming; Dou, Shuo-Xing; Rety, Stephane; Deprez, Eric; Xi, Xu-Guang

2015-10-15

ScPif1 DNA helicase is the prototypical member of a 5'-to-3' helicase superfamily conserved from bacteria to human and plays various roles in the maintenance of genomic homeostasis. While many studies have been performed with eukaryotic Pif1 helicases, including yeast and human Pif1 proteins, the potential functions and biochemical properties of prokaryotic Pif1 helicases remain largely unknown. Here, we report the expression, purification and biochemical analysis of Pif1 helicase from Bacteroides sp. 3_1_23 (BsPif1). BsPif1 binds to a large panel of DNA substrates and, in particular, efficiently unwinds partial duplex DNAs with 5'-overhang, fork-like substrates, D-loop and flap-like substrates, suggesting that BsPif1 may act at stalled DNA replication forks and enhance Okazaki fragment maturation. Like its eukaryotic homologues, BsPif1 resolves R-loop structures and unwinds DNA-RNA hybrids. Furthermore, BsPif1 efficiently unfolds G-quadruplexes and disrupts nucleoprotein complexes. Altogether, these results highlight that prokaryotic Pif1 helicases may resolve common issues that arise during DNA transactions. Interestingly, we found that BsPif1 is different from yeast Pif1, but resembles more human Pif1 with regard to substrate specificity, helicase activity and mode of action. These findings are discussed in the context of the possible functions of prokaryotic Pif1 helicases in vivo. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sun glitter imaging analysis of submarine sand waves in HJ-1A/B satellite CCD images

NASA Astrophysics Data System (ADS)

Zhang, Huaguo; He, Xiekai; Yang, Kang; Fu, Bin; Guan, Weibing

2014-11-01

Submarine sand waves are a widespread bed-form in tidal environment. Submarine sand waves induce current convergence and divergence that affect sea surface roughness thus become visible in sun glitter images. These sun glitter images have been employed for mapping sand wave topography. However, there are lots of effect factors in sun glitter imaging of the submarine sand waves, such as the imaging geometry and dynamic environment condition. In this paper, several sun glitter images from HJ-1A/B in the Taiwan Banks are selected. These satellite sun glitter images are used to discuss sun glitter imaging characteristics in different sensor parameters and dynamic environment condition. To interpret the imaging characteristics, calculating the sun glitter radiance and analyzing its spatial characteristics of the sand wave in different images is the best way. In this study, a simulated model based on sun glitter radiation transmission is adopted to certify the imaging analysis in further. Some results are drawn based on the study. Firstly, the sun glitter radiation is mainly determined by sensor view angle. Second, the current is another key factor for the sun glitter. The opposite current direction will cause exchanging of bright stripes and dark stripes. Third, brightness reversal would happen at the critical angle. Therefore, when using sun glitter image to obtain depth inversion, one is advised to take advantage of image properties of sand waves and to pay attention to key dynamic environment condition and brightness reversal.

Assessment of swine-specific bacteriophages of Bacteroides fragilis in swine farms with different antibiotic practices.

PubMed

Leknoi, Yuranan; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2017-04-01

We assessed the occurrence and specificity of bacteriophages of Bacteroides fragilis in swine farms for their potential application in microbial source tracking. A local B. fragilis host strain, SP25 (DSM29413), was isolated from a pooled swine feces sample taken from a non-antibiotic farm. This strain was highly specific to swine fecal materials because it did not detect bacteriophages in any samples from human sewage, sheep, goats, cattle, dogs, and cats. The reference B. fragilis strain, RYC2056, could detect phages in swine samples but also detected phages in most human sewage and polluted urban canal samples. Phages of SP25 exist in the proximity of certain swine farms, regardless of their antibiotic use (p > 0.05). B. fragilis strain SP25 exhibited relatively high resistance to most of the veterinary antimicrobial agents tested. Interestingly, most farms that were positive for SP25 phages were also positive for RYC2056 phages. In conclusion, the swine-specific SP25 strain has the potential to indicate swine fecal contamination in certain bodies of water. Bacterial isolates with larger distributions are being studied and validated. This study highlights the importance of assessing the abundance of phages in local swine populations before determining their potential applicability for source tracking in local surface waters.

In-vitro activity of ciprofloxacin combined with flomoxef against Bacteroides fragilis, compared with that of ciprofloxacin combined with clindamycin.

PubMed

Kato, Komei; Iwai, Shigetomi; Sato, Takeshi; Harada, Tomohide; Nakagawa, Yoshiteru; Iwanaga, Hitomi; Ito, Yumiko; Takayama, Tadatoshi

2002-06-01

Using checkerboard and time-kill assays, the in-vitro activity of ciprofloxacin alone and in combination with flomoxef against clinical Bacteroides fragilis strains was evaluated. In addition, the microbiological efficacy of this combination was compared with that of ciprofloxacin plus clindamycin. In 88% of the 25 strains tested, the combination of ciprofloxacin plus flomoxef exhibited a synergistic or an additive effect, whereas only 56% of the 25 strains ( P< 0.01, chi(2) test) tested with the combination of ciprofloxacin plus clindamycin exhibited similar effects. In a time-kill study using 7 clinical strains, a synergistic or additive effect of the combination of ciprofloxacin plus flomoxef was observed in all 7 strains. In conclusion, the combination of ciprofloxacin plus flomoxef is very active against B. fragilis, suggesting that this combination may be very useful in the treatment of aerobic and B. fragilis mixed infections, because ciprofloxacin has an expanded spectrum against aerobes.

Detection of human-derived fecal contamination in Puerto Rico using carbamazepine, HF183 Bacteroides, and fecal indicator bacteria.

PubMed

Wade, Christina; Otero, Ernesto; Poon-Kwong, Brennan; Rozier, Ralph; Bachoon, Dave

2015-12-30

The level of fecal pollution in 17 sites in Puerto Rico was determined by Escherichia coli (E.coli) enumeration using an enzyme substrate medium and Quanti-Tray®/2000. Human fecal pollution was identified using an enzyme-linked immunosorbent assay for the detection of carbamazepine (CBZ) and quantitative polymerase chain reaction (qPCR) detection of the human Bacteroides marker, HF183. Carbamazepine was detected in 16 out of 17 sites, including Condado Lagoon, a popular recreational area. Elevated E.coli levels (>410 CFU 100 mL(-1)) were detected in 13 sites. Average CBZ concentrations ranged from 0.005 μg L(-1) to 0.482 μg L(-1) and 7 sites were positive for HF183. Higher CBZ concentrations were associated with the detection of HF183 (Mann-Whitney test; U=42.0; df=7; 1-tailed P value=0.013). This was the second study to determine surface water concentrations of CBZ in the Caribbean and the first in Puerto Rico. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolutionary engineering of Saccharomyces cerevisiae for efficient conversion of red algal biosugars to bioethanol.

PubMed

Lee, Hye-Jin; Kim, Soo-Jung; Yoon, Jeong-Jun; Kim, Kyoung Heon; Seo, Jin-Ho; Park, Yong-Cheol

2015-09-01

The aim of this work was to apply the evolutionary engineering to construct a mutant Saccharomyces cerevisiae HJ7-14 resistant on 2-deoxy-D-glucose and with an enhanced ability of bioethanol production from galactose, a mono-sugar in red algae. In batch and repeated-batch fermentations, HJ7-14 metabolized 5-fold more galactose and produced ethanol 2.1-fold faster than the parental D452-2 strain. Transcriptional analysis of genes involved in the galactose metabolism revealed that moderate relief from the glucose-mediated repression of the transcription of the GAL genes might enable HJ7-14 to metabolize galactose rapidly. HJ7-14 produced 7.4 g/L ethanol from hydrolysates of the red alga Gelidium amansii within 12 h, which was 1.5-times faster than that observed with D452-2. We demonstrate conclusively that evolutionary engineering is a promising tool to manipulate the complex galactose metabolism in S. cerevisiae to produce bioethanol from red alga. Copyright © 2015 Elsevier Ltd. All rights reserved.

Central nervous system demyelinating disease protection by the human commensal Bacteroides fragilis depends on polysaccharide A expression.

PubMed

Ochoa-Repáraz, Javier; Mielcarz, Daniel W; Ditrio, Lauren E; Burroughs, Ashley R; Begum-Haque, Sakhina; Dasgupta, Suryasarathi; Kasper, Dennis L; Kasper, Lloyd H

2010-10-01

The importance of gut commensal bacteria in maintaining immune homeostasis is increasingly understood. We recently described that alteration of the gut microflora can affect a population of Foxp3(+)T(reg) cells that regulate demyelination in experimental autoimmune encephalomyelitis (EAE), the experimental model of human multiple sclerosis. We now extend our previous observations on the role of commensal bacteria in CNS demyelination, and we demonstrate that Bacteroides fragilis producing a bacterial capsular polysaccharide Ag can protect against EAE. Recolonization with wild type B. fragilis maintained resistance to EAE, whereas reconstitution with polysaccharide A-deficient B. fragilis restored EAE susceptibility. Enhanced numbers of Foxp3(+)T(reg) cells in the cervical lymph nodes were observed after intestinal recolonization with either strain of B. fragilis. Ex vivo, CD4(+)T cells obtained from mice reconstituted with wild type B. fragilis had significantly enhanced rates of conversion into IL-10-producing Foxp3(+)T(reg) cells and offered greater protection against disease. Our results suggest an important role for commensal bacterial Ags, in particular B. fragilis expressing polysaccharide A, in protecting against CNS demyelination in EAE and perhaps human multiple sclerosis.

Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.

PubMed

Hemsworth, Glyn R; Thompson, Andrew J; Stepper, Judith; Sobala, Łukasz F; Coyle, Travis; Larsbrink, Johan; Spadiut, Oliver; Goddard-Borger, Ethan D; Stubbs, Keith A; Brumer, Harry; Davies, Gideon J

2016-07-01

The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins. © 2016 The Authors.

Tenacibaculum caenipelagi sp. nov., a member of the family Flavobacteriaceae isolated from tidal flat sediment.

PubMed

Park, Sooyeon; Yoon, Jung-Hoon

2013-08-01

A Gram-stain-negative, non-spore-forming, aerobic, non-flagellated, gliding and rod-shaped bacterial strain, designated HJ-26M(T), was isolated from a tidal flat sediment in the Korean peninsula. It grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that the strain fell within the clade comprising Tenacibaculum species, clustering coherently with the type strains of Tenacibaculum lutimaris and Tenacibaculum aestuarii. Strain HJ-26M(T) exhibited the highest 16S rRNA gene sequence similarity values of 98.4 and 98.2 % to T. lutimaris TF-26(T) and T. aestuarii SMK-4(T), respectively, and of 94.9-97.4 % to the type strains of the other Tenacibaculum species. Strain HJ-26M(T) contained MK-6 as the predominant menaquinone and iso-C15:0 and iso-C17:0 3-OH as the major fatty acids. The DNA G+C content of strain HJ-26M(T) was 34.5 mol% and its mean DNA-DNA relatedness values with the type strains of T. lutimaris and T. aestuarii were 19 and 23 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HJ-26M(T) is separate from other Tenacibaculum species. On the basis of the data presented, strain HJ-26M(T) is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum caenipelagi sp. nov. is proposed. The type strain is HJ-26M(T) (= KCTC 32323(T) = CECT 8283(T)).

Identification and use of the putative Bacteroides ovatus xylanase promoter for the inducible production of recombinant human proteins.

PubMed

Hamady, Zaed Z R; Farrar, Mark D; Whitehead, Terence R; Holland, Keith T; Lodge, J Peter A; Carding, Simon R

2008-10-01

The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ovatus for the production of these molecules, due to its ability to colonize the colon and xylan utilization properties. Here we have identified the putative xylanase promoter. The 5' region of the corresponding mRNA was determined by 5'RACE analysis and the transcription initiation site was identified 216 bp upstream of the ATG start codon. The putative xylanase promoter was regulated by xylan in a dose- and time-dependent manner, and repressed by glucose. This promoter was subsequently used to direct the controlled expression of a gene encoding the human intestinal trefoil factor (TFF-3) after integration as a single copy into the chromosome of B. ovatus. The resulting strain produced biologically active TFF-3 in the presence of xylan. These findings identify the B. ovatus xylanase operon promoter and show that it can be utilized to direct xylan-inducible expression of heterologous eukaryotic genes in B. ovatus.

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium

PubMed Central

Li, Jiaojiao; Mandal, Goutam; Rosen, Barry P.

2016-01-01

The response of the obligate anaerobe Bacteroides vulgatus ATCC 8482, a common human gut microbiota, to arsenic was determined. B. vulgatus ATCC 8482 is highly resistant to pentavalent As(V) and methylarsenate (MAs(V)). It is somewhat more sensitive to trivalent inorganic As(III) but 100-fold more sensitive to methylarsenite (MAs(III)) than to As(III). B. vulgatus ATCC 8482 has eight continuous genes in its genome that we demonstrate form an arsenical-inducible transcriptional unit. The first gene of this ars operon, arsR, encodes a putative ArsR As(III)-responsive transcriptional repressor. The next three genes encode proteins of unknown function. The remaining genes, arsDABC, have well-characterized roles in detoxification of inorganic arsenic, but there are no known genes for MAs(III) resistance. Expression of each gene after exposure to trivalent and pentavalent inorganic and methylarsenicals was analyzed. MAs(III) was the most effective inducer. The arsD gene was the most highly expressed of the ars operon genes. These results demonstrate that this anaerobic microbiome bacterium has arsenic-responsive genes that confer resistance to inorganic arsenic and may be responsible for the organism's ability to maintain its prevalence in the gut following dietary exposure to inorganic arsenic. PMID:27040269

Prevalence and characterization of enterotoxigenic Bacteroides fragilis and toxigenic Clostridium difficile in a Taipei emergency department.

PubMed

Ji, Dar-Der; Huang, I-Hsiu; Lai, Chao-Chih; Wu, Fang-Tzy; Jiang, Donald Dah-Shyong; Hsu, Bing-Mu; Lin, Wei-Chen

2017-02-01

Enterotoxigenic Bacteroides fragilis (ETBF) and toxin-encoding Clostridium difficile (TXCD) are associated with gastroenteritis. Routine anaerobic blood culture for recovery of these anaerobic pathogens is not used for the detection of their toxins, especially for toxin-variant TXCD. The aim of this study was to investigate the prevalence and risk factors of the genotypes of these anaerobes in patients with acute diarrheal illnesses. The data and samples of 513 patients with gastroenteritis were collected in a Taipei emergency department from March 1, 2006 to December 31, 2009. Nonenterotoxigenic B. fragilis (NTBF) and ETBF and the toxin genotypes of TXCD were detected by molecular methods. The prevalence rates of NTBF, ETBF, and TXCD infections were 33.14%, 1.56%, and 2.34%, respectively. ETBF infections often occurred in the elderly (average age = 67.13 years) and during the cold, dry winters. TXCD infections were widely distributed in age and often occurred in the warm, wet springs and summers. The symptoms of ETBF-infected patients were significantly more severe than those of NTBF-infected patients. This study identified and analyzed the prevalence, risk factors, and clinical presentations of these anaerobic infections. Future epidemiologic and clinical studies are needed to understand the role of ETBF and TXCD in human gastroenteritis. Copyright © 2015. Published by Elsevier B.V.

Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system.

PubMed

Huang, Zhitao; Jiang, Yuli; Song, Xiefa; Hallerman, Eric; Peng, Lei; Dong, Dengpan; Ma, Teng; Zhai, Jieming; Li, Wensheng

2018-02-10

While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.

Comparative Analysis of GF-1 and HJ-1 Data to Derive the Optimal Scale for Monitoring Heavy Metal Stress in Rice.

PubMed

Wang, Dongmin; Liu, Xiangnan

2018-03-06

Remote sensing can actively monitor heavy metal contamination in crops, but with the increase of satellite sensors, the optimal scale for monitoring heavy metal stress in rice is still unknown. This study focused on identifying the optimal scale by comparing the ability to detect heavy metal stress in rice at various spatial scales. The 2 m, 8 m, and 16 m resolution GF-1 (China) data and the 30 m resolution HJ-1 (China) data were used to invert leaf area index (LAI). The LAI was the input parameter of the World Food Studies (WOFOST) model, and we obtained the dry weight of storage organs (WSO) and dry weight of roots (WRT) through the assimilation method; then, the mass ratio of rice storage organs and roots (SORMR) was calculated. Through the comparative analysis of SORMR at each spatial scale of data, we determined the optimal scale to monitor heavy metal stress in rice. The following conclusions were drawn: (1) SORMR could accurately and effectively monitor heavy metal stress; (2) the 8 m and 16 m images from GF-1 were suitable for monitoring heavy metal stress in rice; (3) 16 m was considered the optimal scale to assess heavy metal stress in rice.

Identifying Local Scale Climate Zones of Urban Heat Island from HJ-1B Satellite Data Using Self-Organizing Maps

NASA Astrophysics Data System (ADS)

Wei, C. Z.; Blaschke, T.

2016-10-01

With the increasing acceleration of urbanization, the degeneration of the environment and the Urban Heat Island (UHI) has attracted more and more attention. Quantitative delineation of UHI has become crucial for a better understanding of the interregional interaction between urbanization processes and the urban environment system. First of all, our study used medium resolution Chinese satellite data-HJ-1B as the Earth Observation data source to derive parameters, including the percentage of Impervious Surface Areas, Land Surface Temperature, Land Surface Albedo, Normalized Differential Vegetation Index, and object edge detector indicators (Mean of Inner Border, Mean of Outer border) in the city of Guangzhou, China. Secondly, in order to establish a model to delineate the local climate zones of UHI, we used the Principal Component Analysis to explore the correlations between all these parameters, and estimate their contributions to the principal components of UHI zones. Finally, depending on the results of the PCA, we chose the most suitable parameters to classify the urban climate zones based on a Self-Organization Map (SOM). The results show that all six parameters are closely correlated with each other and have a high percentage of cumulative (95%) in the first two principal components. Therefore, the SOM algorithm automatically categorized the city of Guangzhou into five classes of UHI zones using these six spectral, structural and climate parameters as inputs. UHI zones have distinguishable physical characteristics, and could potentially help to provide the basis and decision support for further sustainable urban planning.

The hyperthermophilic α-amylase from Thermococcus sp. HJ21 does not require exogenous calcium for thermostability because of high-binding affinity to calcium.

PubMed

Cheng, Huaixu; Luo, Zhidan; Lu, Mingsheng; Gao, Song; Wang, Shujun

2017-05-01

The hyperthermophilic α-amylase from Thermococcus sp. HJ21 does not require exogenous calcium ions for thermostability, and is a promising alternative to commercially available α-amylases to increase the efficiency of industrial processes like the liquefaction of starch. We analyzed the amino acid sequence of this α-amylase by sequence alignments and structural modeling, and found that this α-amylase closely resembles the α-amylase from Pyrococcus woesei. The gene of this α-amylase was cloned in Escherichia coli and the recombinant α-amylase was overexpressed and purified with a combined renaturation-purification procedure. We confirmed thermostability and exogenous calcium ion independency of the recombinant α-amylase and further investigated the mechanism of the independency using biochemical approaches. The results suggested that the α-amylase has a high calcium ion binding affinity that traps a calcium ion that would not dissociate at high temperatures, providing a direct explanation as to why the addition of calcium ions is not required for thermostability. Understanding of the mechanism offers a strong base on which to further engineer properties of this α-amylase for better potential applications in industrial processes.

Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola.

PubMed

Chen, Yaowen; Li, Zongcheng; Hu, Shuofeng; Zhang, Jian; Wu, Jiaqi; Shao, Ningsheng; Bo, Xiaochen; Ni, Ming; Ying, Xiaomin

2017-02-01

Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or species-level composition and microbial gene sets, while strain-level composition and single-nucleotide polymorphism (SNP) have been overlooked. The gut metagenomes of type 2 diabetes (T2D) patients have been found to be enriched with butyrate-producing bacteria and sulfate reduction functions. However, it is not known whether the gut metagenomes of T2D patients have characteristic strain patterns or SNP distributions. We downloaded public gut metagenome datasets from 170 T2D patients and 174 healthy controls and performed a systematic comparative analysis of their metagenome SNPs. We found that Bacteroides coprocola, whose relative abundance did not differ between the groups, had a characteristic distribution of SNPs in the T2D patient group. We identified 65 genes, all in B. coprocola, that had remarkably different enrichment of SNPs. The first and sixth ranked genes encode glycosyl hydrolases (GenBank accession EDU99824.1 and EDV02301.1). Interestingly, alpha-glucosidase, which is also a glycosyl hydrolase located in the intestine, is an important drug target of T2D. These results suggest that different strains of B. coprocola may have different roles in human gut and a specific set of B. coprocola strains are correlated with T2D.

Effects of the herbal medicine Hachimi-jio-gan (Ba-Wei-Di-Huang-Wan) on insulin secretion and glucose tolerance in type 2 diabetic Goto-Kakizaki rats.

PubMed

Hirotani, Y; Ikeda, K; Myotoku, M

2010-04-01

Hachimi-jio-gan (HJ) is a Chinese medicine that has been widely used for the treatment of nephrotic syndromes, hypertension, and diabetes mellitus. We reported that HJ lowers plasma glucose in type 1 diabetic rats. We investigated the effects of HJ on diabetic hyperglycemia and insulin secretion in type 2 diabetic Goto-Kakizaki (GK) rats. Eight-week-old diabetic GK rats were given free access to pellets containing 1% HJ extract powder for 14 weeks. HJ consumption increased the food intake and body weight of these rats in comparison to control rats. HJ may control the body weight loss observed in GK rats. HJ also reduced hyperglycemia in diabetic GK rats, and it significantly increased insulin secretion in non-fasting GK rats over the experimental period. In oral glucose tolerance tests, HJ significantly improved the insulin response at 30 min and reduced the plasma glucose level at 60 min after glucose administration (p < 0.05). Ten weeks after administration, the plasma leptin levels significantly increased in the HJ group rats. These results demonstrate that in diabetic GK rats, HJ decreased the level of postprandial glucose via enhanced insulin secretion coupled with the regulation of food intake by leptin.

Potential usefulness of bacteriophages that infect Bacteroides fragilis as model organisms for monitoring virus removal in drinking water treatment plants.

PubMed Central

Jofre, J; Ollé, E; Ribas, F; Vidal, A; Lucena, F

1995-01-01

The presence of bacteriophages at different stages in three drinking water treatment plants was evaluated to study the usefulness of phages as model organisms for assessing the efficiency of the processes. The bacteriophages tested were somatic coliphages, F-specific coliphages, and phages infecting Bacteroides fragilis. The presence of enteroviruses and currently used bacterial indicators was also determined. Most bacteriophages were removed during the prechlorination-flocculation-sedimentation step. In these particular treatment plants, which include prechlorination, phages were, in general, more resistant to the treatment processes than present bacterial indicators, with the exception, in some cases, of clostridia. Bacteriophages infecting B. fragilis were found to be more resistant to water treatment than either somatic or F-specific coliphages or even clostridia. Enteric viruses were found only in untreated water in low numbers, and consequently, the efficiency of the plants in the removal of viruses could not be evaluated with precision. The numbers and frequencies of detection of the various microorganisms in water samples taken in the distribution network served by the three plants confirm the results found in the finished water at the plants. PMID:7574632

A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass

PubMed Central

Vija, Heiki; Aasamets, Anneli; Viigand, Katrin

2017-01-01

Bacteroides thetaiotaomicron, an abundant commensal of the human gut, degrades numerous complex carbohydrates. Recently, it was reported to grow on a β-2,6-linked polyfructan levan produced by Zymomonas mobilis degrading the polymer into fructooligosaccharides (FOS) with a cell surface bound endo-levanase BT1760. The FOS are consumed by B. thetaiotaomicron, but also by other gut bacteria, including health-promoting bifidobacteria and lactobacilli. Here we characterize biochemical properties of BT1760, including the activity of BT1760 on six bacterial levans synthesized by the levansucrase Lsc3 of Pseudomonas syringae pv. tomato, its mutant Asp300Asn, levansucrases of Zymomonas mobilis, Erwinia herbicola, Halomonas smyrnensis as well as on levan isolated from timothy grass. For the first time a plant levan is shown as a perfect substrate for an endo-fructanase of a human gut bacterium. BT1760 degraded levans to FOS with degree of polymerization from 2 to 13. At optimal reaction conditions up to 1 g of FOS were produced per 1 mg of BT1760 protein. Low molecular weight (<60 kDa) levans, including timothy grass levan and levan synthesized from sucrose by the Lsc3Asp300Asn, were degraded most rapidly whilst levan produced by Lsc3 from raffinose least rapidly. BT1760 catalyzed finely at human body temperature (37°C) and in moderately acidic environment (pH 5–6) that is typical for the gut lumen. According to differential scanning fluorimetry, the Tm of the endo-levanase was 51.5°C. All tested levans were sufficiently stable in acidic conditions (pH 2.0) simulating the gastric environment. Therefore, levans of both bacterial and plant origin may serve as a prebiotic fiber for B. thetaiotaomicron and contribute to short-chain fatty acids synthesis by gut microbiota. In the genome of Bacteroides xylanisolvens of human origin a putative levan degradation locus was disclosed. PMID:28103254

A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass.

PubMed

Mardo, Karin; Visnapuu, Triinu; Vija, Heiki; Aasamets, Anneli; Viigand, Katrin; Alamäe, Tiina

2017-01-01

Bacteroides thetaiotaomicron, an abundant commensal of the human gut, degrades numerous complex carbohydrates. Recently, it was reported to grow on a β-2,6-linked polyfructan levan produced by Zymomonas mobilis degrading the polymer into fructooligosaccharides (FOS) with a cell surface bound endo-levanase BT1760. The FOS are consumed by B. thetaiotaomicron, but also by other gut bacteria, including health-promoting bifidobacteria and lactobacilli. Here we characterize biochemical properties of BT1760, including the activity of BT1760 on six bacterial levans synthesized by the levansucrase Lsc3 of Pseudomonas syringae pv. tomato, its mutant Asp300Asn, levansucrases of Zymomonas mobilis, Erwinia herbicola, Halomonas smyrnensis as well as on levan isolated from timothy grass. For the first time a plant levan is shown as a perfect substrate for an endo-fructanase of a human gut bacterium. BT1760 degraded levans to FOS with degree of polymerization from 2 to 13. At optimal reaction conditions up to 1 g of FOS were produced per 1 mg of BT1760 protein. Low molecular weight (<60 kDa) levans, including timothy grass levan and levan synthesized from sucrose by the Lsc3Asp300Asn, were degraded most rapidly whilst levan produced by Lsc3 from raffinose least rapidly. BT1760 catalyzed finely at human body temperature (37°C) and in moderately acidic environment (pH 5-6) that is typical for the gut lumen. According to differential scanning fluorimetry, the Tm of the endo-levanase was 51.5°C. All tested levans were sufficiently stable in acidic conditions (pH 2.0) simulating the gastric environment. Therefore, levans of both bacterial and plant origin may serve as a prebiotic fiber for B. thetaiotaomicron and contribute to short-chain fatty acids synthesis by gut microbiota. In the genome of Bacteroides xylanisolvens of human origin a putative levan degradation locus was disclosed.

The validity of two Omron pedometers during treadmill walking is speed dependent.

PubMed

Giannakidou, Dimitra M; Kambas, Antonis; Ageloussis, Nikolaos; Fatouros, Ioannis; Christoforidis, Christos; Venetsanou, Fotini; Douroudos, Ioannis; Taxildaris, Kyriakos

2012-01-01

The purpose of this study was to examine the effects of walking speed on the accuracy of measurement of steps, distance, and energy expenditure of two commercially available Omron pedometers [HJ-720IT-E2 (HJ-720) and HJ-113-E (HJ-113)]. Twenty-four untrained males (age, 22.7 ± 2.8 years; BMI, 24.38 ± 2.19 kg m(-2); body fat (%), 16 ± 2.2; VO(2max), 40.2 ± 6.5 ml kg(-1) min(-1)) and 18 females (age, 22.4 ± 2.9 years; BMI, 21.68 ± 2.43 kg m(-2); body fat (%), 23% ± 1.8; VO(2max), 35.9 ± 2.8 ml kg(-1) min(-1)) walked at five different velocities (54, 67, 80, 94 and 107 m min(-1)) on a treadmill in 5-min stages while wearing three types of pedometers: (a) HJ-720, (b) HJ-113, and (c) Yamax Digi-Walker SW-200 (YAM). Step-count for each pedometer was recorded at the end of each stage and compared with the value of a hand counter. Additionally, Omron pedometers were evaluated on their distance and energy expenditure (against VO(2) measurement with a gas-exchange analyzer) accuracy during each stage. HJ-720 and HJ-113 demonstrated high accuracy (r = 0.80-0.99) at all speeds. YAM underestimated step-count only at 54 m min(-1) (r = 0.46). HJ-720 and HJ-113 overestimated distance at slower speeds and underestimated distance at faster speeds, providing mean distance values that where to within 1.5-4% at 80 m min(-1). HJ-720 and HJ-113 underestimated energy expenditure (gross kilocalories) by 28%, when compared to indirect calorimetry. These results suggest that although the Omron HJ-720 and HJ-113 pedometers are accurate in the measurement of step-count, they demonstrate limited accuracy in the assessment of traveled distance and energy expenditure in a speed-dependent manner.

[Can fixation disparity be detected reliably by measurement and correctional techniques according H.J. Haase (MKH)?].

PubMed

Gerling, J; de Paz, H; Schroth, V; Bach, M; Kommerell, G

2000-06-01

The theory of the "Measuring and Correction Methods of H.-J. Haase" (MCH) states that a small misalignment of one eye, called fixation disparity, indicates a difficulty in overcoming a "vergence position of rest" that is different from ortho position. This difficulty, so the theory, can cause asthenopic complaints, such as headaches, and these complaints can be relieved by prisms. The theory further claims that fixation disparity can be ascertained by a series of tests which depend on the subject's perception. The tests most decisive for the diagnosis of a so-called fixation disparity type 2 consist of stereo displays. The magnitude of the prism that allows the subject to see the test configurations in symmetry is thought to be the one that corrects the "vergence position of rest". Nine subjects with healthy eyes in whom a "fixation disparity type 2" had been diagnosed were selected for the study. Misalignment of the eyes was determined according to the principle of the unilateral cover test. Targets identical for both eyes were presented on the screen of the Polatest E. Then, the target was deleted for one eye and the ensuing position change of the other eye was measured, using the search coil technique. This test was performed both with and without the MCH prism. In all 9 subjects the misalignment was less than 10 minutes of arc, i.e. in the range of normal fixation instability. Averaging across the 9 subjects, the deviation of the eye (misaligned according to MCH) was 0.79 +/- 3.45 minutes of arc in the direction opposed to that predicted by the MCH, a value not significantly different from zero. The MCH prism elicited a fusional vergence movement the magnitude of which corresponded to the magnitude of the MCH prism. Ascertaining fixation disparity with the MCH is unreliable. Accordingly, it appears dubious to correct a "vergence position of rest" on the basis of the MCH.

Monoclonal antibody against Porphyromonas (Bacteroides) endodontalis lipopolysaccharide and application of the antibody for direct identification of the species.

PubMed

Hanazawa, S; Sagiya, T; Kitami, H; Ohta, K; Nishikawa, H; Kitano, S

1991-11-01

The aim of the present study was to develop a monoclonal antibody that recognizes the shared antigen of Porphyromonas endodontalis so that we could use the antibody in direct identification and detection of P. endodontalis in infectious material from apical periodontal patients. We established a hybridoma cell line producing monoclonal antibody (BEB5) specific for P. endodontalis. BEB5 antibody reacted with all of the P. endodontalis strains tested, but not with any of the other black-pigmented Porphyromonas and Bacteroides spp. The antibody reacted specifically with the lipopolysaccharide (LPS) of three P. endodontalis strains of different serotypes (O1K1, O1K2, and O1K-). Western blotting (immunoblotting) analysis confirmed the specificity of the antibody to these LPSs, because the antibody recognized the typical "repetitive ladder" pattern characteristic of LPS on sodium dodecyl sulfate-polyacrylamide electrophoretic gels. These observations demonstrate that P. endodontalis LPS is the shared antigen of this species. The antibody can specifically identify P. endodontalis on nitrocellulose membrane blots of bacterial colonies grown on agar. The antibody is also capable of directly detecting the presence of P. endodontalis in infectious material by immunoslot blot assay. These results indicate that LPS is the shared antigen of P. endodontalis and that BEB5 antibody against LPS is a useful one for direct identification and detection of the organisms in samples from apical periodontal patients.

Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms.

PubMed

Wilson, Marlena M; Anderson, D Eric; Bernstein, Harris D

2015-01-01

Bacteroides fragilis is a widely distributed member of the human gut microbiome and an opportunistic pathogen. Cell surface molecules produced by this organism likely play important roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM) and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under laboratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipoproteins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel family of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipoproteins and other proteins that might be substrates of the putative type I or type VI secretion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM proteins that it produces and the range of secretion strategies that it utilizes.

Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent.

PubMed

Hirsch, P; Ludwig, W; Hethke, C; Sittig, M; Hoffmann, B; Gallikowski, C A

1998-08-01

Aseptically collected sandstone and soil samples from the antarctic Dry Valleys were inoculated into oligotrophic media and incubated under low light intensities. A total of 41 Gram-negative isolates were obtained with reddish colonies spreading on agar. A sandstone isolate and four soil strains were characterized further. They were nearly identical in morphological, physiological, biochemical and chemotaxonomic properties. They produced large amounts of extracellular polymer and utilized for growth: glucose, saccharose, mannitol, sorbitol, L-aspartate, malate and acetate, but not D-ribose, adonitol, DL-alanine, glutamate, glycolate, lactate or succinate. All strains hydrolyzed gelatin, starch, casein, xylan, Tweens 80 or 60 and dead or living yeast cells, but not cellulose or pectin. Nitrate was not reduced, ethanol was not oxidized and acid was not produced from maltose, mannitol or dulcitol. Ammonia was not produced from peptone. They were strictly aerobic. Major fatty acids were n 16:1 d 9, n 16:1 d 11, n 17:1 d 11, and i 15:0. The strains contained the quinone MK-7 and phosphatidylethanolamine as the main phospholipid. The base ratio ranged from 55 to 61 mol% G+C. A 16S rRNA sequence analysis of strains AA-688 and AA-718 showed these to be identical and to represent a special phylogenetic group within the Cytophaga/Flavobacterium/Bacteroides major line of descent. Three soil strains labeled "Taxeobacter" Txc1, Txg1, and Txo1 (Reichenbach, 1992) belonged to the same group but had lower sequence similarities (<95%). Some of their characteristics were different from those of the antarctic strains: the utilization of C-compounds, hydrolysis of polymers, temperature tolerances, major fatty acids and base ratios. Txc1 and Txg1 may later have to be considered as members of this group, possibly on the species level, while Txo1 could represent a different related genus. It is concluded that the five antarctic strains represent a new genus and species for which the name

CROWDING-OUT OF GIANTS BY DWARFS: AN ORIGIN FOR THE LACK OF COMPANION PLANETS IN HOT JUPITER SYSTEMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogihara, Masahiro; Inutsuka, Shu-ichiro; Kobayashi, Hiroshi, E-mail: ogihara@nagoya-u.jp

2013-11-20

We investigate the formation of close-in terrestrial planets from planetary embryos under the influence of a hot Jupiter (HJ) using gravitational N-body simulations that include gravitational interactions between the gas disk and the terrestrial planet (e.g., type I migration). Our simulations show that several terrestrial planets efficiently form outside the orbit of the HJ, making a chain of planets, and all of them gravitationally interact directly or indirectly with the HJ through resonance, which leads to inward migration of the HJ. We call this mechanism of induced migration of the HJ ''crowding-out''. The HJ is eventually lost through collision withmore » the central star, and only several terrestrial planets remain. We also find that the efficiency of the crowding-out effect depends on the model parameters; for example, the heavier the disk is, the more efficient the crowding-out is. When planet formation occurs in a massive disk, the HJ can be lost to the central star and is never observed. On the other hand, for a less massive disk, the HJ and terrestrial planets can coexist; however, the companion planets may be below the detection limit of current observations. In both cases, systems with a HJ and terrestrial planets have little chance of detection. Therefore, our model naturally explains the lack of companion planets in HJ systems regardless of the disk mass. In effect, our model provides a theoretical prediction for future observations; additional planets can be discovered just outside the HJ, and their masses should generally be small.« less

Decolorization of Methyl Orange by a new clay-supported nanoscale zero-valent iron: Synergetic effect, efficiency optimization and mechanism.

