Distribution and Genetic Variability of Fusarium oxysporum Associated with Tomato Diseases in Algeria and a Biocontrol Strategy with Indigenous Trichoderma spp.

PubMed

Debbi, Ali; Boureghda, Houda; Monte, Enrique; Hermosa, Rosa

2018-01-01

Fifty fungal isolates were sampled from diseased tomato plants as result of a survey conducted in seven tomato crop areas in Algeria from 2012 to 2015. Morphological criteria and PCR-based identification, using the primers PF02 and PF03, assigned 29 out of 50 isolates to Fusarium oxysporum ( Fo ). The banding patterns amplified for genes SIX1, SIX3 and SIX4 served to identify races 2 and 3 of Fo f. sp. lycopersici (FOL), and Fo f. sp. radicis lycopersici (FORL) among the Algerian isolates. All FOL isolates showed pathogenicity on the susceptible tomato cv. "Super Marmande," while nine of out 10 Algerian FORL isolates were pathogenic on tomato cv. "Rio Grande." Inter simple sequence repeat (ISSR) fingerprints showed high genetic diversity among Algerian Fo isolates. Seventeen Algerian Trichoderma isolates were also obtained and assigned to the species T. asperellum (12 isolates), T. harzianum (four isolates) and T. ghanense (one isolate) based on ITS and tef1 α gene sequences. Different in vitro tests identified the antagonistic potential of native Trichoderma isolates against FORL and FOL. Greenhouse biocontrol assays performed on "SM" tomato plants with T. ghanense T8 and T. asperellum T9 and T17, and three Fo isolates showed that isolate T8 performed well against FORL and FOL. This finding was based on an incidence reduction of crown and root rot and Fusarium wilt diseases by 53.1 and 48.3%, respectively.

Genetic speciation of environmental Legionella isolates in Thailand.

PubMed

Paveenkittiporn, Wantana; Dejsirilert, Surang; Kalambaheti, Thareerat

2012-10-01

Legionella-like organisms were isolated during 2003-2007 from various water resources by culturing on selective media of Wadowsky-Yee-Okuda agar. The 256 isolates were identified as belonging to the Legionella genus based on detection of 108 bp PCR product of the 5S rRNA gene, while the inclusion as Legionella pneumophila were confirmed by PCR detection of a specific mip gene region of 168 bp. The 50 isolates, identified as non-pneumophila, were then subjected to DNA tree analysis, based on mip gene of ~650 bp and rnpB genes product ranged from 304 to 354 bp. Phylogenetic tree was constructed to predict their species in relative to the available database. The isolates of which their speciation, based on those two genes were inconclusive, were then investigated for the almost full-length of 16S rRNA sequences. The isolates were assigned as 16 known Legionella species, and proposed seven novel species based on their unique 16S rRNA sequence. Copyright © 2012 Elsevier B.V. All rights reserved.

High-purity and label-free isolation of circulating tumor cells (CTCs) in a microfluidic platform by using optically-induced-dielectrophoretic (ODEP) force.

PubMed

Huang, Song-Bin; Wu, Min-Hsien; Lin, Yen-Heng; Hsieh, Chia-Hsun; Yang, Chih-Liang; Lin, Hung-Chih; Tseng, Ching-Ping; Lee, Gwo-Bin

2013-04-07

Negative selection-based circulating tumor cell (CTC) isolation is believed valuable to harvest more native, and in particular all possible CTCs without biases relevant to the properties of surface antigens on the CTCs. Under such a cell isolation strategy, however, the CTC purity is normally compromised. To address this issue, this study reports the integration of optically-induced-dielectrophoretic (ODEP) force-based cell manipulation, and a laminar flow regime in a microfluidic platform for the isolation of untreated, and highly pure CTCs after conventional negative selection-based CTC isolation. In the design, six sections of moving light-bar screens were continuously and simultaneously exerted in two parallel laminar flows to concurrently separate the cancer cells from the leukocytes based on their size difference and electric properties. The separated cell populations were further partitioned, delivered, and collected through the two flows. With this approach, the cancer cells can be isolated in a continuous, effective, and efficient manner. In this study, the operating conditions of ODEP for the manipulation of prostate cancer (PC-3) and human oral cancer (OEC-M1) cells, and leukocytes with minor cell aggregation phenomenon were first characterized. Moreover, performances of the proposed method for the isolation of cancer cells were experimentally investigated. The results showed that the presented CTC isolation scheme was able to isolate PC-3 cells or OEC-M1 cells from a leukocyte background with high recovery rate (PC-3 cells: 76-83%, OEC-M1 cells: 61-68%), and high purity (PC-3 cells: 74-82%, OEC-M1 cells: 64-66%) (set flow rate: 0.1 μl min(-1) and sample volume: 1 μl). The latter is beyond what is currently possible in the conventional CTC isolations. Moreover, the viability of isolated cancer cells was evaluated to be as high as 94 ± 2%, and 95 ± 3% for the PC-3, and OEC-M1 cells, respectively. Furthermore, the isolated cancer cells were also shown to preserve their proliferative capability. As a whole, this study has presented an ODEP-based microfluidic platform that is capable of isolating CTCs in a continuous, label-free, cell-friendly, and particularly highly pure manner. All these traits are found particularly meaningful for exploiting the harvested CTCs for the subsequent cell-based, or biochemical assays.

Multi-resonant electromagnetic shunt in base isolation for vibration damping and energy harvesting

NASA Astrophysics Data System (ADS)

Pei, Yalu; Liu, Yilun; Zuo, Lei

2018-06-01

This paper investigates multi-resonant electromagnetic shunts applied to base isolation for dual-function vibration damping and energy harvesting. Two multi-mode shunt circuit configurations, namely parallel and series, are proposed and optimized based on the H2 criteria. The root-mean-square (RMS) value of the relative displacement between the base and the primary structure is minimized. Practically, this will improve the safety of base-isolated buildings subjected the broad bandwidth ground acceleration. Case studies of a base-isolated building are conducted in both the frequency and time domains to investigate the effectiveness of multi-resonant electromagnetic shunts under recorded earthquake signals. It shows that both multi-mode shunt circuits outperform traditional single mode shunt circuits by suppressing the first and the second vibration modes simultaneously. Moreover, for the same stiffness ratio, the parallel shunt circuit is more effective at harvesting energy and suppressing vibration, and can more robustly handle parameter mistuning than the series shunt circuit. Furthermore, this paper discusses experimental validation of the effectiveness of multi-resonant electromagnetic shunts for vibration damping and energy harvesting on a scaled-down base isolation system.

Distribution and Genetic Variability of Fusarium oxysporum Associated with Tomato Diseases in Algeria and a Biocontrol Strategy with Indigenous Trichoderma spp.

PubMed Central

Debbi, Ali; Boureghda, Houda; Monte, Enrique; Hermosa, Rosa

2018-01-01

Fifty fungal isolates were sampled from diseased tomato plants as result of a survey conducted in seven tomato crop areas in Algeria from 2012 to 2015. Morphological criteria and PCR-based identification, using the primers PF02 and PF03, assigned 29 out of 50 isolates to Fusarium oxysporum (Fo). The banding patterns amplified for genes SIX1, SIX3 and SIX4 served to identify races 2 and 3 of Fo f. sp. lycopersici (FOL), and Fo f. sp. radicis lycopersici (FORL) among the Algerian isolates. All FOL isolates showed pathogenicity on the susceptible tomato cv. “Super Marmande,” while nine of out 10 Algerian FORL isolates were pathogenic on tomato cv. “Rio Grande.” Inter simple sequence repeat (ISSR) fingerprints showed high genetic diversity among Algerian Fo isolates. Seventeen Algerian Trichoderma isolates were also obtained and assigned to the species T. asperellum (12 isolates), T. harzianum (four isolates) and T. ghanense (one isolate) based on ITS and tef1α gene sequences. Different in vitro tests identified the antagonistic potential of native Trichoderma isolates against FORL and FOL. Greenhouse biocontrol assays performed on “SM” tomato plants with T. ghanense T8 and T. asperellum T9 and T17, and three Fo isolates showed that isolate T8 performed well against FORL and FOL. This finding was based on an incidence reduction of crown and root rot and Fusarium wilt diseases by 53.1 and 48.3%, respectively. PMID:29515557

Analysis of the Seismic Performance of Isolated Buildings according to Life-Cycle Cost

PubMed Central

Dang, Yu; Han, Jian-ping; Li, Yong-tao

2015-01-01

This paper proposes an indicator of seismic performance based on life-cycle cost of a building. It is expressed as a ratio of lifetime damage loss to life-cycle cost and determines the seismic performance of isolated buildings. Major factors are considered, including uncertainty in hazard demand and structural capacity, initial costs, and expected loss during earthquakes. Thus, a high indicator value indicates poor building seismic performance. Moreover, random vibration analysis is conducted to measure structural reliability and evaluate the expected loss and life-cycle cost of isolated buildings. The expected loss of an actual, seven-story isolated hospital building is only 37% of that of a fixed-base building. Furthermore, the indicator of the structural seismic performance of the isolated building is much lower in value than that of the structural seismic performance of the fixed-base building. Therefore, isolated buildings are safer and less risky than fixed-base buildings. The indicator based on life-cycle cost assists owners and engineers in making investment decisions in consideration of structural design, construction, and expected loss. It also helps optimize the balance between building reliability and building investment. PMID:25653677

Analysis of the seismic performance of isolated buildings according to life-cycle cost.

PubMed

Dang, Yu; Han, Jian-Ping; Li, Yong-Tao

2015-01-01

This paper proposes an indicator of seismic performance based on life-cycle cost of a building. It is expressed as a ratio of lifetime damage loss to life-cycle cost and determines the seismic performance of isolated buildings. Major factors are considered, including uncertainty in hazard demand and structural capacity, initial costs, and expected loss during earthquakes. Thus, a high indicator value indicates poor building seismic performance. Moreover, random vibration analysis is conducted to measure structural reliability and evaluate the expected loss and life-cycle cost of isolated buildings. The expected loss of an actual, seven-story isolated hospital building is only 37% of that of a fixed-base building. Furthermore, the indicator of the structural seismic performance of the isolated building is much lower in value than that of the structural seismic performance of the fixed-base building. Therefore, isolated buildings are safer and less risky than fixed-base buildings. The indicator based on life-cycle cost assists owners and engineers in making investment decisions in consideration of structural design, construction, and expected loss. It also helps optimize the balance between building reliability and building investment.

Intraspecific variation in Cryptocaryon irritans.

PubMed

Diggles, B K; Adlard, R D

1997-01-01

Intraspecific variation in the ciliate Cryptocaryon irritans was examined using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA) combined with developmental and morphological characters. Amplified rDNA sequences consisting of 151 bases of the flanking 18 S and 5.8 S regions, and the entire ITS-1 region (169 or 170 bases), were determined and compared for 16 isolates of C. irritans from Australia, Israel and the USA. There was one variable base between isolates in the 18 S region and 11 variable bases in the ITS-1 region. Despite their similar morphology, significant sequence variation (4.1% divergence) and developmental differences indicate that Australian C. irritans isolates from estuarine (Moreton Bay) and coral reef (Heron Island) environments are distinct. The Heron Island isolate was genetically closer to morphologically dissimilar isolates from Israel (1.8% divergence) and the USA (2.3% divergence) than it was to the Moreton Bay isolates. Three isolates maintained in our laboratory since February 1994 differed in sequence from earlier laboratory isolates (2.9% to 3.5% divergence), even though all were similar morphologically and originated from the same source. During this time the sequence of the isolates from wild fish in Moreton Bay remained unchanged. These genetic differences indicate the existence of a founder effect in laboratory populations of C. irritans. The genetic variation found here, combined with known morphological and developmental differences, is used to characterise four strains of C. irritans.

Identification of Isolates that Cause a Leaf Spot Disease of Brassicas as Xanthomonas campestris pv. raphani and Pathogenic and Genetic Comparison with Related Pathovars.

PubMed

Vicente, J G; Everett, B; Roberts, S J

2006-07-01

ABSTRACT Twenty-five Xanthomonas isolates, including some isolates received as either X. campestris pv. armoraciae or pv. raphani, caused discrete leaf spot symptoms when spray-inoculated onto at least one Brassica oleracea cultivar. Twelve of these isolates and four other Xanthomonas isolates were spray- and pin-inoculated onto 21 different plant species/cultivars including horseradish (Armoracia rusticana), radish (Raphanus sativus), and tomato (Lycopersicon esculentum). The remaining 13 leaf spot isolates were spray-inoculated onto a subset of 10 plant species/cultivars. The leaf spot isolates were very aggressive on several Brassica spp., radish, and tomato causing leaf spots and dark sunken lesions on the middle vein, petiole, and stem. Based on the differential reactions of several Brassica spp. and radish cultivars, the leaf spot isolates were divided into three races, with races 1 and 3 predominating. A differential series was established to determine the race-type of isolates and a gene-for-gene model based on the interaction of two avirulence genes in the pathogen races and two matching resistance genes in the differential hosts is proposed. Repetitive-DNA polymerase chain reaction-based fingerprinting was used to assess the genetic diversity of the leaf spot isolates and isolates of closely related Xanthomonas pathovars. Although there was variability within each race, the leaf spot isolates were clustered separately from the X. campestris pv. campestris isolates. We propose that X. campestris isolates that cause a nonvascular leaf spot disease on Brassica spp. should be identified as pv. raphani and not pv. armoraciae. Race-type strains and a neopathotype strain for X. campestris pv. raphani are proposed.

Containment testing of isolation rooms.

PubMed

Rydock, J P; Eian, P K

2004-07-01

Results from the tracer containment testing of four 'state-of-the-art' airborne infection isolation rooms, in a new hospital, are presented. A testing technician exited an isolation room several minutes after a small quantity of tracer gas was injected over the patient bed in that room. Easily measurable tracer gas concentrations were then found in the anterooms outside the patient rooms and corridor outside the isolation room suites. Containment factors for the isolation rooms and dilution factors in the anterooms and corridor were calculated, based on the measured tracer concentrations. These results indicate the desirability of evidence-based design standards and guidelines for assessing performance of airborne infection isolation rooms. The study also demonstrates that the tracer testing procedure yields comparable results for equivalent isolation room suites, suggesting good reproducibility of the testing method.

Successful performance of a base-isolated hospital building during the 17 January 1994 northridge earthquake

USGS Publications Warehouse

Celebi, M.

1996-01-01

The purpose of this paper is to examine the response records and thereby the performance of the base-isolated University of Southern California (USC) hospital building during the Ms = 6-8 Northridge (California) earthquake of 17 January 1994. The data retrieved from the building is the first set of data from any base-isolated building that (a) was tested to acceleration levels at the free-field similar to the zero period acceleration (ZPA) level postulated in the seismic design criteria of the building and (b) exhibits levels of relative displacement excursions which puts the isolators into the nonlinear range. The variation of the fundamental frequency as a function of changing instantaneous stiffness of the isolators is identifiable. During the shaking, the isolators (a) performed well and, having attained up to 10% hysteretic damping, effectively dissipated the incoming energy of motions and (b) reduced the drift ratios of the superstructure of the building to a maximum of 10% of the allowable, which should explain the fact that there was no damage to the structure or its contents. The primary conclusion of this study is that this base-isolated building performed well during the Northridge earthquake of 17 January 1994 when only approximately 10% of the displacement capability of the isolators were utilized. Therefore, there is every reason to believe that the building will perform well during future earthquakes in the region.

Identification and molecular epidemiology of dermatophyte isolates by repetitive-sequence-PCR-based DNA fingerprinting using the DiversiLab system in Turkey.

PubMed

Koc, A Nedret; Atalay, Mustafa A; Inci, Melek; Sariguzel, Fatma M; Sav, Hafize

2017-05-01

Dermatophyte species, isolation and identification in clinical samples are still difficult and take a long time. The identification and molecular epidemiology of dermatophytes commonly isolated in a clinical laboratory in Turkey by repetitive sequence-based PCR (rep-PCR) were assessed by comparing the results with those of reference identification. A total of 44 dermatophytes isolated from various clinical specimens of 20 patients with superficial mycoses in Kayseri and 24 patients in Hatay were studied. The identification of dermatophyte isolates was based on the reference identification and rep-PCR using the DiversiLab System (BioMerieux). The genotyping of dermatophyte isolates from different patients was determined by rep-PCR. In the identification of dermatophyte isolates, agreement between rep-PCR and conventional methods was 87.8 % ( 36 of 41). The dermatophyte strains belonged to four clones (A -D) which were determined by the use of rep-PCR. The dermatophyte strains in Clone B, D showed identical patterns with respect to the region. In conclusion, rep-PCR appears to be useful for evaluation of the identification and clonal relationships between Trichophyton rubrum species complex and Trichophyton mentagrophytes species complex isolates. The similarity and diversity of these isolates may be assessed according to different regions by rep-PCR. © 2017 Blackwell Verlag GmbH.

Upstream thinking and health promotion planning for older adults at risk of social isolation.

PubMed

Wilson, Donna M; Harris, Ashley; Hollis, Vivien; Mohankumar, Deepthi

2011-12-01

To raise awareness of social isolation, and provide an approach to first conceptualise and then prevent social isolation among older community-dwelling persons. Older adults comprise a vulnerable population for social isolation and its associated health risks. Literature review. Canada's Population Health Promotion Model was chosen as a comprehensive tool to understand and prevent social isolation. Research studies were sought to identify key health determinants and evidence-based options for preventing social isolation. Around 1 out of 6 older persons are socially isolated and three health determinants are of prime importance: (i) income and social status; (ii) personal health practices and coping skills and (iii) social support networks. Evidence-based interventions targeted to these health determinants are suggested. Nurses are a key group to advocate for actions needed to prevent social isolation. Nurses can play a vital role in minimising social isolation through a variety of educational, prevention and political lobbying activities. © 2010 Blackwell Publishing Ltd.

Phytate degrading activities of lactic acid bacteria isolated from traditional fermented food

NASA Astrophysics Data System (ADS)

Damayanti, Ema; Ratisiwi, Febiyani Ndaru; Istiqomah, Lusty; Sembiring, Langkah; Febrisiantosa, Andi

2017-03-01

The objective of this study was to determine the potential of LAB with phytate degrading activity from fermented traditional food grain-based and legume-based. Lactic acid bacteria were isolated from different sources of traditional fermented food from Gunungkidul Yogyakarta Indonesia such as gembus tempeh (tofu waste), soybean tempeh, lamtoro tempeh (Leucaena bean) and kara tempeh. Isolation of LAB was performed using Total Plate Count (TPC) on de Man Rogosa Sharpe Agar (MRSA) medium supplemented with CaCO3. They were screened for their ability to degrade myo-inositol hexaphosphate or IP6 by using qualitative streak platemethod with modified de Man Rogosa-MorpholinoPropanesulfonic Acid Sharpe (MRS-MOPS) medium contained sodium salt of phytic acid as substrate and cobalt chloride staining (plate assay) method. The selected isolates were further assayed for phytase activities using quantitative method with spectrophotometer and the two selected isolates growth were optimized. Furthermore, thhe isolates that shown the highest phytase activity was characterized and identified using API 50 CH kitand 16S rRNA gene sequencing. The results showed that there were 18 LAB isolates obtained from samplesand 13 isolates were able to degrade sodium phytate based on qualitative screening. According to quantitative assay, the highest phytate degrading activities were found in TG-2(23.562 U/mL) and TG-1 (19.641 U/mL) isolated from gembus tempeh. The phytate activity of TG-2 was optimum at 37 °C with agitation, while the phytate activity of TG-1 was optimum at 45 °C without agitation. Characterization and identification of TG-2 isolate with the highest phytate degrading activity using API 50 CH and 16S rRNA showed that TG-2had homology with Lactobacillus fermentum. It could be concluded that LAB from from fermented traditional food grain-based and legume-based produced the extracellular phytase. Keywords: lactic acid bacteria, tempeh, phytatedegrading activity

Characterization of microbial contamination in United States Air Force aviation fuel tanks.

PubMed

Rauch, Michelle E; Graef, Harold W; Rozenzhak, Sophie M; Jones, Sharon E; Bleckmann, Charles A; Kruger, Randell L; Naik, Rajesh R; Stone, Morley O

2006-01-01

Bacteria and fungi, isolated from United States Air Force (USAF) aviation fuel samples, were identified by gas chromatograph fatty acid methyl ester (GC-FAME) profiling and 16S or 18S rRNA gene sequencing. Thirty-six samples from 11 geographically separated USAF bases were collected. At each base, an above-ground storage tank, a refueling truck, and an aircraft wing tank were sampled at the lowest sample point, or sump, to investigate microbial diversity and dispersion within the fuel distribution chain. Twelve genera, including four Bacillus species and two Staphylococcus species, were isolated and identified. Bacillus licheniformis, the most prevalent organism isolated, was found at seven of the 11 bases. Of the organisms identified, Bacillus sp., Micrococcus luteus, Sphinogmonas sp., Staphylococcus sp., and the fungus Aureobasidium pullulans have previously been isolated from aviation fuel samples. The bacteria Pantoea ananatis, Arthrobacter sp., Alcaligenes sp., Kocuria rhizophilia, Leucobacter komagatae, Dietza sp., and the fungus Discophaerina fagi have not been previously reported in USAF aviation fuel. Only at two bases were the same organisms isolated from all three sample points in the fuel supply distribution chain. Isolation of previously undocumented organisms suggests either, changes in aviation fuel microbial community in response to changes in aviation fuel composition, additives and biocide use, or simply, improvements in isolation and identification techniques.

[Isolation of circulating tumor cells in blood by means of "Isolation by SizE of Tumor cells (ISET)"].

PubMed

Liadov, V K; Skrypnikova, M A; Popova, O P

2014-01-01

There is evidence of the importance of circulating tumor cells in bloodstream as a factor of poor prognosis of cancer. The optimum method for isolating and studying of these cells is not defined. The most common methods are either based on the isolation of tumor genetic material from blood or on immune-mediated isolation of epithelial tumor cells. The first group of methods is characterized by a lack of specificity, while the latter do not allow identifying a pool of cells undergone in bloodstream epithelial-mesenchymal transformation. There is presented an overview of results of clinical trials of a new technique of isolation of tumor cells from bloodstream based on the patients' blood filtration through a membrane with defined pore sizes (ISET-Isolation by SizE of Tumor cells).

Comparative Research on Characteristics of the Isolation Systems with Dry Friction Damping and with Vicious Damping under Base Excitation

NASA Astrophysics Data System (ADS)

Hou, Junfang; jing, Min; Zhang, Weihua; Lu, Yahui; He, Haiwen

2017-12-01

As for the isolation problem of electronic equipments on vehicle, the vibration response characteristics of dry friction damping isolation system under base displacement excitation was analyzed in theory by harmonic balance method, and the displacement response was compared between the isolation systems with dry friction damping and vicious damping separately. The results show that the isolation system with small dry friction damping can’t meet the demands of displacement reduction close to the natural frequency, and it can realize full-frequency vibration isolation by improving dry friction damping when the lock frequency passes beyond the resonance frequency band. The results imply that the damping mechanism of dry friction isolator can’t be described only by dry friction damping, and the composite damping with dry friction and vicious damping is more appropriate.

Anhydronium bases from Rauvolfia serpentina.

PubMed

Wachsmuth, Oliver; Matusch, Rudolf

2002-11-01

Five anhydronium bases were isolated by preparative HPLC from a methanolic extract of Rauvolfia serpentina roots. For the first time 3,4,5,6-tetradehydroyohimbine, 3,4,5,6-tetradehydro-(Z)-geissoschizol, 3,4,5,6-tetradehydrogeissoschizol and 3,4,5,6-tetradehydrogeissoschizine-17-O-beta-D-glucopyranoside were isolated from a natural source. In addition, the well-known anhydronium base serpentine was isolated. The structures of the compounds were determined by 1H and 13C NMR, MS and UV.

Streptococcus loxodontisalivarius sp. nov. and Streptococcus saliviloxodontae sp. nov., isolated from oral cavities of elephants.

PubMed

Saito, Masanori; Shinozaki-Kuwahara, Noriko; Hirasawa, Masatomo; Takada, Kazuko

2014-09-01

Four Gram-stain-positive, catalase-negative, coccoid-shaped organisms were isolated from elephant oral cavities. The isolates were tentatively identified as streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus. Two isolates (NUM 6304(T) and NUM 6312) were related most closely to Streptococcus salivarius with 96.8 % and 93.1 % similarity based on the 16S rRNA gene and the RNA polymerase β subunit encoding gene (rpoB), respectively, and to Streptococcus vestibularis with 83.7 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates (NUM 6306(T) and NUM 6318) were related most closely to S. vestibularis with 97.0 % and 82.9 % similarity based on the 16S rRNA and groEL genes, respectively, and to S. salivarius with 93.5 % similarity based on the rpoB gene. Based on phylogenetic and phenotypic evidence, these isolates are suggested to represent novel species of the genus Streptococcus, for which the names Streptococcus loxodontisalivarius sp. nov. (type strain NUM 6304(T) = JCM 19287(T) = DSM 27382(T)) and Streptococcus saliviloxodontae sp. nov. (type strain NUM 6306(T) = JCM 19288(T) = DSM 27513(T)) are proposed. © 2014 IUMS.

Effect of a Near Fault on the Seismic Response of a Base-Isolated Structure with a Soft Storey

NASA Astrophysics Data System (ADS)

Athamnia, B.; Ounis, A.; Abdeddaim, M.

2017-12-01

This study focuses on the soft-storey behavior of RC structures with lead core rubber bearing (LRB) isolation systems under near and far-fault motions. Under near-fault ground motions, seismic isolation devices might perform poorly because of large isolator displacements caused by large velocity and displacement pulses associated with such strong motions. In this study, four different structural models have been designed to study the effect of soft-storey behavior under near-fault and far-fault motions. The seismic analysis for isolated reinforced concrete buildings is carried out using a nonlinear time history analysis method. Inter-story drifts, absolute acceleration, displacement, base shear forces, hysteretic loops and the distribution of plastic hinges are examined as a result of the analysis. These results show that the performance of a base isolated RC structure is more affected by increasing the height of a story under nearfault motion than under far-fault motion.

Modeling and semi-active fuzzy control of magnetorheological elastomer-based isolator for seismic response reduction

NASA Astrophysics Data System (ADS)

Nguyen, Xuan Bao; Komatsuzaki, Toshihiko; Iwata, Yoshio; Asanuma, Haruhiko

2018-02-01

In this paper, a magnetorheological elastomer (MRE) based isolator was investigated to mitigate excessive vibrations in structures during seismic events. The primary objectives of this research are to propose a numerical model that expresses viscoelastic behaviors of the MRE and predict operation process of the MRE-based isolator for future design of isolator systems for various technical applications. Despite the simplicity in parameter definition in comparison to the conventional models, the proposed model works efficiently in a wide range of frequencies and amplitudes. The model consists of the following components: viscoelasticity of host MRE, magnetic field-induced property, nominal viscosity as well as high stiffness in low excitation frequency that are modeled in analogy with a standard linear solid model (Zener model), a stiffness variable spring, and a smooth Coulomb friction, respectively. Furthermore, a semi-active fuzzy controller was designed to enhance the performance of the isolator in suppressing structural vibrations. The control strategy was built to determine the command applied current. The controller is completely adequate for handling the nonlinearity of the isolator and works independently with the building structure. The efficiency of the MRE-based isolator was evaluated by the responses of the scaled building under seismic excitation. Numerical and experimental results show that the isolator accompanied with a fuzzy controller remarkably reduces the relative displacement and absolute acceleration of the scaled building compared to passive-off and passive-on cases.

Characterization of Metarhizium species and varieties based on molecular analysis, heat tolerance and cold activity

USGS Publications Warehouse

Fernandes, E.K.K.; Keyser, C.A.; Chong, J.P.; Rangel, D.E.N.; Miller, M.P.; Roberts, D.W.

2010-01-01

Aims: The genetic relationships and conidial tolerances to high and low temperatures were determined for isolates of several Metarhizium species and varieties. Methods and Results: Molecular-based techniques [AFLP and rDNA (ITS1, ITS2 and 5??8S) gene sequencing] were used to characterize morphologically identified Metarhizium spp. isolates from a wide range of sources. Conidial suspensions of isolates were exposed to wet heat (45 ?? 0??2??C) and plated on potato dextrose agar plus yeast extract (PDAY) medium. After 8-h exposure, the isolates divided clearly into two groups: (i) all isolates of Metarhizium anisopliae var. anisopliae (Ma-an) and Metarhizium from the flavoviride complex (Mf) had virtually zero conidial relative germination (RG), (ii) Metarhizium anisopliae var. acridum (Ma-ac) isolates demonstrated high heat tolerance (c. 70-100% RG). Conidial suspensions also were plated on PDAY and incubated at 5??C for 15 days, during which time RGs for Ma-an and Ma-ac isolates were virtually zero, whereas the two Mf were highly cold active (100% RG). Conclusions: Heat and cold exposures can be used as rapid tools to tentatively identify some important Metarhizium species and varieties. Significance and Impact of the Study: Identification of Metarhizium spp. currently relies primarily on DNA-based methods; we suggest a simple temperature-based screen to quickly obtain tentative identification of isolates as to species or species complexes. ?? 2009 The Society for Applied Microbiology.

Incidence of Radiologically Isolated Syndrome: A Population-Based Study.

PubMed

Forslin, Y; Granberg, T; Jumah, A Antwan; Shams, S; Aspelin, P; Kristoffersen-Wiberg, M; Martola, J; Fredrikson, S

2016-06-01

Incidental MR imaging findings resembling MS in asymptomatic individuals, fulfilling the Okuda criteria, are termed "radiologically isolated syndrome." Those with radiologically isolated syndrome are at high risk of their condition converting to MS. The epidemiology of radiologically isolated syndrome remains largely unknown, and there are no population-based studies, to our knowledge. Our aim was to study the population-based incidence of radiologically isolated syndrome in a high-incidence region for MS and to evaluate the effect on radiologically isolated syndrome incidence when revising the original radiologically isolated syndrome criteria by using the latest radiologic classification for dissemination in space. All 2272 brain MR imaging scans in 1907 persons obtained during 2013 in the Swedish county of Västmanland, with a population of 259,000 inhabitants, were blindly evaluated by a senior radiologist and a senior neuroradiologist. The Okuda criteria for radiologically isolated syndrome were applied by using both the Barkhof and Swanton classifications for dissemination in space. Assessments of clinical data were performed by a radiology resident and a senior neurologist. The cumulative incidence of radiologically isolated syndrome was 2 patients (0.1%), equaling an incidence rate of 0.8 cases per 100,000 person-years, in a region with an incidence rate of MS of 10.2 cases per 100,000 person-years. There was no difference in the radiologically isolated syndrome incidence rate when applying a modified version of the Okuda criteria by using the newer Swanton classification for dissemination in space. Radiologically isolated syndrome is uncommon in a high-incidence region for MS. Adapting the Okuda criteria to use the dissemination in space-Swanton classification may be feasible. Future studies on radiologically isolated syndrome may benefit from a collaborative approach to ensure adequate numbers of participants. © 2016 by American Journal of Neuroradiology.

Species identification and antifungal susceptibility testing of Candida bloodstream isolates from population-based surveillance studies in two U.S. cities from 2008 to 2011.

PubMed

Lockhart, Shawn R; Iqbal, Naureen; Cleveland, Angela A; Farley, Monica M; Harrison, Lee H; Bolden, Carol B; Baughman, Wendy; Stein, Betsy; Hollick, Rosemary; Park, Benjamin J; Chiller, Tom

2012-11-01

Between 2008 and 2011, population-based candidemia surveillance was conducted in Atlanta, GA, and Baltimore, MD. Surveillance had been previously performed in Atlanta in 1992 to 1993 and in Baltimore in 1998 to 2000, making this the first population-based candidemia surveillance conducted over multiple time points in the United States. From 2,675 identified cases of candidemia in the current surveillance, 2,329 Candida isolates were collected. Candida albicans no longer comprised the majority of isolates but remained the most frequently isolated species (38%), followed by Candida glabrata (29%), Candida parapsilosis (17%), and Candida tropicalis (10%). The species distribution has changed over time; in both Atlanta and Baltimore the proportion of C. albicans isolates decreased, and the proportion of C. glabrata isolates increased, while the proportion of C. parapsilosis isolates increased in Baltimore only. There were 98 multispecies episodes, with C. albicans and C. glabrata the most frequently encountered combination. The new species-specific CLSI Candida MIC breakpoints were applied to these data. With the exception of C. glabrata (11.9% resistant), resistance to fluconazole was very low (2.3% of isolates for C. albicans, 6.2% for C. tropicalis, and 4.1% for C. parapsilosis). There was no change in the proportion of fluconazole resistance between surveillance periods. Overall echinocandin resistance was low (1% of isolates) but was higher for C. glabrata isolates, ranging from 2.1% isolates resistant to caspofungin in Baltimore to 3.1% isolates resistant to anidulafungin in Atlanta. Given the increase at both sites and the higher echinocandin resistance, C. glabrata should be closely monitored in future surveillance.

Species Identification and Antifungal Susceptibility Testing of Candida Bloodstream Isolates from Population-Based Surveillance Studies in Two U.S. Cities from 2008 to 2011

PubMed Central

Iqbal, Naureen; Cleveland, Angela A.; Farley, Monica M.; Harrison, Lee H.; Bolden, Carol B.; Baughman, Wendy; Stein, Betsy; Hollick, Rosemary; Park, Benjamin J.; Chiller, Tom

2012-01-01

Between 2008 and 2011, population-based candidemia surveillance was conducted in Atlanta, GA, and Baltimore, MD. Surveillance had been previously performed in Atlanta in 1992 to 1993 and in Baltimore in 1998 to 2000, making this the first population-based candidemia surveillance conducted over multiple time points in the United States. From 2,675 identified cases of candidemia in the current surveillance, 2,329 Candida isolates were collected. Candida albicans no longer comprised the majority of isolates but remained the most frequently isolated species (38%), followed by Candida glabrata (29%), Candida parapsilosis (17%), and Candida tropicalis (10%). The species distribution has changed over time; in both Atlanta and Baltimore the proportion of C. albicans isolates decreased, and the proportion of C. glabrata isolates increased, while the proportion of C. parapsilosis isolates increased in Baltimore only. There were 98 multispecies episodes, with C. albicans and C. glabrata the most frequently encountered combination. The new species-specific CLSI Candida MIC breakpoints were applied to these data. With the exception of C. glabrata (11.9% resistant), resistance to fluconazole was very low (2.3% of isolates for C. albicans, 6.2% for C. tropicalis, and 4.1% for C. parapsilosis). There was no change in the proportion of fluconazole resistance between surveillance periods. Overall echinocandin resistance was low (1% of isolates) but was higher for C. glabrata isolates, ranging from 2.1% isolates resistant to caspofungin in Baltimore to 3.1% isolates resistant to anidulafungin in Atlanta. Given the increase at both sites and the higher echinocandin resistance, C. glabrata should be closely monitored in future surveillance. PMID:22875889

Phenotypic and molecular characterization of Colletotrichum species associated with anthracnose of banana (Musa spp) in Malaysia.

PubMed

Intan Sakinah, M A; Suzianti, I V; Latiffah, Z

2014-05-09

Anthracnose caused by Colletotrichum species is a common postharvest disease of banana fruit. We investigated and identified Colletotrichum species associated with anthracnose in several local banana cultivars based on morphological characteristics and sequencing of ITS regions and of the β-tubulin gene. Thirty-eight Colletotrichum isolates were encountered in anthracnose lesions of five local banana cultivars, 'berangan', 'mas', 'awak', 'rastali', and 'nangka'. Based on morphological characteristics, 32 isolates were identified as Colletotrichum gloeosporioides and 6 isolates as C. musae. C. gloeosporioides isolates were divided into two morphotypes, with differences in colony color, shape of the conidia and growth rate. Based on ITS regions and β-tubulin sequences, 35 of the isolates were identified as C. gloeosporioides and only 3 isolates as C. musae; the percentage of similarity from BLAST ranged from 95-100% for ITS regions and 97-100% for β-tubulin. C. gloeosporioides isolates were more prevalent compared to C. musae. This is the first record of C. gloeosporioides associated with banana anthracnose in Malaysia. In a phylogenetic analysis of the combined dataset of ITS regions and β-tubulin using a maximum likelihood method, C. gloeosporioides and C. musae isolates were clearly separated into two groups. We concluded that C. gloeosporioides and C. musae isolates are associated with anthracnose in the local banana cultivars and that C. gloeosporioides is more prevalent than C. musae.

Isolation and Characterization of Oil-Degrading Bacteria from One of South Sumatera’s Oilfield

NASA Astrophysics Data System (ADS)

Purwasena, I. A.; Astuti, D. I.; Fatmawati, R.; Afinanisa, Q.

2018-01-01

Microbial Enhanced Oil Recovery (MEOR) is a tertiary oil recovery method that utilizes microbes to enhance oil production. This research was focused on the isolation and characterization of indigenous bacteria from a South Sumatra’s oilfield which were able to degrade heavy crude oil and decrease oil viscosity. The total of 33 colonies were successfully isolated based on sequential isolation method and screened based on oil degradation activity and SARA analysis. Isolate G3, G7, and N6 were choosen as the best candidate as they were able to reduce oil viscosity up to 22,67%; 23,14%; and 24,36% respectively. Based on 16S rRNA analysis, isolate G3 which was able to degrade aromatic fraction (38,27%) and resin (29,26%) was identified as Pseudoxhantomonas taiwanensis. Isolate G7 which degraded aromatic fraction (61,14%) was identified as Brevibacillus agri while N6 which degraded asphaltene fraction (51.76%) was identified as Bacillus subtilis. In addition, the change in nalkana fraction (C11 - C28) abundance relative to phytan showed that all of the bacterial isolates were able to change those fractions of crude oil. This study showed that three bacterial species isolated from South Sumatran Oilfield were able to degrade heavier fraction of crude oil and reduce its viscosity. This result suggests that those bacteria are highly potential to be applied for MEOR technology.

Multiple criteria-based screening of Trichoderma isolates for biological control of Botrytis cinerea on tomato

USDA-ARS?s Scientific Manuscript database

Seventy-two isolates of Trichoderma were obtained from Hubei Province of China and identified to species based on the ITS-rDNA sequences. The isolates were initially tested for invasive growth on the colonies of Botrytis cinerea in the dual cultures with B. cinerea on potato dextrose agar at 20°C. T...

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

Sesigur, Haluk; Cili, Feridun

Seismic isolation is an effective design strategy to mitigate the seismic hazard wherein the structure and its contents are protected from the damaging effects of an earthquake. This paper presents the Hangar Project in Sabiha Goekcen Airport which is located in Istanbul, Turkey. Seismic isolation system where the isolation layer arranged at the top of the columns is selected. The seismic hazard analysis, superstructure design, isolator design and testing were based on the Uniform Building Code (1997) and met all requirements of the Turkish Earthquake Code (2007). The substructure which has the steel vertical trusses on facades and RC Hmore » shaped columns in the middle axis of the building was designed with an R factor limited to 2.0 in accordance with Turkish Earthquake Code. In order to verify the effectiveness of the isolation system, nonlinear static and dynamic analyses are performed. The analysis revealed that isolated building has lower base shear (approximately 1/4) against the non-isolated structure.« less

Low cost friction seismic base-isolation of residential new masonry buildings in developing countries: A small masonry house case study

NASA Astrophysics Data System (ADS)

Habieb, A. B.; Milani, G.; Tavio, T.; Milani, F.

2017-07-01

A Finite element model was established to examine performance of a low-cost friction base-isolation system in reducing seismic vulnerability of rural buildings. This study adopts an experimental investigation of the isolation system which was conducted in India. Four friction isolation interfaces, namely, marble-marble, marble-high-density polyethylene, marble-rubber sheet, and marble-geosynthetic were involved. Those interfaces differ in static and dynamic friction coefficient obtained through previous research. The FE model was performed based on a macroscopic approach and the masonry wall is assumed as an isotropic element. In order to observe structural response of the masonry house, elastic and plastic parameters of the brick wall were studied. Concrete damage plasticity (CDP) model was adopted to determine non-linear behavior of the brick wall. The results of FE model shows that involving these friction isolation systems could much decrease response acceleration at roof level. It was found that systems with marble-marble and marble-geosynthetic interfaces reduce the roof acceleration up to 50% comparing to the system without isolation. Another interesting result is there was no damage appearing in systems with friction isolation during the test. Meanwhile a severe failure was clearly visible for a system without isolation.

Understanding Social Isolation Among Urban Aging Adults: Informing Occupation-Based Approaches.

PubMed

Hand, Carri; Retrum, Jessica; Ware, George; Iwasaki, Patricia; Moaalii, Gabe; Main, Deborah S

2017-10-01

Socially isolated aging adults are at risk of poor health and well-being. Occupational therapy can help address this issue; however, information is needed to guide such work. National surveys characterize social isolation in populations of aging adults but fail to provide meaningful information at a community level. The objective of this study is to describe multiple dimensions of social isolation and related factors among aging adults in diverse urban neighborhoods. Community-based participatory research involving a door-to-door survey of adults 50 years and older was used. Participants ( N = 161) reported social isolation in terms of small social networks (24%) and wanting more social engagement (43%). Participants aged 50 to 64 years reported the highest levels of isolation in most dimensions. Low income, poor health, lack of transportation, and infrequent information access appeared linked to social isolation. Occupational therapists can address social isolation in similar urban communities through policy and practice that facilitate social engagement and network building.

Detection of tet(M) and tet(O) using the polymerase chain reaction in bacteria isolated from patients with periodontal disease.

PubMed

Olsvik, B; Olsen, I; Tenover, F C

1995-04-01

The polymerase chain reaction was used to examine 114 tetracycline-resistant anaerobic and facultative anaerobic bacterial isolates from patients with periodontal disease for the tet(M) and tet(O) genes. A 740-base-pair fragment of the tet(M) gene was amplified from 84 of 114 isolates, and a 519-base-pair fragment of the tet(O) gene was amplified from 13 streptococcal isolates. Six of 7 tetracycline-resistant isolates of Veillonella spp. and tetracycline-resistant isolates of Eubacterium spp. (n = 3), Eubacterium saburreum (n = 1), Streptococcus intermedius (n = 5) and Gemella morbillorum (n = 2) all harbored the tet(M) gene. The tet(M) and tet(O) negative as well as selected positive isolates were tested for the tet(K) and tet(L) genes using DNA probes. All isolates of Staphylococcus spp. (n = 11) hybridized with the tet(K) probe. None of the isolates tested hybridized with the probe for tet(L). This is the first report of the tet(M) gene in the facultative bacterium G. morbillorum and in E. saburreum.

Genetic relatedness of Brazilian Colletotrichum truncatum isolates assessed by vegetative compatibility groups and RAPD analysis.

PubMed

Sant'Anna, Juliane R; Miyamoto, Cláudia T; Rosada, Lúcia J; Franco, Claudinéia C S; Kaneshima, Edilson N; Castro-Prado, Marialba A A

2010-01-01

The genetic variation among nine soybean-originating isolates of Colletotrichum truncatum from different Brazilian states was studied. Nitrate non-utilizing (nit) mutants were obtained with potassium chlorate and used to characterize vegetative compatibility reactions, heterokaryosis and RAPD profile. Based on pairings of nit mutants from the different isolates, five vegetative complementation groups (VCG) were identified, and barriers to the formation of heterokaryons were observed among isolates derived from the same geographic area. No complementation was observed among any of the nit mutants recovered from the isolate A, which was designed heterokaryon-self-incompatible. Based on RAPD analysis, a polymorphism was detected among the wild isolate C and their nit1 and NitM mutants. RAPD amplification, with five different primers, also showed polymorphic profiles among Brazilian C. truncatum isolates. Dendrogram analysis resulted in a similarity degree ranging between 0.331 and 0.882 among isolates and identified three RAPD groups. Despite the lack of a correlation between the RAPD analysis and the vegetative compatibility grouping, results demonstrated the potential of VCG analysis to differentiate C. truncatum isolates genotypically similar when compared by RAPD.

Isolation and characterization of lignin from the oak wood bioethanol production residue for adhesives.

PubMed

Lee, Soo Jung; Kim, Hyun Joo; Cho, Eun Jin; Song, Younho; Bae, Hyeun-Jong

2015-01-01

Lignin was isolated from the residue of bioethanol production with oak wood via alkaline and catalyzed organosolv treatments at ambient temperature to improve the purity of lignin for the materials application. The isolated lignins were analyzed for their chemical composition by nitrobenzene oxidation method and their functionality was characterized via wet chemistry method, element analysis, (1)H NMR, GPC and FTIR-ATR. The isolated lignin by acid catalyzed organosolv treatment (Acid-OSL) contained a higher lignin content, aromatic proton, phenolic hydroxyl group and a lower nitrogen content that is more reactive towards chemical modification. The lignin-based adhesives were prepared and the bond strength was measured to evaluate the enhanced reactivity of lignin by the isolation. Two steps of phenolation and methylolation were applied for the modification of the isolated lignins and their tensile strengths were evaluated for the use as an adhesive. The acid catalyzed organosolv lignin-based adhesives had comparable bond strength to phenol-formaldehyde adhesives. The analysis of lignin-based adhesives by FTIR-ATR and TGA showed structural similarity to phenol adhesive. The results demonstrate that the reactivity of lignin was enhanced by isolation from hardwood bioethanol production residues at ambient temperature and it could be used in a value-added application to produce lignin-based adhesives. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparing Soy Flour Wood Adhesives to Purified Soy Protein Adhesives

Treesearch

Charles R. Frihart; Linda F. Lorenz

2013-01-01

While economics dictate that soy-based wood adhesives be made with soy flour, much of the recent literature on soy-based wood adhesives has involved using soy protein isolate. The obvious assumption is that the additional carbohydrates in the flour but not in the isolate only serve as inert diluents. Our studies have shown that the isolate can provide 10 times the wet...

Qualitative Event-Based Diagnosis: Case Study on the Second International Diagnostic Competition

NASA Technical Reports Server (NTRS)

Daigle, Matthew; Roychoudhury, Indranil

2010-01-01

We describe a diagnosis algorithm entered into the Second International Diagnostic Competition. We focus on the first diagnostic problem of the industrial track of the competition in which a diagnosis algorithm must detect, isolate, and identify faults in an electrical power distribution testbed and provide corresponding recovery recommendations. The diagnosis algorithm embodies a model-based approach, centered around qualitative event-based fault isolation. Faults produce deviations in measured values from model-predicted values. The sequence of these deviations is matched to those predicted by the model in order to isolate faults. We augment this approach with model-based fault identification, which determines fault parameters and helps to further isolate faults. We describe the diagnosis approach, provide diagnosis results from running the algorithm on provided example scenarios, and discuss the issues faced, and lessons learned, from implementing the approach

Genetic variation in Pythium myriotylum based on SNP typing and development of a PCR-RFLP detection of isolates recovered from Pythium soft rot ginger.

PubMed

Le, D P; Smith, M K; Aitken, E A B

2017-10-01

Pythium myriotylum is responsible for severe losses in both capsicum and ginger crops in Australia under different regimes. Intraspecific genomic variation within the pathogen might explain the differences in aggressiveness and pathogenicity on diverse hosts. In this study, whole genome data of four P. myriotylum isolates recovered from three hosts and one Pythium zingiberis isolate were derived and analysed for sequence diversity based on single nucleotide polymorphisms (SNPs). A higher number of true and unique SNPs occurred in P. myriotylum isolates obtained from ginger with symptoms of Pythium soft rot (PSR) in Australia compared to other P. myriotylum isolates. Overall, SNPs were discovered more in the mitochondrial genome than those in the nuclear genome. Among the SNPs, a single substitution from the cytosine (C) to the thymine (T) in the partially sequenced CoxII gene of 14 representatives of PSR P. myriotylum isolates was within a restriction site of HinP1I enzyme which was used in the PCR-RFLP for detection and identification of the isolates without sequencing. The PCR-RFLP was also sensitive to detect PSR P. myriotylum strains from artificially infected ginger without the need for isolation for pure cultures. This is the first study of intraspecific variants of Pythium myriotylum isolates recovered from different hosts and origins based on single nucleotide polymorphism (SNP) genotyping of multiple genes. The SNPs discovered provide valuable makers for detection and identification of P. myriotylum strains initially isolated from Pythium soft rot (PSR) ginger by using PCR-RFLP of the CoxII locus. The PCR-RFLP was also sensitive to detect P. myriotylum directly from PSR ginger sampled from pot trials without the need of isolation for pure cultures. © 2017 The Society for Applied Microbiology.

Genetic variation of pfhrp2 in Plasmodium falciparum isolates from Yemen and the performance of HRP2-based malaria rapid diagnostic test.

PubMed

Atroosh, Wahib M; Al-Mekhlafi, Hesham M; Al-Jasari, Adel; Sady, Hany; Al-Delaimy, Ahmed K; Nasr, Nabil A; Dawaki, Salwa; Abdulsalam, Awatif M; Ithoi, Init; Lau, Yee Ling; Fong, Mun Yik; Surin, Johari

2015-07-22

The genetic variation in the Plasmodium falciparum histidine-rich protein 2 (pfhrp2) gene that may compromise the use of pfhrp2-based rapid diagnostic tests (RDTs) for the diagnosis of malaria was assessed in P. falciparum isolates from Yemen. This study was conducted in Hodeidah and Al-Mahwit governorates, Yemen. A total of 622 individuals with fever were examined for malaria by CareStart malaria HRP2-RDT and Giemsa-stained thin and thick blood films. The Pfhrp2 gene was amplified and sequenced from 180 isolates, and subjected to amino acid repeat types analysis. A total of 188 (30.2%) participants were found positive for P. falciparum by the RDT. Overall, 12 different amino acid repeat types were identified in Yemeni isolates. Six repeat types were detected in all the isolates (100%) namely types 1, 2, 6, 7, 10 and 12 while types 9 and 11 were not detected in any of the isolates. Moreover, the sensitivity and specificity of the used PfHRP2-based RDTs were high (90.5% and 96.1%, respectively). The present study provides data on the genetic variation within the pfhrp2 gene, and its potential impact on the PfHRP2-based RDTs commonly used in Yemen. CareStart Malaria HRP2-based RDT showed high sensitivity and specificity in endemic areas of Yemen.

Study on comparison of special moment frame steel structure (SMF) and base isolation special moment frame steel structure (BI-SMF) in Indonesia

NASA Astrophysics Data System (ADS)

Setiawan, Jody; Nakazawa, Shoji

2017-10-01

This paper discusses about comparison of seismic response behaviors, seismic performance and seismic loss function of a conventional special moment frame steel structure (SMF) and a special moment frame steel structure with base isolation (BI-SMF). The validation of the proposed simplified estimation method of the maximum deformation of the base isolation system by using the equivalent linearization method and the validation of the design shear force of the superstructure are investigated from results of the nonlinear dynamic response analysis. In recent years, the constructions of steel office buildings with seismic isolation system are proceeding even in Indonesia where the risk of earthquakes is high. Although the design code for the seismic isolation structure has been proposed, there is no actual construction example for special moment frame steel structure with base isolation. Therefore, in this research, the SMF and BI-SMF buildings are designed by Indonesian Building Code which are assumed to be built at Padang City in Indonesia. The material of base isolation system is high damping rubber bearing. Dynamic eigenvalue analysis and nonlinear dynamic response analysis are carried out to show the dynamic characteristics and seismic performance. In addition, the seismic loss function is obtained from damage state probability and repair cost. For the response analysis, simulated ground accelerations, which have the phases of recorded seismic waves (El Centro NS, El Centro EW, Kobe NS and Kobe EW), adapted to the response spectrum prescribed by the Indonesian design code, that has, are used.

A Predominant and Virulent Legionella pneumophila Serogroup 1 Strain Detected in Isolates from Patients and Water in Queensland, Australia, by an Amplified Fragment Length Polymorphism Protocol and Virulence Gene-Based PCR Assays

PubMed Central

Huang, Bixing; Heron, Brett A.; Gray, Bruce R.; Eglezos, Sofroni; Bates, John R.; Savill, John

2004-01-01

In epidemiological investigations of community legionellosis outbreaks, knowledge of the prevalence, distribution, and clinical significance (virulence) of environmental Legionella isolates is crucial for interpretation of the molecular subtyping results. To obtain such information for Legionella pneumophila serogroup 1 isolates, we used the standardized amplified fragment length polymorphism (AFLP) protocol of the European Working Group on Legionella Infection to subtype L. pneumophila SG1 isolates obtained from patients and water sources in Queensland, Australia. An AFLP genotype, termed AF1, was predominant in isolates from both patients (40.5%) and water (49.0%). The second most common AFLP genotype found in water isolates was AF16 (36.5%), but this genotype was not identified in the patient isolates. When virulence gene-based PCR assays for lvh and rtxA genes were applied to the isolates from patients and water, nearly all (65 of 66) AF1 strains had both virulence genes, lvh and rtxA. In contrast, neither the lvh nor the rtxA gene was found in the AF16 strains, except for one isolate with the rtxA gene. It appears that this may explain the failure to find this genotype in the isolates from patients even though it may be common in the environment. In view of the evidence that the AF1 genotype is the most common genotype among strains found in patients and water sources in this region, any suggested epidemiological link derived from comparing the AF1 genotype from patient isolates with the AF1 genotype from environmental isolates must be interpreted and acted on with caution. The use of virulence gene-based PCR assays applied to environmental samples may be helpful in determining the infection potential of the isolates involved. PMID:15365006

Characterisation of colletotrichum species associated with anthracnose of banana.

PubMed

Zakaria, Latiffah; Sahak, Shamsiah; Zakaria, Maziah; Salleh, Baharuddin

2009-12-01

A total of 13 Colletotrichum isolates were obtained from different banana cultivars (Musa spp.) with symptoms of anthracnose. Colletotrichum isolates from anthracnose of guava (Psidium guajava) and water apple (Syzygium aqueum) were also included in this study. Based on cultural and morphological characteristics, isolates from banana and guava were identified as Colletotrichum musae and from water apple as Colletotrichum gloeosporiodes. Isolates of C. musae from banana and guava had similar banding patterns in a randomly amplified polymorphic DNA (RAPD) analysis with four random primers, and they clustered together in a UPGMA analysis. C. gloeosporiodes from water apple was clustered in a separate cluster. Based on the present study, C. musae was frequently isolated from anthracnose of different banana cultivars and the RAPD banding patterns of C. musae isolates were highly similar but showed intraspecific variations.

Characterisation of Colletotrichum Species Associated with Anthracnose of Banana

PubMed Central

Zakaria, Latiffah; Sahak, Shamsiah; Zakaria, Maziah; Salleh, Baharuddin

2009-01-01

A total of 13 Colletotrichum isolates were obtained from different banana cultivars (Musa spp.) with symptoms of anthracnose. Colletotrichum isolates from anthracnose of guava (Psidium guajava) and water apple (Syzygium aqueum) were also included in this study. Based on cultural and morphological characteristics, isolates from banana and guava were identified as Colletotrichum musae and from water apple as Colletotrichum gloeosporiodes. Isolates of C. musae from banana and guava had similar banding patterns in a randomly amplified polymorphic DNA (RAPD) analysis with four random primers, and they clustered together in a UPGMA analysis. C. gloeosporiodes from water apple was clustered in a separate cluster. Based on the present study, C. musae was frequently isolated from anthracnose of different banana cultivars and the RAPD banding patterns of C. musae isolates were highly similar but showed intraspecific variations. PMID:24575184

Characterization of Malaysian Trichoderma isolates using random amplified microsatellites (RAMS).

PubMed

Siddiquee, Shafiquzzaman; Tan, Soon Guan; Yusuf, Umi Kalsom; Fatihah, Nur Hasan Nudin; Hasan, Md Mainul

2012-01-01

Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the identification of Trichoderma species from throughout the world based on micro-morphological descriptions is tedious and prone to error. The correct identification of Trichoderma species is important as several traits are species-specific. The Random Amplified Microsatellites (RAMS) analysis done using five primers in this study showed different degrees of the genetic similarity among 42 isolates of this genus. The genetic similarity values were found to be in the range of 12.50-85.11% based on a total of 76 bands scored in the Trichoderma isolates. Of these 76 bands, 96.05% were polymorphic, 3.95% were monomorphic and 16% were exclusive bands. Two bands (250 bp and 200 bp) produced by primer LR-5 and one band (250 bp) by primer P1A were present in all the Trichoderma isolates collected from healthy and infected oil palm plantation soils. Cluster analysis based on UPGMA of the RAMS marker data showed that T. harzianum, T. virens and T. longibrachiatum isolates were grouped into different clades and lineages. In this study we found that although T. aureoviride isolates were morphologically different when compared to T. harzianum isolates, the UPGMA cluster analysis showed that the majority isolates of T. aureoviride (seven from nine) were closely related to the isolates of T. harzianum.

Validation of a "Kane's Dynamics" Model for the Active Rack Isolation System

NASA Technical Reports Server (NTRS)

Beech, Geoffrey S.; Hampton, R. David

2000-01-01

Many microgravity space-science experiments require vibratory acceleration levels unachievable without active isolation. The Boeing Corporation's Active Rack Isolation System (ARIS) employs a novel combination of magnetic actuation and mechanical linkages, to address these isolation requirements on the International Space Station (ISS). ARIS provides isolation at the rack (international Standard Payload Rack, or ISPR) level. Effective model-based vibration isolation requires (1) an isolation device, (2) an adequate dynamic (i.e., mathematical) model of that isolator, and (3) a suitable, corresponding controller, ARIS provides the ISS response to the first requirement. In November 1999, the authors presented a response to the second ("A 'Kane's Dynamics' model for the Active Rack Isolation System", Hampton and Beech) intended to facilitate an optimal-controls approach to the third. This paper documents the validation of that high-fidelity dynamic model of ARIS. As before, this model contains the full actuator dynamics, however, the umbilical models are not included in this presentation. The validation of this dynamics model was achieved by utilizing two Commercial Off the Shelf (COTS) software tools: Deneb's ENVISION, and Online Dynamics' AUTOLEV. ENVISION is a robotics software package developed for the automotive industry that employs 3-dimensional (3-D) Computer Aided Design (CAD) models to facilitate both forward and inverse kinematics analyses. AUTOLEV is a DOS based interpreter that is designed in general to solve vector based mathematical problems and specifically to solve Dynamics problems using Kane's method.

A security-awareness virtual machine management scheme based on Chinese wall policy in cloud computing.

PubMed

Yu, Si; Gui, Xiaolin; Lin, Jiancai; Tian, Feng; Zhao, Jianqiang; Dai, Min

2014-01-01

Cloud computing gets increasing attention for its capacity to leverage developers from infrastructure management tasks. However, recent works reveal that side channel attacks can lead to privacy leakage in the cloud. Enhancing isolation between users is an effective solution to eliminate the attack. In this paper, to eliminate side channel attacks, we investigate the isolation enhancement scheme from the aspect of virtual machine (VM) management. The security-awareness VMs management scheme (SVMS), a VMs isolation enhancement scheme to defend against side channel attacks, is proposed. First, we use the aggressive conflict of interest relation (ACIR) and aggressive in ally with relation (AIAR) to describe user constraint relations. Second, based on the Chinese wall policy, we put forward four isolation rules. Third, the VMs placement and migration algorithms are designed to enforce VMs isolation between the conflict users. Finally, based on the normal distribution, we conduct a series of experiments to evaluate SVMS. The experimental results show that SVMS is efficient in guaranteeing isolation between VMs owned by conflict users, while the resource utilization rate decreases but not by much.

A Security-Awareness Virtual Machine Management Scheme Based on Chinese Wall Policy in Cloud Computing

PubMed Central

Gui, Xiaolin; Lin, Jiancai; Tian, Feng; Zhao, Jianqiang; Dai, Min

2014-01-01

Cloud computing gets increasing attention for its capacity to leverage developers from infrastructure management tasks. However, recent works reveal that side channel attacks can lead to privacy leakage in the cloud. Enhancing isolation between users is an effective solution to eliminate the attack. In this paper, to eliminate side channel attacks, we investigate the isolation enhancement scheme from the aspect of virtual machine (VM) management. The security-awareness VMs management scheme (SVMS), a VMs isolation enhancement scheme to defend against side channel attacks, is proposed. First, we use the aggressive conflict of interest relation (ACIR) and aggressive in ally with relation (AIAR) to describe user constraint relations. Second, based on the Chinese wall policy, we put forward four isolation rules. Third, the VMs placement and migration algorithms are designed to enforce VMs isolation between the conflict users. Finally, based on the normal distribution, we conduct a series of experiments to evaluate SVMS. The experimental results show that SVMS is efficient in guaranteeing isolation between VMs owned by conflict users, while the resource utilization rate decreases but not by much. PMID:24688434

Antimicrobial resistance of Listeria monocytogenes isolated from dairy-based food products.

PubMed

Harakeh, Steve; Saleh, Imane; Zouhairi, Omar; Baydoun, Elias; Barbour, Elie; Alwan, Nisreen

2009-06-15

In this study Listeria monocytogenes (L. monocytogenes) was isolated from three traditionally consumed Lebanese dairy-based food products. One hundred and sixty four samples (45 samples of Baladi cheese, 36 samples of Shankleesh and 83 of Kishk) were collected from the Bekaa Valley in the Northeast region of Lebanon. Suspected Listeria colonies were selected and initially identified by using standard biochemical tests. Initial identification of the positive L. monocytogenes colonies was confirmed at the molecular level by Polymerase Chain Reaction (n=30) and the confirmed isolates were evaluated for their susceptibility to 10 commonly used antimicrobials. All of the 30 isolates were confirmed to be L. monocytogenes yielding a PCR product of approximately 660 base pairs (bp). L. monocytogenes was detected in 26.67%, 13.89% and 7.23% of the Baladi cheese, Shankleesh and Kishk samples, respectively. The highest resistance in L. monocytogenes isolates was noted against oxacillin (93.33%) followed by penicillin (90%). The results provide an indication of the contamination levels of dairy-based foods in Lebanon and highlight the emergence of multi-drug resistant Listeria in the environment.

Mesenteric lymphangitis and sepsis due to RTX toxin-producing Actinobacillus spp in 2 foals with hypothyroidism-dysmaturity syndrome.

PubMed

Löhr, C V; Polster, U; Kuhnert, P; Karger, A; Rurangirwa, F R; Teifke, J P

2012-07-01

Actinobacillus suis-like organisms (ASLOs) have been isolated from the genital, respiratory, and digestive tracts of healthy adult horses, horses with respiratory disease, and septic foals. Two foals with congenital hypothyroidism-dysmaturity syndrome from separate farms developed ASLO infection. At necropsy, both had contracted carpal flexor tendons, thyroid hyperplasia, and thrombotic and necrotizing mesenteric lymphangitis and lymphadenitis; one foal also had mandibular prognathism. Numerous ASLOs were isolated from tissues from both foals, including intestine. Biochemical testing and mass spectrometric analysis of the two Actinobacillus isolates did not allow unequivocal identification. Comparative genetic analysis was done on these and similar isolates, including phylogeny based on 16S rRNA, rpoB and recN genes, as well as RTX (repeat in toxin) toxin typing of apxIA-apxIVA and aqxA genes. One isolate was identified as Actinobacillus suis sensu stricto, based on the presence of apxIA and apxIIA but not aqxA, whereas the other isolate had aqxA but neither apxIA nor apxIIA, consistent with A equuli ssp haemolyticus. Based on genotypic analysis of the isolates included for comparison, 3 of 3 equine ASLOs and 2 of 5 A equuli isolates were reclassified as A equuli subsp haemolyticus, emphasizing the importance of toxin genotyping in accurate classification of actinobacilli.

Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).

PubMed

Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G

2011-07-01

Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

Matrix-Assisted Laser Desorption Ionization (MALDI)-Time of Flight Mass Spectrometry- and MALDI Biotyper-Based Identification of Cultured Biphenyl-Metabolizing Bacteria from Contaminated Horseradish Rhizosphere Soil▿

PubMed Central

Uhlik, Ondrej; Strejcek, Michal; Junkova, Petra; Sanda, Miloslav; Hroudova, Miluse; Vlcek, Cestmir; Mackova, Martina; Macek, Tomas

2011-01-01

Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases. PMID:21821747

Predictive Analytical Model for Isolator Shock-Train Location in a Mach 2.2 Direct-Connect Supersonic Combustion Tunnel

NASA Astrophysics Data System (ADS)

Lingren, Joe; Vanstone, Leon; Hashemi, Kelley; Gogineni, Sivaram; Donbar, Jeffrey; Akella, Maruthi; Clemens, Noel

2016-11-01

This study develops an analytical model for predicting the leading shock of a shock-train in the constant area isolator section in a Mach 2.2 direct-connect scramjet simulation tunnel. The effective geometry of the isolator is assumed to be a weakly converging duct owing to boundary-layer growth. For some given pressure rise across the isolator, quasi-1D equations relating to isentropic or normal shock flows can be used to predict the normal shock location in the isolator. The surface pressure distribution through the isolator was measured during experiments and both the actual and predicted locations can be calculated. Three methods of finding the shock-train location are examined, one based on the measured pressure rise, one using a non-physics-based control model, and one using the physics-based analytical model. It is shown that the analytical model performs better than the non-physics-based model in all cases. The analytic model is less accurate than the pressure threshold method but requires significantly less information to compute. In contrast to other methods for predicting shock-train location, this method is relatively accurate and requires as little as a single pressure measurement. This makes this method potentially useful for unstart control applications.

Laboratory and field evaluations for efficacy of a fast-killing baculovirus isolate from Spodoptera frugiperda

USDA-ARS?s Scientific Manuscript database

Three biopesticide parameters were evaluated for a fast-killing isolate (3AP2) Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) and a wild-type isolate (Sf3) of the same baculovirus. Both isolates were evaluated for virus production using in vivo methods, for speed of kill based on bioas...

Analysis of the nucleoprotein gene identifies three distinct lineages of viral haemorrhagic septicemia virus (VHSV) within the European marine environment

USGS Publications Warehouse

Snow, M.; Cunningham, C.O.; Melvin, W.T.; Kurath, G.

1999-01-01

A ribonuclease (RNase) protection assay (RPA) has been used to detect nucleotide sequence variation within the nucleoprotein gene of 39 viral haemorrhagic septicaemia virus (VHSV) isolates of European marine origin. The classification of VHSV isolates based on RPA cleavage patterns permitted the identification of ten distinct groups of viruses based on differences at the molecular level. The nucleotide sequence of representatives of each of these groupings was determined and subjected to phylogenetic analysis. This revealed grouping of the European marine isolates of VHSV into three genotypes circulating within distinct geographic areas. A fourth genotype was identified comprising isolates originating from North America. Phylogenetic analyses indicated that VHSV isolates recovered from wild caught fish around the British Isles were genetically related to isolates responsible for losses in farmed turbot. Furthermore, a relationship between naturally occurring marine isolates and VHSV isolates causing mortality among rainbow trout in continental Europe was demonstrated. Analysis of the nucleoprotein gene identifies distinct lineages of viral haemorrhagic septicaemia virus within the European marine environment. Virus Res. 63, 35-44. Available from: 

Design of isolated buildings with S-FBI system subjected to near-fault earthquakes using NSGA-II algorithm

NASA Astrophysics Data System (ADS)

Ozbulut, O. E.; Silwal, B.

2014-04-01

This study investigates the optimum design parameters of a superelastic friction base isolator (S-FBI) system through a multi-objective genetic algorithm and performance-based evaluation approach. The S-FBI system consists of a flat steel- PTFE sliding bearing and a superelastic NiTi shape memory alloy (SMA) device. Sliding bearing limits the transfer of shear across the isolation interface and provides damping from sliding friction. SMA device provides restoring force capability to the isolation system together with additional damping characteristics. A three-story building is modeled with S-FBI isolation system. Multiple-objective numerical optimization that simultaneously minimizes isolation-level displacements and superstructure response is carried out with a genetic algorithm (GA) in order to optimize S-FBI system. Nonlinear time history analyses of the building with S-FBI system are performed. A set of 20 near-field ground motion records are used in numerical simulations. Results show that S-FBI system successfully control response of the buildings against near-fault earthquakes without sacrificing in isolation efficacy and producing large isolation-level deformations.

Shared Mycobacterium avium Genotypes Observed among Unlinked Clinical and Environmental Isolates

PubMed Central

Weigel, Kris M.; Yakrus, Mitchell A.; Becker, Annie L.; Chen, Hui-Ling; Fridley, Gina; Sikora, Arthur; Speake, Cate; Hilborn, Elizabeth D.; Pfaller, Stacy

2013-01-01

Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-resolution PCR-based genotyping approach, large-sequence polymorphism (LSP)-mycobacterial interspersed repetitive unit–variable-number tandem repeat (MIRU-VNTR), was selected and used to analyze clinical and environmental isolates of M. avium from geographically diverse sources. Among 127 clinical isolates from seven locations in North America, South America, and Europe, 42 genotypes were observed. Among 12 of these genotypes, matches were seen in isolates from apparently unlinked patients in two or more geographic locations. Six of the 12 were also observed in environmental isolates. A subset of these isolates was further analyzed by alternative strain genotyping methods, pulsed-field gel electrophoresis and MIRU-VNTR, which confirmed the existence of geographically dispersed strain genotypes. These results suggest that caution should be exercised in interpreting high-resolution genotypic matches as evidence for an acquisition event. PMID:23851084

Response of high-rise and base-isolated buildings to a hypothetical M w 7.0 blind thrust earthquake

USGS Publications Warehouse

Heaton, T.H.; Hall, J.F.; Wald, D.J.; Halling, M.W.

1995-01-01

High-rise flexible-frame buildings are commonly considered to be resistant to shaking from the largest earthquakes. In addition, base isolation has become increasingly popular for critical buildings that should still function after an earthquake. How will these two types of buildings perform if a large earthquake occurs beneath a metropolitan area? To answer this question, we simulated the near-source ground motions of a Mw 7.0 thrust earthquake and then mathematically modeled the response of a 20-story steel-frame building and a 3-story base-isolated building. The synthesized ground motions were characterized by large displacement pulses (up to 2 meters) and large ground velocities. These ground motions caused large deformation and possible collapse of the frame building, and they required exceptional measures in the design of the base-isolated building if it was to remain functional.

Component isolation for multi-component signal analysis using a non-parametric gaussian latent feature model

NASA Astrophysics Data System (ADS)

Yang, Yang; Peng, Zhike; Dong, Xingjian; Zhang, Wenming; Clifton, David A.

2018-03-01

A challenge in analysing non-stationary multi-component signals is to isolate nonlinearly time-varying signals especially when they are overlapped in time and frequency plane. In this paper, a framework integrating time-frequency analysis-based demodulation and a non-parametric Gaussian latent feature model is proposed to isolate and recover components of such signals. The former aims to remove high-order frequency modulation (FM) such that the latter is able to infer demodulated components while simultaneously discovering the number of the target components. The proposed method is effective in isolating multiple components that have the same FM behavior. In addition, the results show that the proposed method is superior to generalised demodulation with singular-value decomposition-based method, parametric time-frequency analysis with filter-based method and empirical model decomposition base method, in recovering the amplitude and phase of superimposed components.

Characterization of Methicillin Resistant Staphylococcus aureus isolated from human and animal samples in Egypt.

PubMed

Bendary, M M; Solyman, S M; Azab, M M; Mahmoud, N F; Hanora, A M

2016-02-29

Staphylococcus aureus (S. aureus) has been one of the most problematic pathogens. Methicillin Resistant S. aureus (MRSA) has emerged as a major concern for both human and animal. Antibiotic resistance genes dissemination might be possible between human and animal bacteria. The aim of this study is to show phenotypic and genotypic diversity of human and animal MRSA isolates. Antibiogram typing and biofilm production were used as a primary phenotypic typing tool for the characterization of (40) animal and (38) human MRSA isolates. Genetic typing based on sequencing of 16S rRNA gene and virulence gene profiles were done. Antimicrobial resistance profiles of the animal isolates showed little evidence of widespread of resistance, although this was seen in many human isolates. The biofilm production was detected in higher percentage among animal isolates. Based on the genetic typing and multiple antibiotic resistance (MAR) index, the majority of animal isolates clustered into lineages that were not found in human isolates. Animal and human MRSA isolates showed diversity in antibiotic resistance and virulence gene profiles may be due to host adaptation or chances for contamination between the two hosts were not present in our study.

Label-free isolation of a prostate cancer cell among blood cells and the single-cell measurement of drug accumulation using an integrated microfluidic chip.

PubMed

Khamenehfar, A; Beischlag, T V; Russell, P J; Ling, M T P; Nelson, C; Li, P C H

2015-11-01

Circulating tumor cells (CTCs) are found in the blood of patients with cancer. Although these cells are rare, they can provide useful information for chemotherapy. However, isolation of these rare cells from blood is technically challenging because they are small in numbers. An integrated microfluidic chip, dubbed CTC chip, was designed and fabricated for conducting tumor cell isolation. As CTCs usually show multidrug resistance (MDR), the effect of MDR inhibitors on chemotherapeutic drug accumulation in the isolated single tumor cell is measured. As a model of CTC isolation, human prostate cancer cells were mixed with mouse blood cells and the label-free isolation of the tumor cells was conducted based on cell size difference. The major advantages of the CTC chip are the ability for fast cell isolation, followed by multiple rounds of single-cell measurements, suggesting a potential assay for detecting the drug responses based on the liquid biopsy of cancer patients.

Isolated thermocouple amplifier system for stirred fixed-bed gasifier

DOEpatents

Fasching, George E.

1992-01-01

A sensing system is provided for determining the bed temperature profile of the bed of a stirred, fixed-bed gasifier including a plurality of temperature sensors for sensing the bed temperature at different levels, a transmitter for transmitting data based on the outputs of the sensors to a remote operator's station, and a battery-based power supply. The system includes an isolation amplifier system comprising a plurality of isolation amplifier circuits for amplifying the outputs of the individual sensors. The isolation amplifier circuits each comprise an isolation operational amplifier connected to a sensor; a first "flying capacitor" circuit for, in operation, controlling the application of power from the power supply to the isolation amplifier; an output sample and hold circuit connected to the transmitter; a second "flying capacitor" circuit for, in operation, controlling the transfer of the output of the isolation amplifier to the sample and hold circuit; and a timing and control circuit for activating the first and second capacitor circuits in a predetermined timed sequence.

Lineage II (Serovar 1/2a and 1/2c) Human Listeria monocytogenes Pulsed-Field Gel Electrophoresis Types Divided into PFGE Groups Using the Band Patterns Below 145.5 kb.

PubMed

Lopez-Valladares, Gloria; Danielsson-Tham, Marie-Louise; Goering, Richard V; Tham, Wilhelm

2017-01-01

Among 504 clinical lineage II isolates of Listeria monocytogenes isolated during 1958-2010 in Sweden, 119 pulsed-field gel electrophoresis (PFGE) types (AscI) have been identified based on the number and distribution of all banding patterns in each DNA profile. In this study, these types were further divided into PFGE groups based on the configuration of small bands with sizes <145.5 kb. The 504 isolates included 483 serovar 1/2a isolates distributed into 114 PFGE types and 21 serovar 1/2c isolates distributed into 9 PFGE types; these were further divided into 21 PFGE groups. PFGE group, that is, configuration of small bands below 145.5 kb, and serovars were correlated. L. monocytogenes isolates belonging to PFGE groups A, B, C, E, F, H, K, L, M, S, V, W, Y, and Ö-6 to Ö-12 shared serovar 1/2a, with one exception. PFGE group E also included two PFGE types sharing serovar 1/2c and four PFGE types belonging to either serovar 1/2a or 1/2c. Isolates belonging to PFGE group N shared serovar 1/2c. In contrast to lineage I isolates, small fragments <33.3 kb were visible in all L. monocytogenes isolates belonging to lineage II. In the results from both the present and previous studies, the genomic region of small bands was genetically more conservative than in large bands. The distribution of these small bands established the relatedness of strains and defined a genetic marker for both lineages I and II, while also establishing their serogroup. The division of L. monocytogenes PFGE types into PFGE groups is advantageous as the profile of every new isolate can be identified easily and quickly through first studying the PFGE group affiliation of the isolate based on the smaller band patterns <145.5 kb, and then identifying the PFGE type based on the band patterns >145.5 kb.

Serial recall and presentation schedule: a micro-analysis of local distinctiveness.

PubMed

Lewandowsky, Stephan; Brown, Gordon D A

2005-01-01

According to temporal distinctiveness theories, items that are temporally isolated from their neighbours during presentation are more distinct and thus are recalled better. Event-based theories, which deny that elapsed time plays a role at encoding, explain isolation effects by assuming that temporal isolation provides extra time for rehearsal or consolidation of encoding. The two classes of theories can be differentiated by examining the symmetry of isolation effects: Event-based accounts predict that performance should be affected only by pauses following item presentation (because they allow time for rehearsal or consolidation), whereas distinctiveness predicts that items should also benefit from preceding pauses. The first experiment manipulated inter-item intervals and showed an effect of intervals following but not preceding presentation, in line with event-based accounts. The second experiment showed that the effect of following interval was abolished by articulatory suppression. The data are consistent with event-based theories but can be handled by time-based distinctiveness models if they allow for additional encoding during inter-item pauses.

Molecular Characterization of Group A Streptococcus Strains Isolated during a Scarlet Fever Outbreak

PubMed Central

Perea-Mejía, Luis M.; Inzunza-Montiel, Alma E.; Cravioto, Alejandro

2002-01-01

Forty group A streptococcus (GAS) isolates, recovered during a scarlet fever outbreak, were grouped based on their DdeI restriction profiles from emm amplicons. Twenty-seven isolates were identified by sequencing as emm2. The emm2 isolates showed the speA1, speB1, and speC1 alleles. Isolation of this GAS type from scarlet fever outbreaks is uncommon. PMID:11773132

Prediction of penicillin resistance in Staphylococcus aureus isolates from dairy cows with mastitis, based on prior test results.

PubMed

Grinberg, A; Lopez-Villalobos, N; Lawrence, K; Nulsen, M

2005-10-01

To gauge how well prior laboratory test results predict in vitro penicillin resistance of Staphylococcus aureus isolates from dairy cows with mastitis. Population-based data on the farm of origin (n=79), genotype based on pulsed-field gel electrophoresis (PFGE) results, and the penicillin-resistance status of Staph. aureus isolates (n=115) from milk samples collected from dairy cows with mastitis submitted to two diagnostic laboratories over a 6-month period were used. Data were mined stochastically using the all-possible-pairs method, binomial modelling and bootstrap simulation, to test whether prior test results enhance the accuracy of prediction of penicillin resistance on farms. Of all Staph. aureus isolates tested, 38% were penicillin resistant. A significant aggregation of penicillin-resistance status was evident within farms. The probability of random pairs of isolates from the same farm having the same penicillin-resistance status was 76%, compared with 53% for random pairings of samples across all farms. Thus, the resistance status of randomly selected isolates was 1.43 times more likely to correctly predict the status of other isolates from the same farm than the random population pairwise concordance probability (p=0.011). This effect was likely due to the clonal relationship of isolates within farms, as the predictive fraction attributable to prior test results was close to nil when the effect of within-farm clonal infections was withdrawn from the model. Knowledge of the penicillin-resistance status of a prior Staph. aureus isolate significantly enhanced the predictive capability of other isolates from the same farm. In the time and space frame of this study, clinicians using previous information from a farm would have more accurately predicted the penicillin-resistance status of an isolate than they would by chance alone on farms infected with clonal Staph. aureus isolates, but not on farms infected with highly genetically heterogeneous bacterial strains.

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia

PubMed Central

2010-01-01

Background Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. Results The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. Conclusions The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases. PMID:20691110

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia.

PubMed

Berhanu, Ayalew; Ideris, Aini; Omar, Abdul R; Bejo, Mohd Hair

2010-08-08

Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases.

Enrichment and isolation of neurons from adult mouse brain for ex vivo analysis.

PubMed

Berl, Sabina; Karram, Khalad; Scheller, Anja; Jungblut, Melanie; Kirchhoff, Frank; Waisman, Ari

2017-05-01

Isolation of neurons from the adult mouse CNS is important in order to study their gene expression during development or the course of different diseases. Here we present two different methods for the enrichment or isolation of neurons from adult mouse CNS. These methods: are either based on flow cytometry sorting of eYFP expressing neurons, or by depletion of non-neuronal cells by sorting with magnetic-beads. Enrichment by FACS sorting of eYFP positive neurons results in a population of 62.4% NeuN positive living neurons. qPCR data shows a 3-5fold upregulation of neuronal markers. The isolation of neurons based on depletion of non-neuronal cells using the Miltenyi Neuron Isolation Kit, reaches a purity of up to 86.5%. qPCR data of these isolated neurons shows an increase in neuronal markers and an absence of glial markers, proving pure neuronal RNA isolation. Former data related to neuronal gene expression are mainly based on histology, which does not allow for high-throughput transcriptome analysis to examine differential gene expression. These protocols can be used to study cell type specific gene expression of neurons to unravel their function in the process of damage to the CNS. Copyright © 2017 Elsevier B.V. All rights reserved.

A "Kane's Dynamics" Model for the Active Rack Isolation System Part Two: Nonlinear Model Development, Verification, and Simplification

NASA Technical Reports Server (NTRS)

Beech, G. S.; Hampton, R. D.; Rupert, J. K.

2004-01-01

Many microgravity space-science experiments require vibratory acceleration levels that are unachievable without active isolation. The Boeing Corporation's active rack isolation system (ARIS) employs a novel combination of magnetic actuation and mechanical linkages to address these isolation requirements on the International Space Station. Effective model-based vibration isolation requires: (1) An isolation device, (2) an adequate dynamic; i.e., mathematical, model of that isolator, and (3) a suitable, corresponding controller. This Technical Memorandum documents the validation of that high-fidelity dynamic model of ARIS. The verification of this dynamics model was achieved by utilizing two commercial off-the-shelf (COTS) software tools: Deneb's ENVISION(registered trademark), and Online Dynamics Autolev(trademark). ENVISION is a robotics software package developed for the automotive industry that employs three-dimensional computer-aided design models to facilitate both forward and inverse kinematics analyses. Autolev is a DOS-based interpreter designed, in general, to solve vector-based mathematical problems and specifically to solve dynamics problems using Kane's method. The simplification of this model was achieved using the small-angle theorem for the joint angle of the ARIS actuators. This simplification has a profound effect on the overall complexity of the closed-form solution while yielding a closed-form solution easily employed using COTS control hardware.

Could High Mental Demands at Work Offset the Adverse Association Between Social Isolation and Cognitive Functioning? Results of the Population-Based LIFE-Adult-Study.

PubMed

Rodriguez, Francisca S; Schroeter, Matthias L; Witte, A Veronica; Engel, Christoph; Löffler, Markus; Thiery, Joachim; Villringer, Arno; Luck, Tobias; Riedel-Heller, Steffi G

2017-11-01

The study investigated whether high mental demands at work, which have shown to promote a good cognitive functioning in old age, could offset the adverse association between social isolation and cognitive functioning. Based on data from the population-based LIFE-Adult-Study, the association between cognitive functioning (Verbal Fluency Test, Trail Making Test B) and social isolation (Lubben Social Network Scale) as well as mental demands at work (O*NET database) was analyzed via linear regression analyses adjusted for age, sex, education, and sampling weights. Cognitive functioning was significantly lower in socially isolated individuals and in individuals working in low mental demands jobs-even in old age after retirement and even after taking into account the educational level. An interaction effect suggested stronger effects of mental demands at work in socially isolated than nonisolated individuals. The findings suggest that working in high mental-demand jobs could offset the adverse association between social isolation and cognitive functioning. Further research should evaluate how interventions that target social isolation and enhance mentally demanding activities promote a good cognitive functioning in old age. Copyright © 2017 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

Species Identification and Strain Typing of Staphylococcus agnetis and Staphylococcus hyicus Isolates from Bovine Milk by Use of a Novel Multiplex PCR Assay and Pulsed-Field Gel Electrophoresis.

PubMed

Adkins, P R F; Middleton, J R; Calcutt, M J; Stewart, G C; Fox, L K

2017-06-01

Staphylococcus hyicus and Staphylococcus agnetis are two coagulase-variable staphylococcal species that can be isolated from bovine milk and are difficult to differentiate. The objectives of this study were to characterize isolates of bovine milk origin from a collection that had previously been characterized as coagulase-positive S. hyicus based on phenotypic species identification methods and to develop a PCR-based method for differentiating S. hyicus , S. agnetis , and Staphylococcus aureus Isolates ( n = 62) were selected from a previous study in which milk samples were collected from cows on 15 dairy herds. Isolates were coagulase tested and identified to the species level using housekeeping gene sequencing. A multiplex PCR to differentiate S. hyicus , S. agnetis , and S. aureus was developed. Pulsed-field gel electrophoresis was conducted to strain type the isolates. Based on gene sequencing, 44/62 of the isolates were determined to be either S. agnetis ( n = 43) or S. hyicus ( n = 1). Overall, 88% (37/42) of coagulase-positive S. agnetis isolates were found to be coagulase positive at 4 h. The herd-level prevalence of coagulase-positive S. agnetis ranged from 0 to 2.17%. Strain typing identified 23 different strains. Six strains were identified more than once and from multiple cows within the herd. Three strains were isolated from cows at more than one time point, with 41 to 264 days between samplings. These data suggest that S. agnetis is likely more prevalent on dairy farms than S. hyicus Also, some S. agnetis isolates in this study appeared to be contagious and associated with persistent infections. Copyright © 2017 American Society for Microbiology.

Diversity Analysis of Dairy and Nondairy Lactococcus lactis Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)5-PCR Fingerprinting▿

PubMed Central

Rademaker, Jan L. W.; Herbet, Hélène; Starrenburg, Marjo J. C.; Naser, Sabri M.; Gevers, Dirk; Kelly, William J.; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E. T.

2007-01-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)5-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene. PMID:17890345

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting.

PubMed

Rademaker, Jan L W; Herbet, Hélène; Starrenburg, Marjo J C; Naser, Sabri M; Gevers, Dirk; Kelly, William J; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E T

2007-11-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)(5)-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene.

Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil.

PubMed

Braga, Lívia Fabiana; Oliveira, Fênix Araújo de; Couto, Eva Aparecida Prado do; Santos, Karina Freire d'Eça Nogueira; Ferreira, Enderson Petrônio de Brito; Martin-Didonet, Claudia Cristina Garcia

This work aimed to characterize 20 isolates obtained from upland rice plants, based on phenotypic (morphology, enzymatic activity, inorganic phosphate solubilization, carbon source use, antagonism), genotypic assays (16S rRNA sequencing) and plant growth promotion. Results showed a great morphological, metabolic and genetic variability among bacterial isolates. All isolates showed positive activity for catalase and protease enzymes and, 90% of the isolates showed positive activity for amylase, catalase and, nitrogenase. All isolates were able to metabolize sucrose and malic acid in contrast with mannitol, which was metabolized only by one isolate. For the other carbon sources, we observed a great variability in its use by the isolates. Most isolates showed antibiosis against Rhizoctonia solani (75%) and Sclerotinia sclerotiorum (55%) and, 50% of them showed antibiosis against both pathogens. Six isolates showed simultaneous ability of antibiosis, inorganic phosphate solubilization and protease activity. Based on phylogenetic analysis of the 16S rRNA gene all the isolates belong to Bacillus genus. Under greenhouse conditions, two isolates (S4 and S22) improved to about 24%, 25%, 30% and 31% the Total N, leaf area, shoot dry weight and root dry weight, respectively, of rice plants, indicating that they should be tested for this ability under field conditions. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Involvement of Colonizing Bacillus Isolates in Glucovanillin Hydrolysis during the Curing of Vanilla planifolia Andrews

PubMed Central

Chen, Yonggan; Li, Jihua; He, Shuzhen; Xu, Fei; Fang, Yiming

2015-01-01

Vanilla beans were analyzed using biochemical methods, which revealed that glucovanillin disperses from the inner part to the outer part of the vanilla bean during the curing process and is simultaneously hydrolyzed by β-d-glucosidase. Enzymatic hydrolysis was found to occur on the surface of the vanilla beans. Transcripts of the β-d-glucosidase gene (bgl) of colonizing microorganisms were detected. The results directly indicate that colonizing microorganisms are involved in glucovanillin hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences showed that the colonizing microorganisms mainly belonged to the Bacillus genus. bgl was detected in all the isolates and presented clustering similar to that of the isolate taxonomy. Furthermore, inoculation of green fluorescent protein-tagged isolates showed that the Bacillus isolates can colonize vanilla beans. Glucovanillin was metabolized as the sole source of carbon in a culture of the isolates within 24 h. These isolates presented unique glucovanillin degradation capabilities. Vanillin was the major volatile compound in the culture. Other compounds, such as α-cubebene, β-pinene, and guaiacol, were detected in some isolate cultures. Colonizing Bacillus isolates were found to hydrolyze glucovanillin in culture, indirectly demonstrating the involvement of colonizing Bacillus isolates in glucovanillin hydrolysis during the vanilla curing process. Based on these results, we conclude that colonizing Bacillus isolates produce β-d-glucosidase, which mediates glucovanillin hydrolysis and influences flavor formation. PMID:25979899

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species.