PubMed

Li, Xiaoguang; Zhao, Ying; Xi, Beidou; Meng, Xiaoguang; Gong, Bin; Li, Rui; Peng, Xing; Liu, Hongliang

2017-02-01

In this study, a novel nanoscale zero-valent iron (nZVI) composite material was successfully synthesized using a low-cost natural clay, "Hangjin 2 # clay" (HJ clay) as the support and tested for the decolorization of the azo dye Methyl Orange (MO) in aqueous solution by nZVI particles. According to the characterization and MO decolorization experiments, the sample with 5:1 HJ clay-supported nZVI (HJ/nZVI) mass ratio (HJ-nZVI5) showed the best dispersion and reactivity and the highest MO decolorization efficiency. With the same equivalent Fe 0 dosage, the HJ-nZVI1 and HJ-nZVI5 samples demonstrated a synergetic effect for the decolorization of MO: their decolorization efficiencies were much higher than that achieved by physical mixing of HJ clay and nZVIs, or the sum of HJ clay and nZVIs alone. The synergetic effect was primarily due to the improved dispersion and more effective utilization of the nZVI particles on/in the composite materials. Higher decolorization efficiency of MO was obtained at larger HJ-nZVI dosage, higher temperature and under N 2 atmosphere, while the MO initial concentration and pH were negatively correlated to the efficiency. HJ clay not only works as a carrier for nZVI nanoparticles, but also contributes to the decolorization through an "adsorption-enhanced reduction" mechanism. The high efficiency of HJ-nZVI for decontamination gives it great potential for use in a variety of remediation applications. Copyright © 2016. Published by Elsevier B.V.

Age prediction formulae from radiographic assessment of skeletal maturation at the knee in an Irish population.

PubMed

O'Connor, Jean E; Coyle, Joseph; Bogue, Conor; Spence, Liam D; Last, Jason

2014-01-01

Age estimation in living subjects is primarily achieved through assessment of a hand-wrist radiograph and comparison with a standard reference atlas. Recently, maturation of other regions of the skeleton has also been assessed in an attempt to refine the age estimates. The current study presents a method to predict bone age directly from the knee in a modern Irish sample. Ten maturity indicators (A-J) at the knee were examined from radiographs of 221 subjects (137 males; 84 females). Each indicator was assigned a maturity score. Scores for indicators A-G, H-J and A-J, respectively, were totalled to provide a cumulative maturity score for change in morphology of the epiphyses (AG), epiphyseal union (HJ) and the combination of both (AJ). Linear regression equations to predict age from the maturity scores (AG, HJ, AJ) were constructed for males and females. For males, equation-AJ demonstrated the greatest predictive capability (R(2)=0.775) while for females equation-HJ had the strongest capacity for prediction (R(2)=0.815). When equation-AJ for males and equation-HJ for females were applied to the current sample, the predicted age of 90% of subjects was within ±1.5 years of actual age for male subjects and within +2.0 to -1.9 years of actual age for female subjects. The regression formulae and associated charts represent the most contemporary method of age prediction currently available for an Irish population, and provide a further technique which can contribute to a multifactorial approach to age estimation in non-adults. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Hydrologic and forest management controls on DOC dynamics in the small watersheds of the H.J. Andrews Experimental Forest, OR

NASA Astrophysics Data System (ADS)

Lajtha, K.; Jones, J. A.

2016-12-01

Dissolved organic carbon (DOC) export from hillslopes to streams is an important component of the carbon cycle of a catchment and may be a critical source of energy for the aquatic food web in receiving waters. Using a long-term record of DOC and other dissolved nutrients and elements from paired watersheds from the H.J. Andrews Experimental Forest in Oregon, we explored hydrologic, climatic, and land-use controls on seasonal and inter-annual patterns of DOC flux in a seasonally dry ecosystem. Seasonal patterns of DOC flux demonstrated source limitations to DOC export, with DOC concentrations highest immediately following the first rains after a dry summer, and lowest after winter rains. In contrast, more geochemically-controlled elements showed simple dilution-concentration patterns with no seasonal hysteresis. Inter-annual patterns of DOC flux, however, did not provide evidence of source limitation, with DOC flux within a watershed tightly correlated to total discharge but not temperature. Among watersheds, forest harvest, even over 50 years ago, significantly reduced DOC flux but not fluxes of other elements including N; this response was linked to the loading of coarse woody debris to the forest floor. Chemical fingerprinting of DOC revealed that old-growth watersheds had higher fluxes of DOC characteristic of forest floor organic materials, likely delivered to streams through more surficial preferential flow pathways not subject to microbial alteration, respiration, or sorption losses. Taken together these results suggest that the biogeochemical composition of forested streams reflects both current hydrologic patterns and also processes that occurred many decades ago within the catchment.

Hydrophobicities of human polymorphonuclear leukocytes and oral Bacteroides and Porphyromonas spp., Wolinella recta, and Eubacterium yurii with special reference to bacterial surface structures.

PubMed

Haapasalo, M; Kerosuo, E; Lounatmaa, K

1990-12-01

The hydrophobicities of human polymorphonuclear leukocytes (PMNLs) and Bacteroides buccae, B. oris, B. oralis, B. veroralis, B. buccalis, B. heparinolyticus, B. intermedius, B. denticola, B. loescheii, B. melaninogenicus, Porphyromonas gingivalis, P. endodontalis, Wolinella recta, and Eubacterium yurii were studied by the hexadecane method. The majority of the strains were equally or less hydrophobic than the PMNLs. Only in the case of E. yurii and the only strain of B. buccalis were all strains more hydrophobic than the PMNLs. However, some strains of B. intermedius, B. oris, B. denticola, and P. gingivalis were also more hydrophobic than the PMNLs. With the exception of B. intermedius and species with a crystalline surface protein layer (S-layer), the strains of all other species with a thick capsule were more hydrophilic than the strains with little or no extracellular polymeric material. All strains of the S-layer species were either quite hydrophilic or hydrophobic depending on the species, totally irrespective of the presence of the capsule. The results suggest that the S-layers of oral anaerobic bacteria may be important determinants of cell surface hydrophobicity.

Deficiency of the ferrous iron transporter FeoAB is linked with metronidazole resistance in Bacteroides fragilis

PubMed Central

Veeranagouda, Yaligara; Husain, Fasahath; Boente, Renata; Moore, Jane; Smith, C. Jeffrey; Rocha, Edson R.; Patrick, Sheila; Wexler, Hannah M.

2014-01-01

Background Metronidazole is the most commonly used antimicrobial for Bacteroides fragilis infections and is recommended for prophylaxis of colorectal surgery. Metronidazole resistance is increasing and the mechanisms of resistance are not clear. Methods A transposon mutant library was generated in B. fragilis 638R (BF638R) to identify the genetic loci associated with resistance to metronidazole. Results Thirty-two independently isolated metronidazole-resistant mutants had a transposon insertion in BF638R_1421 that encodes the ferrous transport fusion protein (feoAB). Deletion of feoAB resulted in a 10-fold increased MIC of metronidazole for the strain. The metronidazole MIC for the feoAB mutant was similar to that for the parent strain when grown on media supplemented with excess iron, suggesting that the increase seen in the MIC of metronidazole was due to reduced cellular iron transport in the feoAB mutant. The furA gene repressed feoAB transcription in an iron-dependent manner and disruption of furA resulted in constitutive transcription of feoAB, regardless of whether or not iron was present. However, disruption of feoAB also diminished the capacity of BF638R to grow in a mouse intraperitoneal abscess model, suggesting that inorganic ferrous iron assimilation is essential for B. fragilis survival in vivo. Conclusions Selection for feoAB mutations as a result of metronidazole treatment will disable the pathogenic potential of B. fragilis and could contribute to the clinical efficacy of metronidazole. While mutations in feoAB are probably not a direct cause of clinical resistance, this study provides a key insight into intracellular metronidazole activity and the link with intracellular iron homeostasis. PMID:25028451

Monoclonal antibody against Porphyromonas (Bacteroides) endodontalis lipopolysaccharide and application of the antibody for direct identification of the species.

PubMed Central

Hanazawa, S; Sagiya, T; Kitami, H; Ohta, K; Nishikawa, H; Kitano, S

1991-01-01

The aim of the present study was to develop a monoclonal antibody that recognizes the shared antigen of Porphyromonas endodontalis so that we could use the antibody in direct identification and detection of P. endodontalis in infectious material from apical periodontal patients. We established a hybridoma cell line producing monoclonal antibody (BEB5) specific for P. endodontalis. BEB5 antibody reacted with all of the P. endodontalis strains tested, but not with any of the other black-pigmented Porphyromonas and Bacteroides spp. The antibody reacted specifically with the lipopolysaccharide (LPS) of three P. endodontalis strains of different serotypes (O1K1, O1K2, and O1K-). Western blotting (immunoblotting) analysis confirmed the specificity of the antibody to these LPSs, because the antibody recognized the typical "repetitive ladder" pattern characteristic of LPS on sodium dodecyl sulfate-polyacrylamide electrophoretic gels. These observations demonstrate that P. endodontalis LPS is the shared antigen of this species. The antibody can specifically identify P. endodontalis on nitrocellulose membrane blots of bacterial colonies grown on agar. The antibody is also capable of directly detecting the presence of P. endodontalis in infectious material by immunoslot blot assay. These results indicate that LPS is the shared antigen of P. endodontalis and that BEB5 antibody against LPS is a useful one for direct identification and detection of the organisms in samples from apical periodontal patients. Images PMID:1774262

Process-to-Panel Modeling and Multiprobe Characterization of Silicon Heterojunction Solar Cell Technology

NASA Astrophysics Data System (ADS)

Chavali, Raghu Vamsi Krishna

The large-scale deployment of PV technology is very sensitive to the material and process costs. There are several potential candidates among p-n heterojunction (HJ) solar cells competing for higher efficiencies at lower material and process costs. These systems are, however, generally complex, involve diverse materials, and are not well understood. The direct translation of classical p-n homojunction theory to p-n HJ cells may not always be self-consistent and can lead, therefore, to misinterpretation of experimental results. Ultimately, this translation may not be useful for modeling and characterization of these solar cells. Hence, there is a strong need to redefine/reinterpret the modeling/characterization methodologies for HJ solar cells to produce a self-consistent framework for optimizing HJ solar cell designs. Towards this goal, we explore the physics and interpret characterization experiments of p-n HJs using Silicon HJ (HIT) solar cells. We will: (1) identify the key HJ properties that affect the cell efficiency; (2) analyze the dependence of key HJ properties on the carrier transport under light and dark conditions; (3) provide a selfconsistent multi-probe approach to extract the HJ parameters using several characterization techniques including dark I-V, light I-V, C-V, impedance spectroscopy, and Suns-Voc; (4) propose design guidelines to address the HJ bottlenecks of HIT cells; and (5) develop a process-to-module modeling framework to establish the module performance limits. The guidelines resulting from this multi-scale and self-consistent framework can be used to improve performance of HIT cells as well as other HJ based solar cells.

Modeling Belief in Dynamic Systems. Part 1: Foundations

DTIC Science & Technology

2000-10-24

GB[J(STLJ_H{HDnC`YHJ_BEt HjXkHj\\]HA(J`�OQA%­äSILE`%L[XQHLE`Jy^IdId?HjDs~?BE^ IATF �OQA%­*¶Gw-¿�BED%LW`G^I~I`YHJn¨ÍBEt0ðe8UWH¢NLEArJ(STHjA...FIH¡IAIH¢Â/Xåä,µJ¨|¶ « J(B*~HrJSIHiXkHjLE`>J]^IdId?HjD[~?BE^ IATF �BEtD?̱ Á ®V7Ç:T¨CE wsÐTOQAINH6­ OQ`WNjXkBE`GHFC^TAIFIHjDWXQHLE`JP^IdTdHD

Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains.

PubMed

Joglekar, Payal; Sonnenburg, Erica D; Higginbottom, Steven K; Earle, Kristen A; Morland, Carl; Shapiro-Ward, Sarah; Bolam, David N; Sonnenburg, Justin L

2018-01-01

Genomic differences between gut-resident bacterial strains likely underlie significant interindividual variation in microbiome function. Traditional methods of determining community composition, such as 16S rRNA gene amplicon sequencing, fail to capture this functional diversity. Metagenomic approaches are a significant step forward in identifying strain-level sequence variants; however, given the current paucity of biochemical information, they too are limited to mainly low-resolution and incomplete functional predictions. Using genomic, biochemical, and molecular approaches, we identified differences in the fructan utilization profiles of two closely related Bacteroides thetaiotaomicron strains. B. thetaiotaomicron 8736 ( Bt-8736 ) contains a fructan polysaccharide utilization locus (PUL) with a divergent susC / susD homolog gene pair that enables it to utilize inulin, differentiating this strain from other characterized Bt strains. Transfer of the distinct pair of susC / susD genes from Bt-8736 into the noninulin using type strain B. thetaiotaomicron VPI-5482 resulted in inulin use by the recipient strain, Bt ( 8736-2 ). The presence of the divergent susC / susD gene pair alone enabled the hybrid Bt ( 8736-2 ) strain to outcompete the wild-type strain in vivo in mice fed an inulin diet. Further, we discovered that the susC / susD homolog gene pair facilitated import of inulin into the periplasm without surface predigestion by an endo-acting enzyme, possibly due to the short average chain length of inulin compared to many other polysaccharides. Our data builds upon recent reports of dietary polysaccharide utilization mechanisms found in members of the Bacteroides genus and demonstrates how the acquisition of two genes can alter the functionality and success of a strain within the gut. IMPORTANCE Dietary polysaccharides play a dominant role in shaping the composition and functionality of our gut microbiota. Dietary interventions using these m icrobiota- a

Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains

PubMed Central

Joglekar, Payal; Sonnenburg, Erica D.; Higginbottom, Steven K.; Earle, Kristen A.; Morland, Carl; Shapiro-Ward, Sarah; Bolam, David N.

2018-01-01

ABSTRACT Genomic differences between gut-resident bacterial strains likely underlie significant interindividual variation in microbiome function. Traditional methods of determining community composition, such as 16S rRNA gene amplicon sequencing, fail to capture this functional diversity. Metagenomic approaches are a significant step forward in identifying strain-level sequence variants; however, given the current paucity of biochemical information, they too are limited to mainly low-resolution and incomplete functional predictions. Using genomic, biochemical, and molecular approaches, we identified differences in the fructan utilization profiles of two closely related Bacteroides thetaiotaomicron strains. B. thetaiotaomicron 8736 (Bt-8736) contains a fructan polysaccharide utilization locus (PUL) with a divergent susC/susD homolog gene pair that enables it to utilize inulin, differentiating this strain from other characterized Bt strains. Transfer of the distinct pair of susC/susD genes from Bt-8736 into the noninulin using type strain B. thetaiotaomicron VPI-5482 resulted in inulin use by the recipient strain, Bt(8736-2). The presence of the divergent susC/susD gene pair alone enabled the hybrid Bt(8736-2) strain to outcompete the wild-type strain in vivo in mice fed an inulin diet. Further, we discovered that the susC/susD homolog gene pair facilitated import of inulin into the periplasm without surface predigestion by an endo-acting enzyme, possibly due to the short average chain length of inulin compared to many other polysaccharides. Our data builds upon recent reports of dietary polysaccharide utilization mechanisms found in members of the Bacteroides genus and demonstrates how the acquisition of two genes can alter the functionality and success of a strain within the gut. IMPORTANCE Dietary polysaccharides play a dominant role in shaping the composition and functionality of our gut microbiota. Dietary interventions using these microbiota

Effects of Hachimi-jio-gan (Ba-Wei-Di-Huang-Wan) on hyperglycemia in streptozotocin-induced diabetic rats.

PubMed

Hirotani, Yoshihiko; Ikeda, Takuya; Yamamoto, Kaoru; Kurokawa, Nobuo

2007-05-01

The present study investigated the effects of Hachimi-jio-gan (HJ) on diabetic hyperglycemia in streptozotocin (STZ)-induced diabetic rats. After STZ administration, rats had free access to pellets containing 1% HJ extract powder for four weeks. HJ markedly suppressed hyperglycemia in STZ-induced diabetic rats at three and four weeks after the start of administration. There were also significant increases in serum and pancreatic immunoreactive insulin levels in STZ and HJ co-administering rats. However, in the present study, the number of beta cells in the pancreatic Langerhans' islets did not increase. Next, in order to investigate the action mechanism besides the glycemic control action of insulin, the expression of glucose transporter 2 (GLUT2) protein, which is involved in glucose uptake and release in the liver, was investigated. GLUT2 protein expression was increased by STZ administration but was normalized after four weeks of HJ administration. Therefore, irrespective of the structural changes in pancreatic beta-cells due to STZ, HJ increased insulin production and secretion by the pancreas and significantly suppressed GLUT2 synthesis in the liver. Amylase secretion from the pancreas was measured to assess pancreatic secretion. Amylase activity was decreased by STZ but was increased by HJ. Therefore, the effects of HJ on STZ-induced hyperglycemia in rats could be summarized as follows: besides increasing insulin synthesis and release, HJ normalizes GLUT2 protein expression in the liver to suppress hyperglycemia. Hence, the results of the present study suggest for the first time that HJ affects not only the production and secretion of insulin, but also the release of glucose from the liver.

Removal of nitrobenzene by immobilized nanoscale zero-valent iron: Effect of clay support and efficiency optimization

NASA Astrophysics Data System (ADS)

Li, Xiaoguang; Zhao, Ying; Xi, Beidou; Mao, Xuhui; Gong, Bin; Li, Rui; Peng, Xing; Liu, Hongliang

2016-05-01

In this study, natural clays were used as the support for nanoscale zero-valent iron (nZVI) to fulfill affordable and efficient decontamination materials. In comparison with the kaolinite (K) and montmorillonite (M) supported nZVI materials (K-nZVI and M-nZVI), Hangjin clay supported nZVI (HJ-nZVI) exhibited the best performance for nitrobenzene (NB) removal because of its favorable characteristics, such as higher specific surface area (SSA, 82.0 m2 g-1), larger pore volume (0.1198 cm3 g-1) and bigger average pore diameter (6.2 nm). The NB removal efficiency achieved by HJ-nZVI (93.2 ± 2.8%) was much higher than these achieved by HJ clay alone (38.2 ± 2.3%), nZVI alone (52.3 ± 2.5%) and by the combined use of nZVI and HJ clay (70.2 ± 1.3%). The superior performance of HJ-nZVI was associated with three aspects: the even distribution of nZVIs onto HJ clay, higher payload efficiency of nZVIs and the stronger adsorption capability of HJ clay support. Higher SSA, larger pore volume, favorable cation exchange capacity and structural negative charges all facilitated the payload of iron onto HJ clay. The adsorption process accelerated the reduction via increasing the local concentration of aqueous NB. The high efficiency of HJ-nZVI for decontamination warranted its promising prospect in remediation applications.

Structure of the GH76 α-mannanase homolog, BT2949, from the gut symbiont Bacteroides thetaiotaomicron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Andrew J.; Cuskin, Fiona; Spears, Richard J.

A high-resolution structure of a noncanonical α-mannanase relevant to human health and nutrition has been solved via heavy-atom phasing of a selenomethionine derivative. The large bowel microbiota, a complex ecosystem resident within the gastrointestinal tract of all human beings and large mammals, functions as an essential, nonsomatic metabolic organ, hydrolysing complex dietary polysaccharides and modulating the host immune system to adequately tolerate ingested antigens. A significant member of this community, Bacteroides thetaiotaomicron, has evolved a complex system for sensing and processing a wide variety of natural glycoproducts in such a way as to provide maximum benefit to itself, the widermore » microbial community and the host. The immense ability of B. thetaiotaomicron as a ‘glycan specialist’ resides in its enormous array of carbohydrate-active enzymes, many of which are arranged into polysaccharide-utilization loci (PULs) that are able to degrade sugar polymers that are often inaccessible to other gut residents, notably α-mannan. The B. thetaiotaomicron genome encodes ten putative α-mannanases spread across various PULs; however, little is known about the activity of these enzymes or the wider implications of α-mannan metabolism for the health of both the microbiota and the host. In this study, SAD phasing of a selenomethionine derivative has been used to investigate the structure of one such B. thetaiotaomicron enzyme, BT2949, which belongs to the GH76 family of α-mannanases. BT2949 presents a classical (α/α){sub 6}-barrel structure comprising a large extended surface cleft common to other GH76 family members. Analysis of the structure in conjunction with sequence alignments reveals the likely location of the catalytic active site of this noncanonical GH76.« less

BmeRABC5 is a multidrug efflux system that can confer metronidazole resistance in Bacteroides fragilis.

PubMed

Pumbwe, Lilian; Chang, Abraham; Smith, Rachel L; Wexler, Hannah M

2007-01-01

The RND-family efflux pump gene bmeB5 was previously shown to be overexpressed in metronidazole-resistant laboratory mutants of Bacteroides fragilis. In the present study, we characterized the bmeABC5 genes and an upstream putative TetR-family regulator gene (bmeR5). bmeR5 (645 bp) was located 51 bp upstream of bmeA5 and encoded a 24.9-kDa protein. Deletant strains lacking bmeB5 or bmeR5 were constructed from a wild-type B. fragilis strain ADB77. Strain antimicrobial susceptibility was determined and gene expression was quantified. bmeR5 was overexpressed in Escherichia coli using a 6x-His tag system; BmeR5-His6 was isolated from inclusion bodies and its binding to bmeABC5 promoter regions was determined. BmeR5-His6 bound specifically to the bmeR5-bmeC5 intergenic region (IT1). Deletion of bmeR5 (ADB77DeltabmeR5) resulted in a significant (p < 0.05) increase in expression of bmeA5, bmeB5, and bmeC5, and > two-fold increase in minimum inhibitory concentrations (MICs) of ampicillin, cefoxitin, cefoperazone, ciprofloxacin, imipenem, metronidazole, ethidium bromide, and sodium dodecyl sulfate (SDS). MICs were reduced by the efflux pump inhibitor carbonyl cyanide m-chlorophenyl hydrazone (CCCP). The MICs of ampicillin, cefoperazone, metronidazole, and SDS were reduced by approximately two-fold in ADB77DeltabmeB5. A multidrug (metronidazole)-resistant, nim-negative B. fragilis clinical isolate overexpressed bmeABC5 genes, had a G-->T point mutation in IT1, and significantly reduced binding to BmeR5-His6. These data demonstrate that BmeR5 is a local repressor of bmeABC5 expression and that mutations in IT1 can lead to a derepression and resistance to multiple antimicrobial agents, including metronidazole.

Effects of honey supplementation combined with different jumping exercise intensities on bone mass, serum bone metabolism markers and gonadotropins in female rats

PubMed Central

2014-01-01

Background The effects of high and low jumping exercise intensities combined with honey on bone and gonadotrophins were investigated in eighty four 9 week-old female rats. Methods The experimental groups were 20 or 80 jumps per day combined with or without honey supplementation (HJ20, HJ80, J20 and J80), honey supplementation (H), sedentary without supplementation control (C), and baseline control (C0) groups. Results Study results showed that HJ80 elicited greatest beneficial effects on tibial and femoral mass, serum total calcium and alkaline phosphatase concentrations. There were significantly (p < 0.05) lower levels of serum follicle stimulating hormone concentrations in H, J20, J80 compared to C, with exception of HJ20 and HJ80. Serum luteinizing hormone concentrations were significantly (p < 0.05) greater in HJ20, HJ80 and J20 compared to J80. Conclusions It appears that high intensity jumping exercise combined with honey supplementation resulted more discernable effects on bone. Meanwhile, honey may protect against the adverse effects induced by jumping exercise on gonadotropins in female rats. PMID:24708608

A comparative study on the heavy metal solidification/stabilization performance of four chemical solidifying agents in municipal solid waste incineration fly ash.

PubMed

Wang, Feng-He; Zhang, Fan; Chen, Ya-Jun; Gao, Jay; Zhao, Bin

2015-12-30

Investigated in this paper were the content, specification distribution, and risk assessment code (RAC) determination of six targeted heavy metals and potentially toxic metals in fly ashes from a municipal solid waste incinerator in China. Contained in it is a comparison of the solidification/stabilization performance of two novel solidifying agents of sixthio guanidine acid (SGA) and tetrathio bicarbamic acid (TBA) with sodium dimethyldithiocarbamate (SDD) and Na2S, and analysis of their leachability in accordance with TCLP 1311 of the US EPA and the extraction procedures of China (HJ/T 299-2007 and HJ/T300-2007). The total concentration of Zn, Cu, Ni, Pb, Cr, Cd is 37383.47, 3080.77, 1583.92, 1356.43, 566.15, and 77.83 mg/kg, respectively. Cr (3.7%) and Pb (7.50%) pose low risk; and Ni (12.93%) and Zn (15.45%) have a medium risk; while Cu (69.84%) and Cd (82.5%) have a very high risk according to their RAC score. Compared with SDD and Na2S, SGA and TBA show an excellent overall solidifying performance due to their multiply hydrosulfide groups that bind with heavy metals very efficiently. The obtained results indicate that the leaching content of Cd, Ni, Pb and Zn is higher than the thresholds prescribed in GB5085.3-2007, and the excessive acetic acid makes its binding capacity stronger in HJ/T 300-2007 than in TCLP 1311. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of Hachimi-jio-gan (Ba-Wei-Di-Huang-Wan) on intestinal function in streptozotocin-induced diabetic rats.

PubMed

Hirotani, Yoshihiko; Ikeda, Takuya; Ikeda, Kenji; Yamamoto, Kaoru; Onda, Mitsuko; Arakawa, Yukio; Li, Jun; Kitamura, Kazuyuki; Kurokawa, Nobuo

2007-09-01

We examined the effects of Hachimi-jio-gan (HJ) on the small intestinal function in streptozotocin (STZ)-induced diabetic rats. The rats had free access to pellets containing 1% HJ extract powder for 4 weeks after STZ administration. The intestinal disaccharidase (sucrase and maltase) activity was elevated in STZ-treated rats compared with control rats, whereas it was significantly reduced by HJ administration. This suggested that HJ suppresses or delays monosaccharide production in the small intestinal epithelium. In addition, the intestinal mucosal weights and DNA contents that were significantly increased in the STZ-treated rats were restrained to the control level by HJ treatment. Simultaneously, we examined the changes in the plasma levels of glucagon-like peptide 2 (GLP-2), which is a trophic factor specific for the intestine. The plasma GLP-2 levels significantly increased in the STZ-treated rats, whereas HJ decreased the plasma GLP-2 levels. Thus intestinal mucosal weights and DNA contents correlated with plasma GLP-2 levels in diabetes-associated bowel growth. These results suggest that HJ may normalize or suppress the small intestinal disaccharidase activity and the epithelial cell proliferation mediated by GLP-2 in the animal model rats.

Membrane stability and mitochondrial activity of human-ejaculated spermatozoa during in vitro experimental infection with Escherichia coli, Staphylococcus haemolyticus and Bacteroides ureolyticus.

PubMed

Fraczek, M; Piasecka, M; Gaczarzewicz, D; Szumala-Kakol, A; Kazienko, A; Lenart, S; Laszczynska, M; Kurpisz, M

2012-10-01

The aim of the study was to examine an in vitro effect of the three bacterial strains (Escherichia coli, Staphylococcus haemolyticus and Bacteroides ureolyticus) on ejaculated spermatozoa with reference to sperm membrane integrity and mitochondrial activity. The study was carried out on swim-up-separated spermatozoa from 12 normozoospermic volunteers. Sperm plasma membrane stability was evaluated by the LIVE/DEAD Sperm Viability Kit and by the merocyanine 540 test. Mitochondrial activity was evaluated using the JC-1 test as well as the NADH-dependent NBT assay. The percentage of dead cells was significantly higher in spermatozoa treated with B. ureolyticus as compared to that of control spermatozoa (P < 0.01). All the bacterial strains applied affected sperm plasma membrane architecture measured by M540 test (P < 0.01). Moreover, the presence of E. coli or B. ureolyticus was connected with significant decrease in both the number of cells with high mitochondrial transmembrane potential (ΔΨm) and the cells with normal oxidoreductive function of mitochondria (P < 0.05 as compared to untreated cells). To conclude, the contact of bacteria with ejaculated spermatozoa can be a reason for severe injury of sperm membrane stability and mitochondrial activity with potential consequences for male fertility. © 2012 Blackwell Verlag GmbH.

A Solution Method for Large Deformation Contact Problems.

DTIC Science & Technology

1984-10-01

15] Desai, C.S., Zaman, M.M., Lightner , J.G., and Siriwardane, H.J., "Thin Element for Interfaces and Joints," Int. J. Anal. and Num. Meth. in...Urbana, IL 61801 SMCCR-SPS-IL 1 Massachusetts Institute of Technology Aeroelastic and Structures Research Laboratory ATTN: Dr. E. A. Witmer Cambridge

Characterization of Bacteroides forsythus Strains from Cat and Dog Bite Wounds in Humans and Comparison with Monkey and Human Oral Strains

PubMed Central

Hudspeth, M. K.; Gerardo, S. Hunt; Maiden, M. F. J.; Citron, D. M.; Goldstein, E. J. C.

1999-01-01

Bacteroides forsythus strains recovered from cat and dog bite wound infections in humans (n = 3), monkey oral strains (n = 3), and the human oral ATCC 43037 type strain were characterized by using phenotypic characteristics, enzymatic tests, whole cell fatty acid analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, PCR fingerprinting, and 16S rDNA (genes coding for rRNA) sequencing. All three bite wound isolates grew on brucella agar supplemented with 5% sheep blood, vitamin K1, and hemin. These strains, unlike the ATCC strain and previously described monkey oral and human clinical strains, did not require N-acetylmuramic acid supplementation for growth as pure cultures. However, their phenotypic characteristics, except for catalase production, were similar to those of previously identified strains. PCR fingerprinting analysis showed differences in band patterns from the ATCC strain. Also, SDS-PAGE and whole cell fatty acid analysis indicated that the dog and cat bite wound strains were similar but not identical to the human B. forsythus ATCC 43037 type strain and the monkey oral strains. The rDNA sequence analysis indicated that the three bite wound isolates had 99.93% homology with each other and 98.9 and 99.22% homology with the human ATCC 43037 and monkey oral strains, respectively. These results suggest that there are host-specific variations within each group. PMID:10325363

The Fecal Microbiota Profile and Bronchiolitis in Infants

PubMed Central

Linnemann, Rachel W.; Mansbach, Jonathan M.; Ajami, Nadim J.; Espinola, Janice A.; Petrosino, Joseph F.; Piedra, Pedro A.; Stevenson, Michelle D.; Sullivan, Ashley F.; Thompson, Amy D.; Camargo, Carlos A.

2016-01-01

BACKGROUND: Little is known about the association of gut microbiota, a potentially modifiable factor, with bronchiolitis in infants. We aimed to determine the association of fecal microbiota with bronchiolitis in infants. METHODS: We conducted a case–control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis. We concurrently enrolled 115 age-matched healthy controls. By applying 16S rRNA gene sequencing and an unbiased clustering approach to these 155 fecal samples, we identified microbiota profiles and determined the association of microbiota profiles with likelihood of bronchiolitis. RESULTS: Overall, the median age was 3 months, 55% were male, and 54% were non-Hispanic white. Unbiased clustering of fecal microbiota identified 4 distinct profiles: Escherichia-dominant profile (30%), Bifidobacterium-dominant profile (21%), Enterobacter/Veillonella-dominant profile (22%), and Bacteroides-dominant profile (28%). The proportion of bronchiolitis was lowest in infants with the Enterobacter/Veillonella-dominant profile (15%) and highest in the Bacteroides-dominant profile (44%), corresponding to an odds ratio of 4.59 (95% confidence interval, 1.58–15.5; P = .008). In the multivariable model, the significant association between the Bacteroides-dominant profile and a greater likelihood of bronchiolitis persisted (odds ratio for comparison with the Enterobacter/Veillonella-dominant profile, 4.24; 95% confidence interval, 1.56–12.0; P = .005). In contrast, the likelihood of bronchiolitis in infants with the Escherichia-dominant or Bifidobacterium-dominant profile was not significantly different compared with those with the Enterobacter/Veillonella-dominant profile. CONCLUSIONS: In this case–control study, we identified 4 distinct fecal microbiota profiles in infants. The Bacteroides-dominant profile was associated with a higher likelihood of bronchiolitis. PMID:27354456

Effect of single-strand break on branch migration and folding dynamics of Holliday junctions.