PubMed

Liu, Xia; Xu, Yongdong; Li, Zhi; Jiang, Shengwei; Yao, Shuo; Wu, Rina; An, Yingfeng

2018-04-21

A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.

A protocol for exosome isolation and characterization: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods.

PubMed

Greening, David W; Xu, Rong; Ji, Hong; Tauro, Bow J; Simpson, Richard J

2015-01-01

Exosomes are 40-150 nm extracellular vesicles that are released from a multitude of cell types, and perform diverse cellular functions including intercellular communication, antigen presentation, and transfer of tumorigenic proteins, mRNA and miRNA. Exosomes are important regulators of the cellular niche, and their altered characteristics in many diseases, such as cancer, suggest their importance for diagnostic and therapeutic applications, and as drug delivery vehicles. Exosomes have been purified from biological fluids and in vitro cell cultures using a variety of strategies and techniques. In this chapter, we reveal the protocol and key insights into the isolation, purification and characterization of exosomes, distinct from shed microvesicles and apoptotic blebs. Using the colorectal cancer cell line LIM1863 as a cell model, a comprehensive evaluation of exosome isolation methods including ultracentrifugation (UC-Exos), OptiPrep™ density-based separation (DG-Exos), and immunoaffinity capture using anti-EpCAM-coated magnetic beads (IAC-Exos) were examined. All exosome isolation methodologies contained 40-150 nm vesicles based on electron microscopy, and positive for exosome markers (Alix, TSG101, HSP70) based on immunoblotting. This protocol employed a proteomic profiling approach to characterize the protein composition of exosomes, and label-free spectral counting to evaluate the effectiveness of each method in exosome isolation. Based on the number of MS/MS spectra identified for exosome markers and proteins associated with their biogenesis, trafficking, and release, IAC-Exos was shown to be the most effective method to isolate exosomes. However, the use of density-based separation (DG-Exos) provides significant advantages for exosome isolation when the use of immunoaffinity capture is limited (due to antibody availability and suitability of exosome markers).

Infection prevention and control in nursing homes: a qualitative study of decision-making regarding isolation-based practices.

PubMed

Cohen, Catherine Crawford; Pogorzelska-Maziarz, Monika; Herzig, Carolyn T A; Carter, Eileen J; Bjarnadottir, Ragnhildur; Semeraro, Patricia; Travers, Jasmine L; Stone, Patricia W

2015-10-01

Isolation-based practices in nursing homes (NHs) differ from those in acute care. NHs must promote quality of life while preventing infection transmission. Practices used in NHs to reconcile these goals of care have not been characterised. To explore decision-making in isolation-based infection prevention and control practices in NHs. A qualitative study was conducted with staff (eg, staff nurses, infection prevention directors and directors of nursing) employed in purposefully sampled US NHs. Semistructured, role-specific interview guides were developed and interviews were digitally recorded, transcribed verbatim and analysed using directed content analysis. The research team discussed emerging themes in weekly meetings to confirm consensus. We inferred from 73 interviews in 10 NHs that there was variation between NHs in practices regarding who was isolated, when isolation-based practices took place, how they were implemented, and how they were tailored for each resident. Interviewees' decision-making depended on staff perceptions of acceptable transmission risk and resident quality of life. NH resources also influenced decision-making, including availability of private rooms, extent to which staff can devote time to isolation-based practices and communication tools. A lack of understanding of key infection prevention and control concepts was also revealed. Current clinical guidelines are not specific enough to ensure consistent practice that meets care goals and resource constraints in NHs. However, new epidemiological research regarding effectiveness of varying isolation practices in this setting is needed to inform clinical practice. Further, additional infection prevention and control education for NH staff may be required. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

FACS-based isolation, propagation and characterization of mouse embryonic cardiomyocytes based on VCAM-1 surface marker expression.

PubMed

Pontén, Annica; Walsh, Stuart; Malan, Daniela; Xian, Xiaojie; Schéele, Susanne; Tarnawski, Laura; Fleischmann, Bernd K; Jovinge, Stefan

2013-01-01

Purification of cardiomyocytes from the embryonic mouse heart, embryonic stem (ES) or induced pluripotent stem cells (iPS) is a challenging task and will require specific isolation procedures. Lately the significance of surface markers for the isolation of cardiac cell populations with fluorescence activated cell sorting (FACS) has been acknowledged, and the hunt for cardiac specific markers has intensified. As cardiomyocytes have traditionally been characterized by their expression of specific transcription factors and structural proteins, and not by specific surface markers, this constitutes a significant bottleneck. Lately, Flk-1, c-kit and the cellular prion protein have been reported to specify cardiac progenitors, however, no surface markers have so far been reported to specify a committed cardiomyocyte. Herein show for the first time, that embryonic cardiomyocytes can be isolated with 98% purity, based on their expression of vascular cell adhesion molecule-1 (VCAM-1). The FACS-isolated cells express phenotypic markers for embryonic committed cardiomyocytes but not cardiac progenitors. An important aspect of FACS is to provide viable cells with retention of functionality. We show that VCAM-1 positive cardiomyocytes can be isolated with 95% viability suitable for in vitro culture, functional assays or expression analysis. In patch-clamp experiments we provide evidence of functionally intact cardiomyocytes of both atrial and ventricular subtypes. This work establishes that cardiomyocytes can be isolated with a high degree of purity and viability through FACS, based on specific surface marker expression as has been done in the hematopoietic field for decades. Our FACS protocol represents a significant advance in which purified populations of cardiomyocytes may be isolated and utilized for downstream applications, such as purification of ES-cell derived cardiomyocytes.

FACS-Based Isolation, Propagation and Characterization of Mouse Embryonic Cardiomyocytes Based on VCAM-1 Surface Marker Expression

PubMed Central

Pontén, Annica; Walsh, Stuart; Malan, Daniela; Xian, Xiaojie; Schéele, Susanne; Tarnawski, Laura; Fleischmann, Bernd K.; Jovinge, Stefan

2013-01-01

Purification of cardiomyocytes from the embryonic mouse heart, embryonic stem (ES) or induced pluripotent stem cells (iPS) is a challenging task and will require specific isolation procedures. Lately the significance of surface markers for the isolation of cardiac cell populations with fluorescence activated cell sorting (FACS) has been acknowledged, and the hunt for cardiac specific markers has intensified. As cardiomyocytes have traditionally been characterized by their expression of specific transcription factors and structural proteins, and not by specific surface markers, this constitutes a significant bottleneck. Lately, Flk-1, c-kit and the cellular prion protein have been reported to specify cardiac progenitors, however, no surface markers have so far been reported to specify a committed cardiomyocyte. Herein show for the first time, that embryonic cardiomyocytes can be isolated with 98% purity, based on their expression of vascular cell adhesion molecule-1 (VCAM-1). The FACS-isolated cells express phenotypic markers for embryonic committed cardiomyocytes but not cardiac progenitors. An important aspect of FACS is to provide viable cells with retention of functionality. We show that VCAM-1 positive cardiomyocytes can be isolated with 95% viability suitable for in vitro culture, functional assays or expression analysis. In patch-clamp experiments we provide evidence of functionally intact cardiomyocytes of both atrial and ventricular subtypes. This work establishes that cardiomyocytes can be isolated with a high degree of purity and viability through FACS, based on specific surface marker expression as has been done in the hematopoietic field for decades. Our FACS protocol represents a significant advance in which purified populations of cardiomyocytes may be isolated and utilized for downstream applications, such as purification of ES-cell derived cardiomyocytes. PMID:24386094

Prevalence and Characterization of Cronobacter sakazakii in Retail Milk-Based Infant and Baby Foods in Shaanxi, China.

PubMed

Li, Zhen; Ge, Wupeng; Li, Keting; Gan, Jing; Zhang, Yifan; Zhang, Qiang; Luo, Rong; Chen, Limin; Liang, Yi; Wang, Qianning; Xi, Meili; Xia, Xiaodong; Wang, Xin; Yang, Baowei

2016-04-01

Cronobacter sakazakii (formerly Enterobacter sakazakii) is an opportunistic pathogen that causes meningitis, sepsis, and necrotizing enterocolitis in neonates and infants through consumption of contaminated milk-based foods. In this study, the prevalence of C. sakazakii in 705 retail milk-based infant and baby food samples was investigated in 12 cities in Shaanxi, China, in 2010 and 2012. One hundred and nineteen samples (16.9%) were C. sakazakii positive. The isolates were further characterized for antimicrobial susceptibility to 14 antibiotics, pulsed-field gel electrophoresis profiles, and presence of the virulence genes. Samples of brand W, Y, A, and G in 2010 and 2012 were C. sakazakii positive. All isolates recovered in 2010 and 2012 were susceptible to levofloxacin and cefoperazone. In 2012, no isolate was resistant to gentamicin, cefoxitin, chloramphenicol, gatifloxacin, ciprofloxacin, and ceftriaxone. Antibiotic resistance of the isolates was most commonly found to rifampicin, amoxicillin-clavulanic acid, streptomycin, tetracycline, and ampicillin in both 2010 and 2012, except to trimethoprim/sulfamethoxazole in 2012. Pulsed-field gel electrophoresis profiles indicated that C. sakazakii isolates were genotypically diverse, although these isolates were prevalent in infant and baby foods with the same brand. A total of 34 virulence gene profiles of the C. sakazakii isolates in 2010 and 2012 were detected. Isolates that co-carried hly-ompX-eitCBAD-iucABCD/iutA genes in 2012 were significantly (p < 0.05) more prevalent than those in 2010. The results added new epidemiological evidence for the widespread occurrence of C. sakazakii in retail milk-based infant and baby foods and this should be an indicator of potential health risk for consumers.

Preparation and characterization of bio-nanocomposite films based on soy protein isolate and montmorillonite using melt extrusion

USDA-ARS?s Scientific Manuscript database

The non-biodegradable and non-renewable nature of plastic packaging has led to a renewed interest in packaging materials based on bio-nanocomposites (biopolymer matrix reinforced with nanoparticles such as layered silicates). Bio-nanocomposite films based on soy protein isolate (SPI) and montmorillo...

Prevalence, identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia.

PubMed

Hmaïed, F; Helel, S; Le Berre, V; François, J-M; Leclercq, A; Lecuit, M; Smaoui, H; Kechrid, A; Boudabous, A; Barkallah, I

2014-02-01

We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates. Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for human listeriosis isolated in hospital of Tunis were included. Multiplex PCR serogrouping and pulsed field gel electrophoresis (PFGE) applying the enzyme AscI and ApaI were used for the characterization of isolates of L. monocytogenes. We have developed a rapid microarray-based assay to a reliable discrimination of species within the Listeria genus. The prevalence of Listeria spp. in food samples was estimated at 14% by using classical biochemical identification. Two samples were assigned to L. monocytogenes and 12 to L. innocua. DNA microarray allowed unambiguous identification of Listeria species. Our results obtained by microarray-based assay were in accordance with the biochemical identification. The two food L. monocytogenes isolates were assigned to the PCR serogroup IIa (serovar 1/2a). Whereas human L. monocytogenes isolates were of PCR serogroup IVb, (serovars 4b). These isolates present a high similarity in PFGE. Food L. monocytogenes isolates were classified into two different pulsotypes. These pulsotypes were different from that of the five strains responsible for the human cases. We confirmed the presence of Listeria spp. in variety of food samples in Tunis. Increased food and clinical surveillance must be taken into consideration in Tunisia to identify putative infections sources. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Strain variation in Mycobacterium marinum fish isolates.

PubMed

Ucko, M; Colorni, A; Kvitt, H; Diamant, A; Zlotkin, A; Knibb, W R

2002-11-01

A molecular characterization of two Mycobacterium marinum genes, 16S rRNA and hsp65, was carried out with a total of 21 isolates from various species of fish from both marine and freshwater environments of Israel, Europe, and the Far East. The nucleotide sequences of both genes revealed that all M. marinum isolates from fish in Israel belonged to two different strains, one infecting marine (cultured and wild) fish and the other infecting freshwater (cultured) fish. A restriction enzyme map based on the nucleotide sequences of both genes confirmed the divergence of the Israeli marine isolates from the freshwater isolates and differentiated the Israeli isolates from the foreign isolates, with the exception of one of three Greek isolates from marine fish which was identical to the Israeli marine isolates. The second isolate from Greece exhibited a single base alteration in the 16S rRNA sequence, whereas the third isolate was most likely a new Mycobacterium species. Isolates from Denmark and Thailand shared high sequence homology to complete identity with reference strain ATCC 927. Combined analysis of the two gene sequences increased the detection of intraspecific variations and was thus of importance in studying the taxonomy and epidemiology of this aquatic pathogen. Whether the Israeli M. marinum strain infecting marine fish is endemic to the Red Sea and found extremely susceptible hosts in the exotic species imported for aquaculture or rather was accidentally introduced with occasional imports of fingerlings from the Mediterranean Sea could not be determined.

Microplate-based high throughput screening procedure for the isolation of lipid-rich marine microalgae

PubMed Central

2011-01-01

We describe a new selection method based on BODIPY (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene) staining, fluorescence activated cell sorting (FACS) and microplate-based isolation of lipid-rich microalgae from an environmental sample. Our results show that direct sorting onto solid medium upon FACS can save about 3 weeks during the scale-up process as compared with the growth of the same cultures in liquid medium. This approach enabled us to isolate a biodiverse collection of several axenic and unialgal cultures of different phyla. PMID:22192119

Microplate-based high throughput screening procedure for the isolation of lipid-rich marine microalgae.

PubMed

Pereira, Hugo; Barreira, Luísa; Mozes, André; Florindo, Cláudia; Polo, Cristina; Duarte, Catarina V; Custódio, Luísa; Varela, João

2011-12-22

We describe a new selection method based on BODIPY (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene) staining, fluorescence activated cell sorting (FACS) and microplate-based isolation of lipid-rich microalgae from an environmental sample. Our results show that direct sorting onto solid medium upon FACS can save about 3 weeks during the scale-up process as compared with the growth of the same cultures in liquid medium. This approach enabled us to isolate a biodiverse collection of several axenic and unialgal cultures of different phyla.

Diversity of Streptomyces spp. in Eastern Himalayan region – computational RNomics approach to phylogeny

PubMed Central

Bhattacharjee, Kaushik; Banerjee, Subhro; Joshi, Santa Ram

2012-01-01

Isolation and characterization of actinomycetes from soil samples from altitudinal gradient of North-East India were investigated for computational RNomics based phylogeny. A total of 52 diverse isolates of Streptomyces from the soil samples were isolated on four different media and from these 6 isolates were selected on the basis of cultural characteristics, microscopic and biochemical studies. Sequencing of 16S rDNA of the selected isolates identified them to belong to six different species of Streptomyces. The molecular morphometric and physico-kinetic analysis of 16S rRNA sequences were performed to predict the diversity of the genus. The computational RNomics study revealed the significance of the structural RNA based phylogenetic analysis in a relatively diverse group of Streptomyces. PMID:22829729

Improvement of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of difficult-to-identify bacteria and its impact in the workflow of a clinical microbiology laboratory.

PubMed

Rodríguez-Sánchez, Belén; Marín, Mercedes; Sánchez-Carrillo, Carlos; Cercenado, Emilia; Ruiz, Adrián; Rodríguez-Créixems, Marta; Bouza, Emilio

2014-05-01

This study evaluates matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) capability for the identification of difficult-to-identify microorganisms. A total of 150 bacterial isolates inconclusively identified with conventional phenotypic tests were further assessed by 16S rRNA sequencing and by MALDI-TOF MS following 2 methods: a) a simplified formic acid-based, on-plate extraction and b) performing a tube-based extraction step. Using the simplified method, 29 isolates could not be identified. For the remaining 121 isolates (80.7%), we obtained a reliable identification by MALDI-TOF: in 103 isolates, the identification by 16S rRNA sequencing and MALDI TOF coincided at the species level (68.7% from the total 150 analyzed isolates and 85.1% from the samples with MALDI-TOF result), and in 18 isolates, the identification by both methods coincided at the genus level (12% from the total and 14.9% from the samples with MALDI-TOF results). No discordant results were observed. The performance of the tube-based extraction step allowed the identification at the species level of 6 of the 29 unidentified isolates by the simplified method. In summary, MALDI-TOF can be used for the rapid identification of many bacterial isolates inconclusively identified by conventional methods. Copyright © 2014 Elsevier Inc. All rights reserved.

Biodegradation of 2,4-dichlorophenoxyacetic acid by bacteria with highly antibiotic-resistant pattern isolated from wheat field soils in Kurdistan, Iran.

PubMed

Karami, Solmaz; Maleki, Afshin; Karimi, Ebrahim; Poormazaheri, Helen; Zandi, Shiva; Davari, Behrooz; Salimi, Yahya Zand; Gharibi, Fardin; Kalantar, Enayatollah

2016-12-01

Recently, there has been increasing interest to clean up the soils contaminated with herbicide. Our aim was to determine the bioremediation of 2,4-dichlorophenoxyacetic acid (2,4-D) from wheat fields which have a long history of herbicide in Sanandaj. Based on our literature survey, this study is the first report to isolate and identify antimicrobial resistant bacteria from polluted wheat field soils in Sanandaj which has the capacity to degrade 2,4-D. From 150 2,4-D-exposed soil samples, five different bacteria were isolated and identified based on biochemical tests and 16S ribosomal RNA (rRNA). Pseudomonas has been the most frequently isolated genus. By sequencing the 16S rRNA gene of the isolated bacteria, the strains were detected and identified as a member of the genus Pseudomonas sp, Entrobacter sp, Bacillus sp, Seratia sp, and Staphylococcus sp. The sequence of Sanandaj 1 isolate displayed 87% similarity with the 16S rRNA gene of a Pseudomonas sp (HE995788). Similarly, all the isolates were compared to standard strains based on 16S rRNA. Small amounts of 2,4-D could be transmitted to a depth of 10-20 cm; however, in the depth of 20-40 cm, we could not detect the 2,4-D. The isolates were resistant to various antibiotics particularly, penicillin, ampicillin, and amoxicillin.

Evaluation of Bacillus spp. as dough starters for Adhirasam - A traditional rice based fermented food of Southern India.

PubMed

Anisha, Anvar Hussain Noorul; Anandham, Rangasamy; Kwon, Soon Woo; Gandhi, Pandiyan Indira; Gopal, Nellaiappan Olaganathan

2015-01-01

Adhirasam is a cereal based, doughnut shaped, deep fried dessert consumed in the southern regions of India. The dough used to prepare adhirasam is fermented and contains rice flour and jaggery. The aim of the present study was to characterize the cultivable bacteria associated with this fermented dough and to identify a suitable starter culture for the production of quality adhirasam. In total, one hundred and seventy bacterial isolates were recovered from de Man Rogosa Sharp (MRS) agar, nutrient agar, lysogeny agar and tryptic soy agar media. Out of the 170 bacterial isolates, sixteen isolates were selected based on their ability to tolerate glucose and sucrose. All the bacterial isolates tolerated 15% glucose and 30% sucrose. Analyses of 16S rDNA gene sequences of the bacterial isolates showed that the dominant cultivable bacteria were members of the genus Bacillus. These strains were further used as starters and tested for their ability to ferment rice flour with jaggery to produce adhirasam dough. Organoleptic evaluation was carried out to choose the best starter strain. Adhirasam prepared from Bacillus subtilis isolates S4-P11, S2-G2-A1 and S1-G15, Bacillus tequilensis isolates S2-H16, S3-P9, S3-G10 and Bacillus siamensis isolate S2-G13 were highly acceptable to consumers. Adhirasam prepared using these starter cultures had superior product characteristics such as softness in texture, flavor and enhanced aroma and sweet taste.

Detection and isolation of rare cells by 2-step enrichment high-speed flow cytometry/cell sorting and single cell LEAP laser ablation

NASA Astrophysics Data System (ADS)

Zordan, M. D.; Leary, James F.

2011-02-01

The clonal isolation of rare cells, especially cancer and stem cells, in a population is important to the development of improved medical treatment. We have demonstrated that the Laser-Enabled Analysis and Processing (LEAP, Cyntellect Inc., San Diego, CA) instrument can be used to efficiently produce single cell clones by photoablative dilution. Additionally, we have also shown that cells present at low frequencies can be cloned by photoablative dilution after they are pre-enriched by flow cytometry based cell sorting. Circulating tumor cells were modeled by spiking isolated peripheral blood cells with cells from the lung carcinoma cell line A549. Flow cytometry based cell sorting was used to perform an enrichment sort of A549 cells directly into a 384 well plate. Photoablative dilution was performed with the LEAPTM instrument to remove any contaminating cells, and clonally isolate 1 side population cell per well. We were able to isolate and grow single clones of side population cells using this method at greater than 90% efficiency. We have developed a 2 step method that is able to perform the clonal isolation of rare cells based on a medically relevant functional phenotype.

Dilution-to-extinction cultivation of leaf-inhabiting endophytic fungi in beech (Fagus sylvatica L.)--different cultivation techniques influence fungal biodiversity assessment.

PubMed

Unterseher, Martin; Schnittler, Martin

2009-05-01

Two cultivation-based isolation techniques - the incubation of leaf fragments (fragment plating) and dilution-to-extinction culturing on malt extract agar - were compared for recovery of foliar endophytic fungi from Fagus sylvatica near Greifswald, north-east Germany. Morphological-anatomical characters of vegetative and sporulating cultures and ITS sequences were used to assign morphotypes and taxonomic information to the isolates. Data analysis included species-accumulation curves, richness estimators, multivariate statistics and null model testing. Fragment plating and extinction culturing were significantly complementary with regard to species composition, because around two-thirds of the 35 fungal taxa were isolated with only one of the two cultivation techniques. The difference in outcomes highlights the need for caution in assessing fungal biodiversity based upon single isolation techniques. The efficiency of cultivation-based studies of fungal endophytes was significantly increased with the combination of the two isolation methods and estimations of species richness, when compared with a 20-years old reference study, which needed three times more isolates with fragment plating to attain the same species richness. Intensified testing and optimisation of extinction culturing in endophyte research is advocated.

Seismic isolation of nuclear power plants using elastomeric bearings

NASA Astrophysics Data System (ADS)

Kumar, Manish

Seismic isolation using low damping rubber (LDR) and lead-rubber (LR) bearings is a viable strategy for mitigating the effects of extreme earthquake shaking on safety-related nuclear structures. Although seismic isolation has been deployed in nuclear structures in France and South Africa, it has not seen widespread use because of limited new build nuclear construction in the past 30 years and a lack of guidelines, codes and standards for the analysis, design and construction of isolation systems specific to nuclear structures. The nuclear accident at Fukushima Daiichi in March 2011 has led the nuclear community to consider seismic isolation for new large light water and small modular reactors to withstand the effects of extreme earthquakes. The mechanical properties of LDR and LR bearings are not expected to change substantially in design basis shaking. However, under shaking more intense than design basis, the properties of the lead cores in lead-rubber bearings may degrade due to heating associated with energy dissipation, some bearings in an isolation system may experience net tension, and the compression and tension stiffness may be affected by the horizontal displacement of the isolation system. The effects of intra-earthquake changes in mechanical properties on the response of base-isolated nuclear power plants (NPPs) were investigated using an advanced numerical model of a lead-rubber bearing that has been verified and validated, and implemented in OpenSees and ABAQUS. A series of experiments were conducted at University at Buffalo to characterize the behavior of elastomeric bearings in tension. The test data was used to validate a phenomenological model of an elastomeric bearing in tension. The value of three times the shear modulus of rubber in elastomeric bearing was found to be a reasonable estimate of the cavitation stress of a bearing. The sequence of loading did not change the behavior of an elastomeric bearing under cyclic tension, and there was no significant change in the shear modulus, compressive stiffness, and buckling load of a bearing following cavitation. Response-history analysis of base-isolated NPPs was performed using a two-node macro model and a lumped-mass stick model. A comparison of responses obtained from analysis using simplified and advanced isolator models showed that the variation in buckling load due to horizontal displacement and strength degradation due to heating of lead cores affect the responses of a base-isolated NPP most significantly. The two-node macro model can be used to estimate the horizontal displacement response of a base-isolated NPP, but a three-dimensional model that explicitly considers all of the bearings in the isolation system will be required to estimate demands on individual bearings, and to investigate rocking and torsional responses. The use of the simplified LR bearing model underestimated the torsional and rocking response of the base-isolated NPP. Vertical spectral response at the top of containment building was very sensitive to how damping was defined for the response-history analysis.

Spermatozoa input concentrations and RNA isolation methods on RNA yield and quality in bull (Bos taurus).

PubMed

Parthipan, Sivashanmugam; Selvaraju, Sellappan; Somashekar, Lakshminarayana; Kolte, Atul P; Arangasamy, Arunachalam; Ravindra, Janivara Parameswaraiah

2015-08-01

Sperm RNA can be used to understand the past spermatogenic process, future successful fertilization, and embryo development. To study the sperm RNA composition and function, isolation of good quality RNA with sufficient quantity is essential. The objective of this study was to assess the influence of sperm input concentrations and RNA isolation methods on RNA yield and quality in bull sperm. The fresh semen samples from bulls (n = 6) were snap-frozen in liquid nitrogen and stored at -80 °C. The sperm RNA was isolated using membrane-based methods combined with TRIzol (RNeasy+TRIzol and PureLink+TRIzol) and conventional methods (TRIzol, Double TRIzol, and RNAzol RT). Based on fluorometric quantification, combined methods resulted in significantly (P < 0.05) higher total RNA yields (800-900 ng/30-40 × 10(6)) as compared with other methods and yielded 20 to 30 fg of RNA/spermatozoon. The quality of RNA isolated by membrane-based methods was superior to that isolated by conventional methods. The sperm RNA was observed to be intact as well as fragmented (50-2000 bp). The study revealed that the membrane-based methods with a cocktail of lysis solution and an optimal input concentration of 30 to 40 million sperm were optimal for maximum recovery of RNA from bull spermatozoa. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

USGS Publications Warehouse

Freeman, S.; Pham, M.; Rodriguez, R.J.

1993-01-01

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

Temperature range and degree of acidity growth of isolate of indigenous bacteria on fermented feed “fermege”

NASA Astrophysics Data System (ADS)

Isnawati; Trimulyono, G.

2018-01-01

Fermege is a fermented feed of ruminants, especially goats made from water hyacinth (Eichhornia crassipes). Temperature range and pH need to know in making starter formula for acceleration of fermentation process at making ruminant feed made from this materials. The starter formula expired period can be extended by adjusting starter storage temperature and pH of the starter. This research was aimed to find the temperature and pH range for the growth of isolate of indigenous bacteria “fermege.” This research is an explorative research conducted by growing bacteria isolate indigenous fermege in liquid medium with various pH and incubation in various temperature. Bacterial population was calculated based on turbidity of bacterial suspension with turbidometer. The stages of this research were to isolate the bacteria present in the fermege, purify the isolates found, and then grow the isolates in a liquid medium with various pH values. The isolated bacterials were incubated at different temperature variations. The cell population density of the isolates was calculated after incubation for 24 hours. The results showed there were eight indigenous bacterial isolates. All isolates can grow in the pH range 6 and 7. Two isolates (Bacillus subtilis and B. pumilus) can grow at 4°C. All isolates obtained can grow at a temperature of 30°C. Isolates Bacillus badius, B. subtilis, B. cereus, Pseudomonas stutzeri and P. diminuta can grow at 50°C. Based on research indicates that indigenous fermege bacterial isolates have the ability to grow in the neutral pH range and temperature range between 4°C and 50°C.

Detection and characterization of chicken anemia virus from commercial broiler breeder chickens

PubMed Central

Hailemariam, Zerihun; Omar, Abdul Rahman; Hair-Bejo, Mohd; Giap, Tan Ching

2008-01-01

Background Chicken anemia virus (CAV) is the causative agent of chicken infectious anemia (CIA). Study on the type of CAV isolates present and their genetic diversity, transmission to their progeny and level of protection afforded in the breeder farms is lacking in Malaysia. Hence, the present study was aimed to detect CAV from commercial broiler breeder farms and characterize CAV positive samples based on sequence and phylogenetic analysis of partial VP1 gene. Results A total of 12 CAV isolates from different commercial broiler breeder farms were isolated and characterized. Detection of CAV positive embryos by the PCR assay in the range of 40 to 100% for different farms indicated high level of occurrence of vertical transmission of viral DNA to the progeny. CAV antigen was detected in the thymus and in the bone marrow but not in spleen, liver, duodenum, ovary and oviduct by indirect immunoperoxidase staining. The 12 CAV isolates were characterized based on partial sequences of VP1 gene. Six isolates (MF1A, MF3C, M3B5, NF4A, P12B and P24A) were found to have maximum homology with previously characterized Malaysian isolate SMSC-1, four isolates (M1B1, NF3A, PYT4 and PPW4) with isolate BL-5 and the remaining two (NF1D and NF2C) have maximum homology both with isolates 3-1 and BL-5. Meanwhile, seven of the isolates with amino acid profile of 75-I, 97-L, 139-Q and 144-Q were clustered together in cluster I together with other isolates from different geographical places. The remaining five isolates with amino acid profile of 75-V, 97-M, 139-K and 144-E were grouped under cluster II. All the CAV isolates demonstrated omega values (Ka/Ks) of less than one (the values ranging from 0.07 to 0.5) suggesting the occurrence of purifying (negative) selection in all the studied isolates. Conclusion The present study showed that CAV is widespread in the studied commercial broiler breeder farms. The result also indicated the occurrence of genetic variability in local CAV isolates that can be divided at least into two groups based on characteristic amino acid substitutions at positions 75, 97, 139 and 144 of the VP1 protein. PMID:18954433

Detection and characterization of chicken anemia virus from commercial broiler breeder chickens.

PubMed

Hailemariam, Zerihun; Omar, Abdul Rahman; Hair-Bejo, Mohd; Giap, Tan Ching

2008-10-27

Chicken anemia virus (CAV) is the causative agent of chicken infectious anemia (CIA). Study on the type of CAV isolates present and their genetic diversity, transmission to their progeny and level of protection afforded in the breeder farms is lacking in Malaysia. Hence, the present study was aimed to detect CAV from commercial broiler breeder farms and characterize CAV positive samples based on sequence and phylogenetic analysis of partial VP1 gene. A total of 12 CAV isolates from different commercial broiler breeder farms were isolated and characterized. Detection of CAV positive embryos by the PCR assay in the range of 40 to 100% for different farms indicated high level of occurrence of vertical transmission of viral DNA to the progeny. CAV antigen was detected in the thymus and in the bone marrow but not in spleen, liver, duodenum, ovary and oviduct by indirect immunoperoxidase staining. The 12 CAV isolates were characterized based on partial sequences of VP1 gene. Six isolates (MF1A, MF3C, M3B5, NF4A, P12B and P24A) were found to have maximum homology with previously characterized Malaysian isolate SMSC-1, four isolates (M1B1, NF3A, PYT4 and PPW4) with isolate BL-5 and the remaining two (NF1D and NF2C) have maximum homology both with isolates 3-1 and BL-5. Meanwhile, seven of the isolates with amino acid profile of 75-I, 97-L, 139-Q and 144-Q were clustered together in cluster I together with other isolates from different geographical places. The remaining five isolates with amino acid profile of 75-V, 97-M, 139-K and 144-E were grouped under cluster II. All the CAV isolates demonstrated omega values (Ka/Ks) of less than one (the values ranging from 0.07 to 0.5) suggesting the occurrence of purifying (negative) selection in all the studied isolates. The present study showed that CAV is widespread in the studied commercial broiler breeder farms. The result also indicated the occurrence of genetic variability in local CAV isolates that can be divided at least into two groups based on characteristic amino acid substitutions at positions 75, 97, 139 and 144 of the VP1 protein.

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States.

PubMed

Chen, Yi; Luo, Yan; Curry, Phillip; Timme, Ruth; Melka, David; Doyle, Matthew; Parish, Mickey; Hammack, Thomas S; Allard, Marc W; Brown, Eric W; Strain, Errol A

2017-01-01

A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from different outbreaks/incidents.

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States

PubMed Central

Chen, Yi; Luo, Yan; Curry, Phillip; Timme, Ruth; Melka, David; Doyle, Matthew; Parish, Mickey; Hammack, Thomas S.; Allard, Marc W.; Brown, Eric W.; Strain, Errol A.

2017-01-01

A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from different outbreaks/incidents. PMID:28166293

Molecular typing of Staphylococcus aureus based on coagulase gene.

PubMed

Javid, Faizan; Taku, Anil; Bhat, Mohd Altaf; Badroo, Gulzar Ahmad; Mudasir, Mir; Sofi, Tanveer Ahmad

2018-04-01

This study was conducted to study the coagulase gene-based genetic diversity of Staphylococcus aureus , isolated from different samples of cattle using restriction fragment length polymorphism (RFLP) and their sequence-based phylogenetic analysis. A total of 192 different samples from mastitic milk, nasal cavity, and pus from skin wounds of cattle from Military Dairy Farm, Jammu, India, were screened for the presence of S. aureus . The presumptive isolates were confirmed by nuc gene-based polymerase chain reaction (PCR). The confirmed S. aureus isolates were subjected to coagulase ( coa ) gene PCR. Different coa genotypes observed were subjected to RFLP using restriction enzymes Hae111 and Alu1 , to obtain the different restriction patterns. One isolate from each restriction pattern was sequenced. These sequences were aligned for maximum homology using the Bioedit softwareandsimilarity in the sequences was inferred with the help of sequence identity matrix. Of 192 different samples,39 (20.31%) isolates of S. aureus were confirmed by targeting nuc gene using PCR. Of 39 S. aureus isolates, 25 (64.10%) isolates carried coa gene. Four different genotypes of coa gene, i.e., 514 bp, 595 bp, 757 bp, and 802 bp were obtained. Two coa genotypes, 595 bp (15 isolates) and 802 bp (4 isolates), were observed in mastitic milk. 514 bp (2 isolates) and 757 bp (4 isolates) coa genotypes were observed from nasal cavity and pus from skin wounds, respectively. On RFLP using both restriction enzymes, four different restriction patterns P1, P2, P3, and P4 were observed. On sequencing, four different sequences having unique restriction patterns were obtained. The most identical sequences with the value of 0.810 were found between isolate S. aureus 514 (nasal cavity) and S. aureus 595 (mastitic milk), and thus, they are most closely related. While as the most distant sequences with the value of 0.483 were found between S. aureus 514 and S. aureus 802 isolates. The study, being localized to only one farm, yielded different RFLP patterns as observed from different sampling sites, which indicates that different S . aureus coagulase typeshave a site-specific predilection. Two coa patterns were observed in mastitic milk indicating multiple origins of infection, with 595 bp coa genotype being predominant in mastitic milk. The coa genotypes and their restriction patterns observed in the present study are novel, not published earlier. 514 and 595 coa variants of S. aureus are genetically most related.

Biological features of hepatitis B virus isolates from patients based on full-length genomic analysis.

PubMed

Wen, Yu-Mei; Wang, Yong-Xiang

2009-01-01

The mechanisms for HBV persistence and the pathogenesis of chronic HB have been shown mainly due to defects in host immune responses. However, HBV isolates with different biological features may also contribute to different clinical outcomes and epidemiological implications in viral hepatitis B (HB). This review presents interesting biological features of HBV isolates based on the structural and functional analysis of full-length HBV isolates from various patients. Among isolates from children after failure of HB vaccination, 129L mutant at the 'a' determinant was found with normal binding efficiency to anti-HBs, but with reduced immunogenicity, which could initiate persistent HBV infections. Isolates from fulminant hepatitis (FH) B patients were not all highly replicative, but differences in capacities of anti-HBs induction could be involved in the pathogenesis of FH. The high replicative competency of isolates from hepatocellular carcinoma (HCC) patients could result in enhanced immune-mediated cytopathic effects against HBV viral proteins, and increased transactivating activity by the X protein. The mechanism of a double-spliced variant in enhancing replication of the wild-type virus is presented. The importance of integrating structural and functional analysis to reveal biological features of HBV isolates in viral pathogenesis is discussed.

Isolation and Screening of Pectinolytic Fungi from Orange (Citrus nobilis Tan.) and Banana (Musa acuminata L.) Fruit Peel

NASA Astrophysics Data System (ADS)

Amilia, K. R.; Sari, S. L. A.; Setyaningsih, R.

2017-04-01

Pectinase is the one of most important enzyme which is used in food industry such as fruit and vegetable juice extraction, oil extraction and fermentation of coffee, cocoa and tea. Pectinase can be produced by microorganism such as bacteria and fungi. Fungi are known as potent producer of pectinase. This research was conducted to isolate and screen of the pectinolytic fungi from rotten orange and banana fruit peels. This research succeeded to isolate 10 fungal isolates from rotten orange peels and 5 fungal isolates from rotten banana peels. These isolates were screened in pectinolytic activities based on clear zone formation on pectic medium which is stained by cetyl trimethyl ammonium bromide. The screening result showed that fungal isolates which showed pectinolytic activity were O2, O3, O4, O7, O8, O10, B3, and B5. Based on morphological characters, pectinolytic fungi were identified as Fusarium O4 and O10, Penicillium O2, Aspergillus O3, O7, B3 and B5 and Trichoderma O8. The highest pectinolytic activity was showed by Penicillium O2 which was isolated from orange peel.

Comparative evaluation of an automated repetitive-sequence-based PCR instrument versus pulsed-field gel electrophoresis in the setting of a Serratia marcescens nosocomial infection outbreak.

PubMed

Ligozzi, Marco; Fontana, Roberta; Aldegheri, Marco; Scalet, Giovanna; Lo Cascio, Giuliana

2010-05-01

A semiautomated, repetitive-sequence-based PCR (rep-PCR) instrument (DiversiLab system) was evaluated in comparison with pulsed-field gel electrophoresis (PFGE) to investigate an outbreak of Serratia marcescens infections in a neonatal intensive care unit (NICU). A selection of 36 epidemiologically related and 8 epidemiologically unrelated isolates was analyzed. Among the epidemiologically related isolates, PFGE identified five genetically unrelated patterns. Thirty-two isolates from patients and wet nurses showed the same PFGE profile (pattern A). Genetically unrelated PFGE patterns were found in one patient (pattern B), in two wet nurses (patterns C and D), and in an environmental isolate from the NICU (pattern G). Rep-PCR identified seven different patterns, three of which included the 32 isolates of PFGE type A. One or two band differences in isolates of these three types allowed isolates to be categorized as similar and included in a unique cluster. Isolates of different PFGE types were also of unrelated rep-PCR types. All of the epidemiologically unrelated isolates were of different PFGE and rep-PCR types. The level of discrimination exhibited by rep-PCR with the DiversiLab system allowed us to conclude that this method was able to identify genetic similarity in a spatio-temporal cluster of S. marcescens isolates.

Detection of restriction fragment length polymorphisms in clinical isolates and serially passaged Pseudomonas aeruginosa strains.

PubMed Central

Hjelm, L N; Branstrom, A A; Warren, R L

1990-01-01

An 800-base-pair HindIII-PstI fragment that flanks a hot spot for Tn7 insertion was isolated from the chromosome of Pseudomonas aeruginosa and cloned into pUC12. The fragment was used to probe XhoI digests of genomic DNA from 18 P. aeruginosa isolates collected from sputum samples of seven cystic fibrosis patients. Only two XhoI restriction fragment length polymorphisms (RFLPs), of 3.7 and 7.7 kilobases (kb), were detected. Isolate WSU3531-1 (3.7-kb XhoI fragment) and WSU3860 (7.7-kb XhoI fragment), while isolated from the same patient, showed different RFLPs. Serial passages of isolate WSU3531-1 demonstrated that this strain was phenotypically stable. In contrast, colony and pigment variants were readily isolated at a frequency of 1% from serial passages of isolate WSU3860. When XhoI-digested genomic DNA from phenotypic variants of serially passaged WSU3860 were probed with the 800-base-pair HindIII-PstI fragment, the probe hybridized to a 10.4-kb XhoI fragment from three isolates. Restriction analysis of the genomic DNA digested with a variety of restriction enzymes showed that a 2.7-kb insertion occurred in the same region for all three isolates. There appeared to be no correlation between changes in the RFLP and changes in colony morphology. Images PMID:1977762

Close Genetic Relationship between Legionella pneumophila Serogroup 1 Isolates from Sputum Specimens and Puddles on Roads, as Determined by Sequence-Based Typing

PubMed Central

Kanatani, Jun-ichi; Isobe, Junko; Kimata, Keiko; Shima, Tomoko; Shimizu, Miwako; Kura, Fumiaki; Sata, Tetsutaro

2013-01-01

We investigated the prevalence of Legionella species isolated from puddles on asphalt roads. In addition, we carried out sequence-based typing (SBT) analysis on the genetic relationship between L. pneumophila serogroup 1 (SG 1) isolates from puddles and from stock strains previously obtained from sputum specimens and public baths. Sixty-nine water samples were collected from puddles on roads at 6 fixed locations. Legionella species were detected in 33 samples (47.8%) regardless of season. Among the 325 isolates from puddles, strains of L. pneumophila SG 1, a major causative agent of Legionnaires' disease, were the most frequently isolated (n = 62, 19.1%). Sixty-two isolates of L. pneumophila SG 1 from puddles were classified into 36 sequence types (STs) by SBT. ST120 and ST48 were identified as major STs. Environmental ST120 strains from puddles were found for the first time in this study. Among the 14 STs of the clinical isolates (n = 19), 4 STs (n = 6, 31.6%), including ST120, were also detected in isolates from puddles on roads, and the sources of infection in these cases remained unclear. The lag-1 gene, a tentative marker for clinical isolates, was prevalent in puddle isolates (61.3%). Our findings suggest that puddles on asphalt roads serve as potential reservoirs for L. pneumophila in the environment. PMID:23603681

Close genetic relationship between Legionella pneumophila serogroup 1 isolates from sputum specimens and puddles on roads, as determined by sequence-based typing.

PubMed

Kanatani, Jun-ichi; Isobe, Junko; Kimata, Keiko; Shima, Tomoko; Shimizu, Miwako; Kura, Fumiaki; Sata, Tetsutaro; Watahiki, Masanori

2013-07-01

We investigated the prevalence of Legionella species isolated from puddles on asphalt roads. In addition, we carried out sequence-based typing (SBT) analysis on the genetic relationship between L. pneumophila serogroup 1 (SG 1) isolates from puddles and from stock strains previously obtained from sputum specimens and public baths. Sixty-nine water samples were collected from puddles on roads at 6 fixed locations. Legionella species were detected in 33 samples (47.8%) regardless of season. Among the 325 isolates from puddles, strains of L. pneumophila SG 1, a major causative agent of Legionnaires' disease, were the most frequently isolated (n = 62, 19.1%). Sixty-two isolates of L. pneumophila SG 1 from puddles were classified into 36 sequence types (STs) by SBT. ST120 and ST48 were identified as major STs. Environmental ST120 strains from puddles were found for the first time in this study. Among the 14 STs of the clinical isolates (n = 19), 4 STs (n = 6, 31.6%), including ST120, were also detected in isolates from puddles on roads, and the sources of infection in these cases remained unclear. The lag-1 gene, a tentative marker for clinical isolates, was prevalent in puddle isolates (61.3%). Our findings suggest that puddles on asphalt roads serve as potential reservoirs for L. pneumophila in the environment.