PubMed

Palets, Dmytro; Lushnikov, Alexander Y; Karymov, Mikhail A; Lyubchenko, Yuri L

2010-09-22

The Holliday junction (HJ), or four-way junction, is a central intermediate state of DNA for homologous genetic recombination and other genetic processes such as replication and repair. Branch migration is the process by which the exchange of homologous DNA regions occurs, and it can be spontaneous or driven by proteins. Unfolding of the HJ is required for branch migration. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. Folding of the HJ in one of the folded conformations terminates the branch migration phase. At the same time, in the unfolded state HJ rapidly migrates over entire homology region of the HJ in one hop. This process can be affected by irregularities in the DNA double helical structure, so mismatches almost terminate a spontaneous branch migration. Single-stranded breaks or nicks are the most ubiquitous defects in the DNA helix; however, to date, their effect on the HJ branch migration has not been studied. In addition, although nicked HJs are specific substrates for a number of enzymes involved in DNA recombination and repair, the role of this substrate specificity remains unclear. Our main goal in this work was to study the effect of nicks on the efficiency of HJ branch migration and the dynamics of the HJ. To accomplish this goal, we applied two single-molecule methods: atomic force microscopy and fluorescence resonance energy transfer. The atomic force microscopy data show that the nick does not prevent branch migration, but it does decrease the probability that the HJ will pass the DNA lesion. The single-molecule fluorescence resonance energy transfer approaches were instrumental in detailing the effects of nicks. These studies reveal a dramatic change of the HJ dynamics. The nick changes the structure and conformational dynamics of the junctions, leading to conformations with geometries that are different from those

Tyrosine, Tryptophan and Performance

DTIC Science & Technology

1992-01-22

Indiana, May 15-17, 1991. Deng, M.H., Lynch H.J., Wurtman, R.J. and Lopez G.-Coviella, I. La diferenciacion de celulas de retinoblastoma...effects of chronic pretreatment with d-fenfluramine or p-chloroamphetamine. Society for Neuroscience, New Orleans, LA , Nov. 10-15, 1991. 14 Wurtman, J...Implicaciones en la sistesis de melatonia y sus precursores. IV Meeting of the Spanish Society for Neuroscience, Alicante, Spain, Sept. 30-Oct. 3, 1991. Erfurth

Application of Bacteroides fragilis phage as an alternative indicator of sewage pollution in Tampa Bay, Florida

USGS Publications Warehouse

McLaughlin, M.R.; Rose, J.B.

2006-01-01

Traditional fecal coliform bacterial indicators have been found to be severely limited in determining the significance and sources of fecal contamination in ambient waters of tropical and subtropical regions. The bacteriophages that infect Bacteroides fragilis have been suggested as better fecal indicators and at least one type may be human specific. In this study, the phages that infect B. fragilis host RYC2056 (RYC), including phage B56-3, and host ATCC 51477-HSP40 (HSP), including the human specific phage B40-8, were evaluated in the drainage basins of Tampa Bay, 7 samples (n = 62), or 11%, tested positive for the presence of phages infecting the host HSP, whereas 28 samples, or 45%, tested positive using the host RYC. A survival study was also done to compare the persistence of phages B56-3 and B40-8 to MS2 coliphage in seawater at various temperatures. The decay rates for MS2 were 0.239 log 10 d-1 at 10??C, but increased to 0.896 at 20??C and 2.62 log10 d-1 at 30??C. The two B. fragilis phages persisted much longer in the seawater compared to the coliphage and showed little variation between the temperatures. All sewage influents sampled from area wastewater treatment plants contained phages that infected the two B. fragilis hosts at levels from 1.2 ?? 104 to 1.11 ?? 10 5 pfu 100 ml-1 for host RYC and 67 to 350 pfu 100 ml -1 for host HSP. Of the 7 chlorinated effluent samples tested, 3 were positive for the presence of the phage using the host RYC and the phage enrichment method, with levels estimated to be <10 pfu 100 ml-1. No phages were detected using the host HSP in the treated sewage effluent. Coliphages were found in 3 of the 7 effluent samples at a range of 30 to 1.2 ?? 103 pfu 100 ml-1. ?? 2006 Estuarine Research Federation.

Identification of the alpha-enolase P46 in the extracellular membrane vesicles of Bacteroides fragilis.

PubMed

Ferreira, Thais Gonçalves; Trindade, Camilla Nunes Dos Reis; Bell, Petra; Teixeira-Ferreira, André; Perales, Jonas E; Vommaro, Rossiane C; Domingues, Regina Maria Cavalcanti Pilotto; Ferreira, Eliane de Oliveira

2018-03-01

Members of the Bacteroides fragilis group are the most important components of the normal human gut microbiome, but are also major opportunistic pathogens that are responsible for significant mortality, especially in the case of bacteraemia and other severe infections, such as intra-abdominal abscesses. Up to now, several virulence factors have been described that might explain the involvement of B. fragilis in these infections. The secretion of extracellular membrane vesicles (EMVs) has been proposed to play a role in pathogenesis and symbiosis in gram-negative bacteria, by releasing soluble proteins and other molecules. In B. fragilis, these vesicles are known to have haemagglutination and sialidosis activities, and also contain a capsular polysaccharide (PSA), although their involvement in virulence is still not clear. The aim of this study was to identify proteins in the EMV of the 638R B. fragilis strain by mass spectrometry, and also to assess for the presence of Bfp60, a surface plasminogen (Plg) activator, previously shown in B. fragilis to be responsible for the conversion of inactive Plg to active plasmin, which can also bind to laminin-1. B. fragilis was cultured in a minimum defined media and EMVs were obtained by differential centrifugation, ultracentrifugation, and filtration. The purified EMVs were observed by both transmission electron microscopy (TEM) and immunoelectron microscopy (IM). To identify EMV constituent proteins, EMVs were separated by 1D SDS-PAGE and proteomic analysis of proteins sized 35 kDa to approximately 65 kDa was performed using mass spectrometry (MALDI-TOF MS). TEM micrographs proved the presence of spherical vesicles and IM confirmed the presence of Bfp60 protein on their surface. Mass spectrometry identified 23 proteins with high confidence. One of the proteins from the B. fragilis EMVs was identified as an enolase P46 with a possible lyase activity. Although the Bfp60 protein was not detected by proteomics, α-enolase P46

Identification of the alpha-enolase P46 in the extracellular membrane vesicles of Bacteroides fragilis

PubMed Central

Ferreira, Thais Gonçalves; Trindade, Camilla Nunes dos Reis; Bell, Petra; Teixeira-Ferreira, André; Perales, Jonas E; Vommaro, Rossiane C; Domingues, Regina Maria Cavalcanti Pilotto; Ferreira, Eliane de Oliveira

2018-01-01

BACKGROUND Members of the Bacteroides fragilis group are the most important components of the normal human gut microbiome, but are also major opportunistic pathogens that are responsible for significant mortality, especially in the case of bacteraemia and other severe infections, such as intra-abdominal abscesses. Up to now, several virulence factors have been described that might explain the involvement of B. fragilis in these infections. The secretion of extracellular membrane vesicles (EMVs) has been proposed to play a role in pathogenesis and symbiosis in gram-negative bacteria, by releasing soluble proteins and other molecules. In B. fragilis, these vesicles are known to have haemagglutination and sialidosis activities, and also contain a capsular polysaccharide (PSA), although their involvement in virulence is still not clear. OBJECTIVE The aim of this study was to identify proteins in the EMV of the 638R B. fragilis strain by mass spectrometry, and also to assess for the presence of Bfp60, a surface plasminogen (Plg) activator, previously shown in B. fragilis to be responsible for the conversion of inactive Plg to active plasmin, which can also bind to laminin-1. METHODS B. fragilis was cultured in a minimum defined media and EMVs were obtained by differential centrifugation, ultracentrifugation, and filtration. The purified EMVs were observed by both transmission electron microscopy (TEM) and immunoelectron microscopy (IM). To identify EMV constituent proteins, EMVs were separated by 1D SDS-PAGE and proteomic analysis of proteins sized 35 kDa to approximately 65 kDa was performed using mass spectrometry (MALDI-TOF MS). FINDINGS TEM micrographs proved the presence of spherical vesicles and IM confirmed the presence of Bfp60 protein on their surface. Mass spectrometry identified 23 proteins with high confidence. One of the proteins from the B. fragilis EMVs was identified as an enolase P46 with a possible lyase activity. MAIN CONCLUSIONS Although the Bfp60

Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.

PubMed

Chen, Luan; Shi, Ke; Yin, Zhiqi; Aihara, Hideki

2013-01-07

Holliday junction (HJ) resolvases are structure-specific endonucleases that cleave four-way DNA junctions (HJs) generated during DNA recombination and repair. Bacterial RuvC, a prototypical HJ resolvase, functions as homodimer and nicks DNA strands precisely across the junction point. To gain insights into the mechanisms underlying symmetrical strand cleavages by RuvC, we performed crystallographic and biochemical analyses of RuvC from Thermus thermophilus (T.th. RuvC). The crystal structure of T.th. RuvC shows an overall protein fold similar to that of Escherichia coli RuvC, but T.th. RuvC has a more tightly associated dimer interface possibly reflecting its thermostability. The binding mode of a HJ-DNA substrate can be inferred from the shape/charge complementarity between the T.th. RuvC dimer and HJ-DNA, as well as positions of sulfate ions bound on the protein surface. Unexpectedly, the structure of T.th. RuvC homodimer refined at 1.28 Å resolution shows distinct asymmetry near the dimer interface, in the region harboring catalytically important aromatic residues. The observation suggests that the T.th. RuvC homodimer interconverts between two asymmetric conformations, with alternating subunits switched on for DNA strand cleavage. This model provides a structural basis for the 'nick-counter-nick' mechanism in HJ resolution, a mode of HJ processing shared by prokaryotic and eukaryotic HJ resolvases.

Technology computer aided design of 29.5% efficient perovskite/interdigitated back contact silicon heterojunction mechanically stacked tandem solar cell for energy-efficient applications

NASA Astrophysics Data System (ADS)

Pandey, Rahul; Chaujar, Rishu

2017-04-01

A 29.5% efficient perovskite/SiC passivated interdigitated back contact silicon heterojunction (IBC-SiHJ) mechanically stacked tandem solar cell device has been designed and simulated. This is a substantial improvement of 40% and 15%, respectively, compared to the transparent perovskite solar cell (21.1%) and Si solar cell (25.6%) operated individually. The perovskite solar cell has been used as a top subcell, whereas 250- and 25-μm-thick IBC-SiHJ solar cells have been used as bottom subcells. The realistic technology computer aided design analysis has been performed to understand the physical processes in the device and to make reliable predictions of the behavior. The performance of the top subcell has been obtained for different acceptor densities and hole mobility in Spiro-MeOTAD along with the impact of counter electrode work function. To incorporate the effect of material quality, the influence of carrier lifetimes has also been studied for perovskite top and IBC-SiHJ bottom subcells. The optical and electrical behavior of the devices has been obtained for both standalone as well as tandem configuration. Results reported in this study reveal that the proposed four-terminal tandem device may open a new door for cost-effective and energy-efficient applications.

Small-scale variations of climate change in mountainous forested terrain - a regional study from H.J. Andrews Long Term Ecological Research site in Oregon, USA

NASA Astrophysics Data System (ADS)

Honzakova, Katerina; Hoffmann, Peter; Jones, Julia; Thomas, Christoph

2017-04-01

There has been conflicting evidence as to whether high elevations are experiencing more pronounced climate warming than lower elevations in mountainous regions. In this study we analyze temperature records from H.J. Andrews Long Term Ecological Research, Oregon, USA and several nearby areas, comprising together 28 stations located in Cascade Mountains. The data, starting in 1958, are first checked for quality and homogenized using the Standard Normal Homogeneity Test. As a reference, composite climate time series based on the Global Historic Climate Network is created and together with cross-referencing against station records used to correct breaks and shifts in the data. In the next step, we investigate temperature patterns of the study site from 1958 to 2016 and compare them for valley and hill stations. In particular, we explore seasonality and inter-annual variability of the records and trends of the last day of frost. Additionally, 'cold' sums (positive and negative) are calculated to obtain a link between temperature and ecosystems' responses (such as budbreaks). So far, valley stations seem to be more prone to climate change than ridge or summit stations, contrary to current thinking. Building on previous knowledge, we attempt to provide physical explanations for the temperature records, focusing on wind patterns and associated phenomena such as cold air drainage and pooling. To aid this we analyze wind speed and direction data available for some of the stations since 1996, including seasonality and inter-annual variability of the observed flows.

Catchment scale controls the temporal connection of transpiration and diel fluctuations in streamflow

Treesearch

C.B. Graham; H.R. Barnard; K.L. Kavanagh; J.P. McNamara

2012-01-01

Diel fluctuations can comprise a significant portion of summer discharge in small to medium catchments. The source of these signals and the manner in which they are propagated to stream gauging sites is poorly understood. In this work, we analysed stream discharge from 15 subcatchments in Dry Creek, Idaho, Reynolds Creek, Idaho, and HJ Andrews, Oregon. We identified...

Senior Thai fecal microbiota comparison between vegetarians and non-vegetarians using PCR-DGGE and real-time PCR.

PubMed

Ruengsomwong, Supatjaree; Korenori, Yuki; Sakamoto, Naoshige; Wannissorn, Bhusita; Nakayama, Jiro; Nitisinprasert, Sunee

2014-08-01

The fecal microbiotas were investigated in 13 healthy Thai subjects using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Among the 186 DNA bands detected on the polyacrylamide gel, 37 bands were identified as representing 11 species: Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides uniformis, Bacteroides vulgatus, Clostridium colicanis, Eubacterium eligenes, E. rectale, Faecalibacterium prausnitzii, Megamonas funiformis, Prevotella copri, and Roseburia intestinalis, belonging mainly to the groups of Bacteroides, Prevotella, Clostridium, and F. prausnitzii. A dendrogram of the PCR-DGGE divided the subjects; vegetarians and non-vegetarians. The fecal microbiotas were also analyzed using a quantitative real-time PCR focused on Bacteroides, Bifidobacterium, Enterobacteriaceae, Clostrium coccoides-Eubacterium rectale, C. leptum, Lactobacillus, and Prevotella. The nonvegetarian and vegetarian subjects were found to have significant differences in the high abundance of the Bacteroides and Prevotella genera, respectively. No significant differences were found in the counts of Bifidabacterium, Enterobacteriaceae, C. coccoides-E. rectale group, C. leptum group, and Lactobacillus. Therefore, these findings on the microbiota of healthy Thais consuming different diets could provide helpful data for predicting the health of South East Asians with similar diets.

Average Run Lengths of an Optimal Method of Detecting a Change in Distribution.

DTIC Science & Technology

1983-09-01

Lemna 5 and Theorem 2(i)) P0(Hj < -) is of the order of magnitude of i/CA, choosing A, CA large enough will cause Po(Lj+I< Hj< )/Po(Hj< -) to be...1982) Section 6.3. With minor modifications, the proof is the same. One difference is that Woodroofe’s u n(Y n ) now has (ds) replaced by Wn ’ s W(ds

RbohB, a Phaseolus vulgaris NADPH oxidase gene, enhances symbiosome number, bacteroid size, and nitrogen fixation in nodules and impairs mycorrhizal colonization.

PubMed

Arthikala, Manoj-Kumar; Sánchez-López, Rosana; Nava, Noreide; Santana, Olivia; Cárdenas, Luis; Quinto, Carmen

2014-05-01

The reactive oxygen species (ROS) generated by respiratory burst oxidative homologs (Rbohs) are involved in numerous plant cell signaling processes, and have critical roles in the symbiosis between legumes and nitrogen-fixing bacteria. Previously, down-regulation of RbohB in Phaseolus vulgaris was shown to suppress ROS production and abolish Rhizobium infection thread (IT) progression, but also to enhance arbuscular mycorrhizal fungal (AMF) colonization. Thus, Rbohs function both as positive and negative regulators. Here, we assessed the effect of enhancing ROS concentrations, by overexpressing PvRbohB, on the P. vulgaris--rhizobia and P. vulgaris--AMF symbioses. We estimated superoxide concentrations in hairy roots overexpressing PvRbohB, determined the status of early and late events of both Rhizobium and AMF interactions in symbiont-inoculated roots, and analyzed the nodule ultrastructure of transgenic plants overexpressing PvRbohB. Overexpression of PvRbohB significantly enhanced ROS production, the formation of ITs, nodule biomass, and nitrogen-fixing activity, and increased the density of symbiosomes in nodules, and the density and size of bacteroides in symbiosomes. Furthermore, PvCAT, early nodulin, PvSS1, and PvGOGAT transcript abundances were elevated in these nodules. By contrast, mycorrhizal colonization was reduced in roots that overexpressed RbohB. Overexpression of PvRbohB augmented nodule efficiency by enhancing nitrogen fixation and delaying nodule senescence, but impaired AMF colonization. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Continuing Appropriations Resolution, 2012

THOMAS, 112th Congress

Rep. Rogers, Harold [R-KY-5

2011-09-14

House - 09/15/2011 Rules Committee Resolution H. Res. 399 Reported to House. Rule provides for consideration of H.J. Res. 79 with 1 hour of general debate. Previous question shall be considered as ordered without intervening motions except motion to recommit with or without... (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Xylan-regulated delivery of human keratinocyte growth factor-2 to the inflamed colon by the human anaerobic commensal bacterium Bacteroides ovatus.

PubMed

Hamady, Zaed Z R; Scott, Nigel; Farrar, Mark D; Lodge, J Peter A; Holland, Keith T; Whitehead, Terence; Carding, Simon R

2010-04-01

Human growth factors are potential therapeutic agents for various inflammatory disorders affecting the gastrointestinal tract. However, they are unstable when administered orally and systemic administration requires high doses increasing the risk of unwanted side effects. Live microorganism-based delivery systems can overcome these problems although they suffer from the inability to control heterologous protein production and there are concerns regarding biosafety and environmental contamination. To overcome these limitations we have developed a new live bacteria drug-delivery system using the human commensal gut bacterium Bacteroides ovatus engineered to secrete human growth factors in response to dietary xylan. The anaerobic nature of B ovatus provides an inherent biosafety feature. B ovatus strains expressing human keratinocyte growth factor-2, which plays a central role in intestinal epithelial homeostasis and repair (BO-KGF), were generated by homologous recombination and evaluated using the dextran sodium sulfate (DSS)-induced model of intestinal epithelial injury and colitis. In response to xylan BO-KGF produced biologically active KGF both in vitro and in vivo. In DSS treated mice administration of xylan and BO-KGF had a significant therapeutic effect in reducing weight loss, improving stool consistency, reducing rectal bleeding, accelerating healing of damaged epithelium, reducing inflammation and neutrophil infiltration, reducing expression of pro-inflammatory cytokines, and accelerating production of goblet cells. BO-KGF and xylan treatment also had a marked prophylactic effect limiting the development of inflammation and disruption of the epithelial barrier. This novel, diet-regulated, live bacterial drug delivery system may be applicable to treating various bowel disorders.

Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice

PubMed Central

Dziarski, Roman; Dowd, Scot E.; Gupta, Dipika

2016-01-01

Dysbiosis is a hallmark of inflammatory bowel disease (IBD), but it is unclear which specific intestinal bacteria predispose to and which protect from IBD and how they are regulated. Peptidoglycan recognition proteins (Pglyrps) are antibacterial, participate in maintaining intestinal microflora, and modulate inflammatory responses. Mice deficient in any one of the four Pglyrp genes are more sensitive to dextran sulfate sodium (DSS)-induced colitis, and stools from Pglyrp-deficient mice transferred to wild type (WT) germ-free mice predispose them to much more severe colitis than stools from WT mice. However, the identities of these Pglyrp-regulated bacteria that predispose Pglyrp-deficient mice to colitis or protect WT mice from colitis are not known. Here we identified significant changes in β-diversity of stool bacteria in Pglyrp-deficient mice compared with WT mice. The most consistent changes in microbiome in all Pglyrp-deficient mice were in Bacteroidales, from which we selected four species, two with increased abundance (Prevotella falsenii and Parabacteroides distasonis) and two with decreased abundance (Bacteroides eggerthii and Alistipes finegoldii). We then gavaged WT mice with stock type strains of these species to test the hypothesis that they predispose to or protect from DSS-induced colitis. P. falsenii, P. distasonis, and B. eggerthii all enhanced DSS-induced colitis in both WT mice with otherwise undisturbed intestinal microflora and in WT mice with antibiotic-depleted intestinal microflora. By contrast, A. finegoldii (which is the most abundant species in WT mice) attenuated DSS-induced colitis both in WT mice with otherwise undisturbed intestinal microflora and in WT mice with antibiotic-depleted intestinal microflora, similar to the colitis protective effect of the entire normal microflora. These results identify P. falsenii, P. distasonis, and B. eggerthii as colitis-promoting species and A. finegoldii as colitis-protective species. PMID

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii

PubMed Central

Caffaro-Filho, Roberto A.; Wong, Mayee; Harwood, Valerie J.; Moravcik, Philip; Fujioka, Roger S.

2016-01-01

ABSTRACT Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. IMPORTANCE This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii.

PubMed

Kirs, Marek; Caffaro-Filho, Roberto A; Wong, Mayee; Harwood, Valerie J; Moravcik, Philip; Fujioka, Roger S

2016-11-15

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination

A proteomic network for symbiotic nitrogen fixation efficiency in Bradyrhizobium elkanii

USDA-ARS?s Scientific Manuscript database

Rhizobia bacteroids colonize legumes and reduce N2 to NH3 in root nodules. The current model is that bacteroids avoid assimilating this NH3. Instead, the legume forms glutamine from it, the nitrogen of which is returned to the bacteroid as leucine, isoleucine, valine, dicarboxylates, and peptides. I...

The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c-Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection.

PubMed

Snezhkina, Anastasiya V; Krasnov, George S; Lipatova, Anastasiya V; Sadritdinova, Asiya F; Kardymon, Olga L; Fedorova, Maria S; Melnikova, Nataliya V; Stepanov, Oleg A; Zaretsky, Andrew R; Kaprin, Andrey D; Alekseev, Boris Y; Dmitriev, Alexey A; Kudryavtseva, Anna V

2016-01-01

Colorectal cancer is one of the most common cancers in the world. It is well known that the chronic inflammation can promote the progression of colorectal cancer (CRC). Recently, a number of studies revealed a potential association between colorectal inflammation, cancer progression, and infection caused by enterotoxigenic Bacteroides fragilis (ETBF). Bacterial enterotoxin activates spermine oxidase (SMO), which produces spermidine and H2O2 as byproducts of polyamine catabolism, which, in turn, enhances inflammation and tissue injury. Using qPCR analysis, we estimated the expression of SMOX gene and ETBF colonization in CRC patients. We found no statistically significant associations between them. Then we selected genes involved in polyamine metabolism, metabolic reprogramming, and inflammation regulation and estimated their expression in CRC. We observed overexpression of SMOX, ODC1, SRM, SMS, MTAP, c-Myc, C/EBPβ (CREBP), and other genes. We found that two mediators of metabolic reprogramming, inflammation, and cell proliferation c-Myc and C/EBPβ may serve as regulators of polyamine metabolism genes (SMOX, AZIN1, MTAP, SRM, ODC1, AMD1, and AGMAT) as they are overexpressed in tumors, have binding site according to ENCODE ChIP-Seq data, and demonstrate strong coexpression with their targets. Thus, increased polyamine metabolism in CRC could be driven by c-Myc and C/EBPβ rather than ETBF infection.

The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c-Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection

PubMed Central

Snezhkina, Anastasiya V.; Lipatova, Anastasiya V.; Sadritdinova, Asiya F.; Kardymon, Olga L.; Fedorova, Maria S.; Kaprin, Andrey D.

2016-01-01

Colorectal cancer is one of the most common cancers in the world. It is well known that the chronic inflammation can promote the progression of colorectal cancer (CRC). Recently, a number of studies revealed a potential association between colorectal inflammation, cancer progression, and infection caused by enterotoxigenic Bacteroides fragilis (ETBF). Bacterial enterotoxin activates spermine oxidase (SMO), which produces spermidine and H2O2 as byproducts of polyamine catabolism, which, in turn, enhances inflammation and tissue injury. Using qPCR analysis, we estimated the expression of SMOX gene and ETBF colonization in CRC patients. We found no statistically significant associations between them. Then we selected genes involved in polyamine metabolism, metabolic reprogramming, and inflammation regulation and estimated their expression in CRC. We observed overexpression of SMOX, ODC1, SRM, SMS, MTAP, c-Myc, C/EBPβ (CREBP), and other genes. We found that two mediators of metabolic reprogramming, inflammation, and cell proliferation c-Myc and C/EBPβ may serve as regulators of polyamine metabolism genes (SMOX, AZIN1, MTAP, SRM, ODC1, AMD1, and AGMAT) as they are overexpressed in tumors, have binding site according to ENCODE ChIP-Seq data, and demonstrate strong coexpression with their targets. Thus, increased polyamine metabolism in CRC could be driven by c-Myc and C/EBPβ rather than ETBF infection. PMID:27433286

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS-Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut.

PubMed

Wang, Kai; Jin, Xiaolu; Li, Qiangqiang; Sawaya, Alexandra Christine Helena Frankland; Leu, Richard K Le; Conlon, Michael A; Wu, Liming; Hu, Fuliang

2018-06-11

Dietary supplementation with polyphenol-rich propolis can protect against experimentally-induced colitis. We examined whether different polyphenol compositions of Chinese propolis (CP) and Brazilian propolis (BP) influences their ability to protect against dextran sulfate sodium (DSS)-induced colitis in rats. HPLC-DAD/Q-TOF-MS analysis confirmed that polyphenol compositions of CP and BP were dissimilar. Rats were given CP or BP by gavage (300 mg/kg body weight) throughout the study, starting 1 week prior to DSS treatment for 1 week followed by 3 d without DSS. CP and BP significantly reduced the colitis disease activity index relative to controls not receiving propolis, prevented significant DSS-induced colonic tissue damage and increased resistance to DSS-induced colonic oxidative stress as shown by reduced malonaldehyde levels and increased T-AOC levels. CP and BP significantly reduced DSS-induced colonic apoptosis. Colonic inflammatory markers IL-1β, IL-6 and MCP-1 were suppressed by CP and BP, whereas only BP induced expression of TGF-β. CP, not BP, increased the diversity and richness of gut microbiota populations. Both forms of propolis significantly reduced populations of Bacteroides spp. Despite the dissimilar polyphenol compositions of CP and BP, their ability to protect against DSS-induced colitis is similar. Nevertheless, some different physiological impacts were observed. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Separation of Sperm Whale Click-Trains for Multipath Rejection and Localization

DTIC Science & Technology

2010-03-05

Correlation 12 3.3 Multipath Elimination Rules 13 4 LOCALIZATION 15 4.1 Localization Approach 15 4.2 Inter-Sensor Time-Delay Estimation Approach...Using Bayes’ rule , kj = ’°g kj = >°g< P(H, P(H0 HJ) \\J) (2) />(//,)p(zJ//,) p(H0)p(z,JH0) where p(//o) and p(H\\) are the a priori probabilities...overlapping clicks.) 3.3 MULTIPATH ELIMINATION RULES Multipath click-trains are eliminated if the individual clicks within the click-train are

[Application of small remote sensing satellite constellations for environmental hazards in wetland landscape mapping: taking Liaohe Delta, Liaoning Province of Northeast China as a case].

PubMed

Yang, Yuan-Zheng; Chang, Yu; Hu, Yuan-Man; Liu, Miao; Li, Yue-Hui

2011-06-01

To timely and accurately acquire the spatial distribution pattern of wetlands is of significance for the dynamic monitoring, conservation, and sustainable utilization of wetlands. The small remote sensing satellite constellations A/B stars (HJ-1A/1B stars) for environmental hazards were launched by China for monitoring terrestrial resources, which could provide a new data source of remote sensing image acquisition for retrieving wetland types. Taking Liaohe Delta as a case, this paper compared the accuracy of wetland classification map and the area of each wetland type retrieved from CCD data (HJ CCD data) and TM5 data, and validated and explored the applicability and the applied potential of HJ CCD data in wetland resources dynamic monitoring. The results showed that HJ CCD data could completely replace Landsat TM5 data in feature extraction and remote sensing classification. In real-time monitoring, due to its 2 days of data acquisition cycle, HJ CCD data had the priority to Landsat TM5 data (16 days of data acquisition cycle).

Distribution, Detection of Enterotoxigenic Strains and Antimicrobial Drug Susceptibility Patterns of Bacteroides Fragilis Group in Diarrheic and Non-Diarrheic Feces from Brazilian Infants

PubMed Central

Ferreira, Débora Paula; Silva, Vânia Lúcia; Guimarães, Danielle Aparecida; Coelho, Cíntia Marques; Zauli, Danielle Alves Gomes; Farias, Luiz Macêdo; Carvalho, Maria Auxiliadora Roque; Diniz, Claudio Galuppo

2010-01-01

Despite the importance of gastrointestinal diseases and their global distribution, affecting millions of individuals around the world, the role and antimicrobial susceptibility patterns of anaerobic bacteria such as those in the Bacteroides fragilis group (BFG) are still unclear in young children. This study investigated the occurrence and distribution of species in the BFG and enterotoxigenic strains in the fecal microbiota of children and their antimicrobial susceptibility patterns. Diarrheic (n=110) and non-diarrheic (n=65) fecal samples from children aged 0–5 years old were evaluated. BFG strains were isolated and identified by conventional biochemical, physiological and molecular approaches. Alternatively, bacteria and enterotoxigenic strains were detected directly from feces by molecular biology. Antimicrobial drug susceptibility patterns were determined by the agar dilution method according to the guidelines for isolated bacteria. BFG was detected in 64.3% of the fecal samples (55% diarrheic and 80.4% non-diarrheic), and 4.6% were enterotoxigenic. Antimicrobial resistance was observed against ampicillin, ampicillin/sulbactam, piperacillin/tazobactam, meropenem, ceftriaxone, clindamycin and chloramphenicol. The data show that these bacteria are prevalent in fecal microbiota at higher levels in healthy children. The molecular methodology was more effective in identifying the B. fragilis group when compared to the biochemical and physiological techniques. The observation of high resistance levels stimulates thoughts about the indiscriminate use of antimicrobial drugs in early infancy. Further quantitative studies are needed to gain a better understanding of the role of these bacteria in acute diarrhea in children. PMID:24031535

A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii.

PubMed

Cooper, Bret; Campbell, Kimberly B; Beard, Hunter S; Garrett, Wesley M; Mowery, Joseph; Bauchan, Gary R; Elia, Patrick

2018-03-01

Rhizobia colonize legumes and reduce N 2 to NH 3 in root nodules. The current model is that symbiotic rhizobia bacteroids avoid assimilating this NH 3 . Instead, host legume cells form glutamine from NH 3 , and the nitrogen is returned to the bacteroid as dicarboxylates, peptides, and amino acids. In soybean cells surrounding bacteroids, glutamine also is converted to ureides. One problem for soybean cultivation is inefficiency in symbiotic N 2 fixation, the biochemical basis of which is unknown. Here, the proteomes of bacteroids of Bradyrhizobium elkanii USDA76 isolated from N 2 fixation-efficient Peking and -inefficient Williams 82 soybean nodules were analyzed by mass spectrometry. Nearly half of the encoded bacterial proteins were quantified. Efficient bacteroids produced greater amounts of enzymes to form Nod factors and had increased amounts of signaling proteins, transporters, and enzymes needed to generate ATP to power nitrogenase and to acquire resources. Parallel investigation of nodule proteins revealed that Peking had no significantly greater accumulation of enzymes needed to assimilate NH 3 than Williams 82. Instead, efficient bacteroids had increased amounts of enzymes to produce amino acids, including glutamine, and to form ureide precursors. These results support a model for efficient symbiotic N 2 fixation in soybean where the bacteroid assimilates NH 3 for itself.

78 FR 21604 - Granting of Request for Early Termination of the Waiting Period Under the Premerger Notification...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-11

... Special Situations Fund III, L.P.; H.J. Heinz Company; 3G Special Situations Fund III, L.P. 20130697 G... Premerger Notification Rules Section 7A of the Clayton Act, 15 U.S.C. 18a, as added by Title II of the Hart..., 2013 thru March 29, 2013 03/01/2013 20130612 G Carl C. Icahn; Herbalife Ltd.; Carl C. Icahn. 20130618 G...

The Fumarate Reductase of Bacteroides thetaiotaomicron, unlike That of Escherichia coli, Is Configured so that It Does Not Generate Reactive Oxygen Species

PubMed Central

Lu, Zheng

2017-01-01

ABSTRACT The impact of oxidative stress upon organismal fitness is most apparent in the phenomenon of obligate anaerobiosis. The root cause may be multifaceted, but the intracellular generation of reactive oxygen species (ROS) likely plays a key role. ROS are formed when redox enzymes accidentally transfer electrons to oxygen rather than to their physiological substrates. In this study, we confirm that the predominant intestinal anaerobe Bacteroides thetaiotaomicron generates intracellular ROS at a very high rate when it is aerated. Fumarate reductase (Frd) is a prominent enzyme in the anaerobic metabolism of many bacteria, including B. thetaiotaomicron, and prior studies of Escherichia coli Frd showed that the enzyme is unusually prone to ROS generation. Surprisingly, in this study biochemical analysis demonstrated that the B. thetaiotaomicron Frd does not react with oxygen at all: neither superoxide nor hydrogen peroxide is formed. Subunit-swapping experiments indicated that this difference does not derive from the flavoprotein subunit at which ROS normally arise. Experiments with the related enzyme succinate dehydrogenase discouraged the hypothesis that heme moieties are responsible. Thus, resistance to oxidation may reflect a shift of electron density away from the flavin moiety toward the iron-sulfur clusters. This study shows that the autoxidizability of a redox enzyme can be suppressed by subtle modifications that do not compromise its physiological function. One implication is that selective pressures might enhance the oxygen tolerance of an organism by manipulating the electronic properties of its redox enzymes so they do not generate ROS. PMID:28049145

Characterization of the Bacteroides fragilis bfr Gene Product Identifies a Bacterial DPS-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily

PubMed Central

Gauss, George H.; Reott, Michael A.; Rocha, Edson R.; Young, Mark J.; Douglas, Trevor

2012-01-01

A factor contributing to the pathogenicity of Bacteroides fragilis, the most common anaerobic species isolated from clinical infections, is the bacterium's extreme aerotolerance, which allows survival in oxygenated tissues prior to anaerobic abscess formation. We investigated the role of the bacterioferritin-related (bfr) gene in the B. fragilis oxidative stress response. The bfr mRNA levels are increased in stationary phase or in response to O2 or iron. In addition, bfr null mutants exhibit reduced aerotolerance, and the bfr gene product protects DNA from hydroxyl radical cleavage in vitro. Crystallographic studies revealed a protein with a dodecameric structure and greater similarity to an archaeal DNA protection in starved cells (DPS)-like protein than to the 24-subunit bacterioferritins. Similarity to the DPS-like (DPSL) protein extends to the subunit and includes a pair of conserved cysteine residues juxtaposed to a buried dimetal binding site within the four-helix bundle. Compared to archaeal DPSLs, however, this bacterial DPSL protein contains several unique features, including a significantly different conformation in the C-terminal tail that alters the number and location of pores leading to the central cavity and a conserved metal binding site on the interior surface of the dodecamer. Combined, these characteristics confirm this new class of miniferritin in the bacterial domain, delineate the similarities and differences between bacterial DPSL proteins and their archaeal homologs, allow corrected annotations for B. fragilis bfr and other dpsl genes within the bacterial domain, and suggest an evolutionary link within the ferritin superfamily that connects dodecameric DPS to the (bacterio)ferritin 24-mer. PMID:22020642

Identification of rutin deglycosylated metabolites produced by human intestinal bacteria using UPLC-Q-TOF/MS.

PubMed

Yang, Jing; Qian, Dawei; Jiang, Shu; Shang, Er-xin; Guo, Jianming; Duan, Jin-ao

2012-06-01

In this paper, rutin was metabolized by human intestinal bacteria and five isolated strains including Bacillus sp. 52, Bacteroides sp. 45, 42, 22 and Veillonella sp. 32, the metabolites were identified using ultra performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS). As a result, Bacillus sp. 52 and Bacteroides sp. 45 could metabolize rutin to quercetin 3-O-glucoside and leucocyanidin. Bacteroides sp. 42 and Veillonella sp. 32 could convert rutin to leucocyanidin. Bacteroides sp. 22 could hydrolyze rutin to quercetin-3-O-glucoside. In order to further explain the metabolism pathway of rutin, the β-D-glucosidase and α-L-rhamnosidase activities of five strains were determined. Bacteroides sp. 22 could produce α-L-rhamnosidase but did not produce β-D-glucosidase or β-D-glucosidase activity was too low to be detected. The other four strains all demonstrated α-L-rhamnosidase and β-D-glucosidase activities. Furthermore, α-L-rhamnosidase and β-D-glucosidase activities of Veillonella sp. 32 and Bacteroides sp. 42 were higher than those of Bacteroides sp. 45 and Bacillus sp. 52. Based on these results, we can propose the deglycosylated rout of rutin: rutin was metabolized to be quercetin-3-O-glucoside by α-L-rhamnosidase produced from these bacteria, thereafter, quercetin-3-O-glucoside was further metabolized by β-D-glucosidase to form leucocyanidin. Because of the higher enzyme activity in Veillonella sp. 32 and Bacteroides sp. 42, quercetin-3-O-glucoside was completely metabolized to leucocyanidin by these two bacteria. Due to the lack of β-D-glucosidase activity, Bacteroides sp. 22 could not further metabolize quercetin-3-O-glucoside to leucocyanidin. This study will be helpful for understanding the deglycosylated rout of rutin and the role of different intestinal bacteria on the metabolism of natural compounds. Copyright © 2012 Elsevier B.V. All rights reserved.

Lack of constitutive beta-glucosidase (esculinase) in the genus Fusobacterium.

PubMed Central

Edberg, S C; Bell, S R

1985-01-01

Esculin has been incorporated into both a medium and test with 20% bile for many years to differentiate Bacteroides from Fusobacterium organisms. After 24 to 48 h, all members of the Bacteroides fragilis group grow in 20% bile and hydrolyze esculin. Fusobacterium mortiferum can both grow in bile and hydrolyze esculin, thus limiting the use of the bile-esculin medium and test. The hypothesis that constitutive esculinase (beta-glucosidase) could differentiate Bacteroides from Fusobacterium organisms was investigated. Clinical isolates and American Type Culture Collection clones of the B. fragilis group and other species of Bacteroides and Fusobacterium were tested. All B. fragilis were positive within 30 min. In no case was a Fusobacterium organism positive for constitutive enzyme in a hydrolyzable substrate-based test. The percentage of positive results for other species of Bacteroides agreed with those published in the literature for the esculin test. The genus Fusobacterium can be separated from Bacteroides organisms based on a lack of constitutive beta-glucosidase in the former in a 30-min one-tube test. PMID:3930563

Committee for International Conference on Mechanical Engineering Research (ICMER 2011)

NASA Astrophysics Data System (ADS)

Yusoff, Ahmad Razlan Bin

2012-09-01

Scientific Advisory Committee: 1) Prof. Dr. Ahmad Kamal Ariffin (UKM) 2) Prof. Dr. Hj. Rosli Abu Bakar (UMP) 3) Prof. Dr. Hanafi Ismail (USM) 4) Prof. Ir. Dr. Mohd Jailani Mohd Nor (MoHE) 5) Prof. Dr. Zahari Taha (UMP) 6) Prof. Dr. Masjuki Haji Hassan 7) Prof. Ir. Dr. Ramesh Singh (UNITEN) 8) Prof. Dr. Razali Ayob (UTEM) 9) Prof. Dr. Wan Khairuddin (UTM) 10) Prof. Dr. Sulaiman Hj. Hasan (UTHM) 11) Prof. Dr. Zuraidah Mohd. Zain (UniMAP) 12) Prof. Dr. Horizon Gitano (USM) 13) Prof. Dr. K.V Sharma (UMP) 14) Prof. Dr. Shahrani Anuar (UMP) 15) Assoc. Prof. Dr. Abd Rashid Abd. Aziz (UTP) 16) Assoc. Prof. Dr. Aidy Ali (UPM) 17) Assoc. Prof. Dr. Saidur Rahman (UM) 18) Assoc. Prof. Dr. Md Abdul Maleque (UIA) Organizing Committee Chairman: Prof. Dr. Hj. Rosli Abu Bakar Co-Chair: Prof. Dr. Zahari Taha Co-Chair: Prof. Ir. Dr. Jailani Salihon Secretary: Dr. Rizalman Mamat Committee on Keynote Speaker 1) Kumaran Kadirgama (Chair) 2) Prof. Dr. K.V. Sharma 3) Haji Amirruddin Abdul Kadir 4) Miminorazeansuhaila Loman 5) Mohd Akramin Mohd Romlay Technical Committee (Peer Review & Proceedings) 1) Dr. Abdul Adam Abdullah (Chair) 2) Dr. Ahmad Razlan Yusoff 3) Mohd Yusof Taib 4) Dr. Md. Mustafizur Rahman 5) Dr. Hjh. Yusnita Rahayu 6) Dr. Gigih Priyandoko 7) Dr. Agung Sudrajad 8) Muhammad Hatifi Mansor 9) Mohd Fadzil Abdul Rahim Technical Committee (Panels & Session Chairs) 1) Dr. Mahadzir Ishak (Chair) 2) Prof. Dr. Shahrani Anuar 3) Dr. Maisara Mohyeldin Gasim Mohamed 4) Muhammad Ammar Nik Mu'tasim 5) Ahmad Basirul Subha bin Alias Technical Committee (Journal Publication) 1) Dr. Ahmad Razlan bin Yusoff (Chair) 2) Mohd Yusof Taib 3) Dr. Mahadzir Ishak 4) Dr. Abdul Adam Abdullah 5) Hj. Amirruddin Abdul Kadir 6) Hadi Abdul Salaam Bureau of Publicity & Website 1) Dr. Muhamad Arifpin Mansor (Chair) 2) Amir Abdul Razak 3) Idris Mat Sahat 4) Prof. Dr. Hj. Rosli Abu Bakar 5) Muhamad Zuhairi Sulaiman 6) Dr. Sugeng Ariyono 7) Asnul Hadi Ahmad 8) Mohd Tarmizy Che Kar 9) Mohd Padzly Radzi Bureau of

Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules.

PubMed

Barrière, Quentin; Guefrachi, Ibtissem; Gully, Djamel; Lamouche, Florian; Pierre, Olivier; Fardoux, Joël; Chaintreuil, Clémence; Alunni, Benoît; Timchenko, Tatiana; Giraud, Eric; Mergaert, Peter

2017-08-22

Legumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway.

Comparative In Vitro Activities of ABT-773 against 362 Clinical Isolates of Anaerobic Bacteria

PubMed Central

Citron, Diane M.; Appleman, Maria D.

2001-01-01

The activity of ABT-773, a novel ketolide antibiotic, against clinical isolates of anaerobic bacteria was determined and compared to the activities of other antimicrobial agents. MICs at which 90% of isolates were inhibited (MIC90s) were ≤0.06 μg/ml for Actinomyces spp., Clostridium perfringens, Peptostreptococcus spp., Propionibacterium spp., and Porphyromonas spp. The MIC50s and MIC90s were ≤0.06 and >32 μg/ml, respectively, for Eubacterium spp., Lactobacillus spp., Clostridium difficile, and Clostridium ramosum. The MIC90 for Bilophila wadsworthia, Bacteroides ureolyticus, and Campylobacter gracilis was 1 μg/ml, and that for Prevotella bivia and other Prevotella spp. was 0.5 μg/ml. The MIC90 for Fusobacterium nucleatum was 8 μg/ml, and that for Fusobacterium mortiferum and Fusobacterium varium was >32 μg/ml. The MIC90s for the Bacteroides fragilis group were as follows: for B. fragilis, 8 μg/ml; for Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides distasonis, and Bacteroides uniformis, >32 μg/ml; and for Bacteroides vulgatus, 4 μg/ml. Telithromycin MICs for the B. fragilis group were usually 1 to 2 dilutions higher than ABT-773 MICs. For all strains, ABT-773 was more active than erythromycin by 4 or more dilutions, and for some strains this drug was more active than clindamycin. PMID:11120995

Predominant nonproductive substrate binding by fungal cellobiohydrolase I and implications for activity improvement.

PubMed

Rabinovich, Mikhail L; Melnik, Maria S; Herner, Mikhail L; Voznyi, Yakov V; Vasilchenko, Lilia G

2018-05-21

Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes 9 subsites for β-D-glucose units, 7 of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent k cat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) k cat /K m for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG 4 ). Interaction of substrates with the subsites -6 and -5 proximal to the non-conserved Gln101 residue in HjCel7A decreases K m,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with K d ∼2-9 nM via CBM and CD that captures 6 terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG 4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding. This article is protected by copyright. All rights reserved.

Incorporating Model Parameter Uncertainty into Prostate IMRT Treatment Planning

DTIC Science & Technology

2005-04-01

HD HJ. Fractionation in radiotherapy. London: Taylor & Francis, 1987. 8. Withers HR. Biologic basis for altered fractionation schemes. Cancer 1985; 55...of combined agent regimens. Int J Radiat Biol 1990; 57: 709-722. 15. Thames HD , Jr., Withers HR, Peters LJ, Fletcher GH. Changes in early and late...Oncology, Biology, Physics 2001; 50: 551-560. 30. Turesson I, Thames HD . Repair capacity and kinetics of human skin during fractionated radiotherapy

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 is an Inorganic Pyrophosphatase+

PubMed Central

Huang, Hua; Yury, Patskovsky; Toro, Rafael; Farelli, Jeremiah D.; Pandya, Chetanya; Almo, Steven C.; Allen, Karen N.; Dunaway-Mariano, Debra

2012-01-01

The explosion of protein sequence information requires that current strategies for function assignment must evolve to complement experimental approaches with computationally-based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown Haloalkanoate Dehalogenase superfamily member BT2127 (Uniprot accession # Q8A5V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics/structure/mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with kcat/Km value for pyrophosphate of ∼1 × 105 M−1 s−1), together with the gene context, supports the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of the wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure guided site directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. Based on this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172 and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue β-phosphoglucomutase control the leaving group size (phosphate vs. glucose-phosphate) and the position of the Asp acid/base in the open vs. closed conformations. HADSF pyrophosphatases

Correlation between detection rates of periodontopathic bacterial DNA in coronary stenotic artery plaque [corrected] and in dental plaque samples.

PubMed

Ishihara, Kazuyuki; Nabuchi, Akihiro; Ito, Rieko; Miyachi, Kouji; Kuramitsu, Howard K; Okuda, Katsuji

2004-03-01

Utilizing PCR, the 16S rRNA detection rates for Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Treponema denticola, and Campylobacter rectus in samples of stenotic coronary artery plaques were determined to be 21.6, 23.3, 5.9, 23.5, and 15.7%, respectively. The detection rates for P. gingivalis and C. rectus correlated with their presence in subgingival plaque.

U.S. EPA, Pesticide Product Label, BRULINCIDE #502, 02/25/1975

EPA Pesticide Factsheets

2011-04-13

... j'j I't U; • .t·'Hj w,nlHj I,' ... r ... .Il1li "' .1 ·{d'-'.I: !d/ ~""'lnllnlllq IJI.!)I ",t' Qr-,4 ~ ()d()rll·\\.~. Liquid ('olll'l'ni rall' : .. ' I .' " : . 0 !\\' \\- 0 .... . ...

Concurrent validation of the Actigraph gt3x+, Polar Active accelerometer, Omron HJ-720 and Yamax Digiwalker SW-701 pedometer step counts in lab-based and free-living settings.

PubMed

Lee, Joey A; Williams, Skip M; Brown, Dale D; Laurson, Kelly R

2015-01-01

Activity monitors are frequently used to assess activity in many settings. But as technology advances, so do the mechanisms used to estimate activity causing a continuous need to validate newly developed monitors. The purpose of this study was to examine the step count validity of the Yamax Digiwalker SW-701 pedometer (YX), Omron HJ-720 T pedometer (OP), Polar Active accelerometer (PAC) and Actigraph gt3x+ accelerometer (AG) under controlled and free-living conditions. Participants completed five stages of treadmill walking (n = 43) and a subset of these completed a 3-day free-living wear period (n = 37). Manually counted (MC) steps provided a criterion measure for treadmill walking, whereas the comparative measure during free-living was the YX. During treadmill walking, the OP was the most accurate monitor across all speeds (±1.1% of MC steps), while the PAC underestimated steps by 6.7-16.0% per stage. During free-living, the OP and AG counted 97.5% and 98.5% of YX steps, respectively. The PAC overestimated steps by 44.0%, or 5,265 steps per day. The Omron pedometer seems to provide the most reliable and valid estimate of steps taken, as it was the best performer under lab-based conditions and provided comparable results to the YX in free-living. Future studies should consider these monitors in additional populations and settings.

Efficient Maize and Sunflower Multi-year Mapping with NDVI Time Series of HJ-1A/1B in Hetao Irrigation District of Inner Mongolia, China

NASA Astrophysics Data System (ADS)

Yu, B.; Shang, S.

2016-12-01

Food shortage is one of the major challenges that human beings are facing. It is urgent to improve the monitoring of the plantation and distribution of the main crops to solve the following economic and social issues. Recently, with the extensive use of remote sensing satellite data, it has provided favorable conditions for crop identification in large irrigation district with complex planting structure. Difference of different crop phenology is the main basis for crop identification, and the normalized difference vegetation index (NDVI) time-series could better delineate crop phenology cycle. Therefore, the key of crop identification is to obtain high quality NDVI time-series. MODIS and Landsat TM satellite images are the most frequently used, however, neither of them could guarantee high temporal and spatial resolutions at once. Accordingly, this paper makes use of NDVI time-series extracted from China Environment Satellites data, which has two-day-repeat temporal and 30m spatial resolutions. The NDVI time-series are fitted with an asymmetric logistic curve, the fitting effect is good and the correlation coefficient is greater than 0.9. The phonological parameters are derived from NDVI fitting curves, and crop identification is carried out by different relation ellipses between NDVI and its phonological parameters of different crops. This paper takes Hetao Irrigation District of Inner Mongolia as an example, to identify multi-year maize and sunflower in the district, and the identification result is good. Compared with the official statistics, the relative errors are both lower than 5%. The results show that the NDVI time-series dataset derived from HJ-1A/1B CCD could delineate the crop phenology cycle accurately and demonstrate its application in crop identification in irrigated district.

Isolation and partial characterization of two plasmid deoxyribonucleic acids from endosymbiotic bacteria of Amoeba proteus.

PubMed Central

Han, J H; Jeon, K W

1980-01-01

Obligatory endosymbiotic bacteria in a strain of Amoeba proteus were found to harbor two distinct species of plasmid, pHJ11 and pHJ12. Their molecular weights were 39 x 10(6) and 14 x 10(6), respectively. Images PMID:7364732

Models of Distribution Computation: Behavior Characterization of Intelligent Problem Solving for an Agent Hierarchy in a Competitive (Web) Environment

DTIC Science & Technology

2002-10-04

N^] A U K�C g N hNBDC A U WA �AWL`HjBEHG�C g N E$jW�]E$] L j`1COA E UR tLCy`1COA E U AB;]N^M_GE$M k NW N^A C g N^ Mih �`Hj CON^MOA...y E$ Mih �MON^] j`$XA U KtB_E k N�A U WA �AWL`HjB w\\A C g My` U WE k N^j N k N U CyBiEHG...1COA E U hNXE k NB C g NiE$jW’]E$] L j`1COA E UR e"g N62 C U NBOBEHG"` U A U WA �AWL`Hj x X^` U N^A C g N^ Mih N�WNCON^M k A U NW�h

Resistance of Bacteroides isolates recovered among clinical samples from a major Costa Rican hospital between 2000 and 2008 to ß-lactams, clindamycin, metronidazole, and chloramphenicol.

PubMed

Cordero-Laurent, E; Rodríguez, C; Rodríguez-Cavallini, E; Gamboa-Coronado, M M; Quesada-Gómez, C

2012-12-01

To assess the susceptibility of 100 isolates of Bacteroides spp. recovered in a major Costa Rican hospital between 2000 and 2008 to several ß-lactams, chloramphenicol, clindamycin and metronidazole. Susceptibility to amoxicillin, amoxicillin with clavulanic acid, piperacillin, piperacillin with tazobactam, ticarcillin, ticarcillin with clavulanic acid, cefoxitin, cefotetan, imipenem, chloramphenicol, clindamycin, and metronidazole was determined with the ATB ANA® system. In addition, minimum inhibitory concentrations (MIC) of clindamycin and metronidazole were determined with the broth microdilution method because these drugs are the treatment of choice for anaerobic infections in Costa Rica. Reference strains ATCC® 25285 and ATCC® 29741 were employed as indicated. According to the ATB ANA® system, 93 isolates were resistant to at least one antibiotic. Resistance to ß-lactams was common. By contrast, resistance to ß-lactams supplemented with ß-lactamase inhibitors was rare. All of the strains were inhibited by imipenem and chloramphenicol. By a broth microdilución test, resistance to clindamycin was 20%, with MIC ranging from 64 mg/L to 256 mg/L; all of the strains were susceptible to metronidazole. The high MIC for clindamycin obtained for the majority of the resistant strains is highly suggestive of the presence of mechanisms of acquired resistance among the isolates, therefore surveillance studies are required to determine its efficacy. The low resistance to metronidazole observed underlines its value as a first-line drug. On the other hand, imipenem could be used to treat infections that do not respond well to metronidazole or clindamycin.

Instant screening and verification of carbapenemase activity in Bacteroides fragilis in positive blood culture, using matrix-assisted laser desorption ionization--time of flight mass spectrometry.

PubMed

Johansson, Åsa; Nagy, Elisabeth; Sóki, József

2014-08-01

Rapid identification of isolates in positive blood cultures are of great importance to secure correct treatment of septicaemic patients. As antimicrobial resistance is increasing, rapid detection of resistance is crucial. Carbapenem resistance in Bacteroides fragilis associated with cfiA-encoded class B metallo-beta-lactamase is emerging. In our study we spiked blood culture bottles with 26 B. fragilis strains with various cfiA-status and ertapenem MICs. By using main spectra specific for cfiA-positive and cfiA-negative B. fragilis strains, isolates could be screened for resistance. To verify strains that were positive in the screening, a carbapenemase assay was performed where the specific peaks of intact and hydrolysed ertapenem were analysed with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We show here that it is possible to correctly identify B. fragilis and to screen for enzymic carbapenem resistance directly from the pellet of positive blood cultures. The carbapenemase assay to verify the presence of the enzyme was successfully performed on the pellet from the direct identification despite the presence of blood components. The result of the procedure was achieved in 3 h. Also the Bruker mass spectrometric β-lactamase assay (MSBL assay) prototype software was proven not only to be based on an algorithm that correlated with the manual inspection of the spectra, but also to improve the interpretation by showing the variation in the dataset. © 2014 The Authors.

Detection of Genetic Markers of Fecal Indicator Bacteria in Lake Michigan and Determination of Their Relationship to Escherichia coli Densities Using Standard Microbiological Methods

PubMed Central

Bower, Patricia A.; Scopel, Caitlin O.; Jensen, Erika T.; Depas, Morgan M.; McLellan, Sandra L.

2005-01-01

Lake Michigan surface waters impacted by fecal pollution were assessed to determine the occurrence of genetic markers for Bacteroides and Escherichia coli. Initial experiments with sewage treatment plant influent demonstrated that total Bacteroides spp. could be detected by PCR in a 25- to 125-fold-higher dilution series than E. coli and human-specific Bacteroides spp., which were both found in similar dilution ranges. The limit of detection for the human-specific genetic marker ranged from 0.2 CFU/100 ml to 82 CFU/100 ml culturable E. coli for four wastewater treatment plants in urban and rural areas. The spatial and temporal distributions of these markers were assessed following major rain events that introduced urban storm water, agricultural runoff, and sewage overflows into Lake Michigan. Bacteroides spp. were detected in all of these samples by PCR, including those with <1 CFU/100 ml E. coli. Human-specific Bacteroides spp. were detected as far as 2 km into Lake Michigan during sewage overflow events, with variable detection 1 to 9 days postoverflow, whereas the cow-specific Bacteroides spp. were detected in only highly contaminated samples near the river outflow. Lake Michigan beaches were also assessed throughout the summer season for the same markers. Bacteroides spp. were detected in all beach samples, including 28 of the 74 samples that did not exceed 235 CFU/100 ml of E. coli. Human-specific Bacteroides spp. were detected at three of the seven beaches; one of the sites demonstrating positive results was sampled during a reported sewage overflow, but E. coli levels were below 235 CFU/100 ml. This study demonstrates the usefulness of non-culture-based microbial-source tracking approaches and the prevalence of these genetic markers in the Great Lakes, including freshwater coastal beaches. PMID:16332817

A Novel Phosphatase Gene on 10q23, MINNP, in Hereditary and Sporadic Breast Cancer

DTIC Science & Technology

2002-08-01

surrounding stroma. 14. SUBJECT TERMS 15. NUMBER OF PAGES human cancer genetics, breast cancer 28 16. PRICE CODE 17. SECURITY CLASSIFICATION 18...Genetics. All rights reserved. et al. 1998). CS is a poorly recognized autosomal dom- 0002-929712001/6904-0005$02.00 inant cancer syndrome...58, 1348-1352. 24. Coles, C., Condie, A., Chetty, U., Steel. C.M., Evans, H.J. and Prosser, J. 36. Wolf, C., Rouyer, N., Lutz, Y.. Adida . C., Loriot, M

Recent evolution of antibiotic resistance in the anaerobes as compared to previous decades.

PubMed

Boyanova, Lyudmila; Kolarov, Rossen; Mitov, Ivan

2015-02-01

Evolution of antibiotic resistance in the anaerobes was reviewed using recent data covering 2000-2013 as compared to previous years. All studies reported growing moxifloxacin resistance in Bacteroides/Parabacteroides spp. in Europe and USA and in Clostridium difficile in Europe. In half or more studies, the resistance rates in Bacteroides/Parabacteroides spp. to amoxicillin-clavulanate or ampicillin-sulbactam and clindamycin rose. In some studies, an increase in resistance was found in Bacteroides/Parabacteroides spp. to cefoxitin/cefotetan and carbapenems, in Prevotella spp. to penicillins, in anaerobic cocci to clindamycin and in Bacteroides/Parabacteroides spp. and C. difficile to metronidazole. Decreasing resistance was also observed, e.g. in Bacteroides/Parabacteroides spp. to cephalosporins, in Prevotella spp. and C. difficile to tetracyclines and in C. difficile to rifampin. No resistance changes were found to tigecycline, in Bacteroides/Parabacteroides spp. to chloramphenicol and in C. difficile to vancomycin. Factors influencing the resistance were the species, ribotype, country, hospital centre, antibiotic consumption and specimen type. In conclusion, the antibiotic resistance changes in the anaerobes are diverse and dynamic. Regular national surveys of resistance and both anaerobic microbiology and susceptibility testing of the isolates become more and more valuable. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bacterial Population Adherent to the Epithelium on the Roo of the Dorsal Rumen of Sheep †

PubMed Central

Dehority, Burk A.; Grubb, Jean A.

1981-01-01

By anaerobic procedures, the total number of adherent bacteria was determined on tissue samples obtained from the roof of the dorsal rumen of three sheep. After four washings, 1.91 × 107, 0.34 × 107, and 1.23 × 107 bacteria per cm2 were still attached to the rumen epithelium in sheep 1, 2, and 3, respectively. A total of 95 strains of bacteria were isolated from these three samples. Based on morphology, Gram stain, anaerobiosis, motility, and fermentation end products, they were presumptively identified as follows: Butyrivibrio fibrisolvens, 30 strains; atypical Butyrivibrio, 5 strains; Bacteroides ruminicola, 22 strains; Lactobacillus, 1 strain; and unknown Bacteroides species, 37 strains. For sheep 3, washing the rumen epithelium a total of 10 times reduced the adherent bacterial population by 93% (8.4 × 105 bacteria per cm2). Of 30 strains isolated from this sample, 22 were presumptively identified as Butyrivibrio and Bacteroides types. These results suggest that the epithelium on the roof of the dorsal rumen is primarily colonized by two genera of bacteria, Butyrivibrio and Bacteroides. Most Butyrivibrio and Bacteroides ruminicola strains appeared to be similar to previously isolated rumen strains. However, the unknown Bacteroides species differed considerably from the three species of this genus which are commonly isolated from rumen contents. PMID:16345797

Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides.

PubMed

Thomas, François; Barbeyron, Tristan; Tonon, Thierry; Génicot, Sabine; Czjzek, Mirjam; Michel, Gurvan

2012-09-01

Alginate constitutes a significant part of seaweed biomass and thus a crucial nutrient for numerous marine heterotrophic bacteria. However, the mechanisms for alginate assimilation remain largely unknown in marine microorganisms. We show here that the genome of the marine flavobacterium Zobellia galactanivorans contains seven putative alginate lyase genes, five of them localized within two clusters comprising additional carbohydrate-related genes. The transcription of these genes and the alginolytic activity were strongly induced when Z. galactanivorans used alginate as sole carbon source. These clusters were shown to be transcribed as polycistronic mRNAs and thus to constitute operons. Several candidate enzymes were successfully overexpressed in Escherichia coli, purified and their activity tested. Particularly, AlyA1, AlyA4, AlyA5 and AlyA7 are confirmed as active alginate lyases. Zg2622 and Zg2614 are a dehydrogenase and a kinase, respectively, further converting the terminal unsaturated monosaccharides released by alginate lyases into 2-keto-3-deoxy-6-phosphogluconate. In-depth phylogenomic analyses reveal that such alginolytic operons originated from an ancestral marine flavobacterium and were independently transferred to marine proteobacteria and Japanese gut Bacteroides. These bacteria thus gained the capacity to assimilate the main polysaccharide of brown algae, an adaptive advantage in coastal environments but also in the gut microbiota of specific human population. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Direct analysis of Holliday junction resolving enzyme in a DNA origami nanostructure.

PubMed

Suzuki, Yuki; Endo, Masayuki; Cañas, Cristina; Ayora, Silvia; Alonso, Juan C; Sugiyama, Hiroshi; Takeyasu, Kunio

2014-06-01

Holliday junction (HJ) resolution is a fundamental step for completion of homologous recombination. HJ resolving enzymes (resolvases) distort the junction structure upon binding and prior cleavage, raising the possibility that the reactivity of the enzyme can be affected by a particular geometry and topology at the junction. Here, we employed a DNA origami nano-scaffold in which each arm of a HJ was tethered through the base-pair hybridization, allowing us to make the junction core either flexible or inflexible by adjusting the length of the DNA arms. Both flexible and inflexible junctions bound to Bacillus subtilis RecU HJ resolvase, while only the flexible junction was efficiently resolved into two duplexes by this enzyme. This result indicates the importance of the structural malleability of the junction core for the reaction to proceed. Moreover, cleavage preferences of RecU-mediated reaction were addressed by analyzing morphology of the reaction products. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

N-body simulations of terrestrial planet formation under the influence of a hot Jupiter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogihara, Masahiro; Kobayashi, Hiroshi; Inutsuka, Shu-ichiro, E-mail: omasahiro@oca.eu, E-mail: ogihara@nagoya-u.jp

We investigate the formation of multiple-planet systems in the presence of a hot Jupiter (HJ) using extended N-body simulations that are performed simultaneously with semianalytic calculations. Our primary aims are to describe the planet formation process starting from planetesimals using high-resolution simulations, and to examine the dependences of the architecture of planetary systems on input parameters (e.g., disk mass, disk viscosity). We observe that protoplanets that arise from oligarchic growth and undergo type I migration stop migrating when they join a chain of resonant planets outside the orbit of an HJ. The formation of a resonant chain is almost independentmore » of our model parameters, and is thus a robust process. At the end of our simulations, several terrestrial planets remain at around 0.1 AU. The formed planets are not equal mass; the largest planet constitutes more than 50% of the total mass in the close-in region, which is also less dependent on parameters. In the previous work of this paper, we have found a new physical mechanism of induced migration of the HJ, which is called a crowding-out. If the HJ opens up a wide gap in the disk (e.g., owing to low disk viscosity), crowding-out becomes less efficient and the HJ remains. We also discuss angular momentum transfer between the planets and disk.« less

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

PubMed Central

Bryant, William A.; Stentz, Régis; Le Gall, Gwenaelle; Sternberg, Michael J. E.; Carding, Simon R.; Wilhelm, Thomas

2017-01-01

The interactions between the gut microbiota and its host are of central importance to the health of the host. Outer membrane vesicles (OMVs) are produced ubiquitously by Gram-negative bacteria including the gut commensal Bacteroides thetaiotaomicron. These vesicles can interact with the host in various ways but until now their complement of small molecules has not been investigated in this context. Using an untargeted high-coverage metabolomic approach we have measured the small molecule content of these vesicles in contrasting in vitro conditions to establish what role these metabolites could perform when packed into these vesicles. B. thetaiotaomicron packs OMVs with a highly conserved core set of small molecules which are strikingly enriched with mouse-digestible metabolites and with metabolites previously shown to be associated with colonization of the murine GIT. By use of an expanded genome-scale metabolic model of B. thetaiotaomicron and a potential host (the mouse) we have established many possible metabolic pathways between the two organisms that were previously unknown, and have found several putative novel metabolic functions for mouse that are supported by gene annotations, but that do not currently appear in existing mouse metabolic networks. The lipidome of these OMVs bears no relation to the mouse lipidome, so the purpose of this particular composition of lipids remains unclear. We conclude from this analysis that through intimate symbiotic evolution OMVs produced by B. thetaiotaomicron are likely to have been adopted as a conduit for small molecules bound for the mammalian host in vivo. PMID:29276507

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host.

PubMed

Bryant, William A; Stentz, Régis; Le Gall, Gwenaelle; Sternberg, Michael J E; Carding, Simon R; Wilhelm, Thomas

2017-01-01

The interactions between the gut microbiota and its host are of central importance to the health of the host. Outer membrane vesicles (OMVs) are produced ubiquitously by Gram-negative bacteria including the gut commensal Bacteroides thetaiotaomicron . These vesicles can interact with the host in various ways but until now their complement of small molecules has not been investigated in this context. Using an untargeted high-coverage metabolomic approach we have measured the small molecule content of these vesicles in contrasting in vitro conditions to establish what role these metabolites could perform when packed into these vesicles. B. thetaiotaomicron packs OMVs with a highly conserved core set of small molecules which are strikingly enriched with mouse-digestible metabolites and with metabolites previously shown to be associated with colonization of the murine GIT. By use of an expanded genome-scale metabolic model of B. thetaiotaomicron and a potential host (the mouse) we have established many possible metabolic pathways between the two organisms that were previously unknown, and have found several putative novel metabolic functions for mouse that are supported by gene annotations, but that do not currently appear in existing mouse metabolic networks. The lipidome of these OMVs bears no relation to the mouse lipidome, so the purpose of this particular composition of lipids remains unclear. We conclude from this analysis that through intimate symbiotic evolution OMVs produced by B. thetaiotaomicron are likely to have been adopted as a conduit for small molecules bound for the mammalian host in vivo .

Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov

NASA Technical Reports Server (NTRS)

Gosink, J. J.; Woese, C. R.; Staley, J. T.

1998-01-01

Several psychrophilic, gas vacuolate strains of the Cytophage-Flavobacterium-Bacteroides (CFB) phylogenetic group were isolated from sea ice and water from the Arctic and the Antarctic. The closest taxonomically defined species by 16S rRNA sequence analysis is 'Flectobacillus glomeratus'. However, 'Flc. glomeratus' is phylogenetically distant from the Flectobacillus type species, Flc. major. On the basis of phenotypic, genotypic and 16S rRNA sequence analyses we propose a new genus, Polaribacter, with three new species, Polaribacter irgensii strain 23-P (ATCC 700398), Polaribacter franzmannii strain 301 (ATCC 700399) and Polaribacter filamentus strain 215 (ATCC 700397). P. filamentus is the type species of the genus. None of these species exhibits a cosmopolitan or bipolar distribution. This is the first taxonomic description of gas vacuolate bacteria in the CFB group. Additionally, we propose that 'Flc. glomeratus' be reclassified to the genus Polaribacter as P. glomeratus, comb. nov.

Microstructural, electrical and frequency-dependent properties of Au/p-Cu2ZnSnS4/n-GaN heterojunction.

PubMed

Rajagopal Reddy, V; Janardhanam, V; Won, Jonghan; Choi, Chel-Jong

2017-08-01

An Au/Cu 2 ZnSnS 4 (CZTS)/n-GaN heterojunction (HJ) is fabricated with a CZTS interlayer and probed its chemical states, structural, electrical and frequency-dependent characteristics by XPS, TEM, I-V and C-V measurements. XPS and TEM results confirmed that the CZTS films are formed on the n-GaN surface. The band gap of deposited CZTS film is found to be 1.55eV. The electrical properties of HJ correlated with the Au/n-GaN Schottky junction (SJ). The Au/CZTS/n-GaN HJ reveals a good rectification nature with high barrier height (0.82eV) compared to the Au/n-GaN SJ (0.69eV), which suggests the barrier height is influenced by the CZTS interlayer. The barrier height values assessed by I-V, Cheung's and Norde functions are closely matched with one other, thus the methods used here are reliable and valid. The extracted interface state density (N SS ) of Au/CZTS/n-GaN HJ is lower compared to the Au/n-GaN SJ that suggests the CZTS interlayer plays an important role in the reduction of N SS . Moreover, the capacitance-frequency (C-f) and conductance-frequency (G-f) characteristics of SJ and HJ are measured in the range of 1kHz-1MHz, and found that the capacitance and conductance strappingly dependent on frequency. It is found that the N SS estimated from C-f and G-f characteristics is lower compared to those estimated from I-V characteristics. Analysis confirmed that Poole-Frenkel emission dominates the reverse leakage current in both SJ and HJ, probably related to the structural defects and trap levels in the CZTS interlayer. Copyright © 2017 Elsevier Inc. All rights reserved.

Exposure to human-associated fecal indicators and self-reported illness among swimmers at recreational beaches: a cohort study.