Molecular Diversity of Seed-borne Fusarium Species Associated with Maize in India

PubMed Central

Aiyaz, Mohammed; Divakara, Shetty Thimmappa; Mudili, Venkataramana; Moore, Geromy George; Gupta, Vijai Kumar; Yli-Mattila, Tapani; Nayaka, Siddaiah Chandra; Niranjana, Siddapura Ramachandrappa

2016-01-01

A total of 106 maize seed samples were collected from different agro-climatic regions of India. Sixty-two Fusarium isolates were recovered, 90% of which were identified as Fusarium verticillioides based on morphological and molecular characters. Use of the tef-1α gene corrected/refined the morphological species identifications of 11 isolates, and confirmed those of the remaining isolates. Genetic diversity among the Fusarium isolates involved multilocus fingerprinting profiles by Inter Simple Sequence Repeats (ISSR) UPGMA and tef-1α gene phenetic analyses; for which, we observed no significant differences among the isolates based on geographic origin or fumonisin production; most of the subdivision related to species. Genotyping was performed on the F. verticillioides isolates, using 12 primer sets from the fumonisin pathway, to elucidate the molec-ular basis of fumonisin production or non-production. One fumonisin-negative isolate, UOMMF-16, was unable to amplify nine of the 12 fumonisin cluster genes tested. We also used the CD-ELISA method to confirm fumonisin production for our 62 Fusarium isolates. Only 15 isolates were found to be fumonisin-negative. Interestingly, genotypic characterization re-vealed six isolates with various gene deletion patterns that also tested positive for the production of fumonisins via CD-ELISA. Our findings confirm the importance of molecular studies for species delimitation, and for observing genetic and phenotypic diversity, among the Fusaria. PMID:27226769

Detection of neonatal unit clusters of Candida parapsilosis fungaemia by microsatellite genotyping: Results from laboratory-based sentinel surveillance, South Africa, 2009-2010.

PubMed

Magobo, Rindidzani E; Naicker, Serisha D; Wadula, Jeannette; Nchabeleng, Maphoshane; Coovadia, Yacoob; Hoosen, Anwar; Lockhart, Shawn R; Govender, Nelesh P

2017-05-01

Neonatal candidaemia is a common, deadly and costly hospital-associated disease. To determine the genetic diversity of Candida parapsilosis causing fungaemia in South African neonatal intensive care units (NICUs). From February 2009 through to August 2010, cases of candidaemia were reported through laboratory-based surveillance. C. parapsilosis isolates from neonatal cases were submitted for identification by internal transcribed spacer (ITS) region sequencing, antifungal susceptibility testing and microsatellite genotyping. Cluster analysis was performed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Of 1671 cases with a viable Candida isolate, 393 (24%) occurred among neonates. Isolates from 143 neonatal cases were confirmed as C. parapsilosis sensu stricto. Many isolates were resistant to fluconazole (77/143; 54%) and voriconazole (20/143; 14%). Of 79 closely-related genotypes, 18 were represented by ≥2 isolates; 61 genotypes had a single isolate each. Seven clusters, comprised of 82 isolates, were identified at five hospitals in three provinces. Isolates belonging to certain clusters were significantly more likely to be fluconazole resistant: all cluster 7 isolates and the majority of cluster 4 (78%), 5 (89%) and 6 (67%) isolates (P<.001). Candida parapsilosis-associated candidaemia in public-sector NICUs was caused by closely related genotypes and there was molecular evidence of undetected outbreaks as well as intra-hospital transmission. © 2017 Blackwell Verlag GmbH.

Optimization of analytical parameters for inferring relationships among Escherichia coli isolates from repetitive-element PCR by maximizing correspondence with multilocus sequence typing data.

PubMed

Goldberg, Tony L; Gillespie, Thomas R; Singer, Randall S

2006-09-01

Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a "gold standard" to optimize the analytical parameters for inferring relationships among Escherichia coli isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles ("curve-based" methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were "band-sharing coefficient" methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among E. coli isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.

Exploring the influence of Internet-based caregiver support on experiences of isolation for older spouse caregivers in rural areas: a qualitative interview study.

PubMed

Blusi, Madeleine; Kristiansen, Lisbeth; Jong, Mats

2015-09-01

Many older spouse caregivers are tied to the home by their caring duties and feel isolated. The values of supporting older caregivers are well known. In rural areas with long distances and decline in essential services, attending caregiver support groups can be difficult. Using Internet-based services can provide an opportunity for rural caregivers to participate in caregiver support, regardless of geographical distances and without the need for physical presence. This study aimed to explore how Internet-based caregiver support may influence the experience of isolation among older spouse caregivers in rural areas. An intervention study where 63 older rural caregivers received an Internet-based caregiver support service. A qualitative interview study based on 31 interviews with open-ended questions, analysed using latent content analysis. Two themes represent the findings from the study: Expanding the concept of place and Developing networks. Even though participants still spent their days in the house, they experienced that daily life was being spent in a variety of places, both physically, virtually and emotionally. The Internet-based support service provided them with a tool to reconnect with family and develop new friends. Internet-based caregiver support may reduce the experience of isolation for spouse caregivers in rural areas. Nurses played a crucial part in the development, by encouraging, educating and inspiring caregivers and supporting their independence. Internet-based services ought to be an option for caregiver support in rural areas as it may reduce feelings of isolation for older spouse caregivers. © 2014 John Wiley & Sons Ltd.

Screening and characterization of phosphate solubilizing bacteria from isolate of thermophilic bacteria

NASA Astrophysics Data System (ADS)

Yulianti, Evy; Rakhmawati, Anna

2017-08-01

The aims of this study were to select bacteria that has the ability to dissolve phosphate from thermophilic bacteria isolates after the Merapi eruption. Five isolates of selected bacteria was characterized and continued with identification. Selection was done by using a pikovskaya selective medium. Bacterial isolates were grown in selective medium and incubated for 48 hours at temperature of 55 ° C. Characterization was done by looking at the cell and colony morphology, physiological and biochemical properties. Identification was done with the Profile Matching method based on the reference genus Oscillospira traced through Bergey's Manual of Determinative Bacteriology. Dendogram was created based on similarity index SSM. The results showed there were 14 isolates of bacteria that were able to dissolve phosphate indicated by a clear zone surrounding the bacterial colony on selective media. Five isolates were selected with the largest clear zone. Isolates D79, D92, D110a, D135 and D75 have different characters. The result of phenotypic characters identification with Genus Oscillospira profile has a percentage of 100% similarity to isolate D92 and D110a; 92.31% for isolates D79, and 84.6% for isolates D75 and D135. Dendogram generated from average linkage algorithm / UPGMA using the Simple Matching Coefficient (SSM) algorithms showed, isolate thermophilic bacteria D75 and D135 are combined together to form cluster 1. D110a and D92 form a sub cluster A. Sub cluster A and D79 form cluster 2

Involvement of Colonizing Bacillus Isolates in Glucovanillin Hydrolysis during the Curing of Vanilla planifolia Andrews.

PubMed

Chen, Yonggan; Gu, Fenglin; Li, Jihua; He, Shuzhen; Xu, Fei; Fang, Yiming

2015-08-01

Vanilla beans were analyzed using biochemical methods, which revealed that glucovanillin disperses from the inner part to the outer part of the vanilla bean during the curing process and is simultaneously hydrolyzed by β-d-glucosidase. Enzymatic hydrolysis was found to occur on the surface of the vanilla beans. Transcripts of the β-d-glucosidase gene (bgl) of colonizing microorganisms were detected. The results directly indicate that colonizing microorganisms are involved in glucovanillin hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences showed that the colonizing microorganisms mainly belonged to the Bacillus genus. bgl was detected in all the isolates and presented clustering similar to that of the isolate taxonomy. Furthermore, inoculation of green fluorescent protein-tagged isolates showed that the Bacillus isolates can colonize vanilla beans. Glucovanillin was metabolized as the sole source of carbon in a culture of the isolates within 24 h. These isolates presented unique glucovanillin degradation capabilities. Vanillin was the major volatile compound in the culture. Other compounds, such as α-cubebene, β-pinene, and guaiacol, were detected in some isolate cultures. Colonizing Bacillus isolates were found to hydrolyze glucovanillin in culture, indirectly demonstrating the involvement of colonizing Bacillus isolates in glucovanillin hydrolysis during the vanilla curing process. Based on these results, we conclude that colonizing Bacillus isolates produce β-d-glucosidase, which mediates glucovanillin hydrolysis and influences flavor formation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

PubMed Central

Scaltriti, Erika; Sassera, Davide; Comandatore, Francesco; Morganti, Marina; Mandalari, Carmen; Gaiarsa, Stefano; Bandi, Claudio; Zehender, Gianguglielmo; Bolzoni, Luca; Casadei, Gabriele

2015-01-01

We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n = 15) and food, feed, animal, and environmental sources (n = 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system. PMID:25653407

Differential single nucleotide polymorphism-based analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis.

PubMed

Scaltriti, Erika; Sassera, Davide; Comandatore, Francesco; Morganti, Marina; Mandalari, Carmen; Gaiarsa, Stefano; Bandi, Claudio; Zehender, Gianguglielmo; Bolzoni, Luca; Casadei, Gabriele; Pongolini, Stefano

2015-04-01

We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n=15) and food, feed, animal, and environmental sources (n=24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus.

PubMed

Ferri, D V; Munhoz, C F; Neves, P M O; Ferracin, L M; Sartori, D; Vieira, M L C; Fungaro, M H P

2012-12-01

The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88 % of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5'-TGC GGC TGA GGA GGA CT-3') and BbasCG1024R (5'-TGC GGC TGA GTG TAG AAC-3') were designed for detecting and monitoring this isolate in the field.

LAMP-PCR detection of ochratoxigenic Aspergillus species collected from peanut kernel.

PubMed

Al-Sheikh, H M

2015-01-30

Over the last decade, ochratoxin A (OTA) has been widely described and is ubiquitous in several agricultural products. Ochratoxins represent the second-most important mycotoxin group after aflatoxins. A total of 34 samples were surveyed from 3 locations, including Mecca, Madina, and Riyadh, Saudi Arabia, during 2012. Fungal contamination frequency was determined for surface-sterilized peanut seeds, which were seeded onto malt extract agar media. Aspergillus niger (35%), Aspergillus ochraceus (30%), and Aspergillus carbonarius (25%) were the most frequently observed Aspergillius species, while Aspergillus flavus and Aspergillus phoenicis isolates were only infrequently recovered and in small numbers (10%). OTA production was evaluated on yeast extract sucrose medium, which revealed that 57% of the isolates were A. niger and 60% of A. carbonarius isolates were OTA producers; 100% belonged to A. ochraceus. Only one isolate, morphologically identified as A. carbonarius, and 3 A. niger isolates unstably produced OTA. A polymerase chain reaction (PCR)-based identification and detection assay was used to identify A. ochraceus isolates. Using the primer sets OCRA1/OCRA2, 400-base pair PCR fragments were produced only when genomic DNA from A. ochraceus isolates was used. Recently, the loop-mediated isothermal amplification assay using recombinase polymerase amplification chemistry was used for A. carbonarius and A. niger DNA identification. As a non-gel-based technique, the amplification product was directly visualized in the reaction tube after adding calcein for naked-eye examination.

Parallel evolution of sexual isolation in sticklebacks.

PubMed

Boughman, Janette Wenrick; Rundle, Howard D; Schluter, Dolph

2005-02-01

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

Characterization of rhizobia isolates obtained from nodules of wild genotypes of common bean.

PubMed

Cardoso, Aline Assis; Andraus, Michel de Paula; Borba, Tereza Cristina de Oliveira; Martin-Didonet, Claudia Cristina Garcia; Ferreira, Enderson Petrônio de Brito

This study aimed to evaluate the tolerance to salinity and temperature, the genetic diversity and the symbiotic efficiency of rhizobia isolates obtained from wild genotypes of common bean cultivated in soil samples from the States of Goiás, Minas Gerais and Paraná. The isolates were subjected to different NaCl concentrations (0%, 1%, 2%, 4% and 6%) at different temperatures (28°C, 33°C, 38°C, 43°C and 48°C). Genotypic characterization was performed based on BOX-PCR, REP-PCR markers and 16S rRNA sequencing. An evaluation of symbiotic efficiency was carried out under greenhouse conditions in autoclaved Leonard jars. Among 98 isolates about 45% of them and Rhizobium freirei PRF81 showed a high tolerance to temperature, while 24 isolates and Rhizobium tropici CIAT899 were able to use all of the carbon sources studied. Clustering analysis based on the ability to use carbon sources and on the tolerance to salinity and temperature grouped 49 isolates, R. tropici CIAT899 and R. tropici H12 with a similarity level of 76%. Based on genotypic characterization, 65% of the isolates showed an approximately 66% similarity with R. tropici CIAT899 and R. tropici H12. About 20% of the isolates showed symbiotic efficiency similar to or better than the best Rhizobium reference strain (R. tropici CIAT899). Phylogenetic analysis of the 16S rRNA revealed that two efficient isolates (ALSG5A1 and JPrG6A8) belong to the group of strains used as commercial inoculant for common bean in Brazil and must be assayed in field experiments. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Aspergillus pragensis sp. nov. discovered during molecular reidentification of clinical isolates belonging to Aspergillus section Candidi.

PubMed

Hubka, Vit; Lyskova, Pavlina; Frisvad, Jens C; Peterson, Stephen W; Skorepova, Magdalena; Kolarik, Miroslav

2014-08-01

The identity of nine clinical isolates recovered from Czech patients and presumptively identified as Aspergillus sp. section Candidi based on colony morphology was revised using sequences of β-tubulin, calmodulin gene sequence, and internal transcribed spacer rDNA. Six isolates were from suspected and proven onychomycosis, one from otitis externa, and two associated with probable invasive aspergillosis. The results showed that one Aspergillus candidus isolate was the cause of otitis externa, and both isolates obtained from sputa of patients with probable invasive aspergillosis were reidentified as A. carneus (sect. Terrei) and A. flavus (sect. Flavi). Three isolates from nail scrapings were identified as A. tritici, a verified agent of nondermatophyte onychomycosis. One isolate from toenail was determined to be A. candidus and the two isolates belonged to a hitherto undescribed species, Aspergillus pragensis sp. nov. This species is well supported by phylogenetic analysis based on β-tubulin and calmodulin gene and is distinguishable from other members of sect. Candidi by red-brown reverse on malt extract agar, slow growth on Czapek-Dox agar and inability to grow at 37°C. A secondary metabolite analysis was also provided with comparison of metabolite spectrum to other species. Section Candidi now encompasses five species for which a dichotomous key based on colony characteristics is provided. All clinical isolates were tested for susceptibilities to selected antifungal agents using the Etest and disc diffusion method. Overall sect. Candidi members are highly susceptible to common antifungals. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Size-based separation methods of circulating tumor cells.

PubMed

Hao, Si-Jie; Wan, Yuan; Xia, Yi-Qiu; Zou, Xin; Zheng, Si-Yang

2018-02-01

Circulating tumor cells (CTCs) originate from the primary tumor mass and enter into the peripheral bloodstream. Compared to other "liquid biopsy" portfolios such as exosome, circulating tumor DNA/RNA (ctDNA/RNA), CTCs have incomparable advantages in analyses of transcriptomics, proteomics, and signal colocalization. Hence, CTCs hold the key to understanding the biology of metastasis and play a vital role in cancer diagnosis, treatment monitoring, and prognosis. Size-based enrichment features are prominent in CTC isolation. It is a label-free, simple and fast method. Enriched CTCs remain unmodified and viable for a wide range of subsequent analyses. In this review, we comprehensively summarize the differences of size and deformability between CTCs and blood cells, which would facilitate the development of technologies of size-based CTC isolation. Then we review representative size-/deformability-based technologies available for CTC isolation and highlight the recent achievements in molecular analysis of isolated CTCs. To wrap up, we discuss the substantial challenges facing the field, and elaborate on prospects. Copyright © 2018 Elsevier B.V. All rights reserved.

International Life Science Institute North America Cronobacter (Formerly Enterobacter sakazakii) isolate set.

PubMed

Ivy, Reid A; Farber, Jeffrey M; Pagotto, Franco; Wiedmann, Martin

2013-01-01

Foodborne pathogen isolate collections are important for the development of detection methods, for validation of intervention strategies, and to develop an understanding of pathogenesis and virulence. We have assembled a publicly available Cronobacter (formerly Enterobacter sakazakii) isolate set that consists of (i) 25 Cronobacter sakazakii isolates, (ii) two Cronobacter malonaticus isolates, (iii) one Cronobacter muytjensii isolate, which displays some atypical phenotypic characteristics, biochemical profiles, and colony color on selected differential media, and (iv) two nonclinical Enterobacter asburiae isolates, which show some phenotypic characteristics similar to those of Cronobacter spp. The set consists of human (n = 10), food (n = 11), and environmental (n = 9) isolates. Analysis of partial 16S rDNA sequence and seven-gene multilocus sequence typing data allowed for reliable identification of these isolates to species and identification of 14 isolates as sequence type 4, which had previously been shown to be the most common C. sakazakii sequence type associated with neonatal meningitis. Phenotypic characterization was carried out with API 20E and API 32E test strips and streaking on two selective chromogenic agars; isolates were also assessed for sorbitol fermentation and growth at 45°C. Although these strategies typically produced the same classification as sequence-based strategies, based on a panel of four biochemical tests, one C. sakazakii isolate yielded inconclusive data and one was classified as C. malonaticus. EcoRI automated ribotyping and pulsed-field gel electrophoresis (PFGE) with XbaI separated the set into 23 unique ribotypes and 30 unique PFGE types, respectively, indicating subtype diversity within the set. Subtype and source data for the collection are publicly available in the PathogenTracker database (www. pathogentracker. net), which allows for continuous updating of information on the set, including links to publications that include information on isolates from this collection.

Identification and Characterization of Citrus tristeza virus Isolates Breaking Resistance in Trifoliate Orange in California.

PubMed

Yokomi, Raymond K; Selvaraj, Vijayanandraj; Maheshwari, Yogita; Saponari, Maria; Giampetruzzi, Annalisa; Chiumenti, Michela; Hajeri, Subhas

2017-07-01

Most Citrus tristeza virus (CTV) isolates in California are biologically mild and symptomless in commercial cultivars on CTV tolerant rootstocks. However, to better define California CTV isolates showing divergent serological and genetic profiles, selected isolates were subjected to deep sequencing of small RNAs. Full-length sequences were assembled, annotated and trifoliate orange resistance-breaking (RB) isolates of CTV were identified. Phylogenetic relationships based on their full genomes placed three isolates in the RB clade: CA-RB-115, CA-RB-AT25, and CA-RB-AT35. The latter two isolates were obtained by aphid transmission from Murcott and Dekopon trees, respectively, containing CTV mixtures. The California RB isolates were further distinguished into two subclades. Group I included CA-RB-115 and CA-RB-AT25 with 99% nucleotide sequence identity with RB type strain NZRB-G90; and group II included CA-RB-AT35 with 99 and 96% sequence identity with Taiwan Pumelo/SP/T1 and HA18-9, respectively. The RB phenotype was confirmed by detecting CTV replication in graft-inoculated Poncirus trifoliata and transmission from P. trifoliata to sweet orange. The California RB isolates induced mild symptoms compared with severe isolates in greenhouse indexing tests. Further examination of 570 CTV accessions, acquired from approximately 1960 and maintained in planta at the Central California Tristeza Eradication Agency, revealed 16 RB positive isolates based on partial p65 sequences. Six isolates collected from 1992 to 2011 from Tulare and Kern counties were CA-RB-115-like; and 10 isolates collected from 1968 to 2010 from Riverside, Fresno, and Kern counties were CA-RB-AT35-like. The presence of the RB genotype is relevant because P. trifoliata and its hybrids are the most popular rootstocks in California.

Shared Mycobacterium avium genotypes observed among unlinked clinical and environmental isolates

EPA Science Inventory

Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this, ...

Shared Mycobacterium avium genotypes observed among unlinked clinical and environmental isolates*

EPA Science Inventory

Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this a...

Antibiotic resistance and biofilm formation of some bacteria isolated from sediment, water and fish farms in Malaysia

NASA Astrophysics Data System (ADS)

Faja, Orooba Meteab; Usup, Gires; Ahmad, Asmat

2018-04-01

A total of 90 isolates of bacteria were isolated, from sediment (10) samples, water (10) samples and fish (12) samples (Sea bass, Snapper, Grouper and Tilapia). These include 22 isolates of bacteria from sediment, 28 isolates from water and 40 isolates from fish. All the isolates were tested for sensitivity to 13 antibiotics using disc diffusion method. The isolates showed high resistance to some antibiotics based on samples source. Isolates from sediment showed highest resistance toward novobiocin, kanamycin, ampicillin and streptomycin while isolates from water showed highest resistance against vancomycin, penicillin, streptomycin and tetracycline, in contrast, in fish sample showed highest resistance toward vancomycin, ampicillin, streptomycin and tetracycline. Most of the isolates showed biofilm formation ability with different degrees. Out of 22 bacteria isolates from water, two isolates were weak biofilm formers, six isolates moderate biofilm formers and fourteen isolates strong biofilm formers. While, out of 28 bacteria isolates from water one isolate was weak biofilm former, five isolates moderate biofilm formers and 22 strong biofilm formers Fish isolate showed three isolates (8%) moderate biofilm formers and 27 isolates strong biofilm formers. Biofilm formation was one of the factors that lead to antibiotic resistance of the bacterial isolates from these samples.

Characterization of Phytophthora infestans populations in northwestern Algeria during 2008-2014.

PubMed

Rekad, Fatma Zohra; Cooke, David Edward Llewelyn; Puglisi, Ivana; Randall, Eva; Guenaoui, Yamina; Bouznad, Zouaoui; Evoli, Maria; Pane, Antonella; Schena, Leonardo; Magnano di San Lio, Gaetano; Cacciola, Santa Olga

2017-05-01

A total of 161 Phytophthora infestans isolates, collected from infected potato and tomato plants during 2008-2014, were characterized based on mating type, metalaxyl sensitivity and polymorphism at 12 simple sequence repeat (SSR) loci, in order to investigate the population of P. infestans in the north-west of Algeria, an emerging potato production region. The majority of isolates were of A2 mating type (112 isolates). A high percentage (89 %) of resistance to metalaxyl among isolates was detected. The metalaxyl resistant phenotype was present in both mating types with a higher percentage in A2 mating type isolates. SSR-based genotypic analysis of P. infestans population showed a low diversity. Genotype 13_A2 was the predominant in the population with a frequency of 67 % followed by 2_A1 (21 %) and 23_A1 (5 %). Genotype 23_A1 was detected only in tomato and potato isolates collected in 2013 and 2014. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

PubMed Central

Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

1998-01-01

All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

Effect of type and content of modified montmorillonite on the structure and properties of bio-nanocomposite films based on soy protein isolate and montmorillonite

USDA-ARS?s Scientific Manuscript database

The non-biodegradable and non-renewable nature of plastic packaging has led to a renewed interest in packaging materials based on bio-nanocomposites (biopolymer matrix reinforced with nanoparticles such as layered silicates). Bio-nanocomposite films based on soy protein isolate (SPI) and modified mo...

Detergent-Based Isolation of Yeast Membrane Rafts: An Inquiry-Based Laboratory Series for the Undergraduate Cell Biology or Biochemistry Lab

ERIC Educational Resources Information Center

Willhite, D. Grant; Wright, Stephen E.

2009-01-01

Lipid rafts have been implicated in numerous cellular processes including cell signaling, endocytosis, and even viral infection. Isolation of these lipid rafts often involves detergent treatment of the membrane to dissolve nonraft components followed by separation of raft regions in a density gradient. We present here an inquiry-based lab series…

Phylogenetic relationships of Sarcocystis neurona of horses and opossums to other cyst-forming coccidia deduced from SSU rRNA gene sequences.

PubMed

Elsheikha, Hany M; Lacher, David W; Mansfield, Linda S

2005-11-01

Phylogenetic analyses based on sequences of the nuclear-encoded small subunit rRNA (ssurRNA) gene were performed to examine the origin, phylogeny, and biogeographic relationships of Sarcocystis neurona isolates from opossums and horses from the State of Michigan, USA, in relation to other cyst-forming coccidia. A total of 31 taxa representing all recognized subfamilies and genera of Sarcocystidae were included in the analyses with clonal isolates of two opossum and two horse S. neurona. Phylogenies obtained by the four tree-building methods were consistent with the classical taxonomy based on morphological criteria. The "isosporid" coccidia Neospora, Toxoplasma, Besnoitia, Isospora lacking stieda bodies, and Hyaloklossia formed a sister group to the Sarcocystis spp. Sarcocystis species were divided into three main lineages; S. neurona isolates were located in the second lineage and clustered with S. mucosa, S. dispersa, S. lacertae, S. rodentifelis, S. muris, and Frenkelia spp. Alignment of S. neurona SSU rRNA gene sequences of Michigan opossum isolates (MIOP5, MIOP20) and a S. neurona Michigan horse isolate (MIH8) showed 100% identity. These Michigan isolates differed in 2/1085 bp (0.2%) from a Kentucky S. neurona horse isolate (SN5). Additionally, S. neurona isolates from horses and opossums were identical based on the ultrastructural features and PCR-RFLP analyses thus forming a phylogenetically indistinct group in these regions. These findings revealed the concordance between the morphological and molecular data and confirmed that S. neurona from opossums and horses originated from the same phylogenetic origin.

Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus.

PubMed

Caffier, Valérie; Le Cam, Bruno; Al Rifaï, Mehdi; Bellanger, Marie-Noëlle; Comby, Morgane; Denancé, Caroline; Didelot, Frédérique; Expert, Pascale; Kerdraon, Tifenn; Lemarquand, Arnaud; Ravon, Elisa; Durel, Charles-Eric

2016-10-01

Quantitative plant resistance affects the aggressiveness of pathogens and is usually considered more durable than qualitative resistance. However, the efficiency of a quantitative resistance based on an isolate-specific Quantitative Trait Locus (QTL) is expected to decrease over time due to the selection of isolates with a high level of aggressiveness on resistant plants. To test this hypothesis, we surveyed scab incidence over an eight-year period in an orchard planted with susceptible and quantitatively resistant apple genotypes. We sampled 79 Venturia inaequalis isolates from this orchard at three dates and we tested their level of aggressiveness under controlled conditions. Isolates sampled on resistant genotypes triggered higher lesion density and exhibited a higher sporulation rate on apple carrying the resistance allele of the QTL T1 compared to isolates sampled on susceptible genotypes. Due to this ability to select aggressive isolates, we expected the QTL T1 to be non-durable. However, our results showed that the quantitative resistance based on the QTL T1 remained efficient in orchard over an eight-year period, with only a slow decrease in efficiency and no detectable increase of the aggressiveness of fungal isolates over time. We conclude that knowledge on the specificity of a QTL is not sufficient to evaluate its durability. Deciphering molecular mechanisms associated with resistance QTLs, genetic determinants of aggressiveness and putative trade-offs within pathogen populations is needed to help in understanding the erosion processes. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of Bacillus spp. as dough starters for Adhirasam - A traditional rice based fermented food of Southern India

PubMed Central

Anisha, Anvar Hussain Noorul; Anandham, Rangasamy; Kwon, Soon Woo; Gandhi, Pandiyan Indira; Gopal, Nellaiappan Olaganathan

2015-01-01

Abstract Adhirasam is a cereal based, doughnut shaped, deep fried dessert consumed in the southern regions of India. The dough used to prepare adhirasam is fermented and contains rice flour and jaggery. The aim of the present study was to characterize the cultivable bacteria associated with this fermented dough and to identify a suitable starter culture for the production of quality adhirasam. In total, one hundred and seventy bacterial isolates were recovered from de Man Rogosa Sharp (MRS) agar, nutrient agar, lysogeny agar and tryptic soy agar media. Out of the 170 bacterial isolates, sixteen isolates were selected based on their ability to tolerate glucose and sucrose. All the bacterial isolates tolerated 15% glucose and 30% sucrose. Analyses of 16S rDNA gene sequences of the bacterial isolates showed that the dominant cultivable bacteria were members of the genus Bacillus. These strains were further used as starters and tested for their ability to ferment rice flour with jaggery to produce adhirasam dough. Organoleptic evaluation was carried out to choose the best starter strain. Adhirasam prepared from Bacillus subtilis isolates S4-P11, S2-G2-A1 and S1-G15, Bacillus tequilensis isolates S2-H16, S3-P9, S3-G10 and Bacillus siamensis isolate S2-G13 were highly acceptable to consumers. Adhirasam prepared using these starter cultures had superior product characteristics such as softness in texture, flavor and enhanced aroma and sweet taste. PMID:26691480

Multiplexed Affinity-Based Separation of Proteins and Cells Using Inertial Microfluidics.

PubMed

Sarkar, Aniruddh; Hou, Han Wei; Mahan, Alison E; Han, Jongyoon; Alter, Galit

2016-03-30

Isolation of low abundance proteins or rare cells from complex mixtures, such as blood, is required for many diagnostic, therapeutic and research applications. Current affinity-based protein or cell separation methods use binary 'bind-elute' separations and are inefficient when applied to the isolation of multiple low-abundance proteins or cell types. We present a method for rapid and multiplexed, yet inexpensive, affinity-based isolation of both proteins and cells, using a size-coded mixture of multiple affinity-capture microbeads and an inertial microfluidic particle sorter device. In a single binding step, different targets-cells or proteins-bind to beads of different sizes, which are then sorted by flowing them through a spiral microfluidic channel. This technique performs continuous-flow, high throughput affinity-separation of milligram-scale protein samples or millions of cells in minutes after binding. We demonstrate the simultaneous isolation of multiple antibodies from serum and multiple cell types from peripheral blood mononuclear cells or whole blood. We use the technique to isolate low abundance antibodies specific to different HIV antigens and rare HIV-specific cells from blood obtained from HIV+ patients.

Isolation of circulating tumor cells from pancreatic cancer by automated filtration

PubMed Central

Brychta, Nora; Drosch, Michael; Driemel, Christiane; Fischer, Johannes C.; Neves, Rui P.; Esposito, Irene; Knoefel, Wolfram; Möhlendick, Birte; Hille, Claudia; Stresemann, Antje; Krahn, Thomas; Kassack, Matthias U.; Stoecklein, Nikolas H.; von Ahsen, Oliver

2017-01-01

It is now widely recognized that the isolation of circulating tumor cells based on cell surface markers might be hindered by variability in their protein expression. Especially in pancreatic cancer, isolation based only on EpCAM expression has produced very diverse results. Methods that are independent of surface markers and therefore independent of phenotypical changes in the circulating cells might increase CTC recovery also in pancreatic cancer. We compared an EpCAM-dependent (IsoFlux) and a size-dependent (automated Siemens Healthineers filtration device) isolation method for the enrichment of pancreatic cancer CTCs. The recovery rate of the filtration based approach is dramatically superior to the EpCAM-dependent approach especially for cells with low EpCAM-expression (filtration: 52%, EpCAM-dependent: 1%). As storage and shipment of clinical samples is important for centralized analyses, we also evaluated the use of frozen diagnostic leukapheresis (DLA) as source for isolating CTCs and subsequent genetic analysis such as KRAS mutation detection analysis. Using frozen DLA samples of pancreatic cancer patients we detected CTCs in 42% of the samples by automated filtration. PMID:29156783

Isolation of circulating tumor cells from pancreatic cancer by automated filtration.

PubMed

Brychta, Nora; Drosch, Michael; Driemel, Christiane; Fischer, Johannes C; Neves, Rui P; Esposito, Irene; Knoefel, Wolfram; Möhlendick, Birte; Hille, Claudia; Stresemann, Antje; Krahn, Thomas; Kassack, Matthias U; Stoecklein, Nikolas H; von Ahsen, Oliver

2017-10-17

It is now widely recognized that the isolation of circulating tumor cells based on cell surface markers might be hindered by variability in their protein expression. Especially in pancreatic cancer, isolation based only on EpCAM expression has produced very diverse results. Methods that are independent of surface markers and therefore independent of phenotypical changes in the circulating cells might increase CTC recovery also in pancreatic cancer. We compared an EpCAM-dependent (IsoFlux) and a size-dependent (automated Siemens Healthineers filtration device) isolation method for the enrichment of pancreatic cancer CTCs. The recovery rate of the filtration based approach is dramatically superior to the EpCAM-dependent approach especially for cells with low EpCAM-expression (filtration: 52%, EpCAM-dependent: 1%). As storage and shipment of clinical samples is important for centralized analyses, we also evaluated the use of frozen diagnostic leukapheresis (DLA) as source for isolating CTCs and subsequent genetic analysis such as KRAS mutation detection analysis. Using frozen DLA samples of pancreatic cancer patients we detected CTCs in 42% of the samples by automated filtration.

A combined dynamic analysis method for geometrically nonlinear vibration isolators with elastic rings

NASA Astrophysics Data System (ADS)

Hu, Zhan; Zheng, Gangtie

2016-08-01

A combined analysis method is developed in the present paper for studying the dynamic properties of a type of geometrically nonlinear vibration isolator, which is composed of push-pull configuration rings. This method combines the geometrically nonlinear theory of curved beams and the Harmonic Balance Method to overcome the difficulty in calculating the vibration and vibration transmissibility under large deformations of the ring structure. Using the proposed method, nonlinear dynamic behaviors of this isolator, such as the lock situation due to the coulomb damping and the usual jump resulting from the nonlinear stiffness, can be investigated. Numerical solutions based on the primary harmonic balance are first verified by direct integration results. Then, the whole procedure of this combined analysis method is demonstrated and validated by slowly sinusoidal sweeping experiments with different amplitudes of the base excitation. Both numerical and experimental results indicate that this type of isolator behaves as a hardening spring with increasing amplitude of the base excitation, which makes it suitable for isolating both steady-state vibrations and transient shocks.

Characterization of a novel variant of Mycobacterium chimaera.

PubMed

van Ingen, J; Hoefsloot, W; Buijtels, P C A M; Tortoli, E; Supply, P; Dekhuijzen, P N R; Boeree, M J; van Soolingen, D

2012-09-01

In this study, nonchromogenic mycobacteria were isolated from pulmonary samples of three patients in the Netherlands. All isolates had identical, unique 16S rRNA gene and 16S-23S ITS sequences, which were closely related to those of Mycobacterium chimaera and Mycobacterium marseillense. The biochemical features of the isolates differed slightly from those of M. chimaera, suggesting that the isolates may represent a possible separate species within the Mycobacterium avium complex (MAC). However, the cell-wall mycolic acid pattern, analysed by HPLC, and the partial sequences of the hsp65 and rpoB genes were identical to those of M. chimaera. We concluded that the isolates represent a novel variant of M. chimaera. The results of this analysis have led us to question the currently used methods of species definition for members of the genus Mycobacterium, which are based largely on 16S rRNA or rpoB gene sequencing. Definitions based on a single genetic target are likely to be insufficient. Genetic divergence, especially in the MAC, yields strains that cannot be confidently assigned to a specific species based on the analysis of a single genetic target.

Development and characterization of a multi-layer magnetorheological elastomer isolator based on a Halbach array

NASA Astrophysics Data System (ADS)

Przybylski, Michal; Sun, Shuaishuai; Li, Weihua

2016-10-01

Most existing vibration isolators and dampers based on magnetorheological (MR) materials need electrical power to feed magnetic coils to stimulate the MR material, so if there is a loss of power, such as during a strong earthquake or system failure, they are unable to protect the structure. This paper outlines the design and test of a controllable multilayered magnetorheological elastomer (MRE) isolator based on a circular dipolar Halbach array; which is a set of magnets that generates a strong and uniform magnetic field. Combining an MRE layered isolator system with the Halbach array allows for constant vibration isolation with very low power consumption, where the power generated is only used to adjust the Halbach position. When this system was tested it successfully altered the lateral stiffness and damping force by 81.13% and 148.72%, respectively. This paper also includes an extended analysis of the magnetic field generated by the circular dipolar Halbach array and a discussion of the improvements that may potentially improve the range of magnetic fields generated.

Isolation and culture of human multipotent stromal cells from the pancreas.

PubMed

Seeberger, Karen L; Eshpeter, Alana; Korbutt, Gregory S

2011-01-01

Mesenchymal stem cells, also termed multipotent mesenchymal stromal cells (MSCs), can be isolated from most adult tissues. Although the exact origin of MSCs expanded from the human pancreas has not been resolved, we have developed protocols to isolate and expand MSCs from human pancreatic tissue that remains after islet procurement. Similar to techniques used to isolate MSCs from bone marrow, pancreatic MSCs are isolated based on their cell adherence, expression of several cell surface antigens, and multilineage differentiation. The protocols for isolating, characterizing, and differentiating MSCs from the pancreas are presented in this chapter.

Molecular characterization of an Akabane virus isolate from West Java, Indonesia.

PubMed

Purnomo Edi, Suryo; Ibrahim, Afif; Sukoco, Rinto; Bunali, Lukman; Taguchi, Masaji; Kato, Tomoko; Yanase, Tohru; Shirafuji, Hiroaki

2017-04-08

We isolated an arbovirus from bovine blood in Indonesia. The arbovirus was obtained from the plasma of a cow showing no clinical symptoms in West Java in February 2014, and was identified as Akabane virus (AKAV) by AKAV-specific RT-PCR and subsequent sequence analysis. Phylogenetic analysis based on partial S segment indicated the AKAV isolate, WJ-1SA/P/2014, was most closely related with two isolates from Israel and Turkey reported in 2001 and 2015, respectively, and that WJ-1SA/P/2014 isolate belongs to AKAV genogroup Ib. This is the first isolation of AKAV from Indonesia.

Social isolation in community-dwelling seniors: an evidence-based analysis.

PubMed

2008-01-01

In early August 2007, the Medical Advisory Secretariat began work on the Aging in the Community project, an evidence-based review of the literature surrounding healthy aging in the community. The Health System Strategy Division at the Ministry of Health and Long-Term Care subsequently asked the secretariat to provide an evidentiary platform for the ministry's newly released Aging at Home Strategy.After a broad literature review and consultation with experts, the secretariat identified 4 key areas that strongly predict an elderly person's transition from independent community living to a long-term care home. Evidence-based analyses have been prepared for each of these 4 areas: falls and fall-related injuries, urinary incontinence, dementia, and social isolation. For the first area, falls and fall-related injuries, an economic model is described in a separate report.Please visit the Medical Advisory Secretariat Web site, http://www.health.gov.on.ca/english/providers/program/mas/mas_about.html, to review these titles within the Aging in the Community series.AGING IN THE COMMUNITY: Summary of Evidence-Based AnalysesPrevention of Falls and Fall-Related Injuries in Community-Dwelling Seniors: An Evidence-Based AnalysisBehavioural Interventions for Urinary Incontinence in Community-Dwelling Seniors: An Evidence-Based AnalysisCaregiver- and Patient-Directed Interventions for Dementia: An Evidence-Based AnalysisSocial Isolation in Community-Dwelling Seniors: An Evidence-Based AnalysisThe Falls/Fractures Economic Model in Ontario Residents Aged 65 Years and Over (FEMOR) OBJECTIVE OF THE EVIDENCE-BASED ANALYSIS: The objective was to systematically review interventions aimed at preventing or reducing social isolation and loneliness in community-dwelling seniors, that is, persons ≥ 65 years of age who are not living in long-term care institutions. The analyses focused on the following questions: Are interventions to reduce social isolation and/or loneliness effective?Do these interventions improve health, well-being, and/or quality of life?Do these interventions impact on independent community living by delaying or preventing functional decline or disability?Do the interventions impact on health care utilization, such as physician visits, emergency visits, hospitalization, or admission to long-term care? TARGET POPULATION AND CONDITION Social and family relationships are a core element of quality of life for seniors, and these relationships have been ranked second, next to health, as the most important area of life. Several related concepts-reduced social contact, being alone, isolation, and feelings of loneliness-have all been associated with a reduced quality of life in older people. Social isolation and loneliness have also been associated with a number of negative outcomes such as poor health, maladaptive behaviour, and depressed mood. Higher levels of loneliness have also been associated with increased likelihood of institutionalization. NOTE: It is recognized that the terms "senior" and "elderly" carry a range of meanings for different audiences; this report generally uses the former, but the terms are treated here as essentially interchangeable. METHODS OF THE EVIDENCE-BASED ANALYSIS: The scientific evidence base was evaluated through a systematic literature review. The literature searches were conducted with several computerized bibliographic databases for literature published between January 1980 and February 2008. The search was restricted to English-language reports on human studies and excluded letters, comments and editorials, and case reports. Journal articles eligible for inclusion in the review included those that reported on single, focused interventions directed towards or evaluating social isolation or loneliness; included, in whole or in part, community-dwelling seniors (≥ 65 years); included some quantitative outcome measure on social isolation or loneliness; and included a comparative group. Assessments of current practices were obtained through consultations with various individuals and agencies including the Ontario Community Care Access Centres and the Ontario Assistive Devices Program. An Ontario-based budget impact was also assessed for the identified effective interventions for social isolation. A systematic review of the published literature focusing on interventions for social isolation and loneliness in community-dwelling seniors identified 11 quantitative studies. The studies involved European or American populations with diverse recruitment strategies, intervention objectives, and limited follow-up, with cohorts from 10 to 15 years ago involving mainly elderly women less than 75 years of age. The studies involved 2 classes of interventions: in-person group support activities and technology-assisted interventions. These were delivered to diverse targeted groups of seniors such as those with mental distress, physically inactive seniors, low-income groups, and informal caregivers. The interventions were primarily focused on behaviour-based change. Modifying factors (client attitude or preference) and process issues (targeting methods of at-risk subjects, delivery methods, and settings) influenced intervention participation and outcomes. Both classes of interventions were found to reduce social isolation and loneliness in seniors. Social support groups were found to effectively decrease social isolation for seniors on wait lists for senior apartments and those living in senior citizen apartments. Community-based exercise programs featuring health and wellness for physically inactive community-dwelling seniors also effectively reduced loneliness. Rehabilitation for mild/moderate hearing loss was effective in improving communication disabilities and reducing loneliness in seniors. Interventions evaluated for informal caregivers of seniors with dementia, however, had limited effectiveness for social isolation or loneliness. Research into interventions for social isolation in seniors has not been broadly based, relative to the diverse personal, social, health, economic, and environmentally interrelated factors potentially affecting isolation. Although rehabilitation for hearing-related disability was evaluated, the systematic review did not locate research on interventions for other common causes of aging-related disability and loneliness, such as vision loss or mobility declines. Despite recent technological advances in e-health or telehealth, controlled studies evaluating technology-assisted interventions for social isolation have examined only basic technologies such as phone- or computer-mediated support groups. Although effective interventions were identified for social isolation and loneliness in community-dwelling seniors, they were directed at specifically targeted groups and involved only a few of the many potential causes of social isolation. Little research has been directed at identifying effective interventions that influence the social isolation and other burdens imposed upon caregivers, in spite of the key role that caregivers assume in caring for seniors. The evidence on technology-assisted interventions and their effects on the social health and well-being of seniors and their caregivers is limited, but increasing demand for home health care and the need for efficiencies warrant further exploration. Interventions for social isolation in community-dwelling seniors need to be researched more broadly in order to develop effective, appropriate, and comprehensive strategies for at-risk populations.

Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.

PubMed

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.

A practical examination of RNA isolation methods for European pear (Pyrus communis)

USDA-ARS?s Scientific Manuscript database

With the goal of identifying fast, reliable and broadly applicable RNA isolation methods in European pear fruit for downstream transcriptome analysis, we evaluated several commercially available kit-based RNA isolations methods, plus our modified version of a published cetyl trimethyl ammonium bromi...

Avian Follicular and Interdigitating Dendritic Cells: Isolation and Morphologic, Phenotypic, and Functional Analyses

USDA-ARS?s Scientific Manuscript database

An antiserum against Eimeria tenella sporozoites was used to localize and isolate Ag-binding cells in intestinal cecal tonsils of parasite-infected chickens. Based on their tissue localization, ultrastructural features, and expression of surface markers, two subpopulations of cells were isolated, C...

Plant growth-promoting potential of bacteria isolated from active volcano sites of Barren Island, India.

PubMed

Amaresan, N; Kumar, K; Sureshbabu, K; Madhuri, K

2014-02-01

To elucidate the biodiversity of plant growth-promoting (PGP) bacteria in active volcano sites of Barren Island, India, a total of 102 bacteria were isolated and screened for their multifunctional PGP properties. The results revealed that 21 isolates (20.6%) survived heat shock at 72°C and 11 (10.8%) isolates were able to grow exposed to 25% NaCl (w/v). In assaying for PGP properties, 59 (57.8%) isolates shown indole acetic acid (IAA) like substances production, 57 isolates (55.9%) produced siderophore and 34 (33.3%) solubilized inorganic phosphate qualitatively. Whereas in the production of extracellular enzymes, 42 isolates (41.2%) produced protease and amylase, 26 (25.5%) isolates produced lipase and 24 (23.5%) isolates produced cellulase. In antagonistic activity, 30 isolates (29.4%) were found antagonistic against Macrophomina sp., 20 isolates (19.6%) against Rhizoctonia solani and 15 isolates (14.7%) against Sclerotium rolfsii. The results based on 16 rRNA gene sequencing revealed that the PGP bacteria belonged to 22 different species comprising 13 genera. Based on multifunctional properties, nine isolates were further selected to determine the PGP in brinjal and chilli seeds. Of the bacteria tested, the isolate BAN87 showed increased root and shoot length of both the crops followed in plant growth promotion by BAN86 and BAN43. The outcome of this research proves plausible practical applicability of these PGPB for crop production in soils of saline and arid environments. The present research shows diverse plant growth-promoting (PGP) bacteria could be isolated from the active volcano site and suggests that volcano sites represent an ecological niche, which harbours a diverse and hitherto largely uncharacterized microbial population with yet unknown and untapped potential biotechnological applications, for example, plant growth promoters, as evidenced from this study. The outcome of this research may have a practical effect on crop production methodologies in saline and arid environment soils. © 2013 The Society for Applied Microbiology.