PubMed

Napier, Melanie D; Haugland, Richard; Poole, Charles; Dufour, Alfred P; Stewart, Jill R; Weber, David J; Varma, Manju; Lavender, Jennifer S; Wade, Timothy J

2017-10-02

Fecal indicator bacteria used to assess illness risks in recreational waters (e.g., Escherichia coli, Enterococci) cannot discriminate among pollution sources. To address this limitation, human-associated Bacteroides markers have been proposed, but the risk of illness associated with the presence of these markers in recreational waters is unclear. Our objective was to estimate associations between human-associated Bacteroides markers in water and self-reported illness among swimmers at 6 U.S. beaches spanning 2003-2007. We used data from a prospectively-enrolled cohort of 12,060 swimmers surveyed about beach activities and water exposure on the day of their beach visit. Ten to twelve days later, participants reported gastroinestinal, diarrheal, and respiratory illnesses experienced since the visit. Daily water samples were analyzed for the presence of human-associated Bacteroides genetic markers: HF183, BsteriF1, BuniF2, HumM2. We used model-based standardization to estimate risk differences (RD) and 95% confidence intervals (CI). We assessed whether the presence of Bacteroides markers were modifiers of the association between general Enterococcus and illness among swimmers using interaction contrast. Overall we observed inconsistent associations between the presence of Bacteroides markers and illness. There was a pattern of increased risks of gastrointestinal (RD = 1.9%; 95% CI: 0.1%, 3.7%), diarrheal (RD = 1.3%; 95% CI: -0.2%, 2.7%), and respiratory illnesses (RD = 1.1%; 95% CI: -0.2%, 2.5%) associated with BsteriF1. There was no evidence that Bacteroides markers acted as modifiers of Enterococcus and illness. Patterns were similar when stratified by water matrix. Quantitative measures of fecal pollution using Bacteroides, rather than presence-absence indicators, may be necessary to accurately assess human risk specific to the presence of human fecal pollution.

Degradation of Marine Algae-Derived Carbohydrates by Bacteroidetes Isolated from Human Gut Microbiota.

PubMed

Li, Miaomiao; Shang, Qingsen; Li, Guangsheng; Wang, Xin; Yu, Guangli

2017-03-24

Carrageenan, agarose, and alginate are algae-derived undigested polysaccharides that have been used as food additives for hundreds of years. Fermentation of dietary carbohydrates of our food in the lower gut of humans is a critical process for the function and integrity of both the bacterial community and host cells. However, little is known about the fermentation of these three kinds of seaweed carbohydrates by human gut microbiota. Here, the degradation characteristics of carrageenan, agarose, alginate, and their oligosaccharides, by Bacteroides xylanisolvens , Bacteroides ovatus , and Bacteroides uniforms , isolated from human gut microbiota, are studied.

Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer

PubMed Central

Viljoen, Katie S.; Dakshinamurthy, Amirtha; Goldberg, Paul; Blackburn, Jonathan M.

2015-01-01

Various studies have presented clinical or in vitro evidence linking bacteria to colorectal cancer, but these bacteria have not previously been concurrently quantified by qPCR in a single cohort. We quantify these bacteria (Fusobacterium spp., Streptococcus gallolyticus, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Enteropathogenic Escherichia coli (EPEC), and afaC- or pks-positive E. coli) in paired tumour and normal tissue samples from 55 colorectal cancer patients. We further investigate the relationship between a) the presence and b) the level of colonisation of each bacterial species with site and stage of disease, age, gender, ethnicity and MSI-status. With the exception of S. gallolyticus, we detected all bacteria profiled here in both tumour and normal samples at varying frequencies. ETBF (FDR = 0.001 and 0.002 for normal and tumour samples) and afaC-positive E. coli (FDR = 0.03, normal samples) were significantly enriched in the colon compared to the rectum. ETBF (FDR = 0.04 and 0.002 for normal and tumour samples, respectively) and Fusobacterium spp. (FDR = 0.03 tumour samples) levels were significantly higher in late stage (III/IV) colorectal cancers. Fusobacterium was by far the most common bacteria detected, occurring in 82% and 81% of paired tumour and normal samples. Fusobacterium was also the only bacterium that was significantly higher in tumour compared to normal samples (p = 6e-5). We also identified significant associations between high-level colonisation by Fusobacterium and MSI-H (FDR = 0.05), age (FDR = 0.03) or pks-positive E. coli (FDR = 0.01). Furthermore, we exclusively identified atypical EPEC in our cohort, which has not been previously reported in association with colorectal cancer. By quantifying colorectal cancer-associated bacteria across a single cohort, we uncovered inter- and intra-individual patterns of colonization not previously recognized, as well as important associations with clinicopathological

15 CFR 15.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Definitions. 15.2 Section 15.2 Commerce and Foreign Trade Office of the Secretary of Commerce LEGAL PROCEEDINGS Service of Process § 15.2... States Department of Commerce or other Department employee to whom the General Counsel has delegated...

15 CFR 15.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Definitions. 15.2 Section 15.2 Commerce and Foreign Trade Office of the Secretary of Commerce LEGAL PROCEEDINGS Service of Process § 15.2... States Department of Commerce or other Department employee to whom the General Counsel has delegated...

15 CFR 15.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Definitions. 15.2 Section 15.2 Commerce and Foreign Trade Office of the Secretary of Commerce LEGAL PROCEEDINGS Service of Process § 15.2... States Department of Commerce or other Department employee to whom the General Counsel has delegated...

15 CFR 15.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Definitions. 15.2 Section 15.2 Commerce and Foreign Trade Office of the Secretary of Commerce LEGAL PROCEEDINGS Service of Process § 15.2... States Department of Commerce or other Department employee to whom the General Counsel has delegated...

15 CFR 15.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Definitions. 15.2 Section 15.2 Commerce and Foreign Trade Office of the Secretary of Commerce LEGAL PROCEEDINGS Service of Process § 15.2... States Department of Commerce or other Department employee to whom the General Counsel has delegated...

46 CFR 168.15-15 - Size.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Size. 168.15-15 Section 168.15-15 Shipping COAST GUARD... § 168.15-15 Size. (a) Sleeping accommodations must be divided into rooms, no one of which may berth more... accommodate, must be marked outside the space. (b) Each room must be of such size that there is at least 1.8...

46 CFR 168.15-15 - Size.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 7 2011-10-01 2011-10-01 false Size. 168.15-15 Section 168.15-15 Shipping COAST GUARD... § 168.15-15 Size. (a) Sleeping accommodations must be divided into rooms, no one of which may berth more... accommodate, must be marked outside the space. (b) Each room must be of such size that there is at least 1.8...

Magnet-Facilitated Selection of Electrogenic Bacteria from Marine Sediment

PubMed Central

Kiseleva, Larisa; Briliute, Justina; Khilyas, Irina V.; Simpson, David J. W.; Fedorovich, Viacheslav; Cohen, M.; Goryanin, Igor

2015-01-01

Some bacteria can carry out anaerobic respiration by depositing electrons on external materials, such as electrodes, thereby creating an electrical current. Into the anode chamber of microbial fuel cells (MFCs) having abiotic air-cathodes we inoculated microorganisms cultured from a magnetic particle-enriched portion of a marine tidal sediment, reasoning that since some external electron acceptors are ferromagnetic, electrogenic bacteria should be found in their vicinity. Two MFCs, one inoculated with a mixed bacterial culture and the other with an axenic culture of a helical bacterium isolated from the magnetic particle enrichment, termed strain HJ, were operated for 65 d. Both MFCs produced power, with production from the mixed culture MFC exceeding that of strain HJ. Strain HJ was identified as a Thalassospira sp. by transmission electron microscopic analysis and 16S rRNA gene comparisons. An MFC inoculated with strain HJ and operated in open circuit produced 47% and 57% of the maximal power produced from MFCs inoculated with the known electrogen Geobacter daltonii and the magnetotactic bacterium Desulfamplus magnetomortis, respectively. Further investigation will be needed to determine whether bacterial populations associated with magnetic particles within marine sediments are enriched for electrogens. PMID:26504814

Magnet-Facilitated Selection of Electrogenic Bacteria from Marine Sediment.

PubMed

Kiseleva, Larisa; Briliute, Justina; Khilyas, Irina V; Simpson, David J W; Fedorovich, Viacheslav; Cohen, M; Goryanin, Igor

2015-01-01

Some bacteria can carry out anaerobic respiration by depositing electrons on external materials, such as electrodes, thereby creating an electrical current. Into the anode chamber of microbial fuel cells (MFCs) having abiotic air-cathodes we inoculated microorganisms cultured from a magnetic particle-enriched portion of a marine tidal sediment, reasoning that since some external electron acceptors are ferromagnetic, electrogenic bacteria should be found in their vicinity. Two MFCs, one inoculated with a mixed bacterial culture and the other with an axenic culture of a helical bacterium isolated from the magnetic particle enrichment, termed strain HJ, were operated for 65 d. Both MFCs produced power, with production from the mixed culture MFC exceeding that of strain HJ. Strain HJ was identified as a Thalassospira sp. by transmission electron microscopic analysis and 16S rRNA gene comparisons. An MFC inoculated with strain HJ and operated in open circuit produced 47% and 57% of the maximal power produced from MFCs inoculated with the known electrogen Geobacter daltonii and the magnetotactic bacterium Desulfamplus magnetomortis, respectively. Further investigation will be needed to determine whether bacterial populations associated with magnetic particles within marine sediments are enriched for electrogens.

Effect of freshwater sediment characteristics on the persistence of fecal indicator bacteria and genetic markers within a Southern California Watershed.

EPA Science Inventory

In this study, the relative aging of FIB and genetic markers for Enterococcus spp. (ENT1A), general Bacteroides (GenBac3), and human-associated Bacteroides (HF183) in varying freshwater sediments was evaluated. Freshwater sediment was collected from four different sites within th...

Degradation of Marine Algae-Derived Carbohydrates by Bacteroidetes Isolated from Human Gut Microbiota

PubMed Central

Li, Miaomiao; Shang, Qingsen; Li, Guangsheng; Wang, Xin; Yu, Guangli

2017-01-01

Carrageenan, agarose, and alginate are algae-derived undigested polysaccharides that have been used as food additives for hundreds of years. Fermentation of dietary carbohydrates of our food in the lower gut of humans is a critical process for the function and integrity of both the bacterial community and host cells. However, little is known about the fermentation of these three kinds of seaweed carbohydrates by human gut microbiota. Here, the degradation characteristics of carrageenan, agarose, alginate, and their oligosaccharides, by Bacteroides xylanisolvens, Bacteroides ovatus, and Bacteroides uniforms, isolated from human gut microbiota, are studied. PMID:28338633

[Gardnerella vaginalis in infections of reproductive organs].

PubMed

Kasprowicz, A; Białecka, A

1993-01-01

The study was aimed at multidirectional studies on bacteria isolated from smears from vagina and cervix uteri in 226 patients with inflammatory states of their reproductive organs. Most frequently isolated aerobic bacteria were Gram-negative--27%, mainly E. coli, and Enterococcus faecalis--in 18% of cases. Anaerobic bacteria were isolated in 81% of cases: Gardnerella vaginalis was isolated in 28% and Lactobacillus in 53% of cases. Other anaerobic bacteria were: Peptococcus asaccharolyticus (15.5%), Streptococcus sp. (15.9%), and Bacteroides melaninogenicus (14.1%). Gardnerella vaginalis was most frequently found in chronic cases of vaginosis (41.7%). All strains of G. vaginalis were susceptible to cefotaxime, while 15-40% of them were resistant to gentamycin, tetracycline and metronidazole.

High-Order Central WENO Schemes for 1D Hamilton-Jacobi Equations

NASA Technical Reports Server (NTRS)

Bryson, Steve; Levy, Doron; Biegel, Bryan A. (Technical Monitor)

2002-01-01

In this paper we derive fully-discrete Central WENO (CWENO) schemes for approximating solutions of one dimensional Hamilton-Jacobi (HJ) equations, which combine our previous works. We introduce third and fifth-order accurate schemes, which are the first central schemes for the HJ equations of order higher than two. The core ingredient is the derivation of our schemes is a high-order CWENO reconstructions in space.

Intestinal Microbiota Distinguish Gout Patients from Healthy Humans

PubMed Central

Guo, Zhuang; Zhang, Jiachao; Wang, Zhanli; Ang, Kay Ying; Huang, Shi; Hou, Qiangchuan; Su, Xiaoquan; Qiao, Jianmin; Zheng, Yi; Wang, Lifeng; Koh, Eileen; Danliang, Ho; Xu, Jian; Lee, Yuan Kun; Zhang, Heping

2016-01-01

Current blood-based approach for gout diagnosis can be of low sensitivity and hysteretic. Here via a 68-member cohort of 33 healthy and 35 diseased individuals, we reported that the intestinal microbiota of gout patients are highly distinct from healthy individuals in both organismal and functional structures. In gout, Bacteroides caccae and Bacteroides xylanisolvens are enriched yet Faecalibacterium prausnitzii and Bifidobacterium pseudocatenulatum depleted. The established reference microbial gene catalogue for gout revealed disorder in purine degradation and butyric acid biosynthesis in gout patients. In an additional 15-member validation-group, a diagnosis model via 17 gout-associated bacteria reached 88.9% accuracy, higher than the blood-uric-acid based approach. Intestinal microbiota of gout are more similar to those of type-2 diabetes than to liver cirrhosis, whereas depletion of Faecalibacterium prausnitzii and reduced butyrate biosynthesis are shared in each of the metabolic syndromes. Thus the Microbial Index of Gout was proposed as a novel, sensitive and non-invasive strategy for diagnosing gout via fecal microbiota. PMID:26852926

15 CFR 303.15 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Purpose. 303.15 Section 303.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE MISCELLANEOUS REGULATIONS WATCHES, WATCH MOVEMENTS AND...

The inv dup (15) or idic (15) syndrome (Tetrasomy 15q).

PubMed

Battaglia, Agatino

2008-11-19

The inv dup(15) or idic(15) syndrome displays distinctive clinical findings represented by early central hypotonia, developmental delay and intellectual disability, epilepsy, and autistic behaviour. Incidence at birth is estimated at 1 in 30,000 with a sex ratio of almost 1:1. Developmental delay and intellectual disability affect all individuals with inv dup(15) and are usually moderate to profound. Expressive language is absent or very poor and often echolalic. Comprehension is very limited and contextual. Intention to communicate is absent or very limited. The distinct behavioral disorder shown by children and adolescents has been widely described as autistic or autistic-like. Epilepsy with a wide variety of seizure types can occur in these individuals, with onset between 6 months and 9 years. Various EEG abnormalities have been described. Muscle hypotonia is observed in almost all individuals, associated, in most of them, with joint hyperextensibility and drooling. Facial dysmorphic features are absent or subtle, and major malformations are rare. Feeding difficulties are reported in the newborn period.Chromosome region 15q11q13, known for its instability, is highly susceptible to clinically relevant genomic rearrangements, such as supernumerary marker chromosomes formed by the inverted duplication of proximal chromosome 15. Inv dup(15) results in tetrasomy 15p and partial tetrasomy 15q. The large rearrangements, containing the Prader-Willi/Angelman syndrome critical region (PWS/ASCR), are responsible for the inv dup(15) or idic(15) syndrome. Diagnosis is achieved by standard cytogenetics and FISH analysis, using probes both from proximal chromosome 15 and from the PWS/ASCR. Microsatellite analysis on parental DNA or methylation analysis on the proband DNA, are also needed to detect the parent-of-origin of the inv dup(15) chromosome. Array CGH has been shown to provide a powerful approach for identifying and detecting the extent of the duplication. The possible

47 CFR 15.15 - General technical requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false General technical requirements. 15.15 Section 15.15 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.15 General technical requirements. (a) An intentional or unintentional radiator shall be...

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNulty, Nathan; Wu, Meng; Erickson, Alison L

The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many ofmore » these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising .90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism s 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

PubMed Central

McNulty, Nathan P.; Wu, Meng; Erickson, Alison R.; Pan, Chongle; Erickson, Brian K.; Martens, Eric C.; Pudlo, Nicholas A.; Muegge, Brian D.; Henrissat, Bernard; Hettich, Robert L.; Gordon, Jeffrey I.

2013-01-01

The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight

An antimicrobial peptide essential for bacterial survival in the nitrogen-fixing symbiosis.

PubMed

Kim, Minsoo; Chen, Yuhui; Xi, Jiejun; Waters, Christopher; Chen, Rujin; Wang, Dong

2015-12-08

In the nitrogen-fixing symbiosis between legume hosts and rhizobia, the bacteria are engulfed by a plant cell membrane to become intracellular organelles. In the model legume Medicago truncatula, internalization and differentiation of Sinorhizobium (also known as Ensifer) meliloti is a prerequisite for nitrogen fixation. The host mechanisms that ensure the long-term survival of differentiating intracellular bacteria (bacteroids) in this unusual association are unclear. The M. truncatula defective nitrogen fixation4 (dnf4) mutant is unable to form a productive symbiosis, even though late symbiotic marker genes are expressed in mutant nodules. We discovered that in the dnf4 mutant, bacteroids can apparently differentiate, but they fail to persist within host cells in the process. We found that the DNF4 gene encodes NCR211, a member of the family of nodule-specific cysteine-rich (NCR) peptides. The phenotype of dnf4 suggests that NCR211 acts to promote the intracellular survival of differentiating bacteroids. The greatest expression of DNF4 was observed in the nodule interzone II-III, where bacteroids undergo differentiation. A translational fusion of DNF4 with GFP localizes to the peribacteroid space, and synthetic NCR211 prevents free-living S. meliloti from forming colonies, in contrast to mock controls, suggesting that DNF4 may interact with bacteroids directly or indirectly for its function. Our findings indicate that a successful symbiosis requires host effectors that not only induce bacterial differentiation, but also that maintain intracellular bacteroids during the host-symbiont interaction. The discovery of NCR211 peptides that maintain bacterial survival inside host cells has important implications for improving legume crops.

Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population.

PubMed

Zou, Kai-Nan; Ren, Li-Jie; Ping, Yuan; Ma, Ke; Li, Hui; Cao, Yu; Zhou, Huai-Gu; Wei, Yi-Liang

2016-10-01

In recent years, forensic scientists have focused on the discrimination of body fluids using microbial signatures. In this study, we performed PCR-based detection of microbial signatures of vaginal fluid, saliva, and feces in a Han Chinese population. We investigated the 16S rRNA genes of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae in vaginal fluid, the 16S rRNA and the glucosyltransferase enzyme genes of Streptococcus salivarius and Streptococcus mutans in saliva, and the 16S rRNA genes of Enterococcus species, the RNA polymerase β-subunit gene of Bacteroides uniformis and Bacteroides vulgatus, and the α-1-6 mannanase gene of Bacteroides thetaiotaomicron in feces. As a result, the detection proportions of L. crispatus, L. gasseri, L. jensenii, L. iners, and A. vaginae were 15/16, 5/16, 8/16, 14/16, and 3/16 in 16 vaginal fluid donors, respectively. L. crispatus and L. jensenii were specifically detected in vaginal fluid; L. gasseri, L. iners, and A. vaginae were also detected in non-vaginal fluid. S. salivarius and S. mutans were not specifically detected in saliva. The detection proportions of Enterococcus species, B. uniformis, B. vulgatus, and B. thetaiotaomicron in 16 feces samples were 16/16, 12/16, 15/16, and 11/16, respectively. B. uniformis and B. thetaiotaomicron were specifically detected in feces. In addition, DNA samples prepared for the identification of body fluid can also be used for individual identification by short tandem repeat typing. The mean detection sensitivities of L. crispatus and L. jensenii were 0.362 and 0.249 pg/uL, respectively. In conclusion, L. crispatus, L. jensenii, B. uniformis, and B. thetaiotaomicron can be used as effective markers for forensic identification of vaginal fluid and feces. Copyright © 2016 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

15 CFR 15.11 - Scope.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Scope. 15.11 Section 15.11 Commerce and Foreign Trade Office of the Secretary of Commerce LEGAL PROCEEDINGS Testimony by Employees and the... procedures of the Department of Commerce regarding the testimony of employees, and former employees, as...

15 CFR 30.15 - Introduction.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Introduction. (a) For export shipments to foreign countries, the EEI is used both for statistical and for... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Introduction. 30.15 Section 30.15... control regulations, as well as the requirements of the statistical regulations of this part. For...

GUARD HOUSE AND BARRACKS, SECTIONS AND DETAILS. Navy Department, Bureau ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

GUARD HOUSE AND BARRACKS, SECTIONS AND DETAILS. Navy Department, Bureau of Yards & Docks, Navy Yard, Mare Island, CA. H.J. Brunnier, Structural Engineer, Sharon Building, San Francisco, CA. Sheet 7 of 15, accompanying specification Noy-4675. Submitted May 8, 1941, last revised July 7, 1941. Yards & Docks drawing no. 160692; P.W. (Public Works) drawing no. 10388-31; file no. 930-CR-7. Scale three eighths inch to one foot. 73 cm x 129 cm. Ink on vellum - Mare Island Naval Shipyard, Guard House & Barracks, Railroad Avenue near Eighteenth Street, Vallejo, Solano County, CA

NMR Identification and MS Conformation of the Scopolamine Neurotoxin

DTIC Science & Technology

2007-11-01

8217, Cm and Cm’ (labeled, respectively, as I-h, I-h’, l -m(eq) and I-W’(eq)), all with very similar intensities, suggest that the methyl group occurs at a...trimethylsilyl)- l - propane-sulfonic acid, were purchased from Sigma-Aldrich (St. Louis, MO). HPLC grade 8 ethanol and H20, and (-)-scopolamine hydrochloride...be bound directly to three, magnetically equivalent protons (1 in Figure 4), clearly representing a single methyl group. 15 g,h&il c, d&e f h&j kJ m m

46 CFR 76.15-15 - Piping.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 3 2013-10-01 2013-10-01 false Piping. 76.15-15 Section 76.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PASSENGER VESSELS FIRE PROTECTION EQUIPMENT Carbon Dioxide... forth in this paragraph. Only carbon dioxide or other inert gas shall be used for this test. (2) The...

46 CFR 76.15-15 - Piping.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 3 2012-10-01 2012-10-01 false Piping. 76.15-15 Section 76.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PASSENGER VESSELS FIRE PROTECTION EQUIPMENT Carbon Dioxide... forth in this paragraph. Only carbon dioxide or other inert gas shall be used for this test. (2) The...

46 CFR 76.15-15 - Piping.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 3 2014-10-01 2014-10-01 false Piping. 76.15-15 Section 76.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PASSENGER VESSELS FIRE PROTECTION EQUIPMENT Carbon Dioxide... forth in this paragraph. Only carbon dioxide or other inert gas shall be used for this test. (2) The...

Comparison of the benzoyl-DL-arginine-naphthylamide (BANA) test, DNA probes, and immunological reagents for ability to detect anaerobic periodontal infections due to Porphyromonas gingivalis, Treponema denticola, and Bacteroides forsythus.

PubMed Central

Loesche, W J; Lopatin, D E; Giordano, J; Alcoforado, G; Hujoel, P

1992-01-01

Most forms of periodontal disease are associated with the presence or overgrowth of anaerobic species that could include Treponema denticola, Porphyromonas gingivalis, and Bacteroides forsythus among others. These three organisms are among the few cultivable plaque species that can hydrolyze the synthetic trypsin substrate benzoyl-DL-arginine-naphthylamide (BANA). In turn, BANA hydrolysis by the plaque can be associated with periodontal morbidity and with the presence of these three BANA-positive organisms in the plaque. In this investigation, the results of the BANA test, which simultaneously detects one or more of these organisms, were compared with the detection of these organisms by (i) highly specific antibodies to P. gingivalis, T. denticola, and B. forsythus; (ii) whole genomic DNA probes to P. gingivalis and T. denticola; and (iii) culturing or microscopic procedures. The BANA test, the DNA probes, and an enzyme-linked immunosorbent assay or an indirect immunofluorescence assay procedure exhibited high sensitivities, i.e., 90 ot 96%, and high accuracies, i.e., 83 to 92%, in their ability to detect combinations of these organisms in over 200 subgingival plaque samples taken from the most periodontally diseased sites in 67 patients. This indicated that if P. gingivalis, T. denticola, and B. forsythus are appropriate marker organisms for an anaerobic periodontal infection, then the three detection methods are equally accurate in their ability to diagnose this infection. The same statement could not be made for the culturing approach, where accuracies of 50 to 62% were observed. PMID:1311335

Right and left partial iatrogenic injuries of the biliary tree. Therapeutic options.

PubMed

Mercado, Miguel Angel; Domínguez, Ismael; Arriola, Juan Carlos; Ramirez-Del Val, Fernando; Urencio, Miguel; Sánchez-Fernández, Norberto

2010-01-01

Bile duct injuries (BDI) have a wide array of presentation. Left partial injuries (Strasberg D) of the hepatic duct are the result of excessive traction, which dissects the hepatic hilum and provokes medial perforations without continuity loss. Right partial injuries (Strasberg A, B and C) are produced by direct damage to the hepatic duct or isolated injury to the right and accessory ducts. It is important to determine frequency, spectrum and treatment outcome of this BDI in the surgical scenario. Patients with BDI who underwent surgical treatment in our hospital were reviewed, right and left partial injuries were selected. Demographic, clinical and therapeutic data were analyzed. In a 16-year period, 405 patients underwent surgical treatment of BDI. 31 (8%) were classified as a left partial injury (Strasberg D): 23 injuries at the common hepatic duct treated with a Hepatojejunostomy (HJ); four at the confluence level which received a HJ with neoconfluence construction; two partial injuries in the left hepatic duct underwent a selective left HJ; and two complete occlusions of the left hepatic duct, one treated with a partial hepatectomy and the last case underwent a partial HJ. Right partial injuries (Strasberg A, B or C) were identified in 21 cases (5%), their treatment was tailored according to the type of BDI (conservative, selective HJ, or hepatectomy). In our series the frequency of left and right partial BDI injuries was 8% and 5%, respectively. The spectrum of analyzed injuries included four subtypes for the left partial and eight for the right partial lesions. Most BDI in the two analyzed groups presented concomitant devascularization of the extra-hepatic ducts, therefore receiving surgical treatment rather than endoscopic treatment was done.

CD1b-autoreactive T cells contribute to hyperlipidemia-induced skin inflammation in mice

PubMed Central

Bagchi, Sreya; He, Ying; Zhang, Hong; Cao, Liang; Van Rhijn, Ildiko; Moody, D. Branch; Gudjonsson, Johann E.

2017-01-01

A large proportion of human T cells are autoreactive to group 1 CD1 proteins, which include CD1a, CD1b, and CD1c. However, the physiological role of the CD1 proteins remains poorly defined. Here, we have generated a double-transgenic mouse model that expresses human CD1b and CD1c molecules (hCD1Tg) as well as a CD1b-autoreactive TCR (HJ1Tg) in the ApoE-deficient background (hCD1Tg HJ1Tg Apoe–/– mice) to determine the role of CD1-autoreactive T cells in hyperlipidemia-associated inflammatory diseases. We found that hCD1Tg HJ1Tg Apoe–/– mice spontaneously developed psoriasiform skin inflammation characterized by T cell and neutrophil infiltration and a Th17-biased cytokine response. Anti–IL-17A treatment ameliorated skin inflammation in vivo. Additionally, phospholipids and cholesterol preferentially accumulated in diseased skin and these autoantigens directly activated CD1b-autoreactive HJ1 T cells. Furthermore, hyperlipidemic serum enhanced IL-6 secretion by CD1b+ DCs and increased IL-17A production by HJ1 T cells. In psoriatic patients, the frequency of CD1b-autoreactive T cells was increased compared with that in healthy controls. Thus, this study has demonstrated the pathogenic role of CD1b-autoreactive T cells under hyperlipidemic conditions in a mouse model of spontaneous skin inflammation. As a large proportion of psoriatic patients are dyslipidemic, this finding is of clinical significance and indicates that self-lipid–reactive T cells might serve as a possible link between hyperlipidemia and psoriasis. PMID:28463230

"What Is a Step?" Differences in How a Step Is Detected among Three Popular Activity Monitors That Have Impacted Physical Activity Research.

PubMed

John, Dinesh; Morton, Alvin; Arguello, Diego; Lyden, Kate; Bassett, David

2018-04-15

(1) Background: This study compared manually-counted treadmill walking steps from the hip-worn DigiwalkerSW200 and OmronHJ720ITC, and hip and wrist-worn ActiGraph GT3X+ and GT9X; determined brand-specific acceleration amplitude (g) and/or frequency (Hz) step-detection thresholds; and quantified key features of the acceleration signal during walking. (2) Methods: Twenty participants (Age: 26.7 ± 4.9 years) performed treadmill walking between 0.89-to-1.79 m/s (2-4 mph) while wearing a hip-worn DigiwalkerSW200, OmronHJ720ITC, GT3X+ and GT9X, and a wrist-worn GT3X+ and GT9X. A DigiwalkerSW200 and OmronHJ720ITC underwent shaker testing to determine device-specific frequency and amplitude step-detection thresholds. Simulated signal testing was used to determine thresholds for the ActiGraph step algorithm. Steps during human testing were compared using bias and confidence intervals. (3) Results: The OmronHJ720ITC was most accurate during treadmill walking. Hip and wrist-worn ActiGraph outputs were significantly different from the criterion. The DigiwalkerSW200 records steps for movements with a total acceleration of ≥1.21 g. The OmronHJ720ITC detects a step when movement has an acceleration ≥0.10 g with a dominant frequency of ≥1 Hz. The step-threshold for the ActiLife algorithm is variable based on signal frequency. Acceleration signals at the hip and wrist have distinctive patterns during treadmill walking. (4) Conclusions: Three common research-grade physical activity monitors employ different step-detection strategies, which causes variability in step output.

“What Is a Step?” Differences in How a Step Is Detected among Three Popular Activity Monitors That Have Impacted Physical Activity Research

PubMed Central

John, Dinesh; Arguello, Diego; Lyden, Kate; Bassett, David

2018-01-01

(1) Background: This study compared manually-counted treadmill walking steps from the hip-worn DigiwalkerSW200 and OmronHJ720ITC, and hip and wrist-worn ActiGraph GT3X+ and GT9X; determined brand-specific acceleration amplitude (g) and/or frequency (Hz) step-detection thresholds; and quantified key features of the acceleration signal during walking. (2) Methods: Twenty participants (Age: 26.7 ± 4.9 years) performed treadmill walking between 0.89-to-1.79 m/s (2–4 mph) while wearing a hip-worn DigiwalkerSW200, OmronHJ720ITC, GT3X+ and GT9X, and a wrist-worn GT3X+ and GT9X. A DigiwalkerSW200 and OmronHJ720ITC underwent shaker testing to determine device-specific frequency and amplitude step-detection thresholds. Simulated signal testing was used to determine thresholds for the ActiGraph step algorithm. Steps during human testing were compared using bias and confidence intervals. (3) Results: The OmronHJ720ITC was most accurate during treadmill walking. Hip and wrist-worn ActiGraph outputs were significantly different from the criterion. The DigiwalkerSW200 records steps for movements with a total acceleration of ≥1.21 g. The OmronHJ720ITC detects a step when movement has an acceleration ≥0.10 g with a dominant frequency of ≥1 Hz. The step-threshold for the ActiLife algorithm is variable based on signal frequency. Acceleration signals at the hip and wrist have distinctive patterns during treadmill walking. (4) Conclusions: Three common research-grade physical activity monitors employ different step-detection strategies, which causes variability in step output. PMID:29662048

A deletion in the chromosome of Bacteroides thetaiotaomicron that abolishes production of chondroitinase II does not affect survival of the organism in gastrointestinal tracts of exgermfree mice.

PubMed Central

Salyers, A A; Guthrie, E P

1988-01-01

Bacteroides thetaiotaomicron, an obligate anaerobe normally found in high concentrations in the human colon, is one of the few colon bacteria that can ferment host mucopolysaccharides such as chondroitin sulfate. Previously, we found that a directed insertional mutation in the gene that codes for the chondroitinase II gene of B. thetaiotaomicron did not affect growth on chondroitin sulfate despite the fact that chondroitinase II accounts for 70% of the total cellular chondroitinase activity. Thus, the chondroitinase II gene did not seem to contribute significantly to growth on chondroitin sulfate when the bacteria were grown in laboratory medium. To determine whether this enzyme is important for bacteria growing in the intestinal tract, we tested the ability of a strain that does not produce chondroitinase II to colonize the intestinal tracts of germfree mice and to compete with wild-type B. thetaiotaomicron. The mutant used in these experiments carried a 0.5-kilobase deletion in the chondroitinase II gene and was constructed so that, unlike the original insertion mutant, it contained no exogenous DNA. The deletion mutant colonized the intestinal tracts of germfree mice at the same levels as the wild type. When a mixture of the deletion mutant and wild type was used to colonize germfree mice, the percent wild type, measured by colony hybridization with the deleted 0.5-kilobase fragment as the hybridization probe, did not rise to 100% even after periods as long as 9 weeks. In most experiments, the percent wild type did not rise significantly above the percent in the original mixture.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:3140726

Contribution of enzymatic properties, cell permeability, and enzyme expression to microbiological activities of beta-lactams in three Bacteroides fragilis isolates that harbor a metallo-beta-lactamase gene.

PubMed

Rasmussen, B A; Yang, Y; Jacobus, N; Bush, K

1994-09-01

The metallo-beta-lactamase gene, ccrA, has been cloned from three clinical isolates of Bacteroides fragilis, TAL3636, QMCN3, and QMCN4. Although all three isolates harbored a gene encoding a potent beta-lactamase, the MICs of benzylpenicillin, piperacillin, cefotaxime, ceftazidime, imipenem, and biapenem for the three isolates varied from 4- to > 128-fold. QMCN4 was the most susceptible of the three isolates, followed by QMCN3. TAL3636 was resistant to all of the beta-lactams. Previous DNA sequence analysis of the three ccrA genes revealed that the enzymes differed at 5 amino acid residues (B. A. Rasmussen, Y. Gluzman, and F. P. Tally, Mol. Microbiol. 5:1211-1219, 1991). Biochemical characterization of the three enzymes revealed only small differences in kcat and Km values for the majority of beta-lactams tested. Thus, the 5 amino acid substitutions affected the hydrolyzing activity of the enzymes only modestly. Crypticity differences between the three isolates showed that QMCN4 was the least permeable of the isolates to cephaloridine, followed by TAL3636, and that QMCN3 was highly permeable to cephaloridine. Therefore, neither catalytic activity nor permeability was a major contributor to the dramatic differences in the MICs. Instead, microbiological susceptibility was closely related to the level of metallo-beta-lactamase present in each isolate. Both biochemical and physical studies indicated that TAL3636 produced 5- to 10-fold and 50- to 100-fold more metallo-beta-lactamase than QMCN3 and QMCN4, respectively. Therefore, the level of CcrA enzyme production is the dominant contributing factor to high-level resistance among strains harboring a ccrA gene.

Temporal patterns of genetic variation across a 9-year-old aerial seed bank of the shrub Banksia hookeriana (Proteaceae).

PubMed

Barrett, Luke G; He, Tianhua; Lamont, Byron B; Krauss, Siegfried L

2005-11-01

The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (P(p)) and Shannon's index (I), increased slightly within the seed bank over time, while gene diversity (H(j)), did not change. P(p), I, and H(j) all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for H(j) or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.

Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent

PubMed Central

2013-01-01

Background The intestinal mucus layer plays a key role in the maintenance of host-microbiota homeostasis. To document the crosstalk between the host and microbiota, we used gnotobiotic models to study the influence of two major commensal bacteria, Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii, on this intestinal mucus layer. B. thetaiotaomicron is known to use polysaccharides from mucus, but its effect on goblet cells has not been addressed so far. F. prausnitzii is of particular physiological importance because it can be considered as a sensor and a marker of human health. We determined whether B. thetaiotaomicron affected goblet cell differentiation, mucin synthesis and glycosylation in the colonic epithelium. We then investigated how F. prausnitzii influenced the colonic epithelial responses to B. thetaiotaomicron. Results B. thetaiotaomicron, an acetate producer, increased goblet cell differentiation, expression of mucus-related genes and the ratio of sialylated to sulfated mucins in mono-associated rats. B. thetaiotaomicron, therefore, stimulates the secretory lineage, favoring mucus production. When B. thetaiotaomicron was associated with F. prausnitzii, an acetate consumer and a butyrate producer, the effects on goblet cells and mucin glycosylation were diminished. F. prausnitzii, by attenuating the effects of B. thetaiotaomicron on mucus, may help the epithelium to maintain appropriate proportions of different cell types of the secretory lineage. Using a mucus-producing cell line, we showed that acetate up-regulated KLF4, a transcription factor involved in goblet cell differentiation. Conclusions B. thetaiotaomicron and F. prausnitzii, which are metabolically complementary, modulate, in vivo, the intestinal mucus barrier by modifying goblet cells and mucin glycosylation. Our study reveals the importance of the balance between two main commensal bacteria in maintaining colonic epithelial homeostasis via their respective effects on mucus. PMID

Nitrogen fixation in transposon mutants from Bradyrhizobium japonicum USDA 110 impaired in nitrate reductase.

PubMed

Camacho, María; Burgos, Araceli; Chamber-Pérez, Manuel A

2003-04-01

Tn5 transposon mutagenesis was carried out in Bradyrhizobium japonicum strain USDA 110 to produce defective mutants. From over one thousand clones expressing low levels of nitrate reductase activity as free-living bacteria, approximately five percent had significantly different ratios of nodulation, N2 fixation or nitrate reductase activity compared to the wild strain when determined in bacteroids from soybean nodules. Tn5 insertions were checked previously and mutants were arranged into four different groups. Only one of these groups, designated AN, was less effective at N2 fixation than the wild strain, suggesting a mutation in a domain shared by nitrogenase and NR. The remaining groups of insertions successfully nodulated and were as effective at N2 fixation as the wild strain, but showed diminished ability to reduce nitrate both in nodules and in the isolated bacteroids when assayed in vitro with NADH or methyl viologen as electron donors. PCR amplification demonstrated that Tn5 insertions took place in different genes on each mutant group and the type of mutant (CC) expressing almost no nitrate reductase activity under all treatments seemed to possess transposable elements in two genes. Induction of nitrate reductase activity by nitrate was observed only in those clones expressing a low constitutive activity (AN and AE). Nitrate reductase activity in bacteroids along nodule growth decreased in all groups including the ineffective AN group, whose nodulation was highly inhibited by nitrate at 5 mmol/L N. Host-cultivar interaction seemed to influence the regulation of nitrate reductase activity in bacteroids. Total or partial repression of nitrate reductase activity in bacteroids unaffected by N2 fixation (CC, AJ and AE groups) improved nodule resistance to nitrate and N yields of shoots over those of the wild strain. These observations may suggest that some of the energy supplied to bacteroids was wasted by its constitutive NRA.

Bacteroidaceae in Thromboembolic Disease: Effects of Cell Wall Components on Blood Coagulation In Vivo and In Vitro

PubMed Central

Bjornson, H. S.; Hill, E. O.

1973-01-01

The effects of Bacteroides sp., Fusobacterium mortiferum, Bacteroides fragilis, and Sphaerophorus necrophorus on various parameters of blood coagulation in vivo and in vitro were determined and compared to the coagulation effects of Escherichia coli and Salmonella minnesota, wild type and R595. Intravenous injection of washed cells, culture filtrate, lipopolysaccharide, or lipid A of the anaerobic gram-negative microorganisms into mice resulted in acceleration of coagulation. Lipopolysaccharide and lipid A of the anaerobic microorganisms had no apparent effect on circulating platelets in mice or rabbits and did not cause aggregation of human platelets in vitro. Washed cells, lipopolysaccharide, and lipid A of Bacteroides sp. and F. mortiferum also significantly accelerated the clotting time of recalcified platelet poor normal human plasma and C6-deficient rabbit plasma. Lipid A, but not lipopolysaccharide, of E. coli and washed cells of S. minnesota R595 accelerated coagulation by a similar mechanism. These results indicated that Bacteroides sp. and F. mortiferum can accelerate blood coagulation in vivo and in vitro by a mechanism which does not involve platelets or terminal components of complement. PMID:4594118

15 CFR 752.15 - Export clearance.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 2 2013-01-01 2013-01-01 false Export clearance. 752.15 Section 752.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE EXPORT ADMINISTRATION REGULATIONS SPECIAL...

15 CFR 752.15 - Export clearance.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 2 2011-01-01 2011-01-01 false Export clearance. 752.15 Section 752.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE EXPORT ADMINISTRATION REGULATIONS SPECIAL...

15 CFR 752.15 - Export clearance.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 2 2014-01-01 2014-01-01 false Export clearance. 752.15 Section 752.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE EXPORT ADMINISTRATION REGULATIONS SPECIAL...

15 CFR 752.15 - Export clearance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Export clearance. 752.15 Section 752... OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE EXPORT ADMINISTRATION REGULATIONS SPECIAL COMPREHENSIVE LICENSE § 752.15 Export clearance. (a) Shipper's Export Declaration (SED) or Automated Export...

15 CFR 719.15 - Procedural stipulations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Procedural stipulations. 719.15 Section 719.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS...

15 CFR 719.15 - Procedural stipulations.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 2 2011-01-01 2011-01-01 false Procedural stipulations. 719.15 Section 719.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE CHEMICAL WEAPONS CONVENTION REGULATIONS...

15 CFR 285.15 - Obtaining documents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Obtaining documents. 285.15 Section 285.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY, DEPARTMENT OF COMMERCE ACCREDITATION AND ASSESSMENT PROGRAMS NATIONAL...

15 CFR 285.15 - Obtaining documents.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Obtaining documents. 285.15 Section 285.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY, DEPARTMENT OF COMMERCE ACCREDITATION AND ASSESSMENT PROGRAMS NATIONAL...

15 CFR 285.15 - Obtaining documents.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Obtaining documents. 285.15 Section 285.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY, DEPARTMENT OF COMMERCE ACCREDITATION AND ASSESSMENT PROGRAMS NATIONAL...

15 CFR 285.15 - Obtaining documents.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Obtaining documents. 285.15 Section 285.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY, DEPARTMENT OF COMMERCE ACCREDITATION AND ASSESSMENT PROGRAMS NATIONAL...

Bacteroides Fragilis OmpA: Utility as a Live Vaccine Vector for Biodefense Agents

DTIC Science & Technology

2008-01-01

of handling diseases in large populations. Studies of the immune system and vaccine effectiveness have shown that the ideal way to induce a...the past 15 years, experimental bacterial vaccine vectors have been produced that elicit immune responses against bacterial, viral, protozoan and...given orally, and they can be treated with antibiotics if desired and they effectively induce both humoral and cellular responses. If the organism

46 CFR 34.15-15 - Piping-T/ALL.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Piping-T/ALL. 34.15-15 Section 34.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS FIREFIGHTING EQUIPMENT Carbon Dioxide Extinguishing Systems, Details § 34.15-15 Piping—T/ALL. (a) The piping, valves, and fittings shall have a bursting...

Strategies for Monitoring the Performance of DNAPL Source Zone Remedies. Technical/Regulatory Guidelines

DTIC Science & Technology

2004-08-01

Vinegar , 2002; Bierschenk, et al., 2004; Baker and Kuhlman, 2002). It should be noted that the presence of even small amounts of liquid water will limit...Bioremediation of Trichloroethene.” Environmental Science and Technology, 36(10):2262–68. Stegemeier, G.L., and H.J. Vinegar . 2001. “Thermal Conduction...1134. Vinegar , H.J., G.L. Stegemeier, F.G. Carl, J.D. Stevenson, and R.J. Dudley. 1999. “In Situ Thermal Desorption of Soils Impacted with Chlorinated

Effect of the refractive index on the hawking temperature: an application of the Hamilton-Jacobi method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakalli, I., E-mail: izzet.sakalli@emu.edu.tr; Mirekhtiary, S. F., E-mail: fatemeh.mirekhtiary@emu.edu.tr

2013-10-15

Hawking radiation of a non-asymptotically flat 4-dimensional spherically symmetric and static dilatonic black hole (BH) via the Hamilton-Jacobi (HJ) method is studied. In addition to the naive coordinates, we use four more different coordinate systems that are well-behaved at the horizon. Except for the isotropic coordinates, direct computation by the HJ method leads to the standard Hawking temperature for all coordinate systems. The isotropic coordinates allow extracting the index of refraction from the Fermat metric. It is explicitly shown that the index of refraction determines the value of the tunneling rate and its natural consequence, the Hawking temperature. The isotropicmore » coordinates in the conventional HJ method produce a wrong result for the temperature of the linear dilaton. Here, we explain how this discrepancy can be resolved by regularizing the integral possessing a pole at the horizon.« less

Force field refinement from NMR scalar couplings

NASA Astrophysics Data System (ADS)

Huang, Jing; Meuwly, Markus

2012-03-01

NMR observables contain valuable information about the protein dynamics sampling a high-dimensional potential energy surface. Depending on the observable, the dynamics is sensitive to different time-windows. Scalar coupling constants hJ reflect the pico- to nanosecond motions associated with the intermolecular hydrogen bond network. Including an explicit H-bond in the molecular mechanics with proton transfer (MMPT) potential allows us to reproduce experimentally determined hJ couplings to within 0.02 Hz at best for ubiquitin and protein G. This is based on taking account of the chemically changing environment by grouping the H-bonds into up to seven classes. However, grouping them into two classes already reduces the RMSD between computed and observed hJ couplings by almost 50%. Thus, using ensemble-averaged data with two classes of H-bonds leads to substantially improved scalar couplings from simulations with accurate force fields.

Accuracy of physical activity monitors in pregnant women.

PubMed

Connolly, Christopher P; Coe, Dawn P; Kendrick, Jo M; Bassett, David R; Thompson, Dixie L

2011-06-01

To determine the step count accuracy of three pedometers and one accelerometer in pregnant women during treadmill walking. Participants were 30 women in the second or third trimester (20-34 wk) who were screened for pregnancy-related risk factors. Each participant was fitted with a belt containing three physical activity monitors: Yamax Digiwalker SW-200 (DW), New Lifestyles NL 2000 (NL), and GT3X ActiGraph accelerometer (ACT). The Omron HJ-720ITC (HJ) was placed in the pants' front pocket. Participants walked at 54, 67, 80, and 94 m · min for 2 min each. Actual steps were determined by an investigator using a hand-tally counter. The mean percent of steps recorded was calculated for each device at each speed and compared. Pearson correlations were used to determine the effect of body mass index and tilt angle on pedometer accuracy. There was a significant interaction between speed and device (F9,20 = 7.574, P < 0.001). Across all speeds, the NL and HJ had the lowest error. The ACT and DW underestimated the actual steps taken, particularly at the slower walking speeds. At 54 m · min, the ACT averaged 77.5% of steps and the DW averaged 56.9% of steps. Significant differences in the mean percent of steps recorded were found between devices at all speeds. Body mass index was only significantly correlated with percent of steps recorded by the NL, and there were no significant correlations between steps recorded and tilt angle. In pregnant women, the ACT and DW had more error than the NL and HJ. On the basis of these results, the NL and HJ should be considered for use in further research studies and physical activity programs that focus on walking during pregnancy.

15 CFR 90.15 - Decision by Director.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Decision by Director. 90.15 Section 90.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade BUREAU OF THE CENSUS, DEPARTMENT OF COMMERCE PROCEDURE FOR CHALLENGING CERTAIN POPULATION AND INCOME ESTIMATES § 90.15 Decision by...

15 CFR 90.15 - Decision by Director.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Decision by Director. 90.15 Section 90.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade BUREAU OF THE CENSUS, DEPARTMENT OF COMMERCE PROCEDURE FOR CHALLENGING CERTAIN POPULATION AND INCOME ESTIMATES § 90.15 Decision by...

15 CFR 90.15 - Decision by Director.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Decision by Director. 90.15 Section 90.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade BUREAU OF THE CENSUS, DEPARTMENT OF COMMERCE PROCEDURE FOR CHALLENGING CERTAIN POPULATION AND INCOME ESTIMATES § 90.15 Decision by...

15 CFR 90.15 - Decision by Director.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Decision by Director. 90.15 Section 90.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade BUREAU OF THE CENSUS, DEPARTMENT OF COMMERCE PROCEDURE FOR CHALLENGING CERTAIN POPULATION AND INCOME ESTIMATES § 90.15 Decision by...

Electrochemical control of a DNA Holliday Junction nanoswitch by Mg2+ ions.

PubMed

Ferapontova, E E; Mountford, C P; Crain, J; Buck, A H; Dickinson, P; Beattie, J S; Ghazal, P; Terry, J G; Walton, A J; Mount, A R

2008-11-15

The molecular conformation of a synthetic branched, 4-way DNA Holliday junction (HJ) was electrochemically switched between the open and closed (stacked) conformers. Switching was achieved by electrochemically induced quantitative release of Mg(2+) ions from the oxidised poly(N-methylpyrrole) film (PPy), which contained polyacrylate as an immobile counter anion and Mg(2+) ions as charge compensating mobile cations. This increase in the Mg(2+) concentration screened the electrostatic repulsion between the widely separated arms in the open HJ configuration, inducing switching to the closed conformation. Upon electrochemical reduction of PPy, entrapment of Mg(2+) ions back into the PPy film induced the reverse HJ switching from the closed to open state. The conformational transition was monitored using fluorescence resonance energy transfer (FRET) between donor and acceptor dyes each located at the terminus of one of the arms. The demonstrated electrochemical control of the conformation of the used probe-target HJ complex, previously reported as a highly sequence specific nanodevice for detecting of unlabelled target [Buck, A.H., Campbell, C.J., Dickinson, P., Mountford, C.P., Stoquert, H.C., Terry, J.G., Evans, S.A.G., Keane, L., Su, T.J., Mount, A.R., Walton, A.J., Beattie, J.S., Crain, J., Ghazal, P., 2007. Anal. Chem., 79, 4724-4728], allows the development of electronically addressable DNA nanodevices and label-free gene detection assays.

Lake Michigan Storm: Wave and Water Level Modeling

DTIC Science & Technology

2012-11-01

does appear the ice implementation does well to replicate either iced (flagged for ice coverage), or for a low wave energy environment. Granted there...Jensen, D.T. Resio, R.A. Luettich, C. Dawson, V.J. Cardone , A.T. Cox, M.D. Powell, H.J. Westerink, and H.J. Roberts. (2010). “A high resolution coupled...coast,” In Preparation, US Army Engineer Research and Development Center, Vicksburg, MS. ERDC/CHL TR-12-26 310 Jensen, R.E., V.J. Cardone , and A.T

Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women.

PubMed

Dewulf, Evelyne M; Cani, Patrice D; Claus, Sandrine P; Fuentes, Susana; Puylaert, Philippe G B; Neyrinck, Audrey M; Bindels, Laure B; de Vos, Willem M; Gibson, Glenn R; Thissen, Jean-Paul; Delzenne, Nathalie M

2013-08-01

To highlight the contribution of the gut microbiota to the modulation of host metabolism by dietary inulin-type fructans (ITF prebiotics) in obese women. A double blind, placebo controlled, intervention study was performed with 30 obese women treated with ITF prebiotics (inulin/oligofructose 50/50 mix; n=15) or placebo (maltodextrin; n=15) for 3 months (16 g/day). Blood, faeces and urine sampling, oral glucose tolerance test, homeostasis model assessment and impedancemetry were performed before and after treatment. The gut microbial composition in faeces was analysed by phylogenetic microarray and qPCR analysis of 16S rDNA. Plasma and urine metabolic profiles were analysed by 1H-NMR spectroscopy. Treatment with ITF prebiotics, but not the placebo, led to an increase in Bifidobacterium and Faecalibacterium prausnitzii; both bacteria negatively correlated with serum lipopolysaccharide levels. ITF prebiotics also decreased Bacteroides intestinalis, Bacteroides vulgatus and Propionibacterium, an effect associated with a slight decrease in fat mass and with plasma lactate and phosphatidylcholine levels. No clear treatment clustering could be detected for gut microbial analysis or plasma and urine metabolomic profile analyses. However, ITF prebiotics led to subtle changes in the gut microbiota that may importantly impact on several key metabolites implicated in obesity and/or diabetes. ITF prebiotics selectively changed the gut microbiota composition in obese women, leading to modest changes in host metabolism, as suggested by the correlation between some bacterial species and metabolic endotoxaemia or metabolomic signatures.

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii.

PubMed

Zhang, Wenya; Li, Na; Tang, Xiaolong; Liu, Naifa; Zhao, Wei

2018-05-01

High altitude is an important driving force in animal evolution. However, the effect of altitude on gut microbial communities in reptiles has not been examined in detail. Here, we investigated the intestinal microbiota of three populations of the lizard Phrynocephalus vlangalii living at different altitudes using 16S rRNA gene sequencing. Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla. Bacteroides , Odoribacter , and Parabacteroides were the most abundant genera. Significant differences in the intestinal microbiota composition were found among the three populations from different altitudes. The proportions of Verrucomicrobia and Akkermansia decreased, whereas Bacteroides increased significantly with altitude. Greater abundance of Bacteroides at higher altitude led to the fractional increase in the phylum Bacteroides relative to other phyla. Hypoxia may be the main factor that caused intestinal microbiota variation in P. vlangalii along the altitude gradient. Overall, our study suggested that the community composition and structure of intestinal microbiota of the lizard P. vlangalii varied along altitudes, and such differences likely play a certain role in highland adaptation. Our findings warrant a further study that would determine whether ambient and body temperatures play a key role in the modulation of intestinal microbiota in reptiles.

A low switching voltage organic-on-inorganic heterojunction memory element utilizing a conductive polymer fuse on a doped silicon substrate

NASA Astrophysics Data System (ADS)

Smith, Shawn; Forrest, Stephen R.

2004-06-01

We present a simple, nonvolatile, write-once-read-many-times (WORM) memory device utilizing an organic-on-inorganic heterojunction (OI-HJ) diode with a conductive polymer fuse consisting of polyethylene dioxythiophene:polysterene sulfonic acid (PEDOT:PSS) forming one side of the rectifying junction. Current transients are used to change the fuse from a conducting to a nonconducting state to record a logical "1" or "0", while the nonlinearity of the OI-HJ allows for passive matrix memory addressing. The device switches at 2 and 4 V for 50 nm thick PEDOT:PSS films on p-type Si and n-type Si, respectively. This is significantly lower than the switching voltage used in PEDOT:PSS/p-i-n Si memory elements [J. Appl Phys. 94, 7811 (2003)]. The switching results in a permanent reduction of forward-bias current by approximately five orders of magnitude. These results suggest that the OI-HJ structure has potential for use in low-cost passive matrix WORM memories for archival storage applications.

[Accuracy improvement of spectral classification of crop using microwave backscatter data].

PubMed

Jia, Kun; Li, Qiang-Zi; Tian, Yi-Chen; Wu, Bing-Fang; Zhang, Fei-Fei; Meng, Ji-Hua

2011-02-01

In the present study, VV polarization microwave backscatter data used for improving accuracies of spectral classification of crop is investigated. Classification accuracy using different classifiers based on the fusion data of HJ satellite multi-spectral and Envisat ASAR VV backscatter data are compared. The results indicate that fusion data can take full advantage of spectral information of HJ multi-spectral data and the structure sensitivity feature of ASAR VV polarization data. The fusion data enlarges the spectral difference among different classifications and improves crop classification accuracy. The classification accuracy using fusion data can be increased by 5 percent compared to the single HJ data. Furthermore, ASAR VV polarization data is sensitive to non-agrarian area of planted field, and VV polarization data joined classification can effectively distinguish the field border. VV polarization data associating with multi-spectral data used in crop classification enlarges the application of satellite data and has the potential of spread in the domain of agriculture.

15 CFR 325.15 - Relinquishing a certificate.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Relinquishing a certificate. 325.15 Section 325.15 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE MISCELLANEOUS REGULATIONS EXPORT TRADE CERTIFICATES...

48 CFR 6101.15 - Depositions [Rule 15].

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Depositions [Rule 15..., GENERAL SERVICES ADMINISTRATION CONTRACT DISPUTE CASES 6101.15 Depositions [Rule 15]. (a) When depositions... deposition upon oral examination or written questions before an officer authorized to administer oaths at the...

48 CFR 6101.15 - Depositions [Rule 15].

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 7 2011-10-01 2011-10-01 false Depositions [Rule 15..., GENERAL SERVICES ADMINISTRATION CONTRACT DISPUTE CASES 6101.15 Depositions [Rule 15]. (a) When depositions... deposition upon oral examination or written questions before an officer authorized to administer oaths at the...

46 CFR 72.15-15 - Ventilation for closed spaces.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 3 2011-10-01 2011-10-01 false Ventilation for closed spaces. 72.15-15 Section 72.15-15... ARRANGEMENT Ventilation § 72.15-15 Ventilation for closed spaces. (a) All enclosed spaces within the vessel... spaces and for closing all doorways, ventilators and annular spaces around funnels and other openings to...

46 CFR 72.15-15 - Ventilation for closed spaces.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 3 2013-10-01 2013-10-01 false Ventilation for closed spaces. 72.15-15 Section 72.15-15... ARRANGEMENT Ventilation § 72.15-15 Ventilation for closed spaces. (a) All enclosed spaces within the vessel... spaces and for closing all doorways, ventilators and annular spaces around funnels and other openings to...

46 CFR 72.15-15 - Ventilation for closed spaces.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 3 2010-10-01 2010-10-01 false Ventilation for closed spaces. 72.15-15 Section 72.15-15... ARRANGEMENT Ventilation § 72.15-15 Ventilation for closed spaces. (a) All enclosed spaces within the vessel... spaces and for closing all doorways, ventilators and annular spaces around funnels and other openings to...

46 CFR 72.15-15 - Ventilation for closed spaces.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 3 2014-10-01 2014-10-01 false Ventilation for closed spaces. 72.15-15 Section 72.15-15... ARRANGEMENT Ventilation § 72.15-15 Ventilation for closed spaces. (a) All enclosed spaces within the vessel... spaces and for closing all doorways, ventilators and annular spaces around funnels and other openings to...

46 CFR 72.15-15 - Ventilation for closed spaces.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 3 2012-10-01 2012-10-01 false Ventilation for closed spaces. 72.15-15 Section 72.15-15... ARRANGEMENT Ventilation § 72.15-15 Ventilation for closed spaces. (a) All enclosed spaces within the vessel... spaces and for closing all doorways, ventilators and annular spaces around funnels and other openings to...

The Fumarate Reductase of Bacteroides thetaiotaomicron, unlike That of Escherichia coli, Is Configured so that It Does Not Generate Reactive Oxygen Species.

PubMed

Lu, Zheng; Imlay, James A

2017-01-03

The impact of oxidative stress upon organismal fitness is most apparent in the phenomenon of obligate anaerobiosis. The root cause may be multifaceted, but the intracellular generation of reactive oxygen species (ROS) likely plays a key role. ROS are formed when redox enzymes accidentally transfer electrons to oxygen rather than to their physiological substrates. In this study, we confirm that the predominant intestinal anaerobe Bacteroides thetaiotaomicron generates intracellular ROS at a very high rate when it is aerated. Fumarate reductase (Frd) is a prominent enzyme in the anaerobic metabolism of many bacteria, including B. thetaiotaomicron, and prior studies of Escherichia coli Frd showed that the enzyme is unusually prone to ROS generation. Surprisingly, in this study biochemical analysis demonstrated that the B. thetaiotaomicron Frd does not react with oxygen at all: neither superoxide nor hydrogen peroxide is formed. Subunit-swapping experiments indicated that this difference does not derive from the flavoprotein subunit at which ROS normally arise. Experiments with the related enzyme succinate dehydrogenase discouraged the hypothesis that heme moieties are responsible. Thus, resistance to oxidation may reflect a shift of electron density away from the flavin moiety toward the iron-sulfur clusters. This study shows that the autoxidizability of a redox enzyme can be suppressed by subtle modifications that do not compromise its physiological function. One implication is that selective pressures might enhance the oxygen tolerance of an organism by manipulating the electronic properties of its redox enzymes so they do not generate ROS. Whether in sediments or pathogenic biofilms, the structures of microbial communities are configured around the sensitivities of their members to oxygen. Oxygen triggers the intracellular formation of reactive oxygen species (ROS), and the sensitivity of a microbe to oxygen likely depends upon the rates at which ROS are formed

46 CFR 34.15-15 - Piping-T/ALL.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Piping-T/ALL. 34.15-15 Section 34.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS FIREFIGHTING EQUIPMENT Carbon Dioxide Extinguishing... applied as set forth in this paragraph. Only carbon dioxide or other inert gas shall be used for this test...

46 CFR 34.15-15 - Piping-T/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Piping-T/ALL. 34.15-15 Section 34.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS FIREFIGHTING EQUIPMENT Carbon Dioxide Extinguishing... applied as set forth in this paragraph. Only carbon dioxide or other inert gas shall be used for this test...

46 CFR 34.15-15 - Piping-T/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Piping-T/ALL. 34.15-15 Section 34.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS FIREFIGHTING EQUIPMENT Carbon Dioxide Extinguishing... applied as set forth in this paragraph. Only carbon dioxide or other inert gas shall be used for this test...

On a direct connection of the transition metal impurity levels to the band edge discontinuities in semiconductor heterojunctions

NASA Astrophysics Data System (ADS)

Langer, Jerzy M.; Heinrich, Helmut

1985-11-01

Our recent proposal of using the transition metal impurity levels to predict the isovalent heterojunction (HJ) band-edge discontinuities is further discussed. It is shown that for Ga 1-xAl xAs/GaAs heterojunctions most of the recent discontinuity data follow within experimental error the prediction of the ΔE cb: ΔE vb= 0.64:0.36 discontinuity ratio derived from the Fe 2+ level position in Ga 1-xAl xAs compound. Predictions of valence-band discontinuities for the other III-V and II-VI HJ systems are also given.

The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.

PubMed

Rezazadeh, Akram; Shahabi, Shahram; Bagheri, Morteza; Nabizadeh, Edris; Jazani, Nima Hosseini

2018-06-01

Chronic Urticaria is a common disorder which is defined by recurrent occurrence of wheals and sometimes angioedema. It has a notable influence on the patients' quality of life. Regulation of the immune system is one of the important roles of the gut microbiota. The effect of dysbiosis considering some members of gut microbiota in patients with chronic urticaria has been demonstrated in our previous study. Comparing the frequency and bacterial load of Lactobacillus, Bifidobacterium, and Bacteroides between patients with chronic urticaria and healthy controls. 20 patients with chronic urticaria and 20 age and sex matched healthy individuals were included in the present study. Stool samples were analyzed for determining the frequency and bacterial load of Lactobacillus, Bifidobacterium, and Bacteroides genera. There were no significant differences among the frequencies of detectable Lactobacillus, Bifidobacterium, or Bacteroides in stool samples of patients with chronic urticaria and healthy controls. The relative amounts of Lactobacillus and Bifidobacterium were significantly higher in fecal samples from controls compared to patients with chronic urticaria (P = 0.038 and 0.039, respectively). It is the first study on the implication of Lactobacillus, Bifidobacterium, and Bacteroides genera as gut microbiota members in patients with chronic urticaria. Copyright © 2018 Elsevier B.V. All rights reserved.

5-Nitroimidazole-derived Schiff bases and their copper(II) complexes exhibit potent antimicrobial activity against pathogenic anaerobic bacteria.

PubMed

Oliveira, Alexandre A; Oliveira, Ana P A; Franco, Lucas L; Ferencs, Micael O; Ferreira, João F G; Bachi, Sofia M P S; Speziali, Nivaldo L; Farias, Luiz M; Magalhães, Paula P; Beraldo, Heloisa

2018-05-07

In the present work a family of novel secnidazole-derived Schiff base compounds and their copper(II) complexes were synthesized. The antimicrobial activities of the compounds were evaluated against clinically important anaerobic bacterial strains. The compounds exhibited in vitro antibacterial activity against Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides ovatus, Parabacteroides distasonis and Fusubacterium nucleatum pathogenic anaerobic bacteria. Upon coordination to copper(II) the antibacterial activity significantly increased in several cases. Some derivatives were even more active than the antimicrobial drugs secnidazole and metronidazole. Therefore, the compounds under study are suitable for in vivo evaluation and the microorganisms should be classified as susceptible to them. Electrochemical studies on the reduction of the nitro group revealed that the compounds show comparable reduction potentials, which are in the same range of the bio-reducible drugs secnidazole and benznidazole. The nitro group reduction potential is more favorable for the copper(II) complexes than for the starting ligands. Hence, the antimicrobial activities of the compounds under study might in part be related to intracellular bio-reduction activation. Considering the increasing resistance rates of anaerobic bacteria against a wide range of antimicrobial drugs, the present work constitutes an important contribution to the development of new antibacterial drug candidates.

15 CFR 2008.15 - General restrictions on access.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 3 2013-01-01 2013-01-01 false General restrictions on access. 2008.15 Section 2008.15 Commerce and Foreign Trade Regulations Relating to Foreign Trade Agreements OFFICE OF THE UNITED STATES TRADE REPRESENTATIVE REGULATIONS TO IMPLEMENT E.O. 12065; OFFICE OF THE UNITED...

15 CFR 2008.15 - General restrictions on access.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 3 2011-01-01 2011-01-01 false General restrictions on access. 2008.15 Section 2008.15 Commerce and Foreign Trade Regulations Relating to Foreign Trade Agreements OFFICE OF THE UNITED STATES TRADE REPRESENTATIVE REGULATIONS TO IMPLEMENT E.O. 12065; OFFICE OF THE UNITED...

15 CFR 2008.15 - General restrictions on access.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false General restrictions on access. 2008.15 Section 2008.15 Commerce and Foreign Trade Regulations Relating to Foreign Trade Agreements OFFICE OF THE UNITED STATES TRADE REPRESENTATIVE REGULATIONS TO IMPLEMENT E.O. 12065; OFFICE OF THE UNITED...

15 CFR 2008.15 - General restrictions on access.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 3 2014-01-01 2014-01-01 false General restrictions on access. 2008.15 Section 2008.15 Commerce and Foreign Trade Regulations Relating to Foreign Trade Agreements OFFICE OF THE UNITED STATES TRADE REPRESENTATIVE REGULATIONS TO IMPLEMENT E.O. 12065; OFFICE OF THE UNITED...

15 CFR 2008.15 - General restrictions on access.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 15 Commerce and Foreign Trade 3 2012-01-01 2012-01-01 false General restrictions on access. 2008.15 Section 2008.15 Commerce and Foreign Trade Regulations Relating to Foreign Trade Agreements OFFICE OF THE UNITED STATES TRADE REPRESENTATIVE REGULATIONS TO IMPLEMENT E.O. 12065; OFFICE OF THE UNITED...

Thermodynamic Database for the NdO(1.5)-YO(1.5)-YbO(1.5)-ScO(1.5)-ZrO2 System

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Copland, Evan H.; Kaufman, Larry

2001-01-01

A database for YO(1.5)-NdO(1.5)-YbO(1.5)-ScO(1.5)-ZrO2 for ThermoCalc (ThermoCalc AB, Stockholm, Sweden) has been developed. The basis of this work is the YO(1.5)-ZrO2 assessment by Y. Du, Z. Jin, and P. Huang, 'Thermodynamic Assessment of the ZrO2-YO(1.5) System'. Experimentally only the YO(1.5)-ZrO2 system has been well-studied. All other systems are only approximately known. The major simplification in this work is the treatment of each single cation unit as a component. The pure liquid oxides are taken as reference states and two term lattice stability descriptions are used for each of the components. The limited experimental phase diagrams are reproduced.

15 CFR 14.15 - Metric system of measurement.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Metric system of measurement. 14.15... COMMERCIAL ORGANIZATIONS Pre-Award Requirements § 14.15 Metric system of measurement. The Metric Conversion... activities. Metric implementation may take longer where the use of the system is initially impractical or...

15 CFR 14.15 - Metric system of measurement.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Metric system of measurement. 14.15... COMMERCIAL ORGANIZATIONS Pre-Award Requirements § 14.15 Metric system of measurement. The Metric Conversion... activities. Metric implementation may take longer where the use of the system is initially impractical or...

15 CFR 14.15 - Metric system of measurement.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Metric system of measurement. 14.15... COMMERCIAL ORGANIZATIONS Pre-Award Requirements § 14.15 Metric system of measurement. The Metric Conversion... activities. Metric implementation may take longer where the use of the system is initially impractical or...

15 CFR 14.15 - Metric system of measurement.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Metric system of measurement. 14.15 Section 14.15 Commerce and Foreign Trade Office of the Secretary of Commerce UNIFORM ADMINISTRATIVE... system is the preferred measurement system for U.S. trade and commerce. The Act requires each Federal...

15 CFR 14.15 - Metric system of measurement.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Metric system of measurement. 14.15 Section 14.15 Commerce and Foreign Trade Office of the Secretary of Commerce UNIFORM ADMINISTRATIVE... system is the preferred measurement system for U.S. trade and commerce. The Act requires each Federal...

A new test of multivariate nonlinear causality

PubMed Central

Bai, Zhidong; Jiang, Dandan; Lv, Zhihui; Wong, Wing-Keung; Zheng, Shurong

2018-01-01

The multivariate nonlinear Granger causality developed by Bai et al. (2010) (Mathematics and Computers in simulation. 2010; 81: 5-17) plays an important role in detecting the dynamic interrelationships between two groups of variables. Following the idea of Hiemstra-Jones (HJ) test proposed by Hiemstra and Jones (1994) (Journal of Finance. 1994; 49(5): 1639-1664), they attempt to establish a central limit theorem (CLT) of their test statistic by applying the asymptotical property of multivariate U-statistic. However, Bai et al. (2016) (2016; arXiv: 1701.03992) revisit the HJ test and find that the test statistic given by HJ is NOT a function of U-statistics which implies that the CLT neither proposed by Hiemstra and Jones (1994) nor the one extended by Bai et al. (2010) is valid for statistical inference. In this paper, we re-estimate the probabilities and reestablish the CLT of the new test statistic. Numerical simulation shows that our new estimates are consistent and our new test performs decent size and power. PMID:29304085

High efficiency solar cells combining a perovskite and a silicon heterojunction solar cells via an optical splitting system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uzu, Hisashi, E-mail: Hisashi.Uzu@kaneka.co.jp, E-mail: npark@skku.edu; Ichikawa, Mitsuru; Hino, Masashi

2015-01-05

We have applied an optical splitting system in order to achieve very high conversion efficiency for a full spectrum multi-junction solar cell. This system consists of multiple solar cells with different band gap optically coupled via an “optical splitter.” An optical splitter is a multi-layered beam splitter with very high reflection in the shorter-wave-length range and very high transmission in the longer-wave-length range. By splitting the incident solar spectrum and distributing it to each solar cell, the solar energy can be managed more efficiently. We have fabricated optical splitters and used them with a wide-gap amorphous silicon (a-Si) solar cellmore » or a CH{sub 3}NH{sub 3}PbI{sub 3} perovskite solar cell as top cells, combined with mono-crystalline silicon heterojunction (HJ) solar cells as bottom cells. We have achieved with a 550 nm cutoff splitter an active area conversion efficiency of over 25% using a-Si and HJ solar cells and 28% using perovskite and HJ solar cells.« less

A new test of multivariate nonlinear causality.