Morphological and Genetic Diversity of Rhizobia Nodulating Cowpea (Vigna unguiculata L.) from Agricultural Soils of Lower Eastern Kenya.

PubMed

Ondieki, Damaris K; Nyaboga, Evans N; Wagacha, John M; Mwaura, Francis B

2017-01-01

Limited nitrogen (N) content in the soil is a major challenge to sustainable and high crop production in many developing countries. The nitrogen fixing symbiosis of legumes with rhizobia plays an important role in supplying sufficient N for legumes and subsequent nonleguminous crops. To identify rhizobia strains which are suitable for bioinoculant production, characterization of rhizobia is a prerequisite. The objective of this study was to assess the morphological and genetic diversity of rhizobia that nodulates cowpea in agricultural soils of lower eastern Kenya. Twenty-eight rhizobia isolates were recovered from soil samples collected from farmers' fields in Machakos, Makueni, and Kitui counties in lower eastern Kenya and characterized based on morphological characteristics. Thirteen representative isolates were selected and characterized using BOX repetitive element PCR fingerprinting. Based on the dendrogram generated from morphological characteristics, the test isolates were distributed into two major clusters at a similarity of 75%. Phylogenetic tree, based on BOX repetitive element PCR, grouped the isolates into two clusters at 90% similarity level. The clustering of the isolates did not show a relationship to the origin of soil samples, although the isolates were genetically diverse. This study is a prerequisite to the selection of suitable cowpea rhizobia to develop bioinoculants for sustainable crop production in Kenya.

Discrimination of Scedosporium prolificans against Pseudallescheria boydii and Scedosporium apiospermum by semiautomated repetitive sequence-based PCR.

PubMed

Steinmann, J; Schmidt, D; Buer, J; Rath, P-M

2011-07-01

The laboratory identification of Pseudallescheria and Scedosporium isolates at the species level is important for clinical and epidemiological purposes. This study used semiautomated repetitive sequence-based polymerase chain reaction (rep-PCR) to identify Pseudallescheria/Scedosporium. Reference strains of Pseudallescheria boydii (n = 12), Scedosporium prolificans (n = 8), Scedosporium apiospermum (n = 9), and clinical/environmental isolates (P. boydii, 7; S. prolificans, 7; S. apiospermum, 7) were analyzed by rep-PCR. All clinical isolates were identified by morphological and phenotypic characteristics and by sequence analysis. Species identification of reference strains was based on the results of available databases. Rep-PCR studies were also conducted with various molds to differentiate Pseudallescheria/Scedosporium spp. from other commonly encountered filamentous fungi. All tested Pseudallescheria/Scedosporium isolates were distinguishable from the other filamentous fungi. All Scedosporium prolificans strains clustered within the cutoff of 85%, and species identification by rep-PCR showed an agreement of 100% with sequence analysis. However, several isolates of P. boydii and S. apiospermum did not cluster within the 85% cutoff with the same species by rep-PCR. Although the identification of P. boydii and S. apiospermum was not correct, the semiautomated rep-PCR system is a promising tool for the identification of S. prolificans isolates.

Ultra-low frequency vertical vibration isolator based on LaCoste spring linkage.

PubMed

Li, G; Hu, H; Wu, K; Wang, G; Wang, L J

2014-10-01

For the applications in precision measurement such as absolute gravimeter, we have designed and built an ultra-low frequency vertical vibration isolator based on LaCoste spring linkage. In the system, an arm with test mass is suspended by a mechanical extension spring, and one end of the arm is connected to the frame with flexible pivots. The displacement of the arm is detected by an optical reflection method. With the displacement signal, a feedback control force is exerted on the arm to keep it at the balance position. This method can also correct the systematic drift caused by temperature change. In order to study the vibration isolation performance of the system, we analyze the dynamic characteristics of the spring linkage in the general case, and present key methods to adjust the natural oscillating period of the system. With careful adjustment, the system can achieve a steady oscillation with a natural period up to 32 s. This isolator has been tested based on the T-1 absolute gravimeter. A statistical uncertainty of 2 μGal has been achieved within a typical 12 h measurement. The experimental results verify that the isolator has significant vibration isolation performance, and it is very suitable for applications in high precision absolute gravity measurement.

Salmonella and antimicrobial resistance in an animal-based agriculture river system.

PubMed

Palhares, Julio Cesar Pascale; Kich, Jalusa D; Bessa, Marjo C; Biesus, Luiza L; Berno, Lais G; Triques, Nelise J

2014-02-15

The aim of this study was to examine the Salmonella serovars and antimicrobial resistance within an animal-based agriculture river system. The study area consisted of a 1,345 ha upper part of Pinhal catchment. A total of 384 samples were collected in four years of monitoring. Salmonella was isolated from 241 samples (62.7%), resulting in 324 isolates. The highest number of Salmonella sp. occurred in samples associated with sites with high stoking density animal unit per hectare. It was possible to demonstrate the variability of serovars in the study area: 30 different serovars were found and at least 11 per monitoring site. Thirty-three potentially related isolates were genotyped by PFGE, one major clone was observed in serovar Typhimurium, which occurred in animal feces (swine and bovine), and different sites and samplings proving the cross-contamination and persistence of this specific clone. Among 180 isolates submitted to an antimicrobial susceptibility test, 50.5% were susceptible to all 21 antimicrobials tested and 54 different profiles were found. In the current study, 49.5% of the tested isolates were resistant to at least one antimicrobial, and multi-resistance occurred in 18% of isolates. Results indicate a close interaction between animal-based agriculture, Salmonella, and antimicrobial resistance. Copyright © 2013 Elsevier B.V. All rights reserved.

Ultra-low frequency vertical vibration isolator based on LaCoste spring linkage

NASA Astrophysics Data System (ADS)

Li, G.; Hu, H.; Wu, K.; Wang, G.; Wang, L. J.

2014-10-01

For the applications in precision measurement such as absolute gravimeter, we have designed and built an ultra-low frequency vertical vibration isolator based on LaCoste spring linkage. In the system, an arm with test mass is suspended by a mechanical extension spring, and one end of the arm is connected to the frame with flexible pivots. The displacement of the arm is detected by an optical reflection method. With the displacement signal, a feedback control force is exerted on the arm to keep it at the balance position. This method can also correct the systematic drift caused by temperature change. In order to study the vibration isolation performance of the system, we analyze the dynamic characteristics of the spring linkage in the general case, and present key methods to adjust the natural oscillating period of the system. With careful adjustment, the system can achieve a steady oscillation with a natural period up to 32 s. This isolator has been tested based on the T-1 absolute gravimeter. A statistical uncertainty of 2 μGal has been achieved within a typical 12 h measurement. The experimental results verify that the isolator has significant vibration isolation performance, and it is very suitable for applications in high precision absolute gravity measurement.

Development of a novel and highly efficient method of isolating bacteriophages from water.

PubMed

Liu, Weili; Li, Chao; Qiu, Zhi-Gang; Jin, Min; Wang, Jing-Feng; Yang, Dong; Xiao, Zhong-Hai; Yuan, Zhao-Kang; Li, Jun-Wen; Xu, Qun-Ying; Shen, Zhi-Qiang

2017-08-01

Bacteriophages are widely used to the treatment of drug-resistant bacteria and the improvement of food safety through bacterial lysis. However, the limited investigations on bacteriophage restrict their further application. In this study, a novel and highly efficient method was developed for isolating bacteriophage from water based on the electropositive silica gel particles (ESPs) method. To optimize the ESPs method, we evaluated the eluent type, flow rate, pH, temperature, and inoculation concentration of bacteriophage using bacteriophage f2. The quantitative detection reported that the recovery of the ESPs method reached over 90%. The qualitative detection demonstrated that the ESPs method effectively isolated 70% of extremely low-concentration bacteriophage (10 0 PFU/100L). Based on the host bacteria composed of 33 standard strains and 10 isolated strains, the bacteriophages in 18 water samples collected from the three sites in the Tianjin Haihe River Basin were isolated by the ESPs and traditional methods. Results showed that the ESPs method was significantly superior to the traditional method. The ESPs method isolated 32 strains of bacteriophage, whereas the traditional method isolated 15 strains. The sample isolation efficiency and bacteriophage isolation efficiency of the ESPs method were 3.28 and 2.13 times higher than those of the traditional method. The developed ESPs method was characterized by high isolation efficiency, efficient handling of large water sample size and low requirement on water quality. Copyright © 2017. Published by Elsevier B.V.

Determination of enterotoxigenic and methicillin resistant Staphylococcus aureus in ice cream.

PubMed

Gücükoğlu, Ali; Çadirci, Özgür; Terzi, Göknur; Kevenk, T Onur; Alişarli, Mustafa

2013-05-01

The aim of this study was to determine the prevalence of enterotoxigenic and methicillin-resistant Staphylococcus aureus in ice creams. After culture-based identification of isolates, the presence of 16S rRNA and nuc was confirmed by mPCR. S. aureus was identified in 18 of 56 fruity (32.1%), 4 of 32 vanilla (12.5%), and 1 of 12 chocolate (8.3%) ice creams. S. aureus was identified as 38 isolates in 23 ice cream samples by culture-based techniques, but only 35 isolates were confirmed by PCR as S. aureus. To determine the enterotoxigenic properties of PCR-confirmed S. aureus isolates, a toxin detection kit was used (SET RPLA®). Of the 12 enterotoxigenic S. aureus isolates, 9 SEB (75%), 1 SED (8.3%), 1 SEB+SED (8.3%), and 1 SEA+SEB+SED (8.3%) expressing isolates were found. The presence of enterotoxin genes (sea, seb, sed) was identified in 13 (37.1%) out of 35 isolates by the mPCR technique. In the ice cream isolates, the sea, seb, and sed genes were detected: 1 sea (7.6%), 9 seb (69.2%), 1 sed (7.6%), 1 seb+sed (7.6%), and 1 sea+seb+sed (7.6%), respectively. The sec gene was not detected in any of these isolates. One of the 35 (2.8%) S. aureus strain was mecA positive. © 2013 Institute of Food Technologists®

Phenotypic and genetic characterization of Piscirickettsia salmonis from Chilean and Canadian salmonids.

PubMed

Otterlei, Alexander; Brevik, Øyvind J; Jensen, Daniel; Duesund, Henrik; Sommerset, Ingunn; Frost, Petter; Mendoza, Julio; McKenzie, Peter; Nylund, Are; Apablaza, Patricia

2016-03-15

The study presents the phenotypic and genetic characterization of selected P. salmonis isolates from Atlantic salmon and rainbow trout suffering from SRS (salmonid rickettsial septicemia) in Chile and in Canada. The phenotypic characterization of the P. salmonis isolates were based on growth on different agar media (including a newly developed medium), different growth temperatures, antibiotics susceptibility and biochemical tests. This is the first study differentiating Chilean P. salmonis isolates into two separate genetic groups. Genotyping, based on 16S rRNA-ITS and concatenated housekeeping genes grouped the selected isolates into two clades, constituted by the Chilean strains, while the Canadian isolates form a branch in the phylogenetic tree. The latter consisted of two isolates that were different in both genetic and phenotypic characteristics. The phylogenies and the MLST do not reflect the origin of the isolates with respect to host species. The isolates included were heterogeneous in phenotypic tests. The genotyping methods developed in this study provided a tool for separation of P. salmonis isolates into distinct clades. The SRS outbreaks in Chile are caused by minimum two different genetic groups of P. salmonis. This heterogeneity should be considered in future development of vaccines against this bacterium in Chile. Two different strains of P. salmonis, in regards to genetic and phenotypic characteristics, can occur in the same contemporary outbreak of SRS.

Correction: Shell-isolated nanoparticle-enhanced Raman spectroscopy study of the adsorption behaviour of DNA bases on Au(111) electrode surfaces.

PubMed

Wen, Bao-Ying; Jin, Xi; Li, Yue; Wang, Ya-Hao; Li, Chao-Yu; Liang, Miao-Miao; Panneerselvam, Rajapandiyan; Xu, Qing-Chi; Wu, De-Yin; Yang, Zhi-Lin; Li, Jian-Feng; Tian, Zhong-Qun

2016-06-21

Correction for 'Shell-isolated nanoparticle-enhanced Raman spectroscopy study of the adsorption behaviour of DNA bases on Au(111) electrode surfaces' by Bao-Ying Wen et al., Analyst, 2016, DOI: 10.1039/c6an00180g.

76 FR 32859 - General Schedule Locality Pay Areas

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-07

... remoteness and isolation. (OPM notes, however, that locality pay must be based on pay comparisons, not... locality pay rate due to the effect of remoteness and isolation from the mainland. We respond in detail... * * *''. OPM Response The locality pay statute bases locality pay on comparisons of General Schedule and non...

Friction Effects on Inertia Compensators used for Heliostat Base Motion Isolation.

DTIC Science & Technology

The base motion isolation of an optical beam deflector with a two-axis gimbal support ( heliostat ) is discussed. The use of an auxiliary inertia...coupled between the elevation gimbal and the heliostat mirror to produce a compensating torque referred to as a gear compensator and a belt compensator

Evidence of triple mutant Pfdhps ISGNGA haplotype in Plasmodium falciparum isolates from North-east India: An analysis of sulfadoxine resistant haplotype selection.

PubMed

Das, Manuj K; Chetry, Sumi; Kalita, Mohan C; Dutta, Prafulla

2016-12-01

North-east region of India has consistent role in the spread of multi drug resistant Plasmodium (P.) falciparum to other parts of Southeast Asia. After rapid clinical treatment failure of Artemisinin based combination therapy-Sulphadoxine/Pyrimethamine (ACT-SP) chemoprophylaxis, Artemether-Lumefantrine (ACT-AL) combination therapy was introduced in the year 2012 in this region for the treatment of uncomplicated P. falciparum malaria. In a DNA sequencing based polymorphism analysis, seven codons of P. falciparum dihydropteroate synthetase ( Pf dhps) gene were screened in a total of 127 P. falciparum isolates collected from Assam, Arunachal Pradesh and Tripura of North-east India during the year 2014 and 2015 to document current sulfadoxine resistant haplotypes. Sequences were analyzed to rearrange both nucleotide and protein haplotypes. Molecular diversity indices were analyzed in DNA Sequence Polymorphism software (DnaSP) on the basis of Pf dhps gene sequences. Disappearance from selective neutrality was assessed based on the ratio of non-synonomous to synonomous nucleotide substitutions [dN/dS ratio]. Moreover, two-tailed Z test was performed in search of the significance for probability of rejecting null hypothesis of strict neutrality [dN = dS]. Presence of mutant P. falciparum multidrug resistance protein1 ( Pf mdr1) was also checked in those isolates that were present with new Pf dhps haplotypes. Phylogenetic relationship based on Pf dhps gene was reconstructed in Molecular Evolutionary Genetics Analysis (MEGA). Among eight different sulfadoxine resistant haplotypes found, IS GNG A haplotype was documented in a total of five isolates from Tripura with association of a new mutant M538 R allele. Sequence analysis of Pf mdr1 gene in these five isolates came to notice that not all but only one isolate was mutant at codon 86 (N86 Y ; Y YSND) in the multidrug resistance protein. Molecular diversity based on Pf dhps haplotypes revealed that P. falciparum populations in Assam and Tripura were under balancing selection for sulfadoxine resistant haplotypes but population from Arunachal Pradesh was under positive selection with comparatively high haplotype diversity ( h  = 0.870). In reconstructed phylogenetic analysis, isolates having IS GNG A haplotype were grouped into two separate sub-clusters from the other isolates based on their genetic distances and diversities. This study suggests that sulfadoxine resistant isolates are still migrating from its epicenter to the other parts of Southeast Asia and hence control and elimination of the drug resistant isolates have become impedimental. Moreover, P. falciparum populations in different areas may undergo selection of particular sulfadoxine resistant haplotypes either in the presence of drug or after its removal to maintain their plasticity.

An isolation-enhanced quad-element antenna using suspended solid wires for LTE small-cell base stations

NASA Astrophysics Data System (ADS)

Chen, Yen-Sheng; Zhou, Huang-Cheng

2017-05-01

This paper presents a multiple-input-multiple-output (MIMO) antenna that has four-unit elements enabled by an isolation technique for long-term evolution (LTE) small-cell base stations. While earlier studies on MIMO base-station antennas cope with either a lower LTE band (698-960 MHz) or an upper LTE band (1710-2690 MHz), the proposed antenna meets the full LTE specification, yet it uses the maximum number of unit elements to increase channel capacity. The antenna configuration is optimized for good impedance matching and high radiation efficiency. In particular, as the spacing between unit elements is so small that severe mutual coupling occurs, we propose a simple structure with extremely low costs to enhance the isolation. By using suspended solid wires interconnecting the position having strong coupled current of two adjacent elements, an isolation enhancement of 37 dB is achieved. Although solid wires inherently aim at direct-current applications, this work successfully employs such a low-cost technique to microwave antenna development. Experimental results have validated the design guidelines and the proposed configuration, showing that antenna performances including impedance matching, isolation, radiation features, signal correlation, and channel capacity gain are highly desired for LTE small-cell base stations.

A vector-based failure detection and isolation algorithm for a dual fail-operational redundant strapdown inertial measurement unit

NASA Technical Reports Server (NTRS)

Morrell, Frederick R.; Bailey, Melvin L.

1987-01-01

A vector-based failure detection and isolation technique for a skewed array of two degree-of-freedom inertial sensors is developed. Failure detection is based on comparison of parity equations with a threshold, and isolation is based on comparison of logic variables which are keyed to pass/fail results of the parity test. A multi-level approach to failure detection is used to ensure adequate coverage for the flight control, display, and navigation avionics functions. Sensor error models are introduced to expose the susceptibility of the parity equations to sensor errors and physical separation effects. The algorithm is evaluated in a simulation of a commercial transport operating in a range of light to severe turbulence environments. A bias-jump failure level of 0.2 deg/hr was detected and isolated properly in the light and moderate turbulence environments, but not detected in the extreme turbulence environment. An accelerometer bias-jump failure level of 1.5 milli-g was detected over all turbulence environments. For both types of inertial sensor, hard-over, and null type failures were detected in all environments without incident. The algorithm functioned without false alarm or isolation over all turbulence environments for the runs tested.

Probiotic Candidates from Fish Pond Water in Central Java Indonesia

NASA Astrophysics Data System (ADS)

Harjuno Condro Haditomo, Alfabetian; Desrina; Sarjito; Budi Prayitno, S.

2018-02-01

Aeromonas hydrophilla is a major bacterial pathogen of intensive fresh water fish culture in Indonesia. An alternative method to control the pathogen is using probiotics. Probiotics is usually consist of live microorganisms which when administered in adequate amounts confer a health benefits on host. The aim of this research was to determine the probiotic candidates against A. hydrophilla which identified based on the 16S rDNA gene sequences. This research was started with field survey to obtained the probiotic candidate and continue with laboratory experiment. Probiotic candidates were isolated from fish pond water located in Boyolali, and Banjarnegara Regency, Central Java, Indonesia. A total of 133 isolates bacteria were isolated and cultured on to TSA, TSB and GSP medium. Out of 133 isolates only 30 isolates showed inhibition to A.hydrophilla activity. Three promising isolates were identified with PCR using primer for 16S rDNA. Based on 16S rDNA sequence analysis, all three isolates were belong to Bacillus genus. Isolate CKlA21, CKlA28, and CBA14 respectively were closely related to Bacillus sp. 13843 (GenBank accession no. JN874760.1 -100% homology), Bacillus subtilis strain H13 (GenBank accession no.KT907045.1 -- 99% homology), and Bacillus sp. strain 22-4 (GenBank accession no. KX816417.1 -- 97% homology).

Isolation of Shiga toxin-producing Escherichia coli from fresh produce using STEC heart infusion washed blood agar with mitomycin-C.

PubMed

Lin, Andrew; Nguyen, Lam; Clotilde, Laurie M; Kase, Julie A; Son, Insook; Lauzon, Carol R

2012-11-01

The ability to detect and isolate Shiga toxin-producing Escherichia coli (STEC) remains a major challenge for food microbiologists. Although methods based on nucleic acids and antibodies have improved detection of STECs in foods, isolation of these bacteria remains arduous. STEC isolation is necessary for matching food, environmental, and clinical isolates during outbreak investigations and for distinguishing between pathogenic and nonpathogenic organisms. STEC heart infusion washed blood agar with mitomycin-C (SHIBAM) is a modification of washed sheep blood agar prepared by adding mitomycin-C and optimizing both the washed blood and base agar to better isolate STECs. Most STEC isolates produce a zone of hemolysis on SHIBAM plates and are easily distinguishable from background microbiota. Here, we present data supporting the use of SHIBAM to isolate STECs from fresh produce. SHIBAM was tested for accuracy in identifying STECs (365 of 410 STEC strains were hemolytic, and 63 of 73 E. coli strains that did not produce Shiga toxin were not hemolytic) and for recovery from artificially inoculated fresh produce (11 of 24 romaine lettuce samples and 6 of 24 tomato samples). STEC recovery with SHIBAM agar was greatly improved when compared with recovery on Levine's eosin-methylene blue agar as a reference method.

Diversity and bioprospecting of culturable actinomycetes from marine sediment of the Yellow Sea, China.

PubMed

Xiong, Zhi-Qiang; Liu, Qiao-Xia; Pan, Zhao-Long; Zhao, Na; Feng, Zhi-Xiang; Wang, Yong

2015-03-01

Marine actinomycetes are a potential source of a wide variety of bioactive natural products. In this work, seven pretreatments, three selective isolation media, and five artificial seawater concentrations were used to isolate actinomycetes from the sediments collected from Yellow Sea, China. Statistical analysis showed that only the isolation medium strongly affected the total and bioactive numbers of actinomycete isolates. A total of 613 actinobacterial strains were isolated and screened for antimicrobial activities; 154 isolates showed activity against at least one of nine test drug-resistant microorganisms. Eighty-nine representatives with strong antimicrobial activity were identified phylogenetically based on 16S rRNA gene sequencing, which were assigned to five different actinomycete genera Streptomyces, Kocuria, Saccharomonospora, Micromonospora, and Nocardiopsis. Using PCR-based screening for six biosynthetic genes of secondary metabolites, all 45 isolates with acute activity have at least one biosynthetic gene, 28.8 % of which possess more than three biosynthetic genes. As a case, strain SMA-1 was selected for antimicrobial natural product discovery. Three diketopiperazine dimers including a new compound iso-naseseazine B (1) and two known compounds naseseazine B (2) and aspergilazine A (3) were isolated by bioassay-guided separation. These results suggested that actinomycetes from marine sediments are a potential resource of novel secondary metabolites and drugs.

Comparison of RNA Isolation Methods From Insect Larvae

PubMed Central

Ridgeway, J. A.; Timm, A. E.

2014-01-01

Abstract Isolating RNA from insects is becoming increasingly important in molecular entomology. Four methods including three commercial kits RNeasy Mini Kit (Qiagen), SV Total RNA isolation system (Promega), TRIzol reagent (Invitrogen), and a cetyl trimethylammonium bromide (CTAB)-based method were compared regarding their ability to isolate RNA from whole-body larvae of Thaumatotibia leucotreta (Meyrick), Thanatophilus micans (F.), Plutella xylostella (L.), and Tenebrio molitor (L.). A difference was observed among the four methods regarding RNA quality but not quantity. However, RNA quality and quantity obtained was not dependent on the insect species. The CTAB-based method produced low-quality RNA and the Trizol reagent produced partially degraded RNA, whereas the RNeasy Mini Kit and SV Total RNA isolation system produced RNA of consistently high quality. However, after reverse transcription to cDNA, RNA produced using all four extraction methods could be used to successfully amplify a 708 bp fragment of the cytochrome oxidase I gene. Of the four methods, the SV Total RNA isolation system showed the least amount of DNA contamination with the highest RNA integrity number and is thus recommended for stringent applications where high-quality RNA is required. This is the first comparison of RNA isolation methods among different insect species and the first to compare RNA isolation methods in insects in the last 20 years. PMID:25527580

NASA ground terminal communication equipment automated fault isolation expert systems

NASA Technical Reports Server (NTRS)

Tang, Y. K.; Wetzel, C. R.

1990-01-01

The prototype expert systems are described that diagnose the Distribution and Switching System I and II (DSS1 and DSS2), Statistical Multiplexers (SM), and Multiplexer and Demultiplexer systems (MDM) at the NASA Ground Terminal (NGT). A system level fault isolation expert system monitors the activities of a selected data stream, verifies that the fault exists in the NGT and identifies the faulty equipment. Equipment level fault isolation expert systems are invoked to isolate the fault to a Line Replaceable Unit (LRU) level. Input and sometimes output data stream activities for the equipment are available. The system level fault isolation expert system compares the equipment input and output status for a data stream and performs loopback tests (if necessary) to isolate the faulty equipment. The equipment level fault isolation system utilizes the process of elimination and/or the maintenance personnel's fault isolation experience stored in its knowledge base. The DSS1, DSS2 and SM fault isolation systems, using the knowledge of the current equipment configuration and the equipment circuitry issues a set of test connections according to the predefined rules. The faulty component or board can be identified by the expert system by analyzing the test results. The MDM fault isolation system correlates the failure symptoms with the faulty component based on maintenance personnel experience. The faulty component can be determined by knowing the failure symptoms. The DSS1, DSS2, SM, and MDM equipment simulators are implemented in PASCAL. The DSS1 fault isolation expert system was converted to C language from VP-Expert and integrated into the NGT automation software for offline switch diagnoses. Potentially, the NGT fault isolation algorithms can be used for the DSS1, SM, amd MDM located at Goddard Space Flight Center (GSFC).

Base isolation: Fresh insight

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

Shustov, V.

1993-07-15

The objective of the research is a further development of the engineering concept of seismic isolation. Neglecting the transient stage of seismic loading results in a widespread misjudgement: The force of resistance associated with velocity is mostly conceived as a source of damping vibrations, though it is an active force at the same time, during an earthquake type excitation. For very pliant systems such as base isolated structures with relatively low bearing stiffness and with artificially added heavy damping mechanism, the so called `damping`` force may occur even the main pushing force at an earthquake. Thus, one of the twomore » basic pillars of the common seismic isolation philosophy, namely, the doctrine of usefulness and necessity of a strong damping mechanism, is turning out to be a self-deception, sometimes even jeopardizing the safety of structures and discrediting the very idea of seismic isolation. There is a way out: breaking with damping dependancy.« less

Efficacy of Pulsed-Field Gel Electrophoresis and Repetitive Element Sequence-Based PCR in Typing of Salmonella Isolates from Assam, India.

PubMed

Gogoi, Purnima; Borah, Probodh; Hussain, Iftikar; Das, Leena; Hazarika, Girin; Tamuly, Shantanu; Barkalita, Luit Moni

2018-05-01

A total of 12 Salmonella isolates belonging to different serovars, viz , Salmonella enterica serovar Enteritidis ( n = 4), Salmonella enterica serovar Weltevreden ( n = 4), Salmonella enterica serovar Newport ( n = 1), Salmonella enterica serovar Litchifield ( n = 1), and untypeable strains ( n = 2) were isolated from 332 diarrheic fecal samples collected from animals, birds, and humans. Of the two molecular typing methods applied, viz , repetitive element sequence-based PCR (REP-PCR) and pulsed-field gel electrophoresis (PFGE), PFGE could clearly differentiate the strains belonging to different serovars as well as differentiate between strains of the same serovar with respect to their source of isolation, whereas REP-PCR could not differentiate between strains of the same serovar. Thus, it can be suggested that PFGE is more useful and appropriate for molecular typing of Salmonella isolates during epidemiological investigations than REP-PCR. Copyright © 2018 American Society for Microbiology.

Selective Osmotic Shock (SOS)-Based Islet Isolation for Microencapsulation.

PubMed

Enck, Kevin; McQuilling, John Patrick; Orlando, Giuseppe; Tamburrini, Riccardo; Sivanandane, Sittadjody; Opara, Emmanuel C

2017-01-01

Islet transplantation (IT) has recently been shown to be a promising alternative to pancreas transplantation for reversing diabetes. IT requires the isolation of the islets from the pancreas, and these islets can be used to fabricate a bio-artificial pancreas. Enzymatic digestion is the current gold standard procedure for islet isolation but has lingering concerns. One such concern is that it has been shown to damage the islets due to nonselective tissue digestion. This chapter provides a detailed description of a nonenzymatic method that we are exploring in our lab as an alternative to current enzymatic digestion procedures for islet isolation from human and nonhuman pancreatic tissues. This method is based on selective destruction and protection of specific cell types and has been shown to leave the extracellular matrix (ECM) of islets intact, which may thus enhance islet viability and functionality. We also show that these SOS-isolated islets can be microencapsulated for transplantation.

High-throughput molecular identification of Staphylococcus spp. isolated from a clean room facility in an environmental monitoring program

PubMed Central

2010-01-01

Background The staphylococci are one of the most common environmental isolates found in clean room facility. Consequently, isolation followed by comprehensive and accurate identification is an essential step in any environmental monitoring program. Findings We have used the API Staph identification kit (bioMérieux, France) which depends on the expression of metabolic activities and or morphological features to identify the Staphylococcus isolates. The API staphylococci showed low sensitivity in the identification of some species, so we performed molecular methods based on PCR based fingerprinting of glyceraldehyde-3-phosphate dehydrogenase encoding gene as useful taxonomic tool for examining Staphylococcus isolates. Conclusions Our results showed that PCR protocol used in this study which depends on genotypic features was relatively accurate, rapid, sensitive and superior in the identification of at least 7 species of Staphylococcus than API Staph which depends on phenotypic features. PMID:21047438

High-throughput molecular identification of Staphylococcus spp. isolated from a clean room facility in an environmental monitoring program.

PubMed

Sheraba, Norhan S; Yassin, Aymen S; Amin, Magdy A

2010-11-04

The staphylococci are one of the most common environmental isolates found in clean room facility. Consequently, isolation followed by comprehensive and accurate identification is an essential step in any environmental monitoring program. We have used the API Staph identification kit (bioMérieux, France) which depends on the expression of metabolic activities and or morphological features to identify the Staphylococcus isolates. The API staphylococci showed low sensitivity in the identification of some species, so we performed molecular methods based on PCR based fingerprinting of glyceraldehyde-3-phosphate dehydrogenase encoding gene as useful taxonomic tool for examining Staphylococcus isolates. Our results showed that PCR protocol used in this study which depends on genotypic features was relatively accurate, rapid, sensitive and superior in the identification of at least 7 species of Staphylococcus than API Staph which depends on phenotypic features.

Whole-genome sequencing of Salmonella enterica subsp. enterica serovar Cubana strains isolated from agricultural sources

USDA-ARS?s Scientific Manuscript database

We report draft genomes of Salmonella enterica subsp. enterica Serovar Cubana strain CVM42234 isolated from chick feed in 2012 and Salmonella Cubana strain 76814 isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 base pairs, respectively....

Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

USDA-ARS?s Scientific Manuscript database

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

Electricity-Free, Sequential Nucleic Acid and Protein Isolation

PubMed Central

Pawlowski, David R.; Karalus, Richard J.

2012-01-01

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratory-based identification, common in the United States, is unavailable 1. The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment 2. The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-of-care platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis. Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters 3. CUBRC's proprietary solid-phase extraction chemistry is used to purify protein from chaotropic salt solutions, in this case, from the waste or flow-thru following nucleic acid isolation4. By packaging well-characterized chemistries into a small, inexpensive and simple platform, we have generated a portable system for nucleic acid and protein extraction that can be performed under a variety of conditions. The isolated nucleic acids are stable and can be transported to a position where power is available for PCR amplification while the protein content can immediately be analyzed by hand held or other immunological-based assays. The rapid identification of disease markers in the field could significantly alter the patient's outcome by directing the proper course of treatment at an earlier stage of disease progression. The tool and method described are suitable for use with virtually any infectious agent and offer the user the redundancy of multi-macromolecule type analyses while simultaneously reducing their logistical burden. PMID:22635135

Electricity-free, sequential nucleic acid and protein isolation.

PubMed

Pawlowski, David R; Karalus, Richard J

2012-05-15

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratory-based identification, common in the United States, is unavailable (1). The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment (2). The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-of-care platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis. Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters (3). CUBRC's proprietary solid-phase extraction chemistry is used to purify protein from chaotropic salt solutions, in this case, from the waste or flow-thru following nucleic acid isolation(4). By packaging well-characterized chemistries into a small, inexpensive and simple platform, we have generated a portable system for nucleic acid and protein extraction that can be performed under a variety of conditions. The isolated nucleic acids are stable and can be transported to a position where power is available for PCR amplification while the protein content can immediately be analyzed by hand held or other immunological-based assays. The rapid identification of disease markers in the field could significantly alter the patient's outcome by directing the proper course of treatment at an earlier stage of disease progression. The tool and method described are suitable for use with virtually any infectious agent and offer the user the redundancy of multi-macromolecule type analyses while simultaneously reducing their logistical burden.

Transfer of a Mycobacterium tuberculosis genotyping method, Spoligotyping, from a reverse line-blot hybridization, membrane-based assay to the Luminex multianalyte profiling system.

PubMed

Cowan, Lauren S; Diem, Lois; Brake, Mary Catherine; Crawford, Jack T

2004-01-01

Spoligotyping using Luminex technology was shown to be a highly reproducible method suitable for high-throughput analysis. Spoligotyping of 48 isolates using the traditional membrane-based assay and the Luminex assay yielded concordant results for all isolates. The Luminex platform provides greater flexibility and cost effectiveness than the membrane-based assay.

Genetic analysis of Fasciola isolates from cattle in Korea based on second internal transcribed spacer (ITS-2) sequence of nuclear ribosomal DNA.

PubMed

Choe, Se-Eun; Nguyen, Thuy Thi-Dieu; Kang, Tae-Gyu; Kweon, Chang-Hee; Kang, Seung-Won

2011-09-01

Nuclear ribosomal DNA sequence of the second internal transcribed spacer (ITS-2) has been used efficiently to identify the liver fluke species collected from different hosts and various geographic regions. ITS-2 sequences of 19 Fasciola samples collected from Korean native cattle were determined and compared. Sequence comparison including ITS-2 sequences of isolates from this study and reference sequences from Fasciola hepatica and Fasciola gigantica and intermediate Fasciola in Genbank revealed seven identical variable sites of investigated isolates. Among 19 samples, 12 individuals had ITS-2 sequences completely identical to that of pure F. hepatica, five possessed the sequences identical to F. gigantica type, whereas two shared the sequence of both F. hepatica and F. gigantica. No variations in length and nucleotide composition of ITS-2 sequence were observed within isolates that belonged to F. hepatica or F. gigantica. At the position of 218, five Fasciola containing a single-base substitution (C>T) formed a distinct branch inside the F. gigantica-type group which was similar to those of Asian-origin isolates. The phylogenetic tree of the Fasciola spp. based on complete ITS-2 sequences from this study and other representative isolates in different locations clearly showed that pure F. hepatica, F. gigantica type and intermediate Fasciola were observed. The result also provided additional genetic evidence for the existence of three forms of Fasciola isolated from native cattle in Korea by genetic approach using ITS-2 sequence.

Contact lens disinfecting solutions antibacterial efficacy: comparison between clinical isolates and the standard ISO ATCC strains of Pseudomonas aeruginosa and Staphylococcus aureus.

PubMed

Mohammadinia, M; Rahmani, S; Eslami, G; Ghassemi-Broumand, M; Aghazadh Amiri, M; Aghaie, Gh; Tabatabaee, S M; Taheri, S; Behgozin, A

2012-02-01

To evaluate the disinfectant properties of the three multipurpose contact lens disinfecting solutions available in Iran, against clinical isolates and the standard ISO ATCC strains of Pseudomonas aeruginosa and Staphylococcus aureus, based on the international organization for standardization (ISO) 14729 guidelines. Three multipurpose solutions that were tested were ReNu Multiplus, Solo Care Aqua and All-Clean Soft. The test solutions were challenged with clinical isolates and the standard strains of P. aeruginosa(ATCC 9027) and S. aureus(ATCC 6538), based on the ISO Stand-alone procedure for disinfecting products. Solutions were sampled for surviving microorganisms at manufacturer's minimum recommended disinfection time. The number of viable organisms was determined and log reductions calculated. All of the three test solutions in this study provided a reduction greater than the required mean 3.0 logarithmic reduction against the recommended standard ATCC strains of P. aeruginosa and S. aureus. Antibacterial effectiveness of Solo Care Aqua and All-Clean Soft against clinical isolates of P. aeruginosa and S. aureus were acceptable based on ISO 14729 Stand-alone test. ReNu MultiPlus showed a minimum acceptable efficacy against the clinical isolate of S. aureus, but did not reduce the clinical isolate by the same amount. Although the contact lens disinfecting solutions meet/exceed the ISO 14729 Stand-alone primary acceptance criteria for standard strains of P. aeruginosa and S. aureus, their efficacy may be insufficient against clinical isolates of these organisms.

Contact lens disinfecting solutions antibacterial efficacy: comparison between clinical isolates and the standard ISO ATCC strains of Pseudomonas aeruginosa and Staphylococcus aureus

PubMed Central

Mohammadinia, M; Rahmani, S; Eslami, G; Ghassemi-Broumand, M; Aghazadh Amiri, M; Aghaie, Gh; Tabatabaee, S M; Taheri, S; Behgozin, A

2012-01-01

Purpose To evaluate the disinfectant properties of the three multipurpose contact lens disinfecting solutions available in Iran, against clinical isolates and the standard ISO ATCC strains of Pseudomonas aeruginosaand Staphylococcus aureus, based on the international organization for standardization (ISO) 14729 guidelines. Methods Three multipurpose solutions that were tested were ReNu Multiplus, Solo Care Aqua and All-Clean Soft. The test solutions were challenged with clinical isolates and the standard strains of P. aeruginosa(ATCC 9027) and S. aureus(ATCC 6538), based on the ISO Stand-alone procedure for disinfecting products. Solutions were sampled for surviving microorganisms at manufacturer's minimum recommended disinfection time. The number of viable organisms was determined and log reductions calculated. Results All of the three test solutions in this study provided a reduction greater than the required mean 3.0 logarithmic reduction against the recommended standard ATCC strains of P. aeruginosaand S. aureus. Antibacterial effectiveness of Solo Care Aqua and All-Clean Soft against clinical isolates of P. aeruginosaand S. aureuswere acceptable based on ISO 14729 Stand-alone test. ReNu MultiPlus showed a minimum acceptable efficacy against the clinical isolate of S. aureus, but did not reduce the clinical isolate by the same amount. Conclusions Although the contact lens disinfecting solutions meet/exceed the ISO 14729 Stand-alone primary acceptance criteria for standard strains of P. aeruginosaand S. aureus, their efficacy may be insufficient against clinical isolates of these organisms. PMID:22094301

Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences.

PubMed

Lin, Y-H; Abad, J A; Maroon-Lango, C J; Perry, K L; Pappu, H R

2014-08-01

Five potato virus S (PVS) isolates from the USA and three isolates from Chile were characterized based on biological and molecular properties to delineate these PVS isolates into either ordinary (PVS(O)) or Andean (PVS(A)) strains. Five isolates - 41956, Cosimar, Galaxy, ND2492-2R, and Q1 - were considered ordinary strains, as they induced local lesions on the inoculated leaves of Chenopodium quinoa, whereas the remaining three (FL206-1D, Q3, and Q5) failed to induce symptoms. Considerable variability of symptom expression and severity was observed among these isolates when tested on additional indicator plants and potato cv. Defender. Additionally, all eight isolates were characterized by determining the nucleotide sequences of their coat protein (CP) genes. Based on their biological and genetic properties, the 41956, Cosimar, Galaxy, ND2492-2R, and Q1 isolates were identified as PVS(O). PVS-FL206-1D and the two Chilean isolates (PVS-Q3 and PVS-Q5) could not be identified based on phenotype alone; however, based on sequence comparisons, PVS-FL206-1D was identified as PVS(O), while Q3 and Q5 clustered with known PVS(A) strains. C. quinoa may not be a reliable indicator for distinguishing PVS strains. Sequences of the CP gene should be used as an additional criterion for delineating PVS strains. A global genetic analysis of known PVS sequences from GenBank was carried out to investigate nucleotide substitution, population selection, and genetic recombination and to assess the genetic diversity and evolution of PVS. A higher degree of nucleotide diversity (π value) of the CP gene compared to that of the 11K gene suggested greater variation in the CP gene. When comparing PVS(A) and PVS(O) strains, a higher π value was found for PVS(A). Statistical tests of the neutrality hypothesis indicated a negative selection pressure on both the CP and 11K proteins of PVS(O), whereas a balancing selection pressure was found on PVS(A).