PubMed

Bai, Zhidong; Hui, Yongchang; Jiang, Dandan; Lv, Zhihui; Wong, Wing-Keung; Zheng, Shurong

2018-01-01

The multivariate nonlinear Granger causality developed by Bai et al. (2010) (Mathematics and Computers in simulation. 2010; 81: 5-17) plays an important role in detecting the dynamic interrelationships between two groups of variables. Following the idea of Hiemstra-Jones (HJ) test proposed by Hiemstra and Jones (1994) (Journal of Finance. 1994; 49(5): 1639-1664), they attempt to establish a central limit theorem (CLT) of their test statistic by applying the asymptotical property of multivariate U-statistic. However, Bai et al. (2016) (2016; arXiv: 1701.03992) revisit the HJ test and find that the test statistic given by HJ is NOT a function of U-statistics which implies that the CLT neither proposed by Hiemstra and Jones (1994) nor the one extended by Bai et al. (2010) is valid for statistical inference. In this paper, we re-estimate the probabilities and reestablish the CLT of the new test statistic. Numerical simulation shows that our new estimates are consistent and our new test performs decent size and power.

Hydrothermal growth of n-ZnO films on a patterned p-GaN epilayer and its application in heterojunction light-emitting diodes

NASA Astrophysics Data System (ADS)

Ko, Rong-Ming; Wang, Shui-Jinn; Chen, Ching-Yi; Wu, Cheng-Han; Lin, Yan-Ru; Lo, Hsin-Ming

2017-04-01

The hydrothermal growth (HTG) of crystalline n-ZnO films on both the nonpatterned and patterned p-GaN epilayers with a honeycomb array of etched holes is demonstrated, and its application in n-ZnO/p-GaN heterojunction light-emitting diodes (HJ-LEDs) is reported. The results reveal that an HTG n-ZnO film on a patterned p-GaN layer exhibits a high-quality single crystal with FWHMs of 0.463 and 0.983° obtained from a ω-rocking curve and a ϕ-scan pattern, respectively, which are much better than those obtained on a nonpatterned p-GaN layer. In addition, the n-ZnO/patterned p-GaN HJ-LED exhibited a much better rectifying diode behavior owing to having a higher n-ZnO film crystallinity quality and an improved interface with the p-GaN layer. Strong violet and violet-blue lights emitted from the n-ZnO/patterned p-GaN HJ-LED at around 405, 412, and 430 nm were analyzed.

Hormones, metabolites, and reproduction in Holsteins, Jerseys, and their crosses.

PubMed

Brown, K L; Cassell, B G; McGilliard, M L; Hanigan, M D; Gwazdauskas, F C

2012-02-01

Holsteins (HH), Jerseys (JJ), and their crosses in first (n=157) and second (n=107) lactation were used to determine if reproduction, progesterone (P4), insulin-like growth factor 1 (IGF-1), insulin, nonesterified fatty acids (NEFA), and milk production differed between genetic groups. Thirty-four cows were Holstein-Jersey (HJ) crosses, 46 were Jersey-Holstein (JH) crosses, 48 were purebred Holsteins (HH), and 29 were purebred Jerseys (JJ) in first lactation, whereas the second-lactation animals included 23 HJ, 35 JH, 35 HH, and 14 JJ. Blood samples were collected weekly for the first 10 wk postpartum. Analyses were conducted using the MIXED, chi-square, and GLIMMIX procedures (SAS Institute Inc., Cary, NC). Seasons of calving were cold (November to May) and hot (June to October) and were combined with year to form 8 year-seasons. Days open and number of services were affected by genetic group. The HH were open 169±8 d, which was greater than HJ (143±9 d), JJ (132±10 d), and JH (127±8 d). The HH had 2.4±0.1 services per pregnancy, which was greater than JH (1.9±0.1), but not different from HJ (2.1±0.2) or JJ (2.1±0.2). Concentrations of NEFA were greater in lactation 2 (0.52±0.02 mEq/L) than in lactation 1 (0.45±0.02 mEq/L) and decreased over the 10-wk period. Concentrations of NEFA were greater in the cold season except in yr 3. Insulin in lactation 1 (0.81±0.03 ng/mL) was greater than in lactation 2 (0.72±0.03 ng/mL); insulin decreased to wk 2 then gradually increased. The HJ had the greatest insulin concentrations (0.87±0.04 ng/mL) and the JJ had the lowest (0.66±0.04 ng/mL), and IGF-1 gradually increased over the 10-wk period. Milk production (actual yield in the first 305 d, not adjusted for fat and protein) was affected by genetic group, lactation number, year-season, and wk 1 insulin. The HH produced 10,348±207 kg of milk, which was greater than the HJ (9,129±230 kg), the JH (9,384±190 kg), and the JJ (7,080±240 kg). Milk production in

Task Force Delay Study. Denver Stapleton International Airport, Volume II.

DTIC Science & Technology

1980-03-01

Stephen L. 11. Hockaday Manager Sl H/j c 2nclosure cc: x. Fred Jaeger bcc: Mr. Herb Hubbard, UAL TFD Correspondence H. Fan 0 JI-. *~ ~ E ~ n ti ~’L1 -J (D...34 Attachment E contains a list of additional delay experiments discussed at the previous Task Force meeting. I I P M. M. &6 Co. Mr. Phillip J. LaRochelle March... E -05B Western. C-01, C7.O3, C-05, CO2 , C-04, C-06, Continental,, C-07, C-09, C-11, C-15, C-10, C-12, C-14, C-16 Trans World,, D-01, D-03, D-05, D-07

Levofloxacin plus Metronidazole Administered Once Daily versus Moxifloxacin Monotherapy against a Mixed Infection of Escherichia coli and Bacteroides fragilis in an In Vitro Pharmacodynamic Model

PubMed Central

Hermsen, Elizabeth D.; Hovde, Laurie B.; Sprandel, Kelly A.; Rodvold, Keith A.; Rotschafer, John C.

2005-01-01

Moxifloxacin has been suggested as an option for monotherapy of intra-abdominal infections. Recent data support the use of a once-daily metronidazole regimen. The purpose of this study was to investigate the activity of levofloxacin (750 mg every 24 h [q24h]) plus metronidazole (1,500 mg q24h) compared with that of moxifloxacin (400 mg q24h) monotherapy in a mixed-infection model. By using an in vitro pharmacodynamic model in duplicate, Escherichia coli and Bacteroides fragilis were exposed to peak concentrations of 8.5 mg of levofloxacin/liter q24h, 32 mg of metronidazole/liter q24h, and 2 mg for moxifloxacin/liter q24h for 24 h. The activities of levofloxacin, metronidazole, moxifloxacin, and levofloxacin plus metronidazole were evaluated against E. coli, B. fragilis, and E. coli plus B. fragilis. The targeted half-lives of levofloxacin, metronidazole, and moxifloxacin were 8, 8, and 12 h, respectively. Time-kill curves were analyzed for time to 3-log killing, slope, and regrowth. Pre- and postexposure MICs were determined. The preexposure levofloxacin, metronidazole, and moxifloxacin MICs for E. coli and B. fragilis were 0.5 and 1, >64 and 0.5, and 1 and 0.25 mg/liter, respectively. Levofloxacin and moxifloxacin achieved a 3-log killing against E. coli and B. fragilis in all experiments, as did metronidazole against B. fragilis. Metronidazole did not decrease the starting inoculum of E. coli. The area under the concentration-time curve/MIC ratios for E. coli and B. fragilis were 171.7 and 85.9, respectively, for levofloxacin and 26 and 103.9, respectively, for moxifloxacin. Levofloxacin plus metronidazole exhibited the fastest rates of killing. The levofloxacin and moxifloxacin MICs for B. fragilis increased 8- to 16-fold after the organism was exposed to moxifloxacin. No other changes in the postexposure MICs were found. Levofloxacin plus metronidazole administered once daily exhibited activity similar to that of moxifloxacin against the mixed E. coli and B

Levofloxacin plus metronidazole administered once daily versus moxifloxacin monotherapy against a mixed infection of Escherichia coli and Bacteroides fragilis in an in vitro pharmacodynamic model.

PubMed

Hermsen, Elizabeth D; Hovde, Laurie B; Sprandel, Kelly A; Rodvold, Keith A; Rotschafer, John C

2005-02-01

Moxifloxacin has been suggested as an option for monotherapy of intra-abdominal infections. Recent data support the use of a once-daily metronidazole regimen. The purpose of this study was to investigate the activity of levofloxacin (750 mg every 24 h [q24h]) plus metronidazole (1,500 mg q24h) compared with that of moxifloxacin (400 mg q24h) monotherapy in a mixed-infection model. By using an in vitro pharmacodynamic model in duplicate, Escherichia coli and Bacteroides fragilis were exposed to peak concentrations of 8.5 mg of levofloxacin/liter q24h, 32 mg of metronidazole/liter q24h, and 2 mg for moxifloxacin/liter q24h for 24 h. The activities of levofloxacin, metronidazole, moxifloxacin, and levofloxacin plus metronidazole were evaluated against E. coli, B. fragilis, and E. coli plus B. fragilis. The targeted half-lives of levofloxacin, metronidazole, and moxifloxacin were 8, 8, and 12 h, respectively. Time-kill curves were analyzed for time to 3-log killing, slope, and regrowth. Pre- and postexposure MICs were determined. The preexposure levofloxacin, metronidazole, and moxifloxacin MICs for E. coli and B. fragilis were 0.5 and 1, >64 and 0.5, and 1 and 0.25 mg/liter, respectively. Levofloxacin and moxifloxacin achieved a 3-log killing against E. coli and B. fragilis in all experiments, as did metronidazole against B. fragilis. Metronidazole did not decrease the starting inoculum of E. coli. The area under the concentration-time curve/MIC ratios for E. coli and B. fragilis were 171.7 and 85.9, respectively, for levofloxacin and 26 and 103.9, respectively, for moxifloxacin. Levofloxacin plus metronidazole exhibited the fastest rates of killing. The levofloxacin and moxifloxacin MICs for B. fragilis increased 8- to 16-fold after the organism was exposed to moxifloxacin. No other changes in the postexposure MICs were found. Levofloxacin plus metronidazole administered once daily exhibited activity similar to that of moxifloxacin against the mixed E. coli and B

Bacteroides fragilis Enterotoxin Induces Formation of Autophagosomes in Endothelial Cells but Interferes with Fusion with Lysosomes for Complete Autophagic Flux through a Mitogen-Activated Protein Kinase-, AP-1-, and C/EBP Homologous Protein-Dependent Pathway.

PubMed

Ko, Su Hyuk; Jeon, Jong Ik; Myung, Hyun Soo; Kim, Young-Jeon; Kim, Jung Mogg

2017-10-01

Bacteroides fragilis enterotoxin (BFT), a virulence factor of enterotoxigenic B. fragilis (ETBF), plays an essential role in mucosal inflammation. Although autophagy contributes to the pathogenesis of diverse infectious diseases, little is known about autophagy in ETBF infection. This study was conducted to investigate the role of BFT in the autophagic process in endothelial cells (ECs). Stimulation of human umbilical vein ECs (HUVECs) with BFT increased light chain 3 protein II (LC3-II) conversion from LC3-I and protein expression of p62, Atg5, and Atg12. In addition, BFT-exposed ECs showed increased indices of autophagosomal fusion with lysosomes such as LC3-lysosome-associated protein 2 (LAMP2) colocalization and the percentage of red vesicles monitored by the expression of dual-tagged LC3B. BFT also upregulated expression of C/EBP homologous protein (CHOP), and inhibition of CHOP significantly increased indices of autophagosomal fusion with lysosomes. BFT activated an AP-1 transcription factor, in which suppression of AP-1 activity significantly downregulated CHOP and augmented autophagosomal fusion with lysosomes. Furthermore, suppression of Jun N-terminal protein kinase (JNK) mitogen-activated protein kinase (MAPK) significantly inhibited the AP-1 and CHOP signals, leading to an increase in autophagosomal fusion with lysosomes in BFT-stimulated ECs. These results suggest that BFT induced accumulation of autophagosomes in ECs, but activation of a signaling pathway involving JNK, AP-1, and CHOP may interfere with complete autophagy. Copyright © 2017 American Society for Microbiology.

Data fusion in data scarce areas using a back-propagation artificial neural network model: a case study of the South China Sea

NASA Astrophysics Data System (ADS)

Wang, Zheng; Mao, Zhihua; Xia, Junshi; Du, Peijun; Shi, Liangliang; Huang, Haiqing; Wang, Tianyu; Gong, Fang; Zhu, Qiankun

2018-06-01

The cloud cover for the South China Sea and its coastal area is relatively large throughout the year, which limits the potential application of optical remote sensing. A HJ-charge-coupled device (HJ-CCD) has the advantages of wide field, high temporal resolution, and short repeat cycle. However, this instrument suffers from its use of only four relatively low-quality bands which can't adequately resolve the features of long wavelengths. The Landsat Enhanced Thematic Mapper-plus (ETM+) provides high-quality data, however, the Scan Line Corrector (SLC) stopped working and caused striping of remote sensed images, which dramatically reduced the coverage of the ETM+ data. In order to combine the advantages of the HJ-CCD and Landsat ETM+ data, we adopted a back-propagation artificial neural network (BP-ANN) to fuse these two data types for this study. The results showed that the fused output data not only have the advantage of data intactness for the HJ-CCD, but also have the advantages of the multi-spectral and high radiometric resolution of the ETM+ data. Moreover, the fused data were analyzed qualitatively, quantitatively and from a practical application point of view. Experimental studies indicated that the fused data have a full spatial distribution, multi-spectral bands, high radiometric resolution, a small difference between the observed and fused output data, and a high correlation between the observed and fused data. The excellent performance in its practical application is a further demonstration that the fused data are of high quality.

Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease.

PubMed

Rodrigues, N F; Kästle, J; Coutinho, T J D; Amorim, A T; Campos, G B; Santos, V M; Marques, L M; Timenetsky, J; de Farias, S T

2015-06-12

The microbial community of the reproductive appara-tus, when known, can provide information about the health of the host. Metagenomics has been used to characterize and obtain genetic infor-mation about microbial communities in various environments and can relate certain diseases with changes in this community composition. In this study, samples of vaginal surface mucosal secretions were col-lected from five healthy cows and five cows that showed symptoms of reproductive disorders. Following high-throughput sequencing of the isolated microbial DNA, data were processed using the Mothur soft-ware to remove low-quality sequences and chimeras, and released to the Ribosomal Database Project for classification of operational taxo-nomic units (OTUs). Local BLASTn was performed and results were loaded into the MEGAN program for viewing profiles and taxonomic microbial attributes. The control profile comprised a total of 15 taxa, with Bacteroides, Enterobacteriaceae, and Victivallis comprising the highest representation of OTUs; the reproductive disorder-positive profile comprised 68 taxa, with Bacteroides, Enterobacteriaceae, His-tophilus, Victivallis, Alistipes, and Coriobacteriaceae being the taxa with the most OTU representation. A change was observed in both the community composition as well as in the microbial attributes of the profiles, suggesting that a relationship might exist between the patho-gen and representative taxa, reflecting the production of metabolites to disease progression.

Normal bacterial flora from vaginas of Criollo Limonero cows.

PubMed

Zambrano-Nava, Sunny; Boscán-Ocando, Julio; Nava, Jexenia

2011-02-01

In order to describe the normal bacterial flora in vaginas of Criollo Limonero cows, 51 healthy multiparous cows, at least 90-day postpartum, were selected. Duplicated swabs (N = 102) were taken from the vaginal fornix of cows to perform aerobic and anaerobic cultures as well as conventional biochemical tests. Out of 102 swabs, bacterial growth was obtained in 55 (53.9%) while the remaining 47 (46.1%) did not exhibited any bacterial growth. Of the 55 bacterial growths, 23 (41.8%) were aerobic whereas 32 (58.1%) were anaerobic. Likewise, 29 (52.72%) of bacterial growths were pure and 26 (47.27%) were mixed. Under both aerobic and anaerobic conditions, Gram positive bacteria were predominant (81.82% and 73.08%, respectively) over Gram negative bacteria (18.18% and 26.92%, respectively). Isolated bacteria were Arcanobacterium pyogenes (22.92%), Staphylococcus aureus (15.63%), Staphylococcus coagulase negative (17.71%), Erysipelothrix rhusiopathiae (6.25%), Bacteroides spp. (13.54%), and Peptostreptococcus spp. (7.29%). In conclusion, normal vaginal bacterial flora of Criollo Limonero cows was predominantly Gram positive and included A. pyogenes, S. aureus, coagulase negative Staphylococcus, E. rhusiopathiae, Bacteroides spp., and Peptostreptococcus spp. In Criollo Limonero cattle, adaptive aspects such as development of humoral and physical mechanisms for defense, and bacterial adaptation to host deserve research attention.

The application of remote sensing image sea ice monitoring method in Bohai Bay based on C4.5 decision tree algorithm

NASA Astrophysics Data System (ADS)

Ye, Wei; Song, Wei

2018-02-01

In The Paper, the remote sensing monitoring of sea ice problem was turned into a classification problem in data mining. Based on the statistic of the related band data of HJ1B remote sensing images, the main bands of HJ1B images related with the reflectance of seawater and sea ice were found. On the basis, the decision tree rules for sea ice monitoring were constructed by the related bands found above, and then the rules were applied to Liaodong Bay area seriously covered by sea ice for sea ice monitoring. The result proved that the method is effective.

Sustainable microbial water quality monitoring programme design using phage-lysis and multivariate techniques.

PubMed

Nnane, Daniel Ekane

2011-11-15

Contamination of surface waters is a pervasive threat to human health, hence, the need to better understand the sources and spatio-temporal variations of contaminants within river catchments. River catchment managers are required to sustainably monitor and manage the quality of surface waters. Catchment managers therefore need cost-effective low-cost long-term sustainable water quality monitoring and management designs to proactively protect public health and aquatic ecosystems. Multivariate and phage-lysis techniques were used to investigate spatio-temporal variations of water quality, main polluting chemophysical and microbial parameters, faecal micro-organisms sources, and to establish 'sentry' sampling sites in the Ouse River catchment, southeast England, UK. 350 river water samples were analysed for fourteen chemophysical and microbial water quality parameters in conjunction with the novel human-specific phages of Bacteroides GB-124 (Bacteroides GB-124). Annual, autumn, spring, summer, and winter principal components (PCs) explained approximately 54%, 75%, 62%, 48%, and 60%, respectively, of the total variance present in the datasets. Significant loadings of Escherichia coli, intestinal enterococci, turbidity, and human-specific Bacteroides GB-124 were observed in all datasets. Cluster analysis successfully grouped sampling sites into five clusters. Importantly, multivariate and phage-lysis techniques were useful in determining the sources and spatial extent of water contamination in the catchment. Though human faecal contamination was significant during dry periods, the main source of contamination was non-human. Bacteroides GB-124 could potentially be used for catchment routine microbial water quality monitoring. For a cost-effective low-cost long-term sustainable water quality monitoring design, E. coli or intestinal enterococci, turbidity, and Bacteroides GB-124 should be monitored all-year round in this river catchment. Copyright © 2011 Elsevier B.V. All

Discovery of β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans.

PubMed

Nihira, Takanori; Suzuki, Erika; Kitaoka, Motomitsu; Nishimoto, Mamoru; Ohtsubo, Ken'ichi; Nakai, Hiroyuki

2013-09-20

A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator superfamily transporter, a starch utilization system-like transporter consisting of a TonB-dependent oligosaccharide transporter and an outer membrane lipoprotein, four glycoside hydrolases (α-mannosidase, β-N-acetylhexosaminidase, exo-α-sialidase, and endo-β-N-acetylglucosaminidase), and a phosphorylase (BT1033) with unknown function. It was demonstrated that BT1033 catalyzed the reversible phosphorolysis of β-1,4-D-mannosyl-N-acetyl-D-glucosamine in a typical sequential Bi Bi mechanism. These results indicate that BT1033 plays a crucial role as a key enzyme in the N-glycan catabolism where β-1,4-D-mannosyl-N-acetyl-D-glucosamine is liberated from N-glycans by sequential glycoside hydrolase-catalyzed reactions, transported into the cell, and intracellularly converted into α-D-mannose 1-phosphate and N-acetyl-D-glucosamine. In addition, intestinal anaerobic bacteria such as Bacteroides fragilis, Bacteroides helcogenes, Bacteroides salanitronis, Bacteroides vulgatus, Prevotella denticola, Prevotella dentalis, Prevotella melaninogenica, Parabacteroides distasonis, and Alistipes finegoldii were also suggested to possess the similar metabolic pathway for N-glycans. A notable feature of the new metabolic pathway for N-glycans is the more efficient use of ATP-stored energy, in comparison with the conventional pathway where β-mannosidase and ATP-dependent hexokinase participate, because it is possible to directly phosphorylate the D-mannose residue of β-1,4-D-mannosyl-N-acetyl-D-glucosamine to enter glycolysis. This is the first report of a metabolic pathway for N-glycans that includes a phosphorylase. We propose 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase as the systematic name and β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase as the short name for BT1033.

Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination.

PubMed

Lee, Chang Soo; Lee, Jiyoung

2010-09-01

A rapid and specific gyrB-based real-time PCR system has been developed for detecting Bacteroides fragilis as a human-specific marker of fecal contamination. Its specificity and sensitivity was evaluated by comparison with other 16S rRNA gene-based primers using closely related Bacteroides and Prevotella. Many studies have used 16S rRNA gene-based method targeting Bacteroides because this genus is relatively abundant in human feces and is useful for microbial source tracking. However, 16S rRNA gene-based primers are evolutionarily too conserved among taxa to discriminate between human-specific species of Bacteroides and other closely related genera, such as Prevotella. Recently, one of the housekeeping genes, gyrB, has been used as an alternative target in multilocus sequence analysis (MLSA) to provide greater phylogenetic resolution. In this study, a new B. fragilis-specific primer set (Bf904F/Bf958R) was designed by alignments of 322 gyrB genes and was compared with the performance of the 16S rRNA gene-based primers in the presence of B. fragilis, Bacteroides ovatus and Prevotella melaninogenica. Amplicons were sequenced and a phylogenetic tree was constructed to confirm the specificity of the primers to B. fragilis. The gyrB-based primers successfully discriminated B. fragilis from B. ovatus and P. melaninogenica. Real-time PCR results showed that the gyrB primer set had a comparable sensitivity in the detection of B. fragilis when compared with the 16S rRNA primer set. The host-specificity of our gyrB-based primer set was validated with human, pig, cow, and dog fecal samples. The gyrB primer system had superior human-specificity. The gyrB-based system can rapidly detect human-specific fecal source and can be used for improved source tracking of human contamination. (c) 2010 Elsevier B.V. All rights reserved.

46 CFR 194.15-15 - Chemicals other than compressed gases.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Chemicals other than compressed gases. 194.15-15 Section 194.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) OCEANOGRAPHIC RESEARCH VESSELS HANDLING, USE, AND CONTROL OF EXPLOSIVES AND OTHER HAZARDOUS MATERIALS Chemistry Laboratory and...

46 CFR 194.15-15 - Chemicals other than compressed gases.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 7 2013-10-01 2013-10-01 false Chemicals other than compressed gases. 194.15-15 Section 194.15-15 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) OCEANOGRAPHIC RESEARCH VESSELS HANDLING, USE, AND CONTROL OF EXPLOSIVES AND OTHER HAZARDOUS MATERIALS Chemistry Laboratory and...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salminen, S.O.; Streeter, J.G.

Bradyrhizobium japonicum bacteroids were isolated anaerobically and were supplied with /sup 14/C-labeled trehalose, sucrose, UDP-glucose, glucose, or fructose under low O/sub 2/ (2% in the gas phase). Uptake and conversion of /sup 14/C to CO/sub 2/ were measured at intervals up to 90 minutes. Of the five compounds studied, UDP-glucose was most rapidly absorbed but it was very slowly metabolized. Trehalose was the sugar most rapidly converted to CO/sub 2/, and fructose was respired at a rate of at least double that of glucose. Sucrose and glucose were converted to CO/sub 2/ at a very low but measurable rate (<0.1more » nanomoles per milligram protein per hour). Carbon Number 1 of glucose appeared in CO/sub 2/ at a rate 30 times greater than the conversion of carbon Number 6 to CO/sub 2/, indicating high activity of the pentose phosphate pathway. Enzymes of the Entner-Doudoroff pathway were not detected in bacteroids, but very low activities of sucrose synthase and phosphofructokinase were demonstrated. Although metabolism of sugars by B. japonicum bacteroids was clearly demonstrated, the rate of sugar uptake was only 1/30 to 1/50 the rate of succinate uptake. The overall results support the view that, although bacteroids metabolize sugars, the rates are very low and are inadequate to support nitrogenase.« less

44 CFR 15.15 - Weapons and explosives.

Code of Federal Regulations, 2013 CFR

2013-10-01

... HOMELAND SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.15 Weapons and explosives. No person entering or while at Mt. Weather or the... openly or concealed, except: (a) For official purposes if the Administrator, Mt. Weather Executive...

44 CFR 15.15 - Weapons and explosives.

Code of Federal Regulations, 2010 CFR

2010-10-01

... HOMELAND SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.15 Weapons and explosives. No person entering or while at Mt. Weather or the... openly or concealed, except: (a) For official purposes if the Administrator, Mt. Weather Executive...

44 CFR 15.15 - Weapons and explosives.

Code of Federal Regulations, 2012 CFR

2012-10-01

... HOMELAND SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.15 Weapons and explosives. No person entering or while at Mt. Weather or the... openly or concealed, except: (a) For official purposes if the Administrator, Mt. Weather Executive...

44 CFR 15.15 - Weapons and explosives.

Code of Federal Regulations, 2014 CFR

2014-10-01

... HOMELAND SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.15 Weapons and explosives. No person entering or while at Mt. Weather or the... openly or concealed, except: (a) For official purposes if the Administrator, Mt. Weather Executive...

44 CFR 15.15 - Weapons and explosives.

Code of Federal Regulations, 2011 CFR

2011-10-01

... HOMELAND SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.15 Weapons and explosives. No person entering or while at Mt. Weather or the... openly or concealed, except: (a) For official purposes if the Administrator, Mt. Weather Executive...

46 CFR 194.15-15 - Chemicals other than compressed gases.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 7 2011-10-01 2011-10-01 false Chemicals other than compressed gases. 194.15-15 Section... Scientific Laboratory § 194.15-15 Chemicals other than compressed gases. Chemicals, including those listed in 49 CFR part 172, may be stored in small working quantities in the chemical laboratory. [CGD 86-033...

46 CFR 194.15-15 - Chemicals other than compressed gases.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 7 2012-10-01 2012-10-01 false Chemicals other than compressed gases. 194.15-15 Section... Scientific Laboratory § 194.15-15 Chemicals other than compressed gases. Chemicals, including those listed in 49 CFR part 172, may be stored in small working quantities in the chemical laboratory. [CGD 86-033...

46 CFR 194.15-15 - Chemicals other than compressed gases.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 7 2014-10-01 2014-10-01 false Chemicals other than compressed gases. 194.15-15 Section... Scientific Laboratory § 194.15-15 Chemicals other than compressed gases. Chemicals, including those listed in 49 CFR part 172, may be stored in small working quantities in the chemical laboratory. [CGD 86-033...

46 CFR 97.15-15 - Examination of boilers and machinery.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Examination of boilers and machinery. 97.15-15 Section... VESSELS OPERATIONS Tests, Drills, and Inspections § 97.15-15 Examination of boilers and machinery. It shall be the duty of the chief engineer when assuming charge of the boilers and machinery of a vessel to...

46 CFR 196.15-15 - Examination of boilers and machinery.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Examination of boilers and machinery. 196.15-15 Section... VESSELS OPERATIONS Test, Drills, and Inspections § 196.15-15 Examination of boilers and machinery. (a) It shall be the duty of the chief engineer when he assumes charge of the boilers and machinery of a vessel...

Distinct 15q Genotypes in Russell-Silver and Ring 15 Syndromes

PubMed Central

Rogan, Peter K.; Seip, James R.; Driscoll, Daniel J.; Papenhausen, Peter R.; Johnson, Virginia P.; Raskin, Salmo; Woodward, Amy L.; Butler, Merlin G.

2018-01-01

Individuals with a ring 15 chromosome [r(15)] and those with Russell-Silver syndrome have short stature, developmental delay, triangular face, and clinodactyly. To assess whether the apparent phenotypic overlap of these conditions reflects a common genetic cause, the extent of deletions in chromosome 15q was determined in 5 patients with r(15), 1 patient with del 15q26.1–qter, and 5 patients with Russell- Silver syndrome. All patients with Russell- Silver syndrome were diploid for genetic markers in distal 15q, indicating that Russell-Silver syndrome in these individuals was unlikely to be related to the expression of single alleles at these or linked genetic loci. At least 3 distinct sites of chromosome breakage close to the telomere were found in the r(15) and del 15q25.1–qter patients, with 1 r(15) patient having both a terminal and an interstitial deletion. Although the patient with del 15q25.1–qter exhibited the largest deletion and the most profound growth retardation, the degree of growth impairment among the r(15) patients was not correlated with the size of the deleted interval. Rather, the parental origin of the ring chromosome in several patients was associated with phenotypes that are also seen in patients with either Prader-Willi (PWS) or Angelman (AS) syndromes, conditions that result from uniparental expression of genes on chromosome 15. In fact, unequal representation of chromosome 15 alleles in 1 patient with r(15) suggests the possibility that a mosaic karyotype composed of the constitutional cell line and cell line(s) possibly deficient in the ring chromosome might be present. The PWS-like or AS-like phenotypes could be explained by postzygotic loss of the ring chromosome, leading to uniparental inheritance of the intact chromosome in some tissues of r(15) patients. PMID:8779316

Experimental Shigella Infections in Laboratory Animals I. Antagonism by Human Normal Flora Components in Gnotobiotic Mice 12

PubMed Central

Maier, Bruce R.; Hentges, David J.

1972-01-01

Germfree mice were associated with selected species of human intestinal bacteria and then challenged with a streptomycin-resistant Shigella flexneri strain. Antagonism against Shigella was most pronounced in mice associated with Escherichia coli and least pronounced in mice associated with Bacteroides fragilis. A moderate degree of antagonism could be demonstrated in mice associated with either Streptococcus faecalis or Bifidobacterium adolescentis. Shigella persisted in the cecal contents of E. coli-associated mice at very low, stable levels. Shigella populations were reduced to levels below detection in the ceca of mice diassociated with E. coli and Bacteroides. Upon subsequent administration of streptomycin, Bacteroides disappeared from the ceca. The E. coli population was greatly reduced, and Shigella reappeared at very high population levels as an apparent recombinant which resembled E. coli biochemically. A streptomycin-resistant E. coli population subsequently emerged and became dominant in the ceca. Shigella concomitantly declined to levels below detection. PMID:4631914

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

PubMed

Vatanen, Tommi; Kostic, Aleksandar D; d'Hennezel, Eva; Siljander, Heli; Franzosa, Eric A; Yassour, Moran; Kolde, Raivo; Vlamakis, Hera; Arthur, Timothy D; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Uibo, Raivo; Mokurov, Sergei; Dorshakova, Natalya; Ilonen, Jorma; Virtanen, Suvi M; Szabo, Susanne J; Porter, Jeffrey A; Lähdesmäki, Harri; Huttenhower, Curtis; Gevers, Dirk; Cullen, Thomas W; Knip, Mikael; Xavier, Ramnik J

2016-05-05

According to the hygiene hypothesis, the increasing incidence of autoimmune diseases in western countries may be explained by changes in early microbial exposure, leading to altered immune maturation. We followed gut microbiome development from birth until age three in 222 infants in Northern Europe, where early-onset autoimmune diseases are common in Finland and Estonia but are less prevalent in Russia. We found that Bacteroides species are lowly abundant in Russians but dominate in Finnish and Estonian infants. Therefore, their lipopolysaccharide (LPS) exposures arose primarily from Bacteroides rather than from Escherichia coli, which is a potent innate immune activator. We show that Bacteroides LPS is structurally distinct from E. coli LPS and inhibits innate immune signaling and endotoxin tolerance; furthermore, unlike LPS from E. coli, B. dorei LPS does not decrease incidence of autoimmune diabetes in non-obese diabetic mice. Early colonization by immunologically silencing microbiota may thus preclude aspects of immune education. Copyright © 2016 Elsevier Inc. All rights reserved.

PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples.

PubMed Central

Wang, R F; Cao, W W; Cerniglia, C E

1996-01-01

PCR procedures based on 16S rRNA gene sequences specific for 12 anaerobic bacteria that predominate in the human intestinal tract were developed and used for quantitative detection of these species in human (adult and baby) feces and animal (rat, mouse, cat, dog, monkey, and rabbit) feces. Fusobacterium prausnitzii, Peptostreptococcus productus, and Clostridium clostridiiforme had high PCR titers (the maximum dilutions for positive PCR results ranged from 10(-3) to 10(-8)) in all of the human and animal fecal samples tested. Bacteroides thetaiotaomicron, Bacteroides vulgatus, and Eubacterium limosum also showed higher PCR titers (10(-2) to 10(-6)) in adult human feces. The other bacteria tested, including Escherichia coli, Bifidobacterium adolescentis, Bifidobacterium longum, Lactobacillus acidophilus, Eubacterium biforme, and Bacteroides distasonis, were either at low PCR titers (less than 10(-2)) or not detected by PCR. The reported PCR procedure including the fecal sample preparation method is simplified and rapid and eliminates the DNA isolation steps. PMID:8919784

Results From a Microbial Source-Tracking Study at Villa Angela Beach, Cleveland, Ohio, 2007

USGS Publications Warehouse

Bushon, Rebecca N.; Stelzer, Erin A.; Stoeckel, Donald M.