Social Isolation in Community-Dwelling Seniors

PubMed Central

2008-01-01

Executive Summary In early August 2007, the Medical Advisory Secretariat began work on the Aging in the Community project, an evidence-based review of the literature surrounding healthy aging in the community. The Health System Strategy Division at the Ministry of Health and Long-Term Care subsequently asked the secretariat to provide an evidentiary platform for the ministry’s newly released Aging at Home Strategy. After a broad literature review and consultation with experts, the secretariat identified 4 key areas that strongly predict an elderly person’s transition from independent community living to a long-term care home. Evidence-based analyses have been prepared for each of these 4 areas: falls and fall-related injuries, urinary incontinence, dementia, and social isolation. For the first area, falls and fall-related injuries, an economic model is described in a separate report. Please visit the Medical Advisory Secretariat Web site, http://www.health.gov.on.ca/english/providers/program/mas/mas_about.html, to review these titles within the Aging in the Community series. Aging in the Community: Summary of Evidence-Based Analyses Prevention of Falls and Fall-Related Injuries in Community-Dwelling Seniors: An Evidence-Based Analysis Behavioural Interventions for Urinary Incontinence in Community-Dwelling Seniors: An Evidence-Based Analysis Caregiver- and Patient-Directed Interventions for Dementia: An Evidence-Based Analysis Social Isolation in Community-Dwelling Seniors: An Evidence-Based Analysis The Falls/Fractures Economic Model in Ontario Residents Aged 65 Years and Over (FEMOR) Objective of the Evidence-Based Analysis The objective was to systematically review interventions aimed at preventing or reducing social isolation and loneliness in community-dwelling seniors, that is, persons ≥ 65 years of age who are not living in long-term care institutions. The analyses focused on the following questions: Are interventions to reduce social isolation and/or loneliness effective? Do these interventions improve health, well-being, and/or quality of life? Do these interventions impact on independent community living by delaying or preventing functional decline or disability? Do the interventions impact on health care utilization, such as physician visits, emergency visits, hospitalization, or admission to long-term care? Background: Target Population and Condition Social and family relationships are a core element of quality of life for seniors, and these relationships have been ranked second, next to health, as the most important area of life. Several related concepts—reduced social contact, being alone, isolation, and feelings of loneliness—have all been associated with a reduced quality of life in older people. Social isolation and loneliness have also been associated with a number of negative outcomes such as poor health, maladaptive behaviour, and depressed mood. Higher levels of loneliness have also been associated with increased likelihood of institutionalization. Note: It is recognized that the terms “senior” and “elderly” carry a range of meanings for different audiences; this report generally uses the former, but the terms are treated here as essentially interchangeable. Methods of the Evidence-Based Analysis The scientific evidence base was evaluated through a systematic literature review. The literature searches were conducted with several computerized bibliographic databases for literature published between January 1980 and February 2008. The search was restricted to English-language reports on human studies and excluded letters, comments and editorials, and case reports. Journal articles eligible for inclusion in the review included those that reported on single, focused interventions directed towards or evaluating social isolation or loneliness; included, in whole or in part, community-dwelling seniors (≥ 65 years); included some quantitative outcome measure on social isolation or loneliness; and included a comparative group. Assessments of current practices were obtained through consultations with various individuals and agencies including the Ontario Community Care Access Centres and the Ontario Assistive Devices Program. An Ontario-based budget impact was also assessed for the identified effective interventions for social isolation. Findings A systematic review of the published literature focusing on interventions for social isolation and loneliness in community-dwelling seniors identified 11 quantitative studies. The studies involved European or American populations with diverse recruitment strategies, intervention objectives, and limited follow-up, with cohorts from 10 to 15 years ago involving mainly elderly women less than 75 years of age. The studies involved 2 classes of interventions: in-person group support activities and technology-assisted interventions. These were delivered to diverse targeted groups of seniors such as those with mental distress, physically inactive seniors, low-income groups, and informal caregivers. The interventions were primarily focused on behaviour-based change. Modifying factors (client attitude or preference) and process issues (targeting methods of at-risk subjects, delivery methods, and settings) influenced intervention participation and outcomes. Both classes of interventions were found to reduce social isolation and loneliness in seniors. Social support groups were found to effectively decrease social isolation for seniors on wait lists for senior apartments and those living in senior citizen apartments. Community-based exercise programs featuring health and wellness for physically inactive community-dwelling seniors also effectively reduced loneliness. Rehabilitation for mild/moderate hearing loss was effective in improving communication disabilities and reducing loneliness in seniors. Interventions evaluated for informal caregivers of seniors with dementia, however, had limited effectiveness for social isolation or loneliness. Research into interventions for social isolation in seniors has not been broadly based, relative to the diverse personal, social, health, economic, and environmentally interrelated factors potentially affecting isolation. Although rehabilitation for hearing-related disability was evaluated, the systematic review did not locate research on interventions for other common causes of aging-related disability and loneliness, such as vision loss or mobility declines. Despite recent technological advances in e-health or telehealth, controlled studies evaluating technology-assisted interventions for social isolation have examined only basic technologies such as phone- or computer-mediated support groups. Conclusions Although effective interventions were identified for social isolation and loneliness in community-dwelling seniors, they were directed at specifically targeted groups and involved only a few of the many potential causes of social isolation. Little research has been directed at identifying effective interventions that influence the social isolation and other burdens imposed upon caregivers, in spite of the key role that caregivers assume in caring for seniors. The evidence on technology-assisted interventions and their effects on the social health and well-being of seniors and their caregivers is limited, but increasing demand for home health care and the need for efficiencies warrant further exploration. Interventions for social isolation in community-dwelling seniors need to be researched more broadly in order to develop effective, appropriate, and comprehensive strategies for at-risk populations. PMID:23074510

Identification of Medically Important Yeasts Using PCR-Based Detection of DNA Sequence Polymorphisms in the Internal Transcribed Spacer 2 Region of the rRNA Genes

PubMed Central

Chen, Y. C.; Eisner, J. D.; Kattar, M. M.; Rassoulian-Barrett, S. L.; LaFe, K.; Yarfitz, S. L.; Limaye, A. P.; Cookson, B. T.

2000-01-01

Identification of medically relevant yeasts can be time-consuming and inaccurate with current methods. We evaluated PCR-based detection of sequence polymorphisms in the internal transcribed spacer 2 (ITS2) region of the rRNA genes as a means of fungal identification. Clinical isolates (401), reference strains (6), and type strains (27), representing 34 species of yeasts were examined. The length of PCR-amplified ITS2 region DNA was determined with single-base precision in less than 30 min by using automated capillary electrophoresis. Unique, species-specific PCR products ranging from 237 to 429 bp were obtained from 92% of the clinical isolates. The remaining 8%, divided into groups with ITS2 regions which differed by ≤2 bp in mean length, all contained species-specific DNA sequences easily distinguishable by restriction enzyme analysis. These data, and the specificity of length polymorphisms for identifying yeasts, were confirmed by DNA sequence analysis of the ITS2 region from 93 isolates. Phenotypic and ITS2-based identification was concordant for 427 of 434 yeast isolates examined using sequence identity of ≥99%. Seven clinical isolates contained ITS2 sequences that did not agree with their phenotypic identification, and ITS2-based phylogenetic analyses indicate the possibility of new or clinically unusual species in the Rhodotorula and Candida genera. This work establishes an initial database, validated with over 400 clinical isolates, of ITS2 length and sequence polymorphisms for 34 species of yeasts. We conclude that size and restriction analysis of PCR-amplified ITS2 region DNA is a rapid and reliable method to identify clinically significant yeasts, including potentially new or emerging pathogenic species. PMID:10834993

Characterization of Lactobacillus from Algerian Goat’S Milk Based on Phenotypic, 16S rDNA Sequencing and their Technological Properties

PubMed Central

Marroki, Ahmed; Zúñiga, Manuel; Kihal, Mabrouk; Pérez- Martínez, Gaspar

2011-01-01

Nineteen strains of Lactobacillus isolated from goat’s milk from farms in north-west of Algeria were characterized. Isolates were identified by phenotypic, physiological and genotypic methods and some of their important technological properties were studied. Phenotypic characterization was carried out by studying physiological, morphological characteristics and carbohydrate fermentation patterns using API 50 CHL system. Isolates were also characterized by partial 16S rDNA sequencing. Results obtained with phenotypic methods were correlated with the genotypic characterization and 13 isolates were identified as L. plantarum, two isolates as L. rhamnosus and one isolate as L. fermentum. Three isolates identified as L. plantarum by phenotypic characterization were found to be L. pentosus by the genotypic method. A large diversity in technological properties (acid production in skim milk, exopolysaccharide production, aminopeptidase activity, antibacterial activity and antibiotic susceptibility) was observed. Based on these results, two strains of L. plantarum (LbMS16 and LbMS21) and one strain of L. rhamnosus (LbMF25) have been tentatively selected for use as starter cultures in the manufacture of artisanal fermented dairy products in Algeria. PMID:24031617

Genotype diversity of Escherichia coli isolates in natural waters determined by PFGE and ERIC-PCR.

PubMed

Casarez, Elizabeth A; Pillai, Suresh D; Di Giovanni, George D

2007-08-01

Most library-dependent bacterial source tracking studies using Escherichia coli (E. coli) have focused on strain diversity of isolates obtained from known human and animal faecal sources for library development. In contrast, this study evaluated the genotype variation of E. coli isolated from natural surface water using pulsed field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR) to better understand these naturally occurring populations. A total of 650 water samples were collected over a nine month period from eleven sampling stations from Lake Waco and Belton Lake in Central Texas. Of the 650 water samples collected, 412 were positive for E. coli, yielding a total of 631 E. coli isolates (1-12 isolates collected per sample). PFGE and ERIC-PCR patterns were successfully generated for 555 isolates and were compared using the curve-based Pearson's product-moment correlation coefficient. The 555 E. coli isolates represented 461 PFGE genotypes, with 84% (386/461) of the genotypes being represented by individual isolates. The remaining 75 genotypes were represented by 2-5 isolates each. Using ERIC-PCR, the 555 E. coli isolates represented 175 genotypes, with 63% (109/175) of the genotypes being represented by individual isolates. In contrast to the PFGE results, two ERIC-PCR genotypes represented 37% of the E. coli isolates, (83 and 124 isolates, respectively), and were found throughout the watersheds both spatially and temporally. Based on the PFGE genotype diversity of water isolates, there is little evidence that a small number of environmentally-adapted E. coli represent dominant populations in the studied waterbodies. However, with the lower discriminatory power technique ERIC-PCR, an opposing conclusion might have been drawn. These results emphasize the importance of considering the resolving power of the source tracking technique being used when assessing strain diversity and geographical stability.

High prevalence of the PER-1 gene among carbapenem-resistant Acinetobacter baumannii in Riyadh, Saudi Arabia.

PubMed

Aly, M M; Abu Alsoud, N M; Elrobh, M S; Al Johani, S M; Balkhy, H H

2016-11-01

The prevalence of carbapenem-resistant Acinetobacter baumannii in Saudi Arabia and their resistance genetic mechanisms are yet to be identified. We studied the prevalence and genetic diversity of extended-spectrum beta-lactamase genes, particularly the PER-1 gene, among carbapenem-resistant A. baumannii strains from patients at a tertiary care hospital in Riyadh, Saudi Arabia between 2006 and 2014. Fresh subcultured samples were tested for antimicrobial susceptibility minimum inhibitory concentration (MIC). Total genomic DNA was extracted from each isolate and further used for polymerase chain reaction (PCR) genotyping, sequence-based typing (SBT) of PER-1 and OXA-51-like gene, and multilocus sequence typing (MLST) of positive isolates. Randomly selected clinical isolates (n = 100) were subjected to MLST. A total of 503 isolates were characterized as multidrug-resistant (MDR) using the MIC. Isolates were further PCR tested for bla -TEM and bla -PER-1 resistance genes (n = 503). The genotyping results showed that 68/503 (14 %) isolates were positive to bla TEM. The genotyping results of PER-1-like genes showed that 384/503 (76.3 %) were positive among MDR Acinetobacter isolates. Based on SBT, the majority of these isolates were clustered into three main groups including isolates harboring PER-1: AB11 (bla -PER-1 ), isolate AB16 (bla -PER-1 ), and, finally, the plasmid pAB154 (bla -PER-7 ). Remarkably, many isolates were concealing the PER-1 gene and harboring the TEM resistance genes as well. MLST results for selected isolates (n = 100) identified four main sequence types (STs: 2, 19, 20, and 25) and four novel isolates (ST 486-489). We report 76.3 % prevalence of the PER-1 resistance gene among Acinetobacter clinical isolates from Riyadh, Saudi Arabia. Further work is needed to explore the clinical risks and patient outcome with such resistance related to healthcare-associated infections and investigate the genetic and molecular mechanisms that confer the MDR phenotype.

Two rapid pigmentation tests for identification of Cryptococcus neoformans.

PubMed Central

Kaufmann, C S; Merz, W G

1982-01-01

Two tests were developed for the rapid identification of Cryptococcus neoformans based on pigment produced by the organism's phenoloxidase activity. Caffeic acid was incorporated into cornmeal agar, a medium used routinely for yeast identification. When tested on this medium, only C. neoformans isolates produced brown pigment. All other yeasts maintained their normal morphology and did not produce the reaction product. A non-medium-based test was developed for same-day identification of C. neoformans isolates. Paper strips saturated with a buffered L-beta-3,4-dihydroxyphenylalanine-ferric citrate solution were inoculated with isolates and incubated at 37 degrees C. Pigment production occurred only with C. neoformans isolates, many within 60 to 90 min. All other yeasts remained negative. PMID:7040452

Fowl adenoviruses isolated from chickens with inclusion body hepatitis in Japan, 2009-2010.

PubMed

Mase, Masaji; Nakamura, Kikuyasu; Minami, Fujiko

2012-08-01

Nine fowl adenoviruses (FAdVs) isolated from chickens with inclusion body hepatitis (IBH) in Japan from 2009 to 2010 were characterized serologically and genetically. These isolates were all neutralized by antisera against the SR-48 strain (FAdV-2). Phylogenetic analysis based on the part of the hexon gene that included the L1 region revealed that all isolates were almost identical except one isolate in 2009. This suggests a common ancestor for the FAdVs obtained from chickens with IBH in Japan in 2010.

Preparation, isolation, and characterization of cutin monomers and oligomers from tomato peels.

PubMed

Osman, S F; Irwin, P; Fett, W F; O'Connor, J V; Parris, N

1999-02-01

Cutin in tomato peels was depolymerized in methanolic base to yield cutin monomers or a mixture of cutin oligomers. These products were isolated by typical solvent extraction methods or by precipitation, and the isolates were characterized by chromatographic and spectroscopic analyses. It was determined that the compositions of the isolates from both isolation procedures were similar, although solvent extraction gave higher yields. However, the precipitation method, which is easy to carry out and avoids the use of undesirable organic solvents, may be preferable in commercial processes for recovering these compounds.

Antimicrobial resistance of Staphylococcus species isolated from Lebanese dairy-based products.

PubMed

Zouhairi, O; Saleh, I; Alwan, N; Toufeili, I; Barbour, E; Harakeh, S

2012-12-04

The study evaluated the antimicrobial resistance of molecularly characterized strains of Staphylococcus aureus and S. saprophyticus isolated from 3 Lebanese dairy-based food products that are sometimes consumed raw: kishk, shanklish and baladi cheese. Suspected Staphylococcus isolates were identified initially using standard biochemical tests, then strains that were confirmed by polymerase chain reaction (29 S. aureus and 17 S. saprophyticus) were evaluated for their susceptibility to different antimicrobials. The highest levels of contamination with staphylococci were in baladi cheese. Resistance rates ranged from 67% to gentamicin to 94% to oxacillin and clindamycin. The results suggest that these locally made dairy-based foods may act as vehicles for the transmission of antimicrobial-resistant Staphylococcus spp.

Molecular characterization of an Akabane virus isolate from West Java, Indonesia

PubMed Central

PURNOMO EDI, Suryo; IBRAHIM, Afif; SUKOCO, Rinto; BUNALI, Lukman; TAGUCHI, Masaji; KATO, Tomoko; YANASE, Tohru; SHIRAFUJI, Hiroaki

2017-01-01

We isolated an arbovirus from bovine blood in Indonesia. The arbovirus was obtained from the plasma of a cow showing no clinical symptoms in West Java in February 2014, and was identified as Akabane virus (AKAV) by AKAV-specific RT-PCR and subsequent sequence analysis. Phylogenetic analysis based on partial S segment indicated the AKAV isolate, WJ-1SA/P/2014, was most closely related with two isolates from Israel and Turkey reported in 2001 and 2015, respectively, and that WJ-1SA/P/2014 isolate belongs to AKAV genogroup Ib. This is the first isolation of AKAV from Indonesia. PMID:28302930

Genotyping of Korean isolates of infectious hematopoietic necrosis virus (IHNV) based on the glycoprotein gene

USGS Publications Warehouse

Kim, W.-S.; Oh, M.-J.; Nishizawa, T.; Park, J.-W.; Kurath, G.; Yoshimizu, M.

2007-01-01

Glycoprotein (G) gene nucleotide sequences of four Korean isolates of infectious hematopoietic necrosis virus (IHNV) were analyzed to evaluate their genetic relatedness to worldwide isolates. All Korean isolates were closely related to Japanese isolates of genogroup JRt rather than to those of North American and European genogroups. It is believed that Korean IHNV has been most likely introduced from Japan to Korea by the movement of contaminated fish eggs. Among the Korean isolates, phylogenetically distinct virus types were obtained from sites north and south of a large mountain range, suggesting the possibility of more than one introduction of virus from Japan. ?? 2007 Springer-Verlag.

Differentiation of Colletotrichum species responsible for anthracnose of strawberry by arbitrarily primed PCR

USGS Publications Warehouse

Freeman, S.; Rodriguez, R.J.

1995-01-01

A collection of 39 isolates of Colletotrichum acutatum, C. fragariae and C. gloeosporioides, which cause anthracnose on strawberry, was grouped into species based on the arbitrarily primed polymerase chain reaction (ap-PCR). All isolates used had previously been identified according to classical taxonomic morphology. Ap-PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of C. acutatum, C. fragariae and two genotypes of C. gloeosporioides. Fifteen of the 18 C. acutatum isolates were very similar, although three isolates which produced a red pigment had distinctly different banding patterns. Nearly identical banding patterns were observed for all nine isolates of C. fragariae. The 12 C. gloeosporioides isolates were more diverse and two separate genotypes, Cgl-1 (six isolates) and Cgl-2 (five isolates) were distinguished by ap-PCR. An additional isolate did not conform to either the Cgl-1 or Cgl-2 genotypes. The utility of ap-PCR compared with other molecular techniques for reliable identification of Colletotrichum isolates pathogenic on strawberry is discussed.

[Identification of Candida dubliniensis strains using heat tolerance tests, morphological characteristics and molecular methods].

PubMed

Arikan, Sevtap; Darka, Ozge; Hasçelik, Gülşen; Günalp, Ayfer

2003-01-01

Described in 1995, Candida dubliniensis is a novel Candida species closely related to Candida albicans due primarily to its ability to produce germ tube and chlamydospores. Given these phenotypic similarities between the two species, C. dubliniensis cannot be readily distinguished from Candida albicans by routine laboratory work-up. We explored the frequency of isolation of C. dubliniensis among 213 strains previously defined as C. albicans based on their ability to produce germ tube. The test isolates were initially examined for their morphological features on cornmeal tween 80 agar, inability to grow at 45 degrees C, and the biochemical assimilation profile (ID 32C system, bioMerieux, France). Among all, 2 (0.9%) of the isolates were identified as C. dubliniensis based on the production of numerous chlamydospores in chains on cornmeal tween 80 agar and the lack of growth at 45 degrees C. The assimilation profile of these isolates was found to be in accordance with this identification. In an effort to confirm the identification, polymerase chain reaction (PCR) studies were carried out by using the C. dubliniensis specific primer set, DUBF and DUBR. Both of the isolates yielded C. dubliniensis-specific 288 base pair amplification products, confirming the previous identification obtained with the initial screening tests. The isolates were found to be susceptible to fluconazole and itraconazole, and generated amphotericin B minimal inhibitory concentrations of 0.5-1 microgram/ml by NCCLS M27-A2 microdilution method. These data suggest that the isolation rate of C. dubliniensis among our clinical isolates is low. The morphological features on cornmeal tween 80 agar and the lack of ability to grow at 45 degrees C appear as reliable, cheap, and practical screening tests in initial identification of C. dubliniensis among germ tube-producing Candida strains.

Rapid identification of Campylobacter, Arcobacter, and Helicobacter isolates by PCR-restriction fragment length polymorphism analysis of the 16S rRNA gene.

PubMed

Marshall, S M; Melito, P L; Woodward, D L; Johnson, W M; Rodgers, F G; Mulvey, M R

1999-12-01

A rapid two-step identification scheme based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 16S rRNA gene was developed in order to differentiate isolates belonging to the Campylobacter, Arcobacter, and Helicobacter genera. For 158 isolates (26 reference cultures and 132 clinical isolates), specific RFLP patterns were obtained and species were successfully identified by this assay.

Assessing Technical Writing in Institutional Contexts: Using Outcomes-Based Assessment for Programmatic Thinking.

ERIC Educational Resources Information Center

Carter, Michael; Anson, Chris M.; Miller, Carolyn R.

2003-01-01

Notes that technical writing instruction often operates in isolation from other components of students' communication education. Argues for altering this isolation by moving writing instruction to a place of increased programmatic perspective, which may be attained through a means of assessment based on educational outcomes. Discusses two models…

Performance of sand and shredded rubber tire mixture as a natural base isolator for earthquake protection

NASA Astrophysics Data System (ADS)

Bandyopadhyay, Srijit; Sengupta, Aniruddha; Reddy, G. R.

2015-12-01

The performance of a well-designed layer of sand, and composites like layer of sand mixed with shredded rubber tire (RSM) as low cost base isolators, is studied in shake table tests in the laboratory. The building foundation is modeled by a 200 mm by 200 mm and 40 mm thick rigid plexi-glass block. The block is placed in the middle of a 1m by 1m tank filled with sand. The selected base isolator is placed between the block and the sand foundation. Accelerometers are placed on top of the footing and foundation sand layer. The displacement of the footing is also measured by LVDT. The whole setup is mounted on a shake table and subjected to sinusoidal motions with varying amplitude and frequency. Sand is found to be effective only at very high amplitude (> 0.65 g) of motions. The performance of a composite consisting of sand and 50% shredded rubber tire placed under the footing is found to be most promising as a low-cost effective base isolator.

Transfer of a Mycobacterium tuberculosis Genotyping Method, Spoligotyping, from a Reverse Line-Blot Hybridization, Membrane-Based Assay to the Luminex Multianalyte Profiling System

PubMed Central

Cowan, Lauren S.; Diem, Lois; Brake, Mary Catherine; Crawford, Jack T.

2004-01-01

Spoligotyping using Luminex technology was shown to be a highly reproducible method suitable for high-throughput analysis. Spoligotyping of 48 isolates using the traditional membrane-based assay and the Luminex assay yielded concordant results for all isolates. The Luminex platform provides greater flexibility and cost effectiveness than the membrane-based assay. PMID:14715809

In vitro testing of biological control agents on A1 and A2 isolates of Phytophthora ramorum

Treesearch

Marianne Elliott; Simon Shamoun

2008-01-01

Biological control products were tested in vitro with six isolates of Phytophthora ramorum. These isolates were geographically diverse and were selected based on their pathogenicity to detached Rhododendron leaves. In addition to five commercially available biocontrol products, nine species of Trichoderma were tested. The in vitro...

76 FR 50759 - Applications and Amendments to Facility Operating Licenses Involving Proposed No Significant...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-16

... addition, the requestor/petitioner shall provide a brief explanation of the bases for the contention and a... trip, various pumps and coolers to start, and various valves to open and close), Containment Isolation (closes valves to isolate the Reactor Building interior from the environment), Steam isolation (close all...

A unique Mycobacterium species isolated from an epizootic of striped bass (Morone saxatilis).

PubMed Central

Rhodes, M. W.; Kator, H.; Kotob, S.; van Berkum, P.; Kaattari, I.; Vogelbein, W.; Floyd, M. M.; Butler, W. R.; Quinn, F. D.; Ottinger, C.; Shotts, E.

2001-01-01

We isolated a Mycobacterium sp. resembling Mycobacterium marinum and M. ulcerans from diseased striped bass (Morone saxatilis) during an epizootic of mycobacteriosis in the Chesapeake Bay. This isolate may represent an undescribed Mycobacterium species, based on phenotypic characteristics and comparative 16S rRNA gene sequence. PMID:11747708

Characterization of isolates of meloidogyne from rice-wheat production fields in Nepal.

PubMed

Pokharel, Ramesh R; Abawi, George S; Zhang, Ning; Duxbury, John M; Smart, Christine D

2007-09-01

Thirty-three isolates of root-knot nematode were recovered from soil samples from rice-wheat fields in Nepal and maintained on rice cv. BR 11. The isolates were characterized using morphology, host range and DNA sequence analyses in order to ascertain their identity. Results indicated phenotypic similarity (juvenile measurements, perennial pattern, host range and gall shape) of the Nepalese isolates with Meloidogyne graminicola, with minor variations. The rice varieties LA 110 and Labelle were susceptible to all of the Nepalese isolates, but differences in the aggressiveness of the isolates were observed. Phylogenetic analyses based on the sequences of partial internal transcribed spacer (ITS) of the rRNA genes indicated that all Nepalese isolates formed a distinct clade with known isolates of M. graminicola with high bootstrap support. Furthermore, two groups were identified within the M. graminicola clade. No correlation between ITS haplotype and aggressiveness or host range was found among the tested isolates.

An in vitro protocol for direct isolation of potential probiotic lactobacilli from raw bovine milk and traditional fermented milks.

PubMed

Baruzzi, Federico; Poltronieri, Palmiro; Quero, Grazia Marina; Morea, Maria; Morelli, Lorenzo

2011-04-01

A method for isolating potential probiotic lactobacilli directly from traditional milk-based foods was developed. The novel digestion/enrichment protocol was set up taking care to minimize the protective effect of milk proteins and fats and was validated testing three commercial fermented milks containing well-known probiotic Lactobacillus strains. Only probiotic bacteria claimed in the label were isolated from two out of three commercial fermented milks. The application of the new protocol to 15 raw milk samples and 6 traditional fermented milk samples made it feasible to isolate 11 potential probiotic Lactobacillus strains belonging to Lactobacillus brevis, Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus johnsonii, Lactobacillus plantarum, Lactobacillus reuteri, and Lactobacillus vaginalis species. Even though further analyses need to ascertain functional properties of these lactobacilli, the novel protocol set-up makes it feasible to isolate quickly potential probiotic strains from traditional milk-based foods reducing the amount of time required by traditional procedures that, in addition, do not allow to isolate microorganisms occurring as sub-dominant populations.

Shape Engineering Boosts Magnetic Mesoporous Silica Nanoparticle-Based Isolation and Detection of Circulating Tumor Cells.

PubMed

Chang, Zhi-Min; Wang, Zheng; Shao, Dan; Yue, Juan; Xing, Hao; Li, Li; Ge, Mingfeng; Li, Mingqiang; Yan, Huize; Hu, Hanze; Xu, Qiaobing; Dong, Wen-Fei

2018-04-04

Magnetic mesoporous silica nanoparticles (M-MSNs) are attractive candidates for the immunomagnetic isolation and detection of circulating tumor cells (CTCs). Understanding of the interactions between the effects of the shape of M-MSNs and CTCs is crucial to maximize the binding capacity and capture efficiency as well as to facilitate the sensitivity and efficiency of detection. In this work, fluorescent M-MSNs were rationally designed with sphere and rod morphologies while retaining their robust fluorescence and uniform surface functionality. After conjugation with the antibody of epithelial cell adhesion molecule (EpCAM), both of the differently shaped M-MSNs-EpCAM obtained achieved efficient enrichment of CTCs and fluorescent-based detection. Importantly, rodlike M-MSNs exhibited faster immunomagnetic isolation as well as better performance in the isolation and detection of CTCs in spiked cells and real clinical blood samples than those of their spherelike counterparts. Our results showed that shape engineering contributes positively toward immunomagnetic isolation, which might open new avenues to the rational design of magnetic-fluorescent nanoprobes for the sensitive and efficient isolation and detection of CTCs.

Prevalence and genetic diversity of Bartonella species in sika deer (Cervus nippon) in Japan.

PubMed

Sato, Shingo; Kabeya, Hidenori; Yamazaki, Mari; Takeno, Shinako; Suzuki, Kazuo; Kobayashi, Shinichi; Souma, Kousaku; Masuko, Takayoshi; Chomel, Bruno B; Maruyama, Soichi

2012-12-01

We report the first description of Bartonella prevalence and genetic diversity in 64 Honshu sika deer (Cervus nippon centralis) and 18 Yezo sika deer (Cervus nippon yesoensis) in Japan. Overall, Bartonella bacteremia prevalence was 41.5% (34/82). The prevalence in wild deer parasitized with ticks and deer keds was 61.8% (34/55), whereas no isolates were detected in captive deer (0/27) free of ectoparasites. The isolates belonged to 11 genogroups based on a combination of the gltA and rpoB gene sequences. Phylogenetic analysis of concatenated sequences of the ftsZ, gltA, ribC, and rpoB genes of 11 representative isolates showed that Japanese sika deer harbor three Bartonella species, including B. capreoli and two novel Bartonella species. All Yezo deer's isolates were identical to B. capreoli B28980 strain isolated from an elk in the USA, based on the sequences of the ftsZ, gltA, and rpoB genes. In contrast, the isolates from Honshu deer showed a higher genetic diversity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Analysis of material parameter effects on fluidlastic isolators performance

NASA Astrophysics Data System (ADS)

Cheng, Q. Y.; Deng, J. H.; Feng, Z. Z.; Qian, F.

2018-01-01

Control of vibration in helicopters has always been a complex and challenging task. The fluidlastic isolators become more and more widely used because the fluids are non-toxic, non-corrosive, nonflammable, and compatible with most elastomers and adhesives. In the field of the fluidlastic isolators design, the selection of design parameters of fluid and rubber is very important to obtain efficient vibration-suppressed. Aiming at getting the property of fluidlastic isolator to material design parameters, a dynamic equation is set up based on the dynamic theory. And the dynamic analysis is carried out. The influences of design parameters on the property of fluidlastic isolator are calculated. The material parameters examined are the properties of fluid and rubber. Analysis results showed that the design parameters such as density of fluid, viscosity coefficient of fluid, stiffness of rubber (K1) and loss coefficient of rubber have obvious influence on the performance of isolator. Base on the results of the study it is concluded that the efficient vibration-suppressed can be obtained by the selection of design parameters.

A High Isolation Series-Shunt RF MEMS Switch

PubMed Central

Yu, Yuan-Wei; Zhu, Jian; Jia, Shi-Xing; Shi, Yi

2009-01-01

This paper presents a wide band compact high isolation microelectromechanical systems (MEMS) switch implemented on a coplanar waveguide (CPW) with three ohmic switch cells, which is based on the series-shunt switch design. The ohmic switch shows a low intrinsic loss of 0.1 dB and an isolation of 24.8 dB at 6 GHz. The measured average pull-in voltage is 28 V and switching time is 47 μs. In order to shorten design period of the high isolation switch, a structure-based small-signal model for the 3-port ohmic MEMS switch is developed and parameters are extracted from the measured results. Then a high isolation switch has been developed where each 3-port ohmic MEMS switch is closely located. The agreement of the measured and modeled radio frequency (RF) performance demonstrates the validity of the electrical equivalent model. Measurements of the series-shunt switch indicate an outstanding isolation of more than 40 dB and a low insertion loss of 0.35 dB from DC to 12 GHz with total chip size of 1 mm × 1.2 mm. PMID:22408535

Multistage position-stabilized vibration isolation system for neutron interferometry

NASA Astrophysics Data System (ADS)

Arif, Muhammad; Brown, Dennis E.; Greene, Geoffrey L.; Clothier, R.; Littrell, K.

1994-10-01

A two stage, position stabilized vibration isolation system has been constructed and is now in operation at the Cold Neutron Research Facility of the National Institute of Standards and Technology, Gaithersburg, MD. The system employs pneumatic isolators with a multiple input/multiple output pneumatic servo system based upon pulse width modulation control loops. The first stage consists of a 40,000 kg reinforced concrete table supported by pneumatic isolators. A large environmentally isolated laboratory enclosure rests on the concrete table. The second stage consists of a 3000 kg granite optical table located within the enclosure and supported by another set of pneumatic isolators. The position of the two stages is monitored by proximity sensors and inclinometers with 12 degrees of freedom. The system controls 12 independent pneumatic airsprings. The signals from these sensors are fed into a personal computer based control system. The control system has maintained the position of the two stages to better than 1 micrometers in translation and 5 (mu) rad in orientation for a period of a few months. A description of the system and its characteristics is given.

Pellet-free isolation of human and bovine milk extracellular vesicles by size-exclusion chromatography.

PubMed

Blans, Kristine; Hansen, Maria S; Sørensen, Laila V; Hvam, Michael L; Howard, Kenneth A; Möller, Arne; Wiking, Lars; Larsen, Lotte B; Rasmussen, Jan T

2017-01-01

Studies have suggested that nanoscale extracellular vesicles (EV) in human and bovine milk carry immune modulatory properties which could provide beneficial health effects to infants. In order to assess the possible health effects of milk EV, it is essential to use isolates of high purity from other more abundant milk structures with well-documented bioactive properties. Furthermore, gentle isolation procedures are important for reducing the risk of generating vesicle artefacts, particularly when EV subpopulations are investigated. In this study, we present two isolation approaches accomplished in three steps based on size-exclusion chromatography (SEC) resulting in effective and reproducible EV isolation from raw milk. The approaches do not require any EV pelleting and can be applied to both human and bovine milk. We show that SEC effectively separates phospholipid membrane vesicles from the primary casein and whey protein components in two differently obtained casein reduced milk fractions, with one of the fractions obtained without the use of ultracentrifugation. Milk EV isolates were enriched in lactadherin, CD9, CD63 and CD81 compared to minimal levels of the EV-marker proteins in other relevant milk fractions such as milk fat globules. Nanoparticle tracking analysis and electron microscopy reveals the presence of heterogeneous sized vesicle structures in milk EV isolates. Lipid analysis by thin layer chromatography shows that EV isolates are devoid of triacylglycerides and presents a phospholipid profile differing from milk fat globules surrounded by epithelial cell plasma membrane. Moreover, the milk EV fractions are enriched in RNA with distinct and diverging profiles from milk fat globules. Collectively, our data supports that successful milk EV isolation can be accomplished in few steps without the use of ultracentrifugation, as the presented isolation approaches based on SEC effectively isolates EV in both human and bovine milk.

Pellet-free isolation of human and bovine milk extracellular vesicles by size-exclusion chromatography

PubMed Central

Blans, Kristine; Hansen, Maria S.; Sørensen, Laila V.; Hvam, Michael L.; Howard, Kenneth A.; Möller, Arne; Wiking, Lars; Larsen, Lotte B.; Rasmussen, Jan T.

2017-01-01

ABSTRACT Studies have suggested that nanoscale extracellular vesicles (EV) in human and bovine milk carry immune modulatory properties which could provide beneficial health effects to infants. In order to assess the possible health effects of milk EV, it is essential to use isolates of high purity from other more abundant milk structures with well-documented bioactive properties. Furthermore, gentle isolation procedures are important for reducing the risk of generating vesicle artefacts, particularly when EV subpopulations are investigated. In this study, we present two isolation approaches accomplished in three steps based on size-exclusion chromatography (SEC) resulting in effective and reproducible EV isolation from raw milk. The approaches do not require any EV pelleting and can be applied to both human and bovine milk. We show that SEC effectively separates phospholipid membrane vesicles from the primary casein and whey protein components in two differently obtained casein reduced milk fractions, with one of the fractions obtained without the use of ultracentrifugation. Milk EV isolates were enriched in lactadherin, CD9, CD63 and CD81 compared to minimal levels of the EV-marker proteins in other relevant milk fractions such as milk fat globules. Nanoparticle tracking analysis and electron microscopy reveals the presence of heterogeneous sized vesicle structures in milk EV isolates. Lipid analysis by thin layer chromatography shows that EV isolates are devoid of triacylglycerides and presents a phospholipid profile differing from milk fat globules surrounded by epithelial cell plasma membrane. Moreover, the milk EV fractions are enriched in RNA with distinct and diverging profiles from milk fat globules. Collectively, our data supports that successful milk EV isolation can be accomplished in few steps without the use of ultracentrifugation, as the presented isolation approaches based on SEC effectively isolates EV in both human and bovine milk. PMID:28386391

Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.

PubMed

Runcharoen, Chakkaphan; Raven, Kathy E; Reuter, Sandra; Kallonen, Teemu; Paksanont, Suporn; Thammachote, Jeeranan; Anun, Suthatip; Blane, Beth; Parkhill, Julian; Peacock, Sharon J; Chantratita, Narisara

2017-09-06

Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin. Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.

All-in-one centrifugal microfluidic device for size-selective circulating tumor cell isolation with high purity.

PubMed

Lee, Ada; Park, Juhee; Lim, Minji; Sunkara, Vijaya; Kim, Shine Young; Kim, Gwang Ha; Kim, Mi-Hyun; Cho, Yoon-Kyoung

2014-11-18

Circulating tumor cells (CTCs) have gained increasing attention owing to their roles in cancer recurrence and progression. Due to the rarity of CTCs in the bloodstream, an enrichment process is essential for effective target cell characterization. However, in a typical pressure-driven microfluidic system, the enrichment process generally requires complicated equipment and long processing times. Furthermore, the commonly used immunoaffinity-based positive selection method is limited, as its recovery rate relies on EpCAM expression of target CTCs, which shows heterogeneity among cell types. Here, we propose a centrifugal-force-based size-selective CTC isolation platform that can isolate and enumerate CTCs from whole blood within 30 s with high purity. The device was validated using the MCF-7 breast cancer cell line spiked in phosphate-buffered saline and whole blood, and an average capture efficiency of 61% was achieved, which is typical for size-based filtration. The capture efficiency for whole blood samples varied from 44% to 84% under various flow conditions and dilution factors. Under the optimized operating conditions, a few hundred white blood cells per 1 mL of whole blood were captured, representing a 20-fold decrease compared to those obtained using a commercialized size-based CTC isolation device. In clinical validation, normalized CTC counts varied from 10 to 60 per 7.5 mL of blood from gastric and lung cancer patients, yielding a detection rate of 50% and 38%, respectively. Overall, our CTC isolation device enables rapid and label-free isolation of CTCs with high purity, which should greatly improve downstream molecular analyses of captured CTCs.

Discrimination between Demodex folliculorum (Acari: Demodicidae) isolates from China and Spain based on mitochondrial cox1 sequences*

PubMed Central

Zhao, Ya-e; Ma, Jun-xian; Hu, Li; Wu, Li-ping; De Rojas, Manuel

2013-01-01

For a long time, classification of Demodex mites has been based mainly on their hosts and phenotypic characteristics. A new subspecies of Demodex folliculorum has been proposed, but not confirmed. Here, cox1 partial sequences of nine isolates of three Demodex species from two geographical sources (China and Spain) were studied to conduct molecular identification of D. folliculorum. Sequencing showed that the mitochondrial cox1 fragments of five D. folliculorum isolates from the facial skin of Chinese individuals were 429 bp long and that their sequence identity was 97.4%. The average sequence divergence was 1.24% among the five Chinese isolates, 0.94% between the two geographical isolate groups (China (5) and Spain (1)), and 2.15% between the two facial tissue sources (facial skin (6) and eyelids (1)). The genetic distance and rate of third-position nucleotide transition/transversion were 0.0125, 2.7 (3/1) among the five Chinese isolates, 0.0094, 3.1 (3/1) between the two geographical isolate groups, and 0.0217, 4.4 (3/1) between the two facial tissue sources. Phylogenetic trees showed that D. folliculorum from the two geographical isolate groups did not form sister clades, while those from different facial tissue sources did. According to the molecular characteristics, it appears that subspecies differentiation might not have occurred and that D. folliculorum isolates from the two geographical sources are of the same population. However, population differentiation might be occurring between isolates from facial skin and eyelids. PMID:24009203

Epidemiological study on the penicillin resistance of clinical Streptococcus pneumoniae isolates identified as the common sequence types.

PubMed

Gao, Wei; Shi, Wei; Chen, Chang-hui; Wen, De-nian; Tian, Jin; Yao, Kai-hu

2016-10-20

There were some limitation in the current interpretation about the penicillin resistance mechanism of clinical Streptococcus pneumoniae isolates at the strain level. To explore the possibilities of studying the mechanism based on the sequence types (ST) of this bacteria, 488 isolates collected in Beijing from 1997-2014 and 88 isolates collected in Youyang County, Chongqing and Zhongjiang County, Sichuan in 2015 were analyzed by penicillin minimum inhibitory concentration (MIC) distribution and annual distribution. The results showed that the penicillin MICs of the all isolates covering by the given ST in Beijing have a defined range, either <0.25 mg/L or≥0.25 mg/L, except for the ST342. The isolates with penicillin MIC <0.25 mg/L were mainly collected before 2001, after which the isolates with MIC≥0.25 mg/L occurred and became the major population gradually. This law of year distribution, however, was not obvious for any specific ST. The isolates covering by any given ST could be determined with different penicillin MICs in the first few years after it was identified. The penicillin MIC of isolates identified as common STs and collected in Youyang County, Chongqing and Sichuan Zhongjiang County, including the ST271, ST320 and ST81, was around 0.25~2 mg/L (≥0.25 mg/L). Our study revealed the epidemiological distribution of penicillin MICs of the given STs determined in clinical S. pneumoniae isolates, suggesting that it is reasonable to research the penicillin resistance mechanism based on the STs of this bacteria.

Polymer Film-Based Screening and Isolation of Polylactic Acid (PLA)-Degrading Microorganisms.

PubMed

Kim, Mi Yeon; Kim, Changman; Moon, Jungheun; Heo, Jinhee; Jung, Sokhee P; Kim, Jung Rae

2017-02-28

Polylactic acid (PLA) has been highlighted as an alternative renewable polymer for the replacement of petroleum-based plastic materials, and is considered to be biodegradable. On the other hand, the biodegradation of PLA by terminal degraders, such as microorganisms, requires a lengthy period in the natural environment, and its mechanism is not completely understood. PLA biodegradation studies have been conducted using mainly undefined mixed cultures, but only a few bacterial strains have been isolated and examined. For further characterization of PLA biodegradation, in this study, the PLA-degrading bacteria from digester sludge were isolated and identified using a polymer film-based screening method. The enrichment of sludge on PLA granules was conducted with the serial transference of a subculture into fresh media for 40 days, and the attached biofilm was inoculated on a PLA film on an agar plate. 3D optical microscopy showed that the isolates physically degraded the PLA film due to bacterial degradation. 16S rRNA gene sequencing identified the microbial colonies to be Pseudomonas sp. MYK1 and Bacillus sp. MYK2. The two isolates exhibited significantly higher specific gas production rates from PLA biodegradation compared with that of the initial sludge inoculum.

Distribution of sequence-based types of legionella pneumophila serogroup 1 strains isolated from cooling towers, hot springs, and potable water systems in China.

PubMed

Qin, Tian; Zhou, Haijian; Ren, Hongyu; Guan, Hong; Li, Machao; Zhu, Bingqing; Shao, Zhujun

2014-04-01

Legionella pneumophila serogroup 1 causes Legionnaires' disease. Water systems contaminated with Legionella are the implicated sources of Legionnaires' disease. This study analyzed L. pneumophila serogroup 1 strains in China using sequence-based typing. Strains were isolated from cooling towers (n = 96), hot springs (n = 42), and potable water systems (n = 26). Isolates from cooling towers, hot springs, and potable water systems were divided into 25 sequence types (STs; index of discrimination [IOD], 0.711), 19 STs (IOD, 0.934), and 3 STs (IOD, 0.151), respectively. The genetic variation among the potable water isolates was lower than that among cooling tower and hot spring isolates. ST1 was the predominant type, accounting for 49.4% of analyzed strains (n = 81), followed by ST154. With the exception of two strains, all potable water isolates (92.3%) belonged to ST1. In contrast, 53.1% (51/96) and only 14.3% (6/42) of cooling tower and hot spring, respectively, isolates belonged to ST1. There were differences in the distributions of clone groups among the water sources. The comparisons among L. pneumophila strains isolated in China, Japan, and South Korea revealed that similar clones (ST1 complex and ST154 complex) exist in these countries. In conclusion, in China, STs had several unique allelic profiles, and ST1 was the most prevalent sequence type of environmental L. pneumophila serogroup 1 isolates, similar to its prevalence in Japan and South Korea.

Characterization and Identification of Phosphate Solubilizing Bacteria Isolate GPC3.7 from Limestone Mining Region

NASA Astrophysics Data System (ADS)

Fitriyanti, D.; Mubarik, N. R.; Tjahjoleksono, A.

2017-03-01

Phosphate (P) are one of major macronutrients needed by plants. P in the soil are present in the organic and inorganic form. The amounts of P in marginal soil can be increased with plant growth promoting rhizobacteria (PGPR). The aim of this study was to characterize and identify P solubilizing bacteria (PSB) isolate GPC3.7 that characteristically could fix N from the soil around limestone mining area. There were 44 PSB isolates found from 15 soil samples around limestone mining area, Blindis mountain, Cirebon. The solubility index of all strain were measured about 0.125 to 2.375 on Pikovskaya media. There were 22 PSB isolates were grown on N-free bromothymol blue (NfB) medium and 19 isolates were grown on Congo Red Agar (CRA) medium. Only 10 isolates were indicated as symbiotic living microorganisms whereas 12 others were categorized as N-free fixing bacteria. Isolate GPC3.7 was chosen to be further observed, based on its P solubility index, N-fixing ability and growth stability. Phosphate quantitative estimation assay of isolate GPC3.7 was unmeasured. The P soluble concentration of GPC3.7 might be lower than 1 mg/L. The colony of GPC3.7 morphologically had round shape, entire margin, raised elevation and white color. Isolate GPC3.7 was Gram negative bacteria with coccus cell shape. Based on 16S rRNA gene, GPC3.7 was closely relative to Acinetobacter baumannii.

A Wide Variety of Clostridium perfringens Type A Food-Borne Isolates That Carry a Chromosomal cpe Gene Belong to One Multilocus Sequence Typing Cluster

PubMed Central

Xiao, Yinghua; Wagendorp, Arjen; Moezelaar, Roy; Abee, Tjakko

2012-01-01

Of 98 suspected food-borne Clostridium perfringens isolates obtained from a nationwide survey by the Food and Consumer Product Safety Authority in The Netherlands, 59 strains were identified as C. perfringens type A. Using PCR-based techniques, the cpe gene encoding enterotoxin was detected in eight isolates, showing a chromosomal location for seven isolates and a plasmid location for one isolate. Further characterization of these strains by using (GTG)5 fingerprint repetitive sequence-based PCR analysis distinguished C. perfringens from other sulfite-reducing clostridia but did not allow for differentiation between various types of C. perfringens strains. To characterize the C. perfringens strains further, multilocus sequence typing (MLST) analysis was performed on eight housekeeping genes of both enterotoxic and non-cpe isolates, and the data were combined with a previous global survey covering strains associated with food poisoning, gas gangrene, and isolates from food or healthy individuals. This revealed that the chromosomal cpe strains (food strains and isolates from food poisoning cases) belong to a distinct cluster that is significantly distant from all the other cpe plasmid-carrying and cpe-negative strains. These results suggest that different groups of C. perfringens have undergone niche specialization and that a distinct group of food isolates has specific core genome sequences. Such findings have epidemiological and evolutionary significance. Better understanding of the origin and reservoir of enterotoxic C. perfringens may allow for improved control of this organism in foods. PMID:22865060

Characterization of integron mediated antimicrobial resistance in Salmonella isolated from diseased swine

PubMed Central

White, David G.; Zhao, Shaohua; McDermott, Patrick F.; Ayers, Sherry; Friedman, Sharon; Sherwood, Julie; Breider-Foley, Missy; Nolan, Lisa K.