2009-01-01

During the 2007 recreational season at Villa Angela Beach in Cleveland, Ohio, scientists with the U.S. Geological Survey (USGS) and the Northeast Ohio Regional Sewer District (NEORSD) found high Escherichia coli (E. coli) concentrations that were not easily explained by results obtained to date in ongoing investigations of recreational water quality at the beach. To help understand the sources behind these elevated E. coli concentrations, the USGS and NEORSD sampled beach-area water for Bacteroides DNA markers. Bacteroides are a group of enteric bacteria that are being used in microbial source tracking, in hope that host-associated DNA markers could be used to indicate potential sources of E. coli in the Villa Angela environment. The USGS Ohio Water Microbiology Laboratory analyzed a total of 13 source samples (sewage and waterfowl feces) and 33 beach-area water and sand samples for three Bacteroides DNA markers. This report lists the results of those analyses, along with environmental conditions at Villa Angela on the dates that samples were collected.

15 CFR 15.3 - Acceptance of service of process.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Acceptance of service of process. 15.3... Process § 15.3 Acceptance of service of process. (a) Except as otherwise provided in this subpart, any... employee by law is to be served personally with process. Service of process in this case is inadequate when...

Lifestyle characteristics assessment of Japanese in Pittsburgh, USA.

PubMed

Hirooka, Nobutaka; Takedai, Teiichi; D'Amico, Frank

2012-04-01

Lifestyle-related chronic diseases such as cancer and cardiovascular disease are the greatest public health concerns. Evidence shows Japanese immigrants to a westernized environment have higher incidence of lifestyle-related diseases. However, little is known about lifestyle characteristics related to chronic diseases for Japanese in a westernized environment. This study is examining the gap in lifestyle by comparing the lifestyle prevalence for Japanese in the US with the Japanese National Data (the National Health and Nutrition Survey in Japan, J-NHANS) as well as the Japan National Health Promotion in the twenty-first Century (HJ21) goals. Japanese adults were surveyed in Pittsburgh, USA, regarding their lifestyle (e.g., diet, exercise, smoking, stress, alcohol, and oral hygiene). The prevalence was compared with J-NHANS and HJ21 goals. Ninety-three responded (response rate; 97.9%). Japanese men (n = 38) and women (n = 55) in Pittsburgh smoke less than Japanese in Japan (P < 0.001 for both genders). Japanese in Pittsburgh perform less physical activity in daily life and have lower prevalence of walking more than 1 h per day (P < 0.001 for both genders). Japanese women in Pittsburgh have significantly higher prevalence of stress than in Japan (P = 0.004). Japanese men in Pittsburgh do not reach HJ21 goal in weight management, BMI, use of medicine or alcohol to sleep, and sleep quality. Japanese women in Pittsburgh do not reach HJ21 goal in weight management and sleep quality. In conclusion, healthy lifestyle promotion including exercise and physical activity intervention for Japanese living in a westernized environment is warranted.

Comparison of Huanjing and Landsat satellite remote sensing of the spatial heterogeneity of Qinghai-Tibet alpine grassland

NASA Astrophysics Data System (ADS)

Wang, Junbang; Sun, Wenyi

2014-11-01

Remote sensing is widely applied in the study of terrestrial primary production and the global carbon cycle. The researches on the spatial heterogeneity in images with different sensors and resolutions would improve the application of remote sensing. In this study two sites on alpine meadow grassland in Qinghai, China, which have distinct fractal vegetation cover, were used to test and analyze differences between Normalized Difference Vegetation Index (NDVI) and enhanced vegetation index (EVI) derived from the Huanjing (HJ) and Landsat Thematic Mapper (TM) sensors. The results showed that: 1) NDVI estimated from HJ were smaller than the corresponding values from TM at the two sites whereas EVI were almost the same for the two sensors. 2) The overall variance represented by HJ data was consistently about half of that of Landsat TM although their nominal pixel size is approximately 30m for both sensors. The overall variance from EVI is greater than that from NDVI. The difference of the range between the two sensors is about 6 pixels at 30m resolution. The difference of the range in which there is not more corrective between two vegetation indices is about 1 pixel. 3) The sill decreased when pixel size increased from 30m to 1km, and then decreased very quickly when pixel size is changed to 250m from 30m or 90m but slowly when changed from 250m to 500m. HJ can capture this spatial heterogeneity to some extent and this study provides foundations for the use of the sensor for validation of net primary productivity estimates obtained from ecosystem process models.

Evidence for the role of Mycobacterium tuberculosis RecG helicase in DNA repair and recombination.

PubMed

Thakur, Roshan S; Basavaraju, Shivakumar; Somyajit, Kumar; Jain, Akshatha; Subramanya, Shreelakshmi; Muniyappa, Kalappa; Nagaraju, Ganesh

2013-04-01

In order to survive and replicate in a variety of stressful conditions during its life cycle, Mycobacterium tuberculosis must possess mechanisms to safeguard the integrity of the genome. Although DNA repair and recombination related genes are thought to play key roles in the repair of damaged DNA in all organisms, so far only a few of them have been functionally characterized in the tubercle bacillus. In this study, we show that M. tuberculosis RecG (MtRecG) expression was induced in response to different genotoxic agents. Strikingly, expression of MtRecG in Escherichia coli ∆recG mutant strain provided protection against mitomycin C, methyl methane sulfonate and UV induced cell death. Purified MtRecG exhibited higher binding affinity for the Holliday junction (HJ) compared with a number of canonical recombinational DNA repair intermediates. Notably, although MtRecG binds at the core of the mobile and immobile HJs, and with higher binding affinity for the immobile HJ, branch migration was evident only in the case of the mobile HJ. Furthermore, immobile HJs stimulate MtRecG ATPase activity less efficiently than mobile HJs. In addition to HJ substrates, MtRecG exhibited binding affinity for a variety of branched DNA structures including three-way junctions, replication forks, flap structures, forked duplex and a D-loop structure, but demonstrated strong unwinding activity on replication fork and flap DNA structures. Together, these results support that MtRecG plays an important role in processes related to DNA metabolism under normal as well as stress conditions. © 2013 The Authors Journal compilation © 2013 FEBS.

15 CFR 15.21 - Purpose.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Support Allotments of NOAA Corps Officers § 15.21 Purpose. This subpart provides implementing policies... the National Oceanic and Atmospheric Administration (NOAA), and prescribes applicable procedures. ...

15 CFR 15.21 - Purpose.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Support Allotments of NOAA Corps Officers § 15.21 Purpose. This subpart provides implementing policies... the National Oceanic and Atmospheric Administration (NOAA), and prescribes applicable procedures. ...

15 CFR 15.21 - Purpose.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Support Allotments of NOAA Corps Officers § 15.21 Purpose. This subpart provides implementing policies... the National Oceanic and Atmospheric Administration (NOAA), and prescribes applicable procedures. ...

15 CFR 15.21 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Support Allotments of NOAA Corps Officers § 15.21 Purpose. This subpart provides implementing policies... the National Oceanic and Atmospheric Administration (NOAA), and prescribes applicable procedures. ...

15 CFR 15.21 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Support Allotments of NOAA Corps Officers § 15.21 Purpose. This subpart provides implementing policies... the National Oceanic and Atmospheric Administration (NOAA), and prescribes applicable procedures. ...

Chroma Shift and Gamut Shape: Going Beyond Average Color Fidelity and Gamut Area

DOE Office of Scientific and Technical Information (OSTI.GOV)

Royer, Michael P.; Houser, Kevin W.; David, Aurélien

Though sometimes referred to as a two-measure system for evaluating color rendition, IES TM-30-15 includes other key components that go beyond the high-level average values IES Rf and IES Rg. This article focuses on the Color Vector Graphic and Local Chroma Shift (IES Rcs,hj), discussing the calculation methods for these evaluation tools and providing context for the interpretation of the values. It also presents alternatives for quantifying the same characteristics, which can inform the development of future measures. The Color Vector Graphic (CVG) is a visual representation of hue and chroma shifts across different hues. It quickly communicates complex informationmore » about how object colors will be rendered by a light source, although it is difficult or impossible to use for writing a specification. CVGs demonstrate that increases in chroma for certain hues sometimes means a decrease in chroma for other hues, and illustrates hue shifts for intermediate colors. The combination of shifts over different hues can be referred to as gamut shape. Complementing this information are the IES Rcs,hj values, which quantify the average relative chroma shift for samples in each of the 16 hue-angle bins (j) specified in IES TM-30-15. Unlike measures of average color fidelity and gamut area, gamut shape and hue-specific chroma shift are new concepts with no directly-comparable historical references. It will be critical to incorporate the Color Vector Graphic and Local Chroma Shift values into practice because they capture information about color rendition that is impossible to describe with average measures (such as CIE Ra, IES Rf, or IES Rg), but that is critical to understanding human evaluations of color quality in architectural environments.« less

Hydrogeology Journal in 2004

USGS Publications Warehouse

Voss, Clifford; Olcott, Perry; Schneider, Robert; Watson, Christine

2004-01-01

Hydrogeology Journal continues to flourish. The increase in the size of our yearly volume attests to the success and growing international reputation of the journal. Until 2001, HJ produced about 600 printed pages each year. This number has steadily increased, and in 2005 and 2006, HJ will be allocated 800 pages per year by the publisher. Despite this good news, the journal is having some growing pains. Most pages in next year’s issues are already fully allocated with currently accepted articles and therefore, many accepted articles must now wait up to one year to appear in printed form. Clearly, this is not an acceptable situation for authors or readers.

Enzymatic Synthesis of 6'-Sialyllactose, a Dominant Sialylated Human Milk Oligosaccharide, by a Novel exo-α-Sialidase from Bacteroides fragilis NCTC9343.

PubMed

Guo, Longcheng; Chen, Xiaodi; Xu, Li; Xiao, Min; Lu, Lili

2018-07-01

Gut bacteria provide a rich source of glycosidases that can recognize and/or hydrolyze glycans for nutrition. Interestingly, some glycosidases have also been found to catalyze transglycosylation reactions in vitro and thus can be used for oligosaccharide synthesis. In this work, six putative and one known exo -α-sialidase genes-three from Bacteroides fragilis NCTC9343, three from Clostridium perfringens ATCC 13124, and one known from Bifidobacterium bifidum JCM1254-were subjected to gene cloning and heterogeneous expression in Escherichia coli The recombinant enzymes were purified, characterized for substrate specificity, and screened for transglycosylation activity. A sialidase, named BfGH33C, from B. fragilis NCTC9343 was found to possess excellent transglycosylation activity for the synthesis of sialylated human milk oligosaccharide. The native BfGH33C was a homodimer with a molecular weight of 113.6 kDa. The K m and k cat values for 4-methylumbelliferyl N -acetyl-α-d-neuraminic acid and sialic acid dimer were determined to be 0.06 mM and 283.2 s -1 , and 0.75 mM and 329.6 s -1 , respectively. The enzyme was able to transfer sialyl from sialic acid dimer or oligomer to lactose with high efficiency and strict α2-6 regioselectivity. The influences of the initial substrate concentration, pH, temperature, and reaction time on transglycosylation were investigated in detail. Using 40 mM sialic acid dimer (or 40 mg/ml oligomer) and 1 M lactose (pH 6.5) at 50°C for 10 min, BfGH33C could specifically produce 6'-sialyllactose, a dominant sialylated human milk oligosaccharide, at a maximal conversion ratio above 20%. It provides a promising alternative to the current chemical and enzymatic methods for obtaining sialylated oligosaccharides. IMPORTANCE Sialylated human milk oligosaccharides are significantly beneficial to the neonate, as they play important roles in supporting resistance to pathogens, gut maturation, immune function, and brain and cognitive development

GUARD HOUSE AND BARRACKS; SECOND FLOOR PLAN AND DOOR FRAME ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

GUARD HOUSE AND BARRACKS; SECOND FLOOR PLAN AND DOOR FRAME AND WINDOW DETAILS. Navy Department, Bureau of Yards & Docks, Navy Yard, Mar Island, CA. Albert F. Roller, Architect, San Francisco, CA. H.J. Brunnier, Structural Engineer, Sharon Building, San Francisco, CA. Sheet 2 of 15, accompanying specification Noy-4675. Submitted May 8, 1941, last revised July 14, 1941. Yards & Docks drawing no. 160687; P.W. (Public Works) drawing no. 10388-26; file no. 930-CR-4. Scale one eighth inch to one foot (floor plan) and 3 inches to one foot (details). 73 cm x 129 cm. Ink on vellum - Mare Island Naval Shipyard, Guard House & Barracks, Railroad Avenue near Eighteenth Street, Vallejo, Solano County, CA

X-ray emission from high temperature plasmas

NASA Technical Reports Server (NTRS)

Harries, W. L.

1974-01-01

X-rays from a 25-hJ plasma focus apparatus were observed with pinhole cameras. The cameras consist of 0.4 mm diameter pinholes in 2 cm thick lead housing enclosing an X-ray intensifying screen at the image plane. Pictures recorded through thin aluminum foils or plastic sheets for X-ray energies sub gamma smaller than 15 keV show distributed X-ray emissions from the focussed plasma and from the anode surface. However, when thick absorbers are used, radial filamentary structure in the X-ray emission from the anode surface is revealed. Occasionally larger structures are observed in addition to the filaments. Possible mechanisms for the filamentary structure are discussed.

Habitual dietary intake is associated with stool microbiota composition in monozygotic twins.

PubMed

Simões, Catarina D; Maukonen, Johanna; Kaprio, Jaakko; Rissanen, Aila; Pietiläinen, Kirsi H; Saarela, Maria

2013-04-01

The impact of diet on the gut microbiota has usually been assessed by subjecting people to the same controlled diet and thereafter following the shifts in the microbiota. In the present study, we used habitual dietary intake, clinical data, quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis (DGGE) to characterize the stool microbiota of Finnish monozygotic twins. The effect of diet on the numbers of bacteria was described through a hierarchical linear mixed model that included the twin individuals, stratified by body mass index, and their families as random effects. The abundance and diversity of the bacterial groups studied did not differ between normal-weight, overweight, and obese individuals with the techniques used. Intakes of energy, monounsaturated fatty acids, n3 polyunsaturated fatty acids (PUFAs), n6 PUFAs, and soluble fiber had significant associations with the stool bacterial numbers (e.g., increased energy intake was associated with reduced numbers of Bacteroides spp.). In addition, co-twins with identical energy intake had more similar numbers and DGGE-profile diversities of Bacteroides spp. than did the co-twins with different intake. Moreover, the co-twins who ingested the same amounts of saturated fatty acids had very similar DGGE profiles of Bacteroides spp., whereas the co-twins with similar consumption of fiber had a very low bifidobacterial DGGE-profile similarity. In conclusion, our findings confirm that the diet plays an important role in the modulation of the stool microbiota, in particular Bacteroides spp. and bifidobacteria.

In vitro activity of flomoxef compared to moxalactam, cefoxitin, cefotaxime, and clindamycin against anaerobes.

PubMed

Werner, H; Heizmann, W; Luft, G

1988-11-01

To assess the in vitro activity of flomoxef (6315-S), moxalactam, cefoxitin, cefotaxime, and clindamycin against anaerobes 197 clinical isolates (27 Bacteroides fragilis, 42 B. thetaiotaomicron, 10 B. vulgatus, 7 B. ovatus, 6 B. uniformis, 6 B. distasonis, 7 Bacteroides melaninogenicus group, 11 Bacteroides oralis group, 21 Clostridium difficile, 7 C. perfringens, 3 C. sporogenes, 3 Clostridium spp., 33 Propionibacterium acnes, 14 Peptococcaceae) were studied by means of agar dilution tests. The MIC90 of B. fragilis was less than 2 micrograms/ml for flomoxef, less than 4 micrograms/ml for moxalactam, less than 16 micrograms/ml for cefoxitin, less than 128 micrograms/ml for cefotaxime and less than 2 micrograms/ml for clindamycin. The respective MIC90's of B. thetaiotaomicron were less than 64, less than 128, less than 32, less than 256 and 8 micrograms/ml. Strains of the other Bacteroides species and groups were more susceptible to flomoxef and the other antibiotics than B. thetaiotaomicron. Against Clostridium difficile flomoxef (MIC90 less than 4 micrograms/ml) proved to be superior to the other agents tested. Most of the Clostridium strains other than C. difficile were also susceptible to flomoxef; anaerobic grampositive cocci and Propionibacterium acnes were very sensitive (MIC90's less than 1 and less than or equal to 0.125 micrograms/ml, respectively). Its anti-anaerobic activity, together with its efficacy against aerobes, should make flomoxef a useful adjunct to the arsenal of modern antibiotic therapy.

46 CFR 190.15-15 - Ventilation for living spaces and quarters.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Ventilation for living spaces and quarters. 190.15-15... VESSELS CONSTRUCTION AND ARRANGEMENT Ventilation § 190.15-15 Ventilation for living spaces and quarters. (a) All living spaces shall be adequately ventilated in a manner suitable to the purpose of the space...

46 CFR 190.15-15 - Ventilation for living spaces and quarters.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 7 2011-10-01 2011-10-01 false Ventilation for living spaces and quarters. 190.15-15... VESSELS CONSTRUCTION AND ARRANGEMENT Ventilation § 190.15-15 Ventilation for living spaces and quarters. (a) All living spaces shall be adequately ventilated in a manner suitable to the purpose of the space...

46 CFR 190.15-15 - Ventilation for living spaces and quarters.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 7 2014-10-01 2014-10-01 false Ventilation for living spaces and quarters. 190.15-15... VESSELS CONSTRUCTION AND ARRANGEMENT Ventilation § 190.15-15 Ventilation for living spaces and quarters. (a) All living spaces shall be adequately ventilated in a manner suitable to the purpose of the space...

46 CFR 190.15-15 - Ventilation for living spaces and quarters.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 7 2012-10-01 2012-10-01 false Ventilation for living spaces and quarters. 190.15-15... VESSELS CONSTRUCTION AND ARRANGEMENT Ventilation § 190.15-15 Ventilation for living spaces and quarters. (a) All living spaces shall be adequately ventilated in a manner suitable to the purpose of the space...

46 CFR 190.15-15 - Ventilation for living spaces and quarters.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 7 2013-10-01 2013-10-01 false Ventilation for living spaces and quarters. 190.15-15... VESSELS CONSTRUCTION AND ARRANGEMENT Ventilation § 190.15-15 Ventilation for living spaces and quarters. (a) All living spaces shall be adequately ventilated in a manner suitable to the purpose of the space...

Antimicrobial susceptibility of pathogens isolated from surgical site infections in Japan: Comparison of data from nationwide surveillance studies conducted in 2010 and 2014-2015.

PubMed

Takesue, Yoshio; Kusachi, Shinya; Mikamo, Hiroshige; Sato, Junko; Watanabe, Akira; Kiyota, Hiroshi; Iwata, Satoshi; Kaku, Mitsuo; Hanaki, Hideaki; Sumiyama, Yoshinobu; Kitagawa, Yuko; Mizuguchi, Toru; Ambo, Yoshiyasu; Konosu, Masafumi; Ishibashi, Keiichiro; Matsuda, Akihisa; Hase, Kazuo; Harihara, Yasushi; Okabayashi, Koji; Seki, Shiko; Hara, Takuo; Matsui, Koshi; Matsuo, Yoichi; Kobayashi, Minako; Kubo, Shoji; Uchiyama, Kazuhisa; Shimizu, Junzo; Kawabata, Ryohei; Ohge, Hiroki; Akagi, Shinji; Oka, Masaaki; Wakatsuki, Toshiro; Suzuki, Katsunori; Okamoto, Kohji; Yanagihara, Katsunori

2017-06-01

A nationwide survey was conducted in Japan from 2014 to 2015 to investigate the antimicrobial susceptibility of pathogens isolated from surgical site infections (SSI). The resulting data were compared with that obtained in an earlier survey, conducted in 2010. Seven main organisms were collected, and 883 isolates were studied. A significant reduction in methicillin resistance was observed among Staphylococcus aureus isolates, dropping from 72.5% in 2010 to 53.8% in 2014-2015 (p < 0.001). MRSA isolates with a vancomycin minimum inhibitory concentration (MIC) of 2 μg/mL accounted for 1.2% of all MRSA isolates, which was significantly lower than in 2010 (9.7%, p = 0.029). Of the Escherichia coli isolates, 23.0% produced an extended spectrum β-lactamase (ESBL) in the 2014-2015 survey, which was a significant increase from 9.5% in 2010 (p = 0.011). The geometric mean MICs for ESBL-producing isolates were 0.07 μg/mL for meropenem, 9.51 μg/mL for tazobactam/piperacillin, 0.15 μg/mL for flomoxef, and 1.56 μg/mL for gentamycin. There was a significant increase in the isolation rate of non-fragilis Bacteroides among Bacteroides fragilis group species between the two study periods (35.2% vs. 53.1%, p = 0.007). More than 90% of isolates belonging to the B. fragilis group remained susceptible to tazobactam/piperacillin, meropenem, and metronidazole. In contrast, lower levels of susceptibility were observed for cefmetazole (49.6%), moxifloxacin (61.9%), and clindamycin (46.9%). Non-fragilis Bacteroides isolates had lower rates of antibiotic susceptibility compared with B. fragilis. Overall, the surveillance data clarified trends in antimicrobial susceptibility for organisms commonly associated with SSI. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

The crystal structure of the mixed-layer Aurivillius phase Bi 5Ti 1.5W 1.5O 15

NASA Astrophysics Data System (ADS)

Tellier, J.; Boullay, Ph.; Créon, N.; Mercurio, D.

2005-09-01

The crystal structure of the 1+2 mixed-layer Aurivillius phase Bi 5Ti 1.5W 1.5O 15 (SG I2cm n o 46: -cba, Z=4, a=5.4092(3) Å, b=5.3843(3) Å and c=41.529(3) Å) consisting of the ordered intergrowth of one and two octahedra thick perovskite-type blocks separated by [Bi 2O 2] 2+ slabs is reported. Supported by an electron diffraction investigation and, using the Rietveld analysis, it is shown that this compound should be described using a I-centering lattice in agreement with the generalised structural model of the Aurivillius type compounds recently presented by the authors. The structure of this Bi 5Ti 1.5W 1.5O 15 phase is analyzed in comparison with the related simple members (Bi 2WO 6 and Bi 3Ti 1.5W 0.5O 9). The crystal structure of Bi 3Ti 1.5W 0.5O 9 is also reported.

15 CFR 15.24 - Policy.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Support Allotments of NOAA Corps Officers § 15.24 Policy. (a) It is the policy of the Department of Commerce to require Commissioned Officers of the NOAA Corps on active duty to make involuntary allotments...

15 CFR 15.24 - Policy.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Support Allotments of NOAA Corps Officers § 15.24 Policy. (a) It is the policy of the Department of Commerce to require Commissioned Officers of the NOAA Corps on active duty to make involuntary allotments...

15 CFR 15.24 - Policy.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Support Allotments of NOAA Corps Officers § 15.24 Policy. (a) It is the policy of the Department of Commerce to require Commissioned Officers of the NOAA Corps on active duty to make involuntary allotments...

15 CFR 15.24 - Policy.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Support Allotments of NOAA Corps Officers § 15.24 Policy. (a) It is the policy of the Department of Commerce to require Commissioned Officers of the NOAA Corps on active duty to make involuntary allotments...

15 CFR 15.24 - Policy.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Support Allotments of NOAA Corps Officers § 15.24 Policy. (a) It is the policy of the Department of Commerce to require Commissioned Officers of the NOAA Corps on active duty to make involuntary allotments...

Simultaneous isolation of anaerobic bacteria from udder abscesses and mastitic milk in lactating dairy cows.

PubMed

Greeff, A S; du Preez, J H

1985-12-01

A variety of non-sporulating anaerobic bacterial species were isolated from udder abscesses in 10 lactating dairy cows. Fifty percent of the abscesses yielded multiple anaerobic species and the other 50% only 1 species. The anaerobic bacteria, however, were always accompanied by classical facultative anaerobic mastitogenic bacteria. In four of the five cows also afflicted with mastitis in the quarters with abscesses, the anaerobic and facultative anaerobic bacteria were identical. Peptococcus indolicus was the most commonly isolated organism followed by Eubacterium and Bacteroides spp. Bacteroides fragilis was resistant to penicillin, ampicillin and tetracycline.

46 CFR 52.15-1 - General (modifies PWT-1 through PWT-15).

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 2 2014-10-01 2014-10-01 false General (modifies PWT-1 through PWT-15). 52.15-1 Section 52.15-1 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Requirements for Watertube Boilers § 52.15-1 General (modifies PWT-1 through PWT-15). Watertube boilers and parts thereof shall be as...

46 CFR 52.15-1 - General (modifies PWT-1 through PWT-15).

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false General (modifies PWT-1 through PWT-15). 52.15-1 Section 52.15-1 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Requirements for Watertube Boilers § 52.15-1 General (modifies PWT-1 through PWT-15). Watertube boilers and parts thereof shall be as...

46 CFR 52.15-1 - General (modifies PWT-1 through PWT-15).

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 2 2013-10-01 2013-10-01 false General (modifies PWT-1 through PWT-15). 52.15-1 Section 52.15-1 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Requirements for Watertube Boilers § 52.15-1 General (modifies PWT-1 through PWT-15). Watertube boilers and parts thereof shall be as...

46 CFR 52.15-1 - General (modifies PWT-1 through PWT-15).

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 2 2012-10-01 2012-10-01 false General (modifies PWT-1 through PWT-15). 52.15-1 Section 52.15-1 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Requirements for Watertube Boilers § 52.15-1 General (modifies PWT-1 through PWT-15). Watertube boilers and parts thereof shall be as...

46 CFR 52.15-1 - General (modifies PWT-1 through PWT-15).

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false General (modifies PWT-1 through PWT-15). 52.15-1 Section 52.15-1 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Requirements for Watertube Boilers § 52.15-1 General (modifies PWT-1 through PWT-15). Watertube boilers and parts thereof shall be as...

Comparison of the intestinal mucosal microbiota in dogs diagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment.

PubMed

Kalenyak, Katja; Isaiah, Anitha; Heilmann, Romy M; Suchodolski, Jan S; Burgener, Iwan A

2018-02-01

We report the first study to evaluate the intestinal mucosal microbiota of dogs with inflammatory bowel disease (IBD) and dogs with food-responsive diarrhea (FRD) before and after treatment. It was hypothesized that differences in the microbial composition exist between both disease groups and within groups pre- vs. post-treatment. Duodenal and colonic biopsies were obtained endoscopically from 24 dogs (15 FRD, 9 IBD) before and after treatment. The intestinal microbiota was evaluated by Illumina sequencing of the bacterial 16S rRNA gene. The global bacterial composition did not differ between IBD and FRD dogs, nor between treatment status. However, several bacterial taxa showed a difference in abundance. Comparing disease groups, an unclassified genus of Neisseriaceae was abundant in the duodenum in the IBD group, whereas Bilophila occurred more frequently in the duodenum and Burkholderia in the colon of FRD dogs. Comparing the microbiota pre- and post-treatment revealed Enterococcus, Corynebacterium and Proteobacteria to be enriched in the duodenum of FRD dogs pre-treatment, while Bacteroides was abundant in the colon post-treatment. In dogs with IBD, Bacteroides also reached significant abundance in the colon post-treatment. In conclusion, some differences in individual bacterial taxa were identified between IBD and FRD dogs and between treatment status. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Immunosuppression induced in vivo by 15 hydroxyeicosatetraenoic acid (15 HETE).

PubMed

Aldigier, J C; Gualde, N; Mexmain, S; Chable-Rabinovitch, H; Ratinaud, M H; Rigaud, M

1984-01-01

We have investigated the in vivo effects of 15 HETE on C57Bl/6 (H-2b) mice injected IP daily with this product. After that the 15 HETE treated animals and the controls were challenged in vivo by DBA/2 (H-2d) cells. Splenocytes from 15 HETE injected animals were either stimulated in vitro by lectins or cocultivated with DBA/2 irradiated splenocytes. It was observed that the response of splenocytes from in vivo treated animals is weaker than the control's response. The data suggest that 15 HETE induce the generation of suppressor cells.

49 CFR 15.15 - SSI disclosed by DOT.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Transportation Office of the Secretary of Transportation PROTECTION OF SENSITIVE SECURITY INFORMATION § 15.15 SSI... Freedom of Information Act (5 U.S.C. 552), the Privacy Act (5 U.S.C. 552a), and other laws, records... persons without a need to know. (b) Disclosure under the Freedom of Information Act and the Privacy Act...

49 CFR 15.15 - SSI disclosed by DOT.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Transportation Office of the Secretary of Transportation PROTECTION OF SENSITIVE SECURITY INFORMATION § 15.15 SSI... Freedom of Information Act (5 U.S.C. 552), the Privacy Act (5 U.S.C. 552a), and other laws, records... persons without a need to know. (b) Disclosure under the Freedom of Information Act and the Privacy Act...

15. "TEST STANDS NOS. 11, 13, & 15; STRUCTURAL STEEL; ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. "TEST STANDS NOS. 1-1, 1-3, & 1-5; STRUCTURAL STEEL; PLAN & DETAILS." Specifications No. ENG 04-353-50-10; Drawing No. 60-09-04; no sheet number within title block. D.O. SERIES 1109/34, Rev. A. Stamped: RECORD DRAWING - AS CONSTRUCTED. Below stamp: Contract DA-04353 Eng. 177, Rev. A, no change; Date: 21 Dec. 1951. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Test Stand 1-5, Test Area 1-115, northwest end of Saturn Boulevard, Boron, Kern County, CA

[Do prisms according to Hans-Joachim Haase improve stereoacuity?].

PubMed

Kromeier, Miriam; Schmitt, Christina; Bach, Michael; Kommerell, Guntram

2002-06-01

The "Measuring and Correcting Methodology" after H.-J. Haase (MKH) aims at converting "fixation disparity" into bicentral fixation, using prismatic spectacles. In the context of the MKH, fixation disparity is diagnosed by a series of subjective tests. According to H.-J. Haase, a long-standing fixation disparity can lead to "disparate correspondence" between the central areas of both retinae, which consolidates the fixation disparity and gradually converts a "young" into an "old fixation disparity". In "old fixation disparity" it is thought that bicentral fixation does not occur anymore, so that stereoacuity is impaired. However, prismatic spectacles can, according to H.-J. Haase, restitute bicentral fixation and consequently improve stereoacuity, even in some cases of "old fixation disparity". Ten non-strabismic subjects with a visual acuity of >/= 1.0 in both eyes were examined. It turned out that all ten had, according to MKH, a "disparate correspondence", 5 subjects with a "young" and 5 with an "old fixation disparity". According to the MKH, a correcting prism was determined. All 10 subjects underwent the automatic Freiburg Stereoacuity Test, without and with the MKH-prism. Without the MKH-prism, the stereoscopic threshold ranged between 1.5 and 14.5 arcsec. With the MKH-prism, the values were not significantly different. Stereoacuity ranged between good and excellent in the 5 subjects with "young" as well as in the 5 subjects with "old fixation disparity". The MKH-prism did not improve the stereoacuity in any of the subjects. These results cast doubt on Haase's assertion that an "old fixation disparity" implies a reduced stereoacuity. Hence, the premise for a benefit of the MKH-prism with respect of stereoacuity is not substantiated. In the 5 subjects with a "young fixation disparity", the good stereoacuity is consistent with Haase's theory, so that a benefit of the MKH-prism for stereoacuity was not expected. In previous studies, stereoacuity was found to be

Solution-processed, barrier-confined, and 1D nanostructure supported quasi-quantum well with large photoluminescence enhancement.

PubMed

Yan, Keyou; Zhang, Lixia; Kuang, Qin; Wei, Zhanhua; Yi, Ya; Wang, Jiannong; Yang, Shihe

2014-04-22

Planar substrate supported semiconductor quantum well (QW) structures are not amenable to manipulation in miniature devices, while free-standing QW nanostructures, e.g., ultrathin nanosheets and nanoribbons, suffer from mechanical and environmental instability. Therefore, it is tempting to fashion high-quality QW structures on anisotropic and mechanically robust supporting nanostructures such as nanowires and nanoplates. Herein, we report a solution quasi-heteroepitaxial route for growing a barrier-confined quasi-QW structure (ZnSe/CdSe/ZnSe) on the supporting arms of ZnO nanotetrapods, which have a 1D nanowire structure, through the combination of ion exchange and successive deposition assembly. This resulted in highly crystalline and highly oriented quasi-QWs along the whole axial direction of the arms of the nanotetrapod because a transition buffer layer (Zn(x)Cd(1-x)Se) was formed and in turn reduced the lattice mismatch and surface defects. Significantly, such a barrier-confined QW emits excitonic light ∼17 times stronger than the heterojunction (HJ)-type structure (ZnSe/CdSe, HJ) at the single-particle level. Time-resolved photoluminescence from ensemble QWs exhibits a lifetime of 10 ns, contrasting sharply with ∼300 ps for the control HJ sample. Single-particle PL and Raman spectra suggest that the barrier layer of QW has completely removed the surface trap states on the HJ and restored or upgraded the photoelectric properties of the semiconductor layer. Therefore, this deliberate heteroepitaxial growth protocol on the supporting nanotetrapod has realized a several micrometer long QW structure with high mechanical robustness and high photoelectric quality. We envision that such QWs integrated on 1D nanostructures will largely improve the performance of solar cells and bioprobes, among others.

X-15 cockpit

NASA Technical Reports Server (NTRS)

1963-01-01

This photo shows the X-15 cockpit. The X-15 was unique for many reasons, including the fact that it had two types of controls for the pilot. For flight in the dense air of the usable atmosphere, the X-15 used conventional aerodynamic controls such as rudder surfaces on the vertical stabilizers to control yaw and movable horizontal stabilizers to control pitch when moving in synchronization or roll when moved differentially. For flight in the thin air outside of the appreciable Earth's atmosphere, the X-15 used a reaction control system. Hydrogen peroxide thrust rockets located on the nose of the aircraft provided pitch and yaw control. Those on the wing provided roll control. The conventional aerodynamic controls used a stick, located in the middle of the floor, and pedals. The reaction control system used a side arm controller, seen in this photo on the left. The X-15 was a rocket-powered aircraft 50 ft long with a wingspan of 22 ft. It was a missile-shaped vehicle with an unusual wedge-shaped vertical tail, thin stubby wings, and unique side fairings that extended along the side of the fuselage. The X-15 weighed about 14,000 lb empty and approximately 34,000 lb at launch. The XLR-99 rocket engine, manufactured by Thiokol Chemical Corp., was pilot controlled and was capable of developing 57,000 lb of thrust. North American Aviation built three X-15 aircraft for the program. The X-15 research aircraft was developed to provide in-flight information and data on aerodynamics, structures, flight controls, and the physiological aspects of high-speed, high-altitude flight. A follow-on program used the aircraft as a testbed to carry various scientific experiments beyond the Earth's atmosphere on a repeated basis. Because of the large fuel consumption, the X-15 was air launched from a B-52 aircraft at 45,000 ft and a speed of about 500 mph. Depending on the mission, the rocket engine provided thrust for the first 80 to 120 sec of flight. The remainder of the normal 10 to