2003-01-01

Forty-two Salmonella isolates obtained from diseased swine were genetically characterized for the presence of specific antimicrobial resistance mechanisms. Twenty of these isolates were characterized as S. Typhimurium DT104 strains. Pulsed-field gel electrophoresis was used to determine genetic relatedness and revealed 20 distinct genetic patterns among the 42 isolates. However, all DT104 isolates fell within 2 closely related genetic clusters. Other Salmonella isolates were genetically grouped together according to serotype. All DT104 isolates displayed the penta-resistance phenotype to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline. Resistance to sulfamethoxazole, tetracycline, streptomycin, kanamycin, and ampicillin was most common among the non-DT104 Salmonella isolates. All DT104 strains contained 2 chromosomal integrons of 1000 and 1200 base pairs. The DNA sequencing revealed that the 2 integrons contained genes encoding a resistance to streptomycin and ampicillin, respectively. None of the non-DT104 strains showed the same pattern, although several strains possessed integrons of 1000 base pairs or larger. However, the majority of non-DT104 Salmonella strains did not possess any integrons. Two Salmonella isolates displayed tolerance to the organic solvent cyclohexane, indicating the possibility that they are overexpressing chromosomal regulatory genes marA or soxS or the associated multidrug efflux pump, acrAB. This research suggests that integrons contribute to antimicrobial resistance among specific swine Salmonella serotypes; however, they are not as widely disseminated among non-Typhimurium swine Salmonella serotypes as previously thought. PMID:12528827

Resistance of Strains Producing Extended-Spectrum β-Lactamases Among Salmonella from Duck Carcasses at Slaughterhouses in Three Major Provinces of South Korea.

PubMed

Lee, Soo Kyoung; Choi, Dasom; Chon, Jung Whan; Seo, Kun Ho

2016-03-01

The current study was carried out to estimate Salmonella spp. contamination of duck carcasses and to determine the antibiotic susceptibility profiles and serotype distribution of the isolates. Salmonella spp. was detected in 21.7% (26/120) of fresh raw duck carcasses sampled at different slaughterhouses in South Korea. Eight Salmonella serovars were identified; the most prevalent serovar was S. Typhimurium (34.6%), followed by S. Virchow (30.8%). All isolates were resistant to at least one antibiotic, and five remarkable isolates were resistant to more than 10 antibiotics, including third- and fourth-generation cephalosporins. Additional phenotypic and genetic characterization demonstrated that these isolates harbored resistance genes to broad-spectrum β-lactams, blaCTX-M-15 and blaCMY-2 genes, among the most prevalent β-lactamase enzymes worldwide. Based on molecular subtyping performed using the DiversiLab™ automated repetitive-sequence-based PCR system, isolates were classified into cluster A and cluster B. Among β-lactamase-producing Salmonellas, the isolate showing >98% similarity in their repetitive-sequence-based PCR banding pattern seemed to have acquired the resistance gene (blaCMY-2) and thus a distinct multiresistance profile. Given that antibiotic-resistant genes might be transferred by plasmid-mediated conjugation, periodic microbiological assessment within slaughterhouses is recommended for pathogens not to be transmitted through cross-contamination during slaughtering and dressing.

Mycorrhizal fungi isolated from native terrestrial orchids of pristine regions in Cordoba (Argentina).

PubMed

Fernández Di Pardo, Agustina; Chiocchio, Viviana M; Barrera, Viviana; Colombo, Roxana P; Martinez, Alicia E; Gasoni, Laura; Godeas, Alicia M

2015-03-01

Orchidaceae is a highly dependent group on the Rhizoctonia complex that includes Ceratorhiza, Moniliopsis, Epulorhiza and Rhizoctonia, for seed germination and the development of new orchid plants. Thus, the isolation and identification of orchid mycorrhizal fungi are important to understand the orchid-fungus relationship, which can lead to the development of efficient conservation strategies by in vivo germination of seeds from endangered orchid plants. The aim of our work was to isolate and characterize the different mycorrhizal fungi found in roots of terrestrial orchids from Cordoba (Argentina), and, to learn about the natural habit and fungal associations in the Chaco Serrano woodland pristine region. In this study, bloomed orchid root and rhizosphere soil samples were obtained in two times from Valle de Punilla during spring of 2007; samples were kept in plastic bags until processed within 48 hours, and mycorrhizal condition confirmed assessing peloton presence. A total of 23 isolates of the orchideous mycorrhizal Rhizoctonia complex were obtained. The isolates were studied based on morphological characters and ITS-rDNA sequences. Morphological characteristics as color of colonies, texture, growth rate, hyphal diameter and length and presence of sclerotia were observed on culture media. To define the number of nuclei per cell, the isolates were grown in Petri dishes containing water-agar (WA) for three days at 25 degrees C and stained with Safranine-O solution. The mycorrhizal fungi were grouped into binucleate (MSGib, 10 isolates) and multinucleate (MSGim, 13 isolates) based on morphological characteristics of the colonies. We obtained the ITS1-5.8s-ITS4 region that was amplified using primers ITSI and ITS4. Based on DNA sequencing, isolates Q23 and Q29 were found to be related to species of Ceratobasidium. Isolates Q24 and Q4 were related to the binucleated anastomosis group AG-C of Rhizoctonia sp. The rest of the isolates grouped in the Ceratobasidium clade without grouping. From our knowledge this is the first report of the asso- ciation of the AG-C testers with terrestrial orchids. A high specificity was observed in the symbiotic relationship. As the mycorrhizal fungal isolates were obtained from native orchids, they could be incorporated in conservation programes of endangered orchids in Argentina.

Isolation, characterization, virulence and immunogenicity testing of field isolates of Pasteurella multocida, Staphylococcus aureus, and Streptococcus agalactiae in laboratory settings.

PubMed

Qudratullah; Muhammad, G; Saqib, M; Bilal, M Qamar

2017-08-01

The present study was designed to investigate isolation, characterization, virulence and immunogenicity testing of field isolates of Pasteurella multocida, Staphylococcus aureus, and Streptococcus agalactiae in rabbits and mice. Isolates of P. multocida, S. aureus and Str. agalactiae recovered from field cases of Hemorragic septicemia and mastitis were scrutinized for virulence/pathogenicity and immunogenicity. Mouse LD 50 of P. multocida showed that P. multocida isolate No.1 was more virulent than isolates No. 2 and 3. Virulence of isolate No.1S. aureus and Str. agalactiae revealed that 100, 80% rabbits died within 18h of inoculation. Seven-digit numerical profiles of these 4 isolates with API ® Staph test strips isolates, No.1 (6736153) showed good identification (S. aureus id=90.3%). Indirect ELISA-based serum antibody titers to P. multocida isolate No.1, S. aureus No.1, Str. agalactiae, isolate No.1 elicited high antibody titers 1.9, 1.23, 1.12 respectively. All the pathogens of Isolate No. 1 (P. multocida, S. aureus Str. agalactiae), were high antibody than others isolates. Copyright © 2017 Elsevier B.V. All rights reserved.

Complete genomic sequence of a Tobacco rattle virus isolate from Michigan-grown potatoes.

PubMed

Crosslin, James M; Hamm, Philip B; Kirk, William W; Hammond, Rosemarie W

2010-04-01

Tobacco rattle virus (TRV) causes stem mottle on potato leaves and necrotic arcs and rings in potato tubers, known as corky ringspot disease. Recently, TRV was reported in Michigan potato tubers cv. FL1879 exhibiting corky ringspot disease. Sequence analysis of the RNA-1-encoded 16-kDa gene of the Michigan isolate, designated MI-1, revealed homology to TRV isolates from Florida and Washington. Here, we report the complete genomic sequence of RNA-1 (6,791 nt) and RNA-2 (3,685 nt) of TRV MI-1. RNA-1 is predicted to contain four open reading frames, and the genome structure and phylogenetic analyses of the RNA-1 nucleotide sequence revealed significant homologies to the known sequences of other TRV-1 isolates. The relationships based on the full-length nucleotide sequence were different from than those based on the 16-kDa gene encoded on genomic RNA-1 and reflect sequence variation within a 20-25-aa residue region of the 16-kDa protein. MI-1 RNA-2 is predicted to contain three ORFs, encoding the coat protein (CP), a 37.6-kDa protein (ORF 2b), and a 33.6-kDa protein (ORF 2c). In addition, it contains a region of similarity to the 3' terminus of RNA-1, including a truncated portion of the 16-kDa cistron. Phylogenetic analysis of RNA-2, based on a comparison of nucleotide sequences with other members of the genus Tobravirus, indicates that TRV MI-1 and other North American isolates cluster as a distinct group. TRV M1-1 is only the second North American isolate for which there is a complete sequence of the genome, and it is distinct from the North American isolate TRV ORY. The relationship of the TRV MI-1 isolate to other tobravirus isolates is discussed.

A planar shock isolation system with high-static-low-dynamic-stiffness characteristic based on cables

NASA Astrophysics Data System (ADS)

Ma, Yanhui; He, Minghua; Shen, Wenhou; Ren, Gexue

2015-12-01

In this paper, a simple and designable shock isolation system with ideal high-static-low-dynamic-stiffness (HSLDS) is proposed, which is intended for the horizontal plane shock isolation application. In this system, the isolated object is suspended by several bearing cables and constrained by a number of uniformly distributed pretensioned cables in the horizontal plane, where the low dynamic stiffness of the system is main controlled by the pretension of the planar cables, whilst the high static stiffness is determined by the axial stiffness of the planar cables and their geometric settings. To obtain the HSLDS characteristic of the system, a brief theoretical description of the relationship between the restoring force and displacement is derived. By obtaining the three-order Taylor expansion with sufficient accuracy of the restoring force, influence of planar cable parameters on the low dynamic and high static stiffness is thus given, therefore, the required HSLDS isolator can be easily designed by adjusting the planar cable length, pretension and tensile stiffness. Finally, the isotropy characteristic of the restoring force of the system with different numbers of planar cables is investigated. To evaluate the performance of the system, a rigid isolated object and flexible cables coupling simulation model considering the contacts of the system is established by using multibody dynamics approach. In this model, flexible cables are simulated by 3-node cable element based on the absolute nodal coordinate formulation; the contact between cable and isolated object is simulated based on Hertz contact theory. Finally, the time-domain shock excitation is converted from the design shock spectrum on the basis of BV043/85 criterion. The design procedure of this isolator and some useful guidelines for choosing cable parameters are presented. In addition, a summary about the performance of the isolators with different numbers of cables shocking in an arbitrary direction is given in the conclusion.

Anticancer property of sediment actinomycetes against MCF-7 and MDA-MB-231 cell lines.

PubMed

Ravikumar, S; Fredimoses, M; Gnanadesigan, M

2012-02-01

To investigate the anticancer property of marine sediment actinomycetes against two different breast cancer cell lines. In vitro anticancer activity was carried out against breast (MCF-7 and MDA-MB-231) cancer cell lines. Partial sequences of the 16s rRNA gene, phylogenetic tree construction, multiple sequence analysis and secondary structure analysis were also carried out with the actinomycetes isolates. Of the selected five actinomycete isolates, ACT01 and ACT02 showed the IC50 value with (10.13±0.92) and (22.34±5.82) µg/mL concentrations, respectively for MCF-7 cell line at 48 h, but ACT01 showed the minimum (18.54±2.49 µg/mL) level of IC50 value with MDA-MB-231 cell line. Further, the 16s rRNA partial sequences of ACT01, ACT02, ACT03, ACT04 and ACT05 isolates were also deposited in NCBI data bank with the accession numbers of GQ478246, GQ478247, GQ478248, GQ478249 and GQ478250, respectively. The phylogenetic tree analysis showed that, the isolates of ACT02 and ACT03 were represented in group I and III, respectively, but ACT01 and ACT02 were represented in group II. The multiple sequence alignment of the actinomycete isolates showed that, the maximum identical conserved regions were identified with the nucleotide regions of 125 to 221st base pairs, 65 to 119th base pairs and 55, 48 and 31st base pairs. Secondary structure prediction of the 16s rRNA showed that, the maximum free energy was consumed with ACT03 isolate (-45.4 kkal/mol) and the minimum free energy was consumed with ACT04 isolate (-57.6 kkal/mol). The actinomycete isolates of ACT01 and ACT02 (GQ478246 and GQ478247) which are isolated from sediment sample can be further used as anticancer agents against breast cancer cell lines.

A "Kanes's Dynamics" Model for the Active Rack Isolation System

NASA Technical Reports Server (NTRS)

Hampton, R. David; Beech, Geoffrey

1999-01-01

Many microgravity space-science experiments require vibratory acceleration levels unachievable without active isolation. The Boeing Corporation's Active Rack Isolation System (ARIS) employs a novel combination of magnetic actuation and mechanical linkages, to address these isolation requirements on the International Space Station (ISS). ARIS provides isolation at the rack (international Standard Payload Rack, or ISPR) level. Effective model-based vibration isolation requires (1) an appropriate isolation device, (2) an adequate dynamic (i.e., mathematical) model of that isolator, and (3) a suitable, corresponding controller. ARIS provides the ISS response to the first requirement. This paper presents one response to the second, in a state-space framework intended to facilitate an optimal-controls approach to the third. The authors use "Kane's Dynamics" to develop an state-space, analytical (algebraic) set of linearized equations of motion for ARIS.

A "Kane's Dynamics" Model for the Active Rack Isolation System

NASA Technical Reports Server (NTRS)

Hampton, R. D.; Beech, G. S.; Rao, N. N. S.; Rupert, J. K.; Kim, Y. K.

2001-01-01

Many microgravity space science experiments require vibratory acceleration levels unachievable without active isolation. The Boeing Corporation's Active Rack Isolation System (ARIS) employs a novel combination of magnetic actuation and mechanical linkages to address these isolation requirements on the International Space Station (ISS). ARIS provides isolation at the rack (International Standard Payload Rack (ISPR)) level. Effective model-based vibration isolation requires: (1) an appropriate isolation device, (2) an adequate dynamic (i.e., mathematical) model of that isolator, and (3) a suitable, corresponding controller. ARIS provides the ISS response to the first requirement. This paper presents one response to the second, in a state space framework intended to facilitate an optimal-controls approach to the third. The authors use "Kane's Dynamics" to develop a state-space, analytical (algebraic) set of linearized equations of motion for ARIS.

Isolation and identification of multidrug-resistant Staphylococcus haemolyticus from a laboratory-breeding mouse.

PubMed

Huang, Fengying; Meng, Qiuping; Tan, Guanghong; Huang, Yonghao; Wang, Hua; Mei, Wenli; Dai, Haofu

2011-06-01

To analysis and identify a bacterium strain isolated from laboratory breeding mouse far away from a hospital. Phenotype of the isolate was investigated by conventional microbiological methods, including Gram-staining, colony morphology, tests for haemolysis, catalase, coagulase, and antimicrobial susceptibility test. The mecA and 16S rRNA genes were amplified by the polymerase chain reaction (PCR) and sequenced. The base sequence of the PCR product was compared with known 16S rRNA gene sequences in the GenBank database by phylogenetic analysis and multiple sequence alignment. The isolate in this study was a gram positive, coagulase negative, and catalase positive coccus. The isolate was resistant to oxacillin, methicillin, penicillin, ampicillin, cefazolin, ciprofloxacin erythromycin, et al. PCR results indicated that the isolate was mecA gene positive and its 16S rRNA was 1 465 bp. Phylogenetic analysis of the resultant 16S rRNA indicated the isolate belonged to genus Saphylococcus, and multiple sequence alignment showed that the isolate was Saphylococcus haemolyticus with only one base difference from the corresponding 16S rRNA deposited in the GenBank. 16S rRNA gene sequencing is a suitable technique for non-specialist researchers. Laboratory animals are possible sources of lethal pathogens, and researchers must adapt protective measures when they manipulate animals. Copyright © 2011 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

Isolation of exosomes from whole blood by integrating acoustics and microfluidics.

PubMed

Wu, Mengxi; Ouyang, Yingshi; Wang, Zeyu; Zhang, Rui; Huang, Po-Hsun; Chen, Chuyi; Li, Hui; Li, Peng; Quinn, David; Dao, Ming; Suresh, Subra; Sadovsky, Yoel; Huang, Tony Jun

2017-10-03

Exosomes are nanoscale extracellular vesicles that play an important role in many biological processes, including intercellular communications, antigen presentation, and the transport of proteins, RNA, and other molecules. Recently there has been significant interest in exosome-related fundamental research, seeking new exosome-based biomarkers for health monitoring and disease diagnoses. Here, we report a separation method based on acoustofluidics (i.e., the integration of acoustics and microfluidics) to isolate exosomes directly from whole blood in a label-free and contact-free manner. This acoustofluidic platform consists of two modules: a microscale cell-removal module that first removes larger blood components, followed by extracellular vesicle subgroup separation in the exosome-isolation module. In the cell-removal module, we demonstrate the isolation of 110-nm particles from a mixture of micro- and nanosized particles with a yield greater than 99%. In the exosome-isolation module, we isolate exosomes from an extracellular vesicle mixture with a purity of 98.4%. Integrating the two acoustofluidic modules onto a single chip, we isolated exosomes from whole blood with a blood cell removal rate of over 99.999%. With its ability to perform rapid, biocompatible, label-free, contact-free, and continuous-flow exosome isolation, the integrated acoustofluidic device offers a unique approach to investigate the role of exosomes in the onset and progression of human diseases with potential applications in health monitoring, medical diagnosis, targeted drug delivery, and personalized medicine.

Isolation of exosomes from whole blood by integrating acoustics and microfluidics

PubMed Central

Wu, Mengxi; Ouyang, Yingshi; Wang, Zeyu; Zhang, Rui; Huang, Po-Hsun; Chen, Chuyi; Li, Hui; Li, Peng; Quinn, David; Dao, Ming; Suresh, Subra

2017-01-01

Exosomes are nanoscale extracellular vesicles that play an important role in many biological processes, including intercellular communications, antigen presentation, and the transport of proteins, RNA, and other molecules. Recently there has been significant interest in exosome-related fundamental research, seeking new exosome-based biomarkers for health monitoring and disease diagnoses. Here, we report a separation method based on acoustofluidics (i.e., the integration of acoustics and microfluidics) to isolate exosomes directly from whole blood in a label-free and contact-free manner. This acoustofluidic platform consists of two modules: a microscale cell-removal module that first removes larger blood components, followed by extracellular vesicle subgroup separation in the exosome-isolation module. In the cell-removal module, we demonstrate the isolation of 110-nm particles from a mixture of micro- and nanosized particles with a yield greater than 99%. In the exosome-isolation module, we isolate exosomes from an extracellular vesicle mixture with a purity of 98.4%. Integrating the two acoustofluidic modules onto a single chip, we isolated exosomes from whole blood with a blood cell removal rate of over 99.999%. With its ability to perform rapid, biocompatible, label-free, contact-free, and continuous-flow exosome isolation, the integrated acoustofluidic device offers a unique approach to investigate the role of exosomes in the onset and progression of human diseases with potential applications in health monitoring, medical diagnosis, targeted drug delivery, and personalized medicine. PMID:28923936

Frequency of Resistance and Susceptible Bacteria Isolated from Houseflies

PubMed Central

Davari, B; Kalantar, E; Zahirnia, A; Moosa-Kazemi, SH

2010-01-01

Background: In this study, we determine the vector competence of Musca domestica with reference to the transmission of susceptible and resistance bacterial strains in hospitals and slaughter house in Sanandaj City, west Iran. Methods: Totally 908 houseflies were collected to isolate bacteria from their external body based on standard procedures.Antibiotic susceptibility testing was performed by Kirby-Bauer disc diffusion method on Mueller Hinton agar based on recommendations of CLSI (formerly the National Committee for Clinical Laboratory Standards). Results: From collected houseflies, 366 bacteria species were isolated. The most common isolated bacterium at hospitals was Klebsiella pneumoniae 43.3% (n= 90) followed by Pseudomonas aeruginosa 37% (n= 77), while that of slaughterhouse was Proteus mirabilis. 29.1% (n= 46) followed by Citrobacter freundii 28.4% (n= 45). Among all the isolates from hospitals, cephalexin, chloramphenicol, ampicillin, and tetracycline, resistance rates were above 32.5% and gentamicin expressed the highest susceptibility among all the isolates from hospitals. It is worth to note that K. pneumoniae showed 61% and 44.5% resistance to cephalexin and chloramphenicol respectively. Similarly, all isolates from slaughterhouse were more than 28% and 30% resistant to cephalexin and chloramphenicol respectively. Surprisingly, among all the isolates, Citrobacter freundii were highly resistant to gentamicin. Conclusion: Houseflies collected from hospitals and slaughterhouse may be involved in the spread of drug resistant bacteria and may increase the potential of human exposure to drug resistant bacteria. PMID:22808400

Frequency of resistance and susceptible bacteria isolated from houseflies.

PubMed

Davari, B; Kalantar, E; Zahirnia, A; Moosa-Kazemi, Sh

2010-01-01

In this study, we determine the vector competence of Musca domestica with reference to the transmission of susceptible and resistance bacterial strains in hospitals and slaughter house in Sanandaj City, west Iran. Totally 908 houseflies were collected to isolate bacteria from their external body based on standard procedures.Antibiotic susceptibility testing was performed by Kirby-Bauer disc diffusion method on Mueller Hinton agar based on recommendations of CLSI (formerly the National Committee for Clinical Laboratory Standards). From collected houseflies, 366 bacteria species were isolated. The most common isolated bacterium at hospitals was Klebsiella pneumoniae 43.3% (n= 90) followed by Pseudomonas aeruginosa 37% (n= 77), while that of slaughterhouse was Proteus mirabilis. 29.1% (n= 46) followed by Citrobacter freundii 28.4% (n= 45). Among all the isolates from hospitals, cephalexin, chloramphenicol, ampicillin, and tetracycline, resistance rates were above 32.5% and gentamicin expressed the highest susceptibility among all the isolates from hospitals. It is worth to note that K. pneumoniae showed 61% and 44.5% resistance to cephalexin and chloramphenicol respectively. Similarly, all isolates from slaughterhouse were more than 28% and 30% resistant to cephalexin and chloramphenicol respectively. Surprisingly, among all the isolates, Citrobacter freundii were highly resistant to gentamicin. Houseflies collected from hospitals and slaughterhouse may be involved in the spread of drug resistant bacteria and may increase the potential of human exposure to drug resistant bacteria.

Cloning and sequence analysis of chitin synthase gene fragments of Demodex mites.

PubMed

Zhao, Ya-e; Wang, Zheng-hang; Xu, Yang; Xu, Ji-ru; Liu, Wen-yan; Wei, Meng; Wang, Chu-ying

2012-10-01

To our knowledge, few reports on Demodex studied at the molecular level are available at present. In this study our group, for the first time, cloned, sequenced and analyzed the chitin synthase (CHS) gene fragments of Demodex folliculorum, Demodex brevis, and Demodex canis (three isolates from each species) from Xi'an China, by designing specific primers based on the only partial sequence of the CHS gene of D. canis from Japan, retrieved from GenBank. Results show that amplification was successful only in three D. canis isolates and one D. brevis isolate out of the nine Demodex isolates. The obtained fragments were sequenced to be 339 bp for D. canis and 338 bp for D. brevis. The CHS gene sequence similarities between the three Xi'an D. canis isolates and one Japanese D. canis isolate ranged from 99.7% to 100.0%, and those between four D. canis isolates and one D. brevis isolate were 99.1%-99.4%. Phylogenetic trees based on maximum parsimony (MP) and maximum likelihood (ML) methods shared the same clusters, according with the traditional classification. Two open reading frames (ORFs) were identified in each CHS gene sequenced, and their corresponding amino acid sequences were located at the catalytic domain. The relatively conserved sequences could be deduced to be a CHS class A gene, which is associated with chitin synthesis in the integument of Demodex mites.

Cloning and sequence analysis of chitin synthase gene fragments of Demodex mites*

PubMed Central

Zhao, Ya-e; Wang, Zheng-hang; Xu, Yang; Xu, Ji-ru; Liu, Wen-yan; Wei, Meng; Wang, Chu-ying

2012-01-01

To our knowledge, few reports on Demodex studied at the molecular level are available at present. In this study our group, for the first time, cloned, sequenced and analyzed the chitin synthase (CHS) gene fragments of Demodex folliculorum, Demodex brevis, and Demodex canis (three isolates from each species) from Xi’an China, by designing specific primers based on the only partial sequence of the CHS gene of D. canis from Japan, retrieved from GenBank. Results show that amplification was successful only in three D. canis isolates and one D. brevis isolate out of the nine Demodex isolates. The obtained fragments were sequenced to be 339 bp for D. canis and 338 bp for D. brevis. The CHS gene sequence similarities between the three Xi’an D. canis isolates and one Japanese D. canis isolate ranged from 99.7% to 100.0%, and those between four D. canis isolates and one D. brevis isolate were 99.1%–99.4%. Phylogenetic trees based on maximum parsimony (MP) and maximum likelihood (ML) methods shared the same clusters, according with the traditional classification. Two open reading frames (ORFs) were identified in each CHS gene sequenced, and their corresponding amino acid sequences were located at the catalytic domain. The relatively conserved sequences could be deduced to be a CHS class A gene, which is associated with chitin synthesis in the integument of Demodex mites. PMID:23024043

Minimizing the Workup of Blood Culture Contaminants: Implementation and Evaluation of a Laboratory-Based Algorithm

PubMed Central

Richter, S. S.; Beekmann, S. E.; Croco, J. L.; Diekema, D. J.; Koontz, F. P.; Pfaller, M. A.; Doern, G. V.

2002-01-01

An algorithm was implemented in the clinical microbiology laboratory to assess the clinical significance of organisms that are often considered contaminants (coagulase-negative staphylococci, aerobic and anaerobic diphtheroids, Micrococcus spp., Bacillus spp., and viridans group streptococci) when isolated from blood cultures. From 25 August 1999 through 30 April 2000, 12,374 blood cultures were submitted to the University of Iowa Clinical Microbiology Laboratory. Potential contaminants were recovered from 495 of 1,040 positive blood cultures. If one or more additional blood cultures were obtained within ±48 h and all were negative, the isolate was considered a contaminant. Antimicrobial susceptibility testing (AST) of these probable contaminants was not performed unless requested. If no additional blood cultures were submitted or there were additional positive blood cultures (within ±48 h), a pathology resident gathered patient clinical information and made a judgment regarding the isolate's significance. To evaluate the accuracy of these algorithm-based assignments, a nurse epidemiologist in approximately 60% of the cases performed a retrospective chart review. Agreement between the findings of the retrospective chart review and the automatic classification of the isolates with additional negative blood cultures as probable contaminants occurred among 85.8% of 225 isolates. In response to physician requests, AST had been performed on 15 of the 32 isolates with additional negative cultures considered significant by retrospective chart review. Agreement of pathology resident assignment with the retrospective chart review occurred among 74.6% of 71 isolates. The laboratory-based algorithm provided an acceptably accurate means for assessing the clinical significance of potential contaminants recovered from blood cultures. PMID:12089259

Complex multifractal nature in Mycobacterium tuberculosis genome

PubMed Central

Mandal, Saurav; Roychowdhury, Tanmoy; Chirom, Keilash; Bhattacharya, Alok; Brojen Singh, R. K.

2017-01-01

The mutifractal and long range correlation (C(r)) properties of strings, such as nucleotide sequence can be a useful parameter for identification of underlying patterns and variations. In this study C(r) and multifractal singularity function f(α) have been used to study variations in the genomes of a pathogenic bacteria Mycobacterium tuberculosis. Genomic sequences of M. tuberculosis isolates displayed significant variations in C(r) and f(α) reflecting inherent differences in sequences among isolates. M. tuberculosis isolates can be categorised into different subgroups based on sensitivity to drugs, these are DS (drug sensitive isolates), MDR (multi-drug resistant isolates) and XDR (extremely drug resistant isolates). C(r) follows significantly different scaling rules in different subgroups of isolates, but all the isolates follow one parameter scaling law. The richness in complexity of each subgroup can be quantified by the measures of multifractal parameters displaying a pattern in which XDR isolates have highest value and lowest for drug sensitive isolates. Therefore C(r) and multifractal functions can be useful parameters for analysis of genomic sequences. PMID:28440326

Complex multifractal nature in Mycobacterium tuberculosis genome

NASA Astrophysics Data System (ADS)

Mandal, Saurav; Roychowdhury, Tanmoy; Chirom, Keilash; Bhattacharya, Alok; Brojen Singh, R. K.

2017-04-01

The mutifractal and long range correlation (C(r)) properties of strings, such as nucleotide sequence can be a useful parameter for identification of underlying patterns and variations. In this study C(r) and multifractal singularity function f(α) have been used to study variations in the genomes of a pathogenic bacteria Mycobacterium tuberculosis. Genomic sequences of M. tuberculosis isolates displayed significant variations in C(r) and f(α) reflecting inherent differences in sequences among isolates. M. tuberculosis isolates can be categorised into different subgroups based on sensitivity to drugs, these are DS (drug sensitive isolates), MDR (multi-drug resistant isolates) and XDR (extremely drug resistant isolates). C(r) follows significantly different scaling rules in different subgroups of isolates, but all the isolates follow one parameter scaling law. The richness in complexity of each subgroup can be quantified by the measures of multifractal parameters displaying a pattern in which XDR isolates have highest value and lowest for drug sensitive isolates. Therefore C(r) and multifractal functions can be useful parameters for analysis of genomic sequences.

Effect of Plant Extracts Formulated in Different Ointment Bases on MDR Strains.

PubMed

Pawar, Pallavi L; Nabar, Bela M

2010-05-01

Extracts of Aloe vera whole plant, Eucalyptus globulus leaves, Ficus infectoria bark, Ficus religiosa bark and Piper betel leaves were studied for antibacterial activity on resistant and sensitive strains, isolated from skin and soft tissue infections. A combination of hot alcoholic extracts of Ficus infectoria, Ficus religiosa and Piper betel were found to be more effective against all the isolates. The combined extract was formulated in different ointment bases such as polyethylene glycol, gelatin, sodium alginate, carbopol, cream base and honey. These were then evaluated to find a suitable base for preparation of an ointment. In vitro study of the release of antimicrobials and kill-time studies of the herbal ointments was carried out against multi-drug resistant isolate of Pseudomonas. The ointment showed bactericidal activity within 2 h against the resistant strain of Pseudomonas spp.

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

PubMed Central

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE. PMID:24688314

Microfluidic devices for the isolation of circulating rare cells: a focus on affinity-based, dielectrophoresis, and hydrophoresis.

PubMed

Hyun, Kyung-A; Jung, Hyo-Il

2013-04-01

Circulating rare cells have attracted interest because they can be good indicators of various types of diseases. For example, enumeration of circulating tumor cells is used for cancer diagnosis and prognosis, while DNA analysis or enumeration of nucleated red blood cells is useful for prenatal diagnosis or hypoxic anemia, and that of circulating stem cells to diagnose cancer metastasis. Isolation of these cells and their downstream analyses can provide significant information such as the origin and characteristics of a disease. Novel approaches based on microfluidics have many advantages, including the continuous process and integration with other components for analysis. For these reasons, a variety of microfluidic devices have been developed to isolate and characterize rare cells. In this article, we review several microfluidic devices, with a focus on affinity-based isolation (e.g. antigen-antibody reaction) and label-free separation (DEP and hydrophoresis). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adding Value to Goat Meat: Biochemical and Technological Characterization of Autochthonous Lactic Acid Bacteria to Achieve High-Quality Fermented Sausages

PubMed Central

Nediani, Miriam T.; García, Luis; Saavedra, Lucila; Martínez, Sandra; López Alzogaray, Soledad; Fadda, Silvina

2017-01-01

Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product. PMID:28513575

Adding Value to Goat Meat: Biochemical and Technological Characterization of Autochthonous Lactic Acid Bacteria to Achieve High-Quality Fermented Sausages.

PubMed

Nediani, Miriam T; García, Luis; Saavedra, Lucila; Martínez, Sandra; López Alzogaray, Soledad; Fadda, Silvina

2017-05-17

Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product.

Development of a selective myclobutanil agar (MBA) medium for the isolation of Fusarium species from asparagus fields.

PubMed

Vujanovic, Vladimir; Hamel, Chantal; Jabaji-Hare, Suha; St-Arnaud, Marc

2002-09-01

A new selective myclobutanil agar medium for the detection of Fusarium, species is proposed. Ten media formulations based on various selective agents (pentachloronitrobenzene (PCNB), Rose Bengal, malachite green, sodium hypochlorite, captan, benomyl, chlorotalonil, myclobutanil, thiram, and cupric sulfate) were compared. First, mycelium growth and colony appearance of Alternaria alternata, Aspergillus flavus, Cladosporium cladosporioides, Epicoccum nigrum, Fusarium sp., Fuisarium solani, Fusarium moniliforme, Fusarium oxysporum f.sp. dianthi, Penicillium sp., and Trichoderma viride isolates were compared. Second, the ability of the different media to isolate and enumerate fusaria from asparagus fields was evaluated. The myclobutanil-based medium showed the highest selectivity to Fusarium spp. growth but required a slightly longer incubation time (>5 d) than peptone-pentachloronitrobenzene-based agar (PPA) (< 5 d). PPA allowed a faster fusaria growth but also permited the growth of other moulds. The other media were less selective and did not allow to isolate fusaria or to differenciate them from other growing fungi.

Molecular typing and exopolysaccharide biosynthesis of Burkholderia cepacia isolates from a Portuguese cystic fibrosis center.

PubMed

Richau, J A; Leitão, J H; Correia, M; Lito, L; Salgado, M J; Barreto, C; Cescutti, P; Sá-Correia, I

2000-04-01

This work describes the first epidemiological survey of Burkholderia cepacia involved in pulmonary infections among the Portuguese population with cystic fibrosis (CF) who attended the major CF treatment Center in Lisbon at Sta. Maria Hospital from 1995 to the end of 1997. The characterization of the genomic relatedness of the isolates was based on the analysis of their ribopatterns (with EcoRI) followed by construction of a ribotype-based phylogenetic tree. This study was complemented with macrorestriction fragment analysis by pulsed-field gel electrophoresis. After optimization of the solid growth medium, we found that exopolysaccharide (EPS) production by B. cepacia CF isolates is not as rare a phenomenon as was thought before; indeed, 70% of the isolates examined were EPS producers.

Molecular Typing and Exopolysaccharide Biosynthesis of Burkholderia cepacia Isolates from a Portuguese Cystic Fibrosis Center

PubMed Central

Richau, João A.; Leitão, Jorge H.; Correia, Manuela; Lito, Luís; Salgado, Maria José; Barreto, Celeste; Cescutti, Paola; Sá-Correia, Isabel

2000-01-01

This work describes the first epidemiological survey of Burkholderia cepacia involved in pulmonary infections among the Portuguese population with cystic fibrosis (CF) who attended the major CF treatment Center in Lisbon at Sta. Maria Hospital from 1995 to the end of 1997. The characterization of the genomic relatedness of the isolates was based on the analysis of their ribopatterns (with EcoRI) followed by construction of a ribotype-based phylogenetic tree. This study was complemented with macrorestriction fragment analysis by pulsed-field gel electrophoresis. After optimization of the solid growth medium, we found that exopolysaccharide (EPS) production by B. cepacia CF isolates is not as rare a phenomenon as was thought before; indeed, 70% of the isolates examined were EPS producers. PMID:10747161

Coagulase gene typing of Staphylococcus aureus isolated from cows with mastitis in southeastern Brazil

PubMed Central

2005-01-01

Abstract A typing procedure based on polymorphism of the coagulase gene (coa) was used to discriminate Staphylococcus aureus isolated from Minas Gerais dairy cows with mastitis. Amplification of the gene from the 64 S. aureus isolates produced 27 different polymerase chain reaction (PCR) products; 60 isolates showed only 1 amplicon, and 4 showed 2 amplicons. The isolates were grouped into 49 types by analyzing the restriction fragment length polymorphism (RFLP) of the coa gene; the 10 most common types accounted for 39% of the isolates. The results demonstrate that many variants of the coa gene are present in the studied region, although only a few predominate. PMID:16479723

Performance assessment of conventional and base-isolated nuclear power plants for earthquake and blast loadings

NASA Astrophysics Data System (ADS)

Huang, Yin-Nan

Nuclear power plants (NPPs) and spent nuclear fuel (SNF) are required by code and regulations to be designed for a family of extreme events, including very rare earthquake shaking, loss of coolant accidents, and tornado-borne missile impacts. Blast loading due to malevolent attack became a design consideration for NPPs and SNF after the terrorist attacks of September 11, 2001. The studies presented in this dissertation assess the performance of sample conventional and base isolated NPP reactor buildings subjected to seismic effects and blast loadings. The response of the sample reactor building to tornado-borne missile impacts and internal events (e.g., loss of coolant accidents) will not change if the building is base isolated and so these hazards were not considered. The sample NPP reactor building studied in this dissertation is composed of containment and internal structures with a total weight of approximately 75,000 tons. Four configurations of the reactor building are studied, including one conventional fixed-base reactor building and three base-isolated reactor buildings using Friction Pendulum(TM), lead rubber and low damping rubber bearings. The seismic assessment of the sample reactor building is performed using a new procedure proposed in this dissertation that builds on the methodology presented in the draft ATC-58 Guidelines and the widely used Zion method, which uses fragility curves defined in terms of ground-motion parameters for NPP seismic probabilistic risk assessment. The new procedure improves the Zion method by using fragility curves that are defined in terms of structural response parameters since damage and failure of NPP components are more closely tied to structural response parameters than to ground motion parameters. Alternate ground motion scaling methods are studied to help establish an optimal procedure for scaling ground motions for the purpose of seismic performance assessment. The proposed performance assessment procedure is used to evaluate the vulnerability of the conventional and base-isolated NPP reactor buildings. The seismic performance assessment confirms the utility of seismic isolation at reducing spectral demands on secondary systems. Procedures to reduce the construction cost of secondary systems in isolated reactor buildings are presented. A blast assessment of the sample reactor building is performed for an assumed threat of 2000 kg of TNT explosive detonated on the surface with a closest distance to the reactor building of 10 m. The air and ground shock waves produced by the design threat are generated and used for performance assessment. The air blast loading to the sample reactor building is computed using a Computational Fluid Dynamics code Air3D and the ground shock time series is generated using an attenuation model for soil/rock response. Response-history analysis of the sample conventional and base isolated reactor buildings to external blast loadings is performed using the hydrocode LS-DYNA. The spectral demands on the secondary systems in the isolated reactor building due to air blast loading are greater than those for the conventional reactor building but much smaller than those spectral demands associated with Safe Shutdown Earthquake shaking. The isolators are extremely effective at filtering out high acceleration, high frequency ground shock loading.

Asperger syndrome, violent thoughts and clinically isolated syndrome.

PubMed

Vanderbruggen, N; Van Geit, N; Bissay, V; Zeeuws, D; Santermans, L; Baeken, C

2010-12-01

A young man, 23 years old, with a clinically isolated syndrome (CIS), presented violent thoughts during a neurological consultation. He was diagnosed with Asperger Syndrome based on a psychiatric and (neuro)psychological examination. Possible risk factors for acting-out and the implications for treatment, if CIS would evolve to MS, are discussed based on a review of the literature.

RNase One Gene Isolation, Expression, and Affinity Purification Models Research Experimental Progression and Culminates with Guided Inquiry-Based Experiments

ERIC Educational Resources Information Center

Bailey, Cheryl P.

2009-01-01

This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry-based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations…

Optical isolators for 2-micron fibre lasers

NASA Astrophysics Data System (ADS)

Stevens, Gary; Legg, Thomas H.; Shardlow, Peter

2015-02-01

We report on the development and testing of optical isolators for use in 2-micron fiber laser systems. A variety of potential Faraday rotator materials were characterised to identify the most suitable materials for use in the 1700-2100nm wavelength range. Isolators based on the three best performing materials were then developed and packaged as fiber-in, fiber-out and fiber-in, beam-out devices. The isolators were then tested in CW, pulsed and ultrafast laser systems. The three different designs produced different performance characteristics, but all designs demonstrated isolation >25dB and insertion losses of <1.2 dB.

Ultra-wideband design of waveguide magneto-optical isolator operating in 1.31mum and 1.55mum band.

PubMed

Shoji, Yuya; Mizumoto, Tetsuya

2007-01-22

The design of an ultra-wideband waveguide magneto-optical isolator is described. The isolator is based on a Mach-Zehnder interferometer employing nonreciprocal phase shift. The ultra-wideband design is realized by adjusting the wavelength dependence of reciprocal phase difference to compensate for that of nonreciprocal phase difference in the backward direction. We obtained the ultra-wideband design that provides isolation > 35dB from 1.25mum to >1.65mum. This is the proposal of magneto-optical isolator that operates both in 1.31mum band and 1.55mum band.

Technology transfer package on seismic base isolation - Volume II

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

NONE

1995-02-14

This Technology Transfer Package provides some detailed information for the U.S. Department of Energy (DOE) and its contractors about seismic base isolation. Intended users of this three-volume package are DOE Design and Safety Engineers as well as DOE Facility Managers who are responsible for reducing the effects of natural phenomena hazards (NPH), specifically earthquakes, on their facilities. The package was developed as part of DOE's efforts to study and implement techniques for protecting lives and property from the effects of natural phenomena and to support the International Decade for Natural Disaster Reduction. Volume II contains the proceedings for the Shortmore » Course on Seismic Base Isolation held in Berkeley, California, August 10-14, 1992.« less

Post-synthetic modifications of cadmium-based knots and links.

PubMed

Prakasam, Thirumurugan; Bilbeisi, Rana A; Lusi, Matteo; Olsen, John-Carl; Platas-Iglesias, Carlos; Trabolsi, Ali

2016-05-31

Three topologically non-trivial cadmium(ii)-based complexes-Cd-[2]C, Cd-TK and Cd-SL-were simultaneously self-assembled in a dynamic library, individually isolated and fully characterized using solid-state, gas-phase and solution-phase techniques. Post-synthetic modifications, including reduction and transmetalation, were subsequently achieved. Imine bond reduction followed by demetallation led to the isolation of the corresponding organic molecules [2]C, TK and SL. Transmetalation of Cd-TK and Cd-SL with the zinc(ii) cation resulted in isolation of the corresponding zinc(ii)-containing complexes Zn-TK and Zn-SL.

Thermally-isolated silicon-based integrated circuits and related methods

DOEpatents

Wojciechowski, Kenneth; Olsson, Roy H.; Clews, Peggy J.; Bauer, Todd

2017-05-09

Thermally isolated devices may be formed by performing a series of etches on a silicon-based substrate. As a result of the series of etches, silicon material may be removed from underneath a region of an integrated circuit (IC). The removal of the silicon material from underneath the IC forms a gap between remaining substrate and the integrated circuit, though the integrated circuit remains connected to the substrate via a support bar arrangement that suspends the integrated circuit over the substrate. The creation of this gap functions to release the device from the substrate and create a thermally-isolated integrated circuit.

Development of the self-learning machine for creating models of microprocessor of single-phase earth fault protection devices in networks with isolated neutral voltage above 1000 V

NASA Astrophysics Data System (ADS)

Utegulov, B. B.; Utegulov, A. B.; Meiramova, S.

2018-02-01

The paper proposes the development of a self-learning machine for creating models of microprocessor-based single-phase ground fault protection devices in networks with an isolated neutral voltage higher than 1000 V. Development of a self-learning machine for creating models of microprocessor-based single-phase earth fault protection devices in networks with an isolated neutral voltage higher than 1000 V. allows to effectively implement mathematical models of automatic change of protection settings. Single-phase earth fault protection devices.

Accelerated lifetime test of vibration isolator made of Metal Rubber material

NASA Astrophysics Data System (ADS)

Ao, Hongrui; Ma, Yong; Wang, Xianbiao; Chen, Jianye; Jiang, Hongyuan

2017-01-01

The Metal Rubber material (MR) is a kind of material with nonlinear damping characteristics for its application in the field of aerospace, petrochemical industry and so on. The study on the lifetime of MR material is impendent to its application in engineering. Based on the dynamic characteristic of MR, the accelerated lifetime experiments of vibration isolators made of MR working under random vibration load were conducted. The effects of structural parameters of MR components on the lifetime of isolators were studied and modelled with the fitting curves of degradation data. The lifetime prediction methods were proposed based on the models.

Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting.

PubMed

Purves, Kevin; Macintyre, Lynsey; Brennan, Debra; Hreggviðsson, Guðmundur Ó; Kuttner, Eva; Ásgeirsdóttir, Margrét E; Young, Louise C; Green, David H; Edrada-Ebel, Ruangelie; Duncan, Katherine R

2016-01-08

The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149-2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations.

Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting

PubMed Central

Purves, Kevin; Macintyre, Lynsey; Brennan, Debra; Hreggviðsson, Guðmundur Ó.; Kuttner, Eva; Ásgeirsdóttir, Margrét E.; Young, Louise C.; Green, David H.; Edrada-Ebel, Ruangelie; Duncan, Katherine R.

2016-01-01

The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149–2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations. PMID:26761036

Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers.

PubMed

Rafiei, Vahideh; Banihashemi, Ziaeddin; Bautista-Jalon, Laura S; Del Mar Jiménez-Gasco, Maria; Turgeon, B Gillian; Milgroom, Michael G

2018-06-01

Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B 824 ; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B 824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B 824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.

Phylogenetic identification of fungi isolated from the marine sponge Tethya aurantium and identification of their secondary metabolites.

PubMed

Wiese, Jutta; Ohlendorf, Birgit; Blümel, Martina; Schmaljohann, Rolf; Imhoff, Johannes F

2011-01-01

Fungi associated with the marine sponge Tethya aurantium were isolated and identified by morphological criteria and phylogenetic analyses based on internal transcribed spacer (ITS) regions. They were evaluated with regard to their secondary metabolite profiles. Among the 81 isolates which were characterized, members of 21 genera were identified. Some genera like Acremonium, Aspergillus, Fusarium, Penicillium, Phoma, and Trichoderma are quite common, but we also isolated strains belonging to genera like Botryosphaeria, Epicoccum, Parasphaeosphaeria, and Tritirachium which have rarely been reported from sponges. Members affiliated to the genera Bartalinia and Volutella as well as to a presumably new Phoma species were first isolated from a sponge in this study. On the basis of their classification, strains were selected for analysis of their ability to produce natural products. In addition to a number of known compounds, several new natural products were identified. The scopularides and sorbifuranones have been described elsewhere. We have isolated four additional substances which have not been described so far. The new metabolite cillifuranone (1) was isolated from Penicillium chrysogenum strain LF066. The structure of cillifuranone (1) was elucidated based on 1D and 2D NMR analysis and turned out to be a previously postulated intermediate in sorbifuranone biosynthesis. Only minor antibiotic bioactivities of this compound were found so far.

Morphological and molecular characterization of Fusarium. solani and F. oxysporum associated with crown disease of oil palm.

PubMed

Hafizi, R; Salleh, B; Latiffah, Z

2013-01-01

Crown disease (CD) is infecting oil palm in the early stages of the crop development. Previous studies showed that Fusarium species were commonly associated with CD. However, the identity of the species has not been resolved. This study was carried out to identify and characterize through morphological approaches and to determine the genetic diversity of the Fusarium species. 51 isolates (39%) of Fusarium solani and 40 isolates (31%) of Fusarium oxysporum were recovered from oil palm with typical CD symptoms collected from nine states in Malaysia, together with samples from Padang and Medan, Indonesia. Based on morphological characteristics, isolates in both Fusarium species were classified into two distinct morphotypes; Morphotypes I and II. Molecular characterization based on IGS-RFLP analysis produced 27 haplotypes among the F. solani isolates and 33 haplotypes for F. oxysporum isolates, which indicated high levels of intraspecific variations. From UPGMA cluster analysis, the isolates in both Fusarium species were divided into two main clusters with the percentage of similarity from 87% to 100% for F. solani, and 89% to 100% for F. oxysporum isolates, which was in accordance with the Morphotypes I and II. The results of the present study indicated that F. solani and F. oxysporum associated with CD of oil palm in Malaysia and Indonesia were highly variable.

Molecular evidence of Burkholderia pseudomallei genotypes based on geographical distribution.

PubMed

Zulkefli, Noorfatin Jihan; Mariappan, Vanitha; Vellasamy, Kumutha Malar; Chong, Chun Wie; Thong, Kwai Lin; Ponnampalavanar, Sasheela; Vadivelu, Jamuna; Teh, Cindy Shuan Ju

2016-01-01

Background. Central intermediary metabolism (CIM) in bacteria is defined as a set of metabolic biochemical reactions within a cell, which is essential for the cell to survive in response to environmental perturbations. The genes associated with CIM are commonly found in both pathogenic and non-pathogenic strains. As these genes are involved in vital metabolic processes of bacteria, we explored the efficiency of the genes in genotypic characterization of Burkholderia pseudomallei isolates, compared with the established pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) schemes. Methods. Nine previously sequenced B. pseudomallei isolates from Malaysia were characterized by PFGE, MLST and CIM genes. The isolates were later compared to the other 39 B. pseudomallei strains, retrieved from GenBank using both MLST and sequence analysis of CIM genes. UniFrac and hierachical clustering analyses were performed using the results generated by both MLST and sequence analysis of CIM genes. Results. Genetic relatedness of nine Malaysian B. pseudomallei isolates and the other 39 strains was investigated. The nine Malaysian isolates were subtyped into six PFGE profiles, four MLST profiles and five sequence types based on CIM genes alignment. All methods demonstrated the clonality of OB and CB as well as CMS and THE. However, PFGE showed less than 70% similarity between a pair of morphology variants, OS and OB. In contrast, OS was identical to the soil isolate, MARAN. To have a better understanding of the genetic diversity of B. pseudomallei worldwide, we further aligned the sequences of genes used in MLST and genes associated with CIM for the nine Malaysian isolates and 39 B. pseudomallei strains from NCBI database. Overall, based on the CIM genes, the strains were subtyped into 33 profiles where majority of the strains from Asian countries were clustered together. On the other hand, MLST resolved the isolates into 31 profiles which formed three clusters. Hierarchical clustering using UniFrac distance suggested that the isolates from Australia were genetically distinct from the Asian isolates. Nevertheless, statistical significant differences were detected between isolates from Malaysia, Thailand and Australia. Discussion. Overall, PFGE showed higher discriminative power in clustering the nine Malaysian B. pseudomallei isolates and indicated its suitability for localized epidemiological study. Compared to MLST, CIM genes showed higher resolution in distinguishing those non-related strains and better clustering of strains from different geographical regions. A closer genetic relatedness of Malaysian isolates with all Asian strains in comparison to Australian strains was observed. This finding was supported by UniFrac analysis which resulted in geographical segregation between Australia and the Asian countries.

Molecular Characterization of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae in the Countries of the Gulf Cooperation Council: Dominance of OXA-48 and NDM Producers

PubMed Central

Sartor, Anna L.; Balkhy, Hanan H.; Walsh, Timothy R.; Al Johani, Sameera M.; AlJindan, Reem Y.; Alfaresi, Mubarak; Ibrahim, Emad; Al-Jardani, Amina; Al-Abri, Seif; Al Salman, Jameela; Dashti, Ali A.; Kutbi, Abdullah H.; Schlebusch, Sanmarié; Sidjabat, Hanna E.; Paterson, David L.

2014-01-01

The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Enterobacteriaceae (CRE) were determined in hospitals in the countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic-resistant genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Sixty-two isolates which screened positive for potential carbapenemase production were assessed, and 45 were found to produce carbapenemase. The most common carbapenemases were of the OXA-48 (35 isolates) and NDM (16 isolates) types; 6 isolates were found to coproduce the OXA-48 and NDM types. No KPC-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with seven clusters of clonally related Klebsiella pneumoniae. Awareness of CRE in GCC countries has important implications for controlling the spread of CRE in the Middle East and in hospitals accommodating patients transferred from the region. PMID:24637692

Model-based fault detection and isolation for intermittently active faults with application to motion-based thruster fault detection and isolation for spacecraft

NASA Technical Reports Server (NTRS)

Wilson, Edward (Inventor)

2008-01-01

The present invention is a method for detecting and isolating fault modes in a system having a model describing its behavior and regularly sampled measurements. The models are used to calculate past and present deviations from measurements that would result with no faults present, as well as with one or more potential fault modes present. Algorithms that calculate and store these deviations, along with memory of when said faults, if present, would have an effect on the said actual measurements, are used to detect when a fault is present. Related algorithms are used to exonerate false fault modes and finally to isolate the true fault mode. This invention is presented with application to detection and isolation of thruster faults for a thruster-controlled spacecraft. As a supporting aspect of the invention, a novel, effective, and efficient filtering method for estimating the derivative of a noisy signal is presented.

Absolute quantification of olive oil DNA by droplet digital-PCR (ddPCR): Comparison of isolation and amplification methodologies.

PubMed

Scollo, Francesco; Egea, Leticia A; Gentile, Alessandra; La Malfa, Stefano; Dorado, Gabriel; Hernandez, Pilar

2016-12-15

Olive oil is considered a premium product for its nutritional value and health benefits, and the ability to define its origin and varietal composition is a key step towards ensuring the traceability of the product. However, isolating the DNA from such a matrix is a difficult task. In this study, the quality and quantity of olive oil DNA, isolated using four different DNA isolation protocols, was evaluated using the qRT-PCR and ddPCR techniques. The results indicate that CTAB-based extraction methods were the best for unfiltered oil, while Nucleo Spin-based extraction protocols showed greater overall reproducibility. The use of both qRT-PCR and ddPCR led to the absolute quantification of the DNA copy number. The results clearly demonstrate the importance of the choice of DNA-isolation protocol, which should take into consideration the qualitative aspects of DNA and the evaluation of the amplified DNA copy number. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of novel Theileria genotypes from Grant's gazelle

PubMed Central

Hooge, Janis; Howe, Laryssa; Ezenwa, Vanessa O.

2015-01-01

Blood samples collected from Grant's gazelles (Nanger granti) in Kenya were screened for hemoparasites using a combination of microscopic and molecular techniques. All 69 blood smears examined by microscopy were positive for hemoparasites. In addition, Theileria/Babesia DNA was detected in all 65 samples screened by PCR for a ~450-base pair fragment of the V4 hypervariable region of the 18S rRNA gene. Sequencing and BLAST analysis of a subset of PCR amplicons revealed widespread co-infection (25/39) and the existence of two distinct Grant's gazelle Theileria subgroups. One group of 11 isolates clustered as a subgroup with previously identified Theileria ovis isolates from small ruminants from Europe, Asia and Africa; another group of 3 isolates clustered with previously identified Theileria spp. isolates from other African antelope. Based on extensive levels of sequence divergence (1.2–2%) from previously reported Theileria species within Kenya and worldwide, the Theileria isolates detected in Grant's gazelles appear to represent at least two novel Theileria genotypes. PMID:25973394

Identification of novel Theileria genotypes from Grant's gazelle.

PubMed

Hooge, Janis; Howe, Laryssa; Ezenwa, Vanessa O

2015-08-01

Blood samples collected from Grant's gazelles (Nanger granti) in Kenya were screened for hemoparasites using a combination of microscopic and molecular techniques. All 69 blood smears examined by microscopy were positive for hemoparasites. In addition, Theileria/Babesia DNA was detected in all 65 samples screened by PCR for a ~450-base pair fragment of the V4 hypervariable region of the 18S rRNA gene. Sequencing and BLAST analysis of a subset of PCR amplicons revealed widespread co-infection (25/39) and the existence of two distinct Grant's gazelle Theileria subgroups. One group of 11 isolates clustered as a subgroup with previously identified Theileria ovis isolates from small ruminants from Europe, Asia and Africa; another group of 3 isolates clustered with previously identified Theileria spp. isolates from other African antelope. Based on extensive levels of sequence divergence (1.2-2%) from previously reported Theileria species within Kenya and worldwide, the Theileria isolates detected in Grant's gazelles appear to represent at least two novel Theileria genotypes.

Assessment of six different collagenase-based methods to isolate feline pancreatic islets.

PubMed

Zini, Eric; Franchini, Marco; Guscetti, Franco; Osto, Melania; Kaufmann, Karin; Ackermann, Mathias; Lutz, Thomas A; Reusch, Claudia E

2009-12-01

Isolation of pancreatic islets is necessary to study the molecular mechanisms underlying beta-cell demise in diabetic cats. Six collagenase-based methods of isolation were compared in 10 cat pancreata, including single and double course of collagenase, followed or not by Ficoll centrifugation or accutase, and collagenase plus accutase. Morphometric analysis was performed to measure the relative area of islet and exocrine tissue. Islet specific mRNA transcripts were quantified in isolates by real-time PCR. The single and double course of collagenase digestion was successful in each cat and provided similar islet-to-exocrine tissue ratio. Quantities of insulin mRNA did not differ between the two methods. However, on histological examination either method yielded only approximately 2% of pure islets. The other methods provided disrupted islets or insufficient samples in 1-7 cats. Although pancreas digestion with single and double course of collagenase was superior, further studies are needed to improve islet isolation in cats.

Bacteria contributing to behaviour of radiocarbon in sodium acetate.

PubMed

Ishii, Nobuyoshi; Uchida, Shigeo

2011-07-01

An acetate-utilising bacterium was isolated and identified from deionised water that was used for flooding of paddy soils in this study's batch culture experiments. Bacteria in the deionised water samples formed colonies on agar plates containing [1,2-(14)C] sodium acetate, and the autoradiograms showed that all the colonies were positive for (14)C utilisation. Then one of the acetate-utilising bacteria was isolated. The isolate was characterised by phylogenetic analysis, cell morphology, Gram staining and growth at 30 °C. Phylogenetic analysis based on 16S rRNA sequencing showed that the isolate belonged to the genus Burkholderia. The bacterium was gram-negative rods and grew at 30 °C under aerobic conditions. Based on these characteristics, the isolate was identified as Burkholderia gladioli. Because B. gladioli is often found in soil, water and the rhizosphere, attention must be paid to the relationships between bacteria and the behaviour of (14)C to for the safety assessment of geological disposal of transuranic waste.

Phenotypic and genetic characterizations of Streptococcus dysgalactiae strains isolated from fish collected in Japan and other Asian countries.

PubMed

Abdelsalam, Mohamed; Chen, Shih-Chu; Yoshida, Terutoyo

2010-01-01

Lancefield group C Streptococcus dysgalactiae is an emerging fish pathogen, which was first isolated in 2002 in Japan. Streptococcus dysgalactiae isolates collected from diseased fish in Japan (n=12), Taiwan (n=12), China (n=2), Malaysia (n=3), and Indonesia (n=1) were characterized using biased sinusoidal field gel electrophoresis (BSFGE), sodA gene sequence analysis, and antimicrobial susceptibility. These isolates exhibited high phenotypic homogeneity irrespective of the countries from where the strains were collected. Seventeen isolates were found to be resistant to oxytetracycline and carried the tet(M) gene, except for the strains collected in Taiwan and the PP1564 strain collected in China. The sodA gene sequence analysis revealed that 23 isolates were identical, except for one Japanese isolate (KNH07902), in which a single nucleotide differed from that of the other isolates. Based on BSFGE typing by ApaI macrorestriction, the isolates - including the Japanese, Taiwanese, and Chinese isolates - could be grouped into one main cluster at a 70% similarity level. However, the macrorestriction genotypes of some isolates were apparently distinct from those of the main cluster.

Fault detection and isolation

NASA Technical Reports Server (NTRS)

Bernath, Greg

1994-01-01

In order for a current satellite-based navigation system (such as the Global Positioning System, GPS) to meet integrity requirements, there must be a way of detecting erroneous measurements, without help from outside the system. This process is called Fault Detection and Isolation (FDI). Fault detection requires at least one redundant measurement, and can be done with a parity space algorithm. The best way around the fault isolation problem is not necessarily isolating the bad measurement, but finding a new combination of measurements which excludes it.

Detailed molecular analyses of the hexon loop-1 and fibers of fowl aviadenoviruses reveal new insights into the antigenic relationship and confirm that specific genotypes are involved in field outbreaks of inclusion body hepatitis.

PubMed

Schachner, Anna; Marek, Ana; Grafl, Beatrice; Hess, Michael

2016-04-15

Forty-eight fowl aviadenoviruses (FAdVs) isolated from recent IBH outbreaks across Europe were investigated, by utilizing for the first time the two major adenoviral antigenic domains, hexon loop-1 and fiber, for compound molecular characterization of IBH-associated FAdVs. Successful target gene amplification, following virus isolation in cell culture or from FTA-card samples, demonstrated presence of FAdVs in all cases indicative for IBH. Based on hexon loop-1 analysis, 31 European field isolates exhibited highest nucleotide identity (>97.2%) to reference strains FAdV-2 or -11 representing FAdV-D, while 16 and one European isolates shared >96.0% nucleotide identity with FAdV-8a and -8b, or FAdV-7, the prototype strains representing FAdV-E. These results extend recognition of specific FAdV-D and FAdV-E affiliate genotypes as causative agents of IBH to the European continent. In all isolates, species specificity determined by fiber gene analysis correlated with hexon-based typing. A threshold of 72.0% intraspecies nucleotide identity between fibers from investigated prototype and field strains corresponded with demarcation criteria proposed for hexon, suggesting fiber-based analysis as a complementary tool for molecular FAdV typing. A limited number of strains exhibited inconsistencies between hexon and fiber subclustering, indicating potential constraints for single-gene based typing of those FAdVs. Within FAdV-D, field isolate fibers shared a high degree of nucleotide (>96.7%) and aa (>95.8%) identity, while FAdV-E field isolate fibers displayed greater nucleotide divergence of up to 22.6%, resulting in lower aa identities of >81.7%. Furthermore, comparison with FAdVs from IBH outbreaks outside Europe revealed close genetic relationship in the fiber, independent of the strains' geographic origin. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparing genome versus proteome-based identification of clinical bacterial isolates.

PubMed

Galata, Valentina; Backes, Christina; Laczny, Cédric Christian; Hemmrich-Stanisak, Georg; Li, Howard; Smoot, Laura; Posch, Andreas Emanuel; Schmolke, Susanne; Bischoff, Markus; von Müller, Lutz; Plum, Achim; Franke, Andre; Keller, Andreas

2018-05-01

Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard', the expert-driven taxonomy was compared with identifications based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis. Additionally, the tools were also evaluated using a data set of 200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31) performed best with 626 (100%) and 193 (99.5%) correct species classifications for the gram-negative and S. aureus isolates, respectively. Moreover, CLARK and Kraken demonstrated highest mean F-measure values (85.5/87.9% and 94.4/94.7% for the two data sets, respectively) in comparison with DIAMOND/MEGAN (71 and 85.3%), Kaiju (41.8 and 18.9%) and TUIT (34.5 and 86.5%). Finally, CLARK, Kaiju and Kraken outperformed the other tools by a factor of 30 to 170 fold in terms of runtime.We conclude that the application of nucleotide-based tools using k-mers-e.g. CLARK or Kraken-allows for accurate and fast taxonomic characterization of bacterial isolates from WGS data. Hence, our results suggest WGS-based genotyping to be a promising alternative to the MS-based biotyping in clinical settings. Moreover, we suggest that complementary information should be used for the evaluation of taxonomic classification tools, as public databases may suffer from suboptimal annotations.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolates in the Gulf Cooperation Council States: Dominance of OXA-23-Type Producers

PubMed Central

Sartor, Anna L.; Sidjabat, Hanna E.; Balkhy, Hanan H.; Walsh, Timothy R.; Al Johani, Sameera M.; AlJindan, Reem Y.; Alfaresi, Mubarak; Ibrahim, Emad; Al-Jardani, Amina; Al Salman, Jameela; Dashti, Ali A.; Johani, Khalid; Paterson, David L.

2015-01-01

The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic resistance genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Selected isolates were subjected to multilocus sequence typing (MLST). We investigated 117 isolates resistant to carbapenem antibiotics (either imipenem or meropenem). All isolates were positive for OXA-51. The most common carbapenemases were the OXA-23-type, found in 107 isolates, followed by OXA-40-type (OXA-24-type), found in 5 isolates; 3 isolates carried the ISAba1 element upstream of blaOXA-51-type. No OXA-58-type, NDM-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with 16 clusters of clonally related CRAB. Some clusters involved hospitals in different states. MLST analysis of 15 representative isolates from different clusters identified seven different sequence types (ST195, ST208, ST229, ST436, ST450, ST452, and ST499), as well as three novel STs. The vast majority (84%) of the isolates in this study were associated with health care exposure. Awareness of multidrug-resistant organisms in GCC states has important implications for optimizing infection control practices; establishing antimicrobial stewardship programs within hospital, community, and agricultural settings; and emphasizing the need for establishing regional active surveillance systems. This will help to control the spread of CRAB in the Middle East and in hospitals accommodating transferred patients from this region. PMID:25568439

Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolates in the Gulf Cooperation Council States: dominance of OXA-23-type producers.

PubMed

Zowawi, Hosam M; Sartor, Anna L; Sidjabat, Hanna E; Balkhy, Hanan H; Walsh, Timothy R; Al Johani, Sameera M; AlJindan, Reem Y; Alfaresi, Mubarak; Ibrahim, Emad; Al-Jardani, Amina; Al Salman, Jameela; Dashti, Ali A; Johani, Khalid; Paterson, David L

2015-03-01

The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic resistance genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Selected isolates were subjected to multilocus sequence typing (MLST). We investigated 117 isolates resistant to carbapenem antibiotics (either imipenem or meropenem). All isolates were positive for OXA-51. The most common carbapenemases were the OXA-23-type, found in 107 isolates, followed by OXA-40-type (OXA-24-type), found in 5 isolates; 3 isolates carried the ISAba1 element upstream of blaOXA-51-type. No OXA-58-type, NDM-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with 16 clusters of clonally related CRAB. Some clusters involved hospitals in different states. MLST analysis of 15 representative isolates from different clusters identified seven different sequence types (ST195, ST208, ST229, ST436, ST450, ST452, and ST499), as well as three novel STs. The vast majority (84%) of the isolates in this study were associated with health care exposure. Awareness of multidrug-resistant organisms in GCC states has important implications for optimizing infection control practices; establishing antimicrobial stewardship programs within hospital, community, and agricultural settings; and emphasizing the need for establishing regional active surveillance systems. This will help to control the spread of CRAB in the Middle East and in hospitals accommodating transferred patients from this region. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Molecular characterization of infectious bursal disease virus isolates from Nepal based on hypervariable region of VP2 gene.

PubMed

Sharma, K; Hair-Bejo, M; Omar, A R; Aini, I

2005-01-01

Two Infectious bursal disease virus (IBDV) isolates, NP1SSH and NP2K were obtained from a severe infectious bursal disease (IBD) outbreak in Nepal in 2002. The hypervariable (HV) region of VP2 gene (1326 bp) of the isolates was generated by RT-PCR and sequenced. The obtained nucleotide sequences were compared with those of twenty other IBDV isolates/strains. Phylogenetic analysis based on this comparison revealed that NP1SSH and NP2K clustered with very virulent (vv) IBDV strains of serotype 1. In contrast, classical, Australian classical and attenuated strains of serotype 1 and avirulent IBDV strains of serotype 2 formed a different cluster. The deduced amino acid sequences of the two isolates showed a 98.3% identity with each other and 97.1% and 98.3% identities, respectively with very virulent IBDV (vvIBDV) isolates/strains. Three amino acids substitutions at positions 300 (E-->A), 308 (I-->F) and 334 (A-->P) within the HV region were common for both the isolates. The amino acids substitutions at positions 27 (S-->T), 28 (I-->T), 31 (D-->A), 36 (H-->Y), 135 (E-->G), 223 (G-->S), 225 (V-->I), 351 (L-->I), 352 (V-->E) and 399 (I-->S) for NP1SSH and at position 438 (I-->S) for NP2K were unique and differed from other IBDV isolates/strains. NP1SSH and NP2K showed highest similarity (97.8%) with the BD399 strain from Bangladesh as compared with other vvIBDV isolates/strains. We conclude that the NP1SSH and NP2K isolates of IBDV from Nepal represent vvIBDV of serotype 1.

Two distinct Epichloë species symbiotic with Achnatherum inebrians, drunken horse grass.

PubMed

Chen, Li; Li, Xiuzhang; Li, Chunjie; Swoboda, Ginger A; Young, Carolyn A; Sugawara, Koya; Leuchtmann, Adrian; Schardl, Christopher L

2015-01-01

Achnatherum inebrians, colloquially known as drunken horse grass, is associated with livestock toxicity in northern China. Epichloë gansuensis (Eg) was described from endophyte isolates from A. inebrians in Sunan County, Gansu Province, whereas a morphologically distinct variety, E. gansuensis var. inebrians (Ei), was described based on two isolates from A. inebrians seeds collected in Urumqi County, Xinjiang Province. Genome sequencing and alkaloid analyses also distinguish these taxa; the Ei isolates produce neurotropic lysergic acid amides (ergot alkaloids), and an Eg isolate produces paxilline (an indole-diterpene alkaloid). To better elucidate the taxonomic diversity of Epichloë spp. symbiotic with A. inebrians, we surveyed eight populations in Xinjiang, Gansu and Inner Mongolia provinces of China and analyzed their genotypes by multiplex PCR for alkaloid biosynthesis genes and mating-type genes. Genotypes consistent with Ei were present in all eight populations, of which they dominated seven. The Ei isolates were all mating type A and tested positive for the ergot alkaloid gene, dmaW. In contrast Eg isolates were all mating type B and had the indole-diterpene gene, idtG. The genome was sequenced from an Ei isolate from seeds collected in Xiahe County, Gansu, and compared to that of the varietal ex type isolate from Urumqi. Alkaloid genes and four different housekeeping genes were nearly identical between the two sequenced Ei isolates and were distinct from a sequenced Eg isolate. Phylogenetic analysis placed Ei, Eg and Epichloë sibirica into respective subclades of a clade that emanated from the base of the Epichloë phylogeny. Given its chemotypic, genotypic, morphological and phylogenetic distinctiveness, its widespread occurrence in rangelands of northern China, and its importance in livestock toxicity, we propose raising Ei to species rank as Epichloë inebrians. © 2015 by The Mycological Society of America.

Antibiotic resistance and molecular typing among cockle (Anadara granosa) strains of Vibrio parahaemolyticus by polymerase chain reaction (PCR)-based analysis.

PubMed

Sahilah, A M; Laila, R A S; Sallehuddin, H Mohd; Osman, H; Aminah, A; Ahmad Azuhairi, A

2014-02-01

Genomic DNA of Vibrio parahaemolyticus were characterized by antibiotic resistance, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis. These isolates originated from 3 distantly locations of Selangor, Negeri Sembilan and Melaka (East coastal areas), Malaysia. A total of 44 (n = 44) of tentatively V. parahaemolyticus were also examined for the presence of toxR, tdh and trh gene. Of 44 isolates, 37 were positive towards toxR gene; while, none were positive to tdh and trh gene. Antibiotic resistance analysis showed the V. parahaemolyticus isolates were highly resistant to bacitracin (92%, 34/37) and penicillin (89%, 33/37) followed by resistance towards ampicillin (68%, 25/37), cefuroxime (38%, 14/37), amikacin (6%, 2/37) and ceftazidime (14%, 5/37). None of the V. parahaemolyticus isolates were resistant towards chloramphenicol, ciprofloxacin, ceftriaxone, enrofloxacin, norfloxacin, streptomycin and vancomycin. Antibiogram patterns exhibited, 9 patterns and phenotypically less heterogenous when compared to PCR-based techniques using ERIC- and RAPD-PCR. The results of the ERIC- and RAPD-PCR were analyzed using GelCompare software. ERIC-PCR with primers ERIC1R and ERIC2 discriminated the V. parahaemolyticus isolates into 6 clusters and 21 single isolates at a similarity level of 80%. While, RAPD-PCR with primer Gen8 discriminated the V. parahaemolyticus isolates into 11 clusters and 10 single isolates and Gen9 into 8 clusters and 16 single isolates at the same similarity level examined. Results in the presence study demonstrated combination of phenotypically and genotypically methods show a wide heterogeneity among cockle isolates of V. parahaemolyticus.

Isolation, characterization and exploring biotechnological potential of halophilic archaea from salterns of western India.

PubMed

Singh, Aparna; Singh, Anil Kumar

2018-01-01

Thirteen halophilic archaea were isolated from Kandla and Bhayander salt pans. These isolates were grouped into three different genera Halobacterium, Haloferax and Haloarcula based on morphological and biochemical characterization, polar lipid analysis, Amplified 16S rDNA restriction analysis (ARDRA) and 16S rDNA sequence analysis. Biochemical characterization suggested the ability of isolates to produce protease, amylase and poly-hydroxybutyrate (PHB) indicating their biotechnological potential. The isolates were further screened for the amount of extracellular protease produced. Halobacterium sp. SP1(1) showed significant protease production compared to other isolates. Protease producing ability of the isolate was influenced by several factors such as NaCl concentration, type of protein source, metal ions and surfactants, and presence of amino acid supplements in the production medium. Soybean flour, FeCl 3 and dicotylsulfosuccinate were found to increase protease production by 2.36, 1.54 and 1.26 folds, respectively compared to production in basal medium. Effect of organic solvents used in paints (n-decane, n-undecane and n-dodecane) was also investigated on protease production by the isolate. Protease production by Halobacterium sp. SP1(1) was enhanced by 1.2 folds in presence of n-decane compared to control. Furthermore, the ability of isolate to hydrolyse fish protein was investigated using three different edible fishes (Pomfret, Flat fish and Seer fish) as sole protein source. Pomfret was found to be a good protein source for protease production by the isolate. These results revealed that Halobacterium sp. SP1(1) may have potential for paint-based antifouling coating preparations and fish sauce preparation by virtue of its extracellular protease.

Isolation of Streptococcus pyogenes from children with pharyngitis and emm type analysis.

PubMed

Khosravi, Azar D; Ebrahimifard, Nasim; Shamsizadeh, Ahmad; Shoja, Saeed

2016-05-01

The group A streptococcus (GAS) M protein, encoded by the emm gene, acts as a major virulence factor. Emm-typing is the GAS gold standard molecular typing and is based on the DNA sequence of the nucleotides of the emm gene. The aim of the present study was to isolate GAS from patients and to detect the emm types of the isolates using emm typing. A total of 1000 throat samples were collected from patients with pharyngitis referred to Aboozar Children's Hospital in Ahvaz, Iran. We performed antimicrobial susceptibility testing on all isolates using the Kirby-Bauer disk diffusion method. Additionally, amplification of the emm gene was performed using polymerase chain reaction using the standard primers and described protocol. From all throat samples screened, 25 isolates (2.5%) were identified as GAS. Antibiotic susceptibility testing revealed that all the GAS isolates were susceptible to penicillin and erythromycin, but 44% showed resistance to vancomycin. Based on polymerase chain reaction for the emm gene, the obtained emm types were: emm-3, observed in 20 isolates (80%); emm-1 observed in four isolates (16%); and emm-75 observed in one isolate (4%). The result of the present study showed that penicillin and erythromycin are still the most effective antibiotics against the organism. The emm typing revealed that emm type-3 was detected in most of the isolates from patients with purulent pharyngitis. On the basis of the findings of this study, we may conclude that emm typing provides new insights on the genetic diversity of the M proteins, and is of demonstrable value for molecular studies of GAS. Copyright © 2016. Published by Elsevier Taiwan LLC.

Costs and benefits of rapid screening of methicillin-resistant Staphylococcus aureus carriage in intensive care units: a prospective multicenter study

PubMed Central

2012-01-01

Introduction Pre-emptive isolation of suspected methicillin-resistant Staphylococcus aureus (MRSA) carriers is a cornerstone of successful MRSA control policies. Implementation of such strategies is hampered when using conventional cultures with diagnostic delays of three to five days, as many non-carriers remain unnecessarily isolated. Rapid diagnostic testing (RDT) reduces the amount of unnecessary isolation days, but costs and benefits have not been accurately determined in intensive care units (ICUs). Methods Embedded in a multi-center hospital-wide study in 12 Dutch hospitals we quantified cost per isolation day avoided using RDT for MRSA, added to conventional cultures, in ICUs. BD GeneOhm™ MRSA PCR (IDI) and Xpert MRSA (GeneXpert) were subsequently used during 17 and 14 months, and their test characteristics were calculated with conventional culture results as reference. We calculated the number of pre-emptive isolation days avoided and incremental costs of adding RDT. Results A total of 163 patients at risk for MRSA carriage were screened and MRSA prevalence was 3.1% (n = 5). Duration of isolation was 27.6 and 21.4 hours with IDI and GeneXpert, respectively, and would have been 96.0 hours when based on conventional cultures. The negative predictive value was 100% for both tests. Numbers of isolation days were reduced by 44.3% with PCR-based screening at the additional costs of €327.84 (IDI) and €252.14 (GeneXpert) per patient screened. Costs per isolation day avoided were €136.04 (IDI) and €121.76 (GeneXpert). Conclusions In a low endemic setting for MRSA, RDT safely reduced the number of unnecessary isolation days on ICUs by 44%, at the costs of €121.76 to €136.04 per isolation day avoided. PMID:22314204

Phenotypic and molecular characterizations of Yersinia pestis isolates from Kazakhstan and adjacent regions.

PubMed

Lowell, Jennifer L; Zhansarina, Aigul; Yockey, Brook; Meka-Mechenko, Tatyana; Stybayeva, Gulnaz; Atshabar, Bakyt; Nekrassova, Larissa; Tashmetov, Rinat; Kenghebaeva, Kuralai; Chu, May C; Kosoy, Michael; Antolin, Michael F; Gage, Kenneth L

2007-01-01

Recent interest in characterizing infectious agents associated with bioterrorism has resulted in the development of effective pathogen genotyping systems, but this information is rarely combined with phenotypic data. Yersinia pestis, the aetiological agent of plague, has been well defined genotypically on local and worldwide scales using multi-locus variable number tandem repeat analysis (MLVA), with emphasis on evolutionary patterns using old isolate collections from countries where Y. pestis has existed the longest. Worldwide MLVA studies are largely based on isolates that have been in long-term laboratory culture and storage, or on field material from parts of the world where Y. pestis has potentially circulated in nature for thousands of years. Diversity in these isolates suggests that they may no longer represent the wild-type organism phenotypically, including the possibility of altered pathogenicity. This study focused on the phenotypic and genotypic properties of 48 Y. pestis isolates collected from 10 plague foci in and bordering Kazakhstan. Phenotypic characterization was based on diagnostic tests typically performed in reference laboratories working with Y. pestis. MLVA was used to define the genotypic relationships between the central-Asian isolates and a group of North American isolates, and to examine Kazakh Y. pestis diversity according to predefined plague foci and on an intermediate geographical scale. Phenotypic properties revealed that a large portion of this collection lacks one or more plasmids necessary to complete the blocked flea/mammal transmission cycle, has lost Congo red binding capabilities (Pgm-), or both. MLVA analysis classified isolates into previously identified biovars, and in some cases groups of isolates collected within the same plague focus formed a clade. Overall, MLVA did not distinguish unique phylogeographical groups of Y. pestis isolates as defined by plague foci and indicated higher genetic diversity among older biovars.

Optimum design of bridges with superelastic-friction base isolators against near-field earthquakes

NASA Astrophysics Data System (ADS)

Ozbulut, Osman E.; Hurlebaus, Stefan

2010-04-01

The seismic response of a multi-span continuous bridge isolated with novel superelastic-friction base isolator (S-FBI) is investigated under near-field earthquakes. The isolation system consists of a flat steel-Teflon sliding bearing and a superelastic NiTi shape memory alloy (SMA) device. Sliding bearings limit the maximum seismic forces transmitted to the superstructure to a certain value that is a function of friction coefficient of sliding interface. Superelastic SMA device provides restoring capability to the isolation system together with additional damping characteristics. The key design parameters of an S-FBI system are the natural period of the isolated, yielding displacement of SMA device, and the friction coefficient of the sliding bearings. The goal of this study is to obtain optimal values for each design parameter by performing sensitivity analyses of the isolated bridge. First, a three-span continuous bridge is modeled as a two-degrees-of-freedom with S-FBI system. A neuro-fuzzy model is used to capture rate-dependent nonlinear behavior of SMA device. A time-dependent method which employs wavelets to adjust accelerograms to match a target response spectrum with minimum changes on the other characteristics of ground motions is used to generate ground motions used in the simulations. Then, a set of nonlinear time history analyses of the isolated bridge is performed. The variation of the peak response quantities of the isolated bridge is shown as a function of design parameters. Also, the influence of temperature variations on the effectiveness of S-FBI system is evaluated. The results show that the optimum design of the isolated bridge with S-FBI system can be achieved by a judicious specification of design parameters.

Comparative genomic analysis of two isolates of Vibrio cholerae O1 Ogawa El Tor isolated during outbreak in Mariupol in 2011.

PubMed

Kuleshov, Konstantin V; Kostikova, Anna; Pisarenko, Sergey V; Kovalev, Dmitry A; Tikhonov, Sergey N; Savelievа, Irina V; Saveliev, Vilory N; Vasilieva, Oksana V; Zinich, Liliia S; Pidchenko, Nadiia N; Kulichenko, Alexander N; Shipulin, German A

2016-10-01

Cholera is a water-borne, severe enteric infection essentially caused by toxigenic strains of Vibrio cholera O1 and O139 serogroups. An outbreak of cholera was registered during May-July 2011 in Mariupol, Ukraine, with 33 cholera cases and 25 carriers of cholera. Following this outbreak, the toxigenic strain of V. cholerae 2011EL-301 was isolated from seawater in the recreation area of Taganrog city on the territory of Russia. The aim of our study was to understand genomic features of Mariupol isolates as well as to evaluate hypothesis about possible interconnection between the outbreak of cholera in Mariupol and the single case of isolation of V. cholerae from the Sea of Azov in Russia. Mariupol isolates were phenotypically characterized and subsequently subjected to whole genome sequencing procedure. Phylogenetic analysis based on high-quality SNPs of V. cholera O1 El Tor isolates of the 7th pandemic clade from different regions showed that clinical and environmental isolates from Mariupol outbreak were attributable to a unique phylogenetic clade within wave 3 of V. cholera O1 El Tor isolates and characterized by six clade-specific SNPs. Whereas Taganrog isolate belonged to distantly related clade which allows us to reject the hypothesis of transmission the outbreak strain of V. cholerae O1 from Ukraine to Russia in 2011. Mariupol isolates shared a common ancestor with Haiti\\Nepal-4\\India clade indicating that outbreak progenitor strain most likely originated in the South Asia region and later was introduced to Ukraine. Moreover, genomic data both based on hqSNPs and similarity of virulence-associated mobile genomic elements of Mariupol isolates suggests that environmental and clinical isolates are a part of joint outbreak which confirms the role of contaminated domestic sewage, as an element of the complex chain of infection spread during cholera outbreak. In general, the genome-wide comparative analysis of both genes and genomic regions of epidemiological importance indicates accessory of this isolates to 'new' clone of toxigenic multiple drug resistance atypical variant of V. cholerae O1 El Tor. Copyright © 2016 Elsevier B.V. All rights reserved.

High frequency of silver resistance genes in invasive isolates of Enterobacter and Klebsiella species.

PubMed

Sütterlin, S; Dahlö, M; Tellgren-Roth, C; Schaal, W; Melhus, Å

2017-07-01

Silver-based products have been marketed as an alternative to antibiotics, and their consumption has increased. Bacteria may, however, develop resistance to silver. To study the presence of genes encoding silver resistance (silE, silP, silS) over time in three clinically important Enterobacteriaceae genera. Using polymerase chain reaction (PCR), 752 bloodstream isolates from the years 1990-2010 were investigated. Age, gender, and ward of patients were registered, and the susceptibility to antibiotics and silver nitrate was tested. Clonality and single nucleotide polymorphism were assessed with repetitive element sequence-based PCR, multi-locus sequence typing, and whole-genome sequencing. Genes encoding silver resistance were detected most frequently in Enterobacter spp. (48%), followed by Klebsiella spp. (41%) and Escherichia coli 4%. Phenotypical resistance to silver nitrate was found in Enterobacter (13%) and Klebsiella (3%) isolates. The lowest carriage rate of sil genes was observed in blood isolates from the neonatology ward (24%), and the highest in blood isolates from the oncology/haematology wards (66%). Presence of sil genes was observed in international high-risk clones. Sequences of the sil and pco clusters indicated that a single mutational event in the silS gene could have caused the phenotypic resistance. Despite a restricted consumption of silver-based products in Swedish health care, silver resistance genes are widely represented in clinical isolates of Enterobacter and Klebsiella species. To avoid further selection and spread of silver-resistant bacteria with a high potential for healthcare-associated infections, the use of silver-based products needs to be controlled and the silver resistance monitored. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Nonlinear damping based semi-active building isolation system

NASA Astrophysics Data System (ADS)

Ho, Carmen; Zhu, Yunpeng; Lang, Zi-Qiang; Billings, Stephen A.; Kohiyama, Masayuki; Wakayama, Shizuka

2018-06-01

Many buildings in Japan currently have a base-isolation system with a low stiffness that is designed to shift the natural frequency of the building below the frequencies of the ground motion due to earthquakes. However, the ground motion observed during the 2011 Tohoku earthquake contained strong long-period waves that lasted for a record length of 3 min. To provide a novel and better solution against the long-period waves while maintaining the performance of the standard isolation range, the exploitation of the characteristics of nonlinear damping is proposed in this paper. This is motivated by previous studies of the authors, which have demonstrated that nonlinear damping can achieve desired performance over both low and high frequency regions and the optimal nonlinear damping force can be realized by closed loop controlled semi-active dampers. Simulation results have shown strong vibration isolation performance on a building model with identified parameters and have indicated that nonlinear damping can achieve low acceleration transmissibilities round the structural natural frequency as well as the higher ground motion frequencies that have been frequently observed during most earthquakes in Japan. In addition, physical building model based laboratory experiments are also conducted, The results demonstrate the advantages of the proposed nonlinear damping technologies over both traditional linear damping and more advanced Linear-Quadratic Gaussian (LQG) feedback control which have been used in practice to address building isolation system design and implementation problems. In comparison with the tuned-mass damper and other active control methods, the proposed solution offers a more pragmatic, low-cost, robust and effective alternative that can be readily installed into the base-isolation system of most buildings.

Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere.

PubMed

Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

2016-01-01

The use of Trichoderma isolates with efficient antagonistic activity represents a potentially effective and alternative disease management strategy to replace health hazardous chemical control. In this context, twenty isolates were obtained from tomato rhizosphere and evaluated by their antagonistic activity against four fungal pathogens ( Fusarium oxysporum f. sp. lycopersici , Alternaria alternata , Colletotrichum gloeosporoides and Rhizoctonia solani ). The production of extracellular cell wall degrading enzymes of tested isolates was also measured. All the isolates significantly reduced the mycelial growth of tested pathogens but the amount of growth reduction varied significantly as well. There was a positive correlation between the antagonistic capacity of Trichoderma isolates towards fungal pathogens and their lytic enzyme production. The Trichoderma isolates were initially sorted according to morphology and based on the translation elongation factor 1-α gene sequence similarity, the isolates were designated as Trichoderma harzianum , T. koningii , T. asperellum , T. virens and T. viride . PCA analysis explained 31.53, 61.95, 62.22 and 60.25% genetic variation among Trichoderma isolates based on RAPD, REP-, ERIC- and BOX element analysis, respectively. ERG - 1 gene, encoding a squalene epoxidase has been used for the first time for diversity analysis of antagonistic Trichoderma from tomato rhizosphere. Phylogenetic analysis of ERG -1 gene sequences revealed close relatedness of ERG -1sequences with earlier reported sequences of Hypocrea lixii , T. arundinaceum and T. reesei. However, ERG -1 gene also showed heterogeneity among some antagonistic isolates and indicated the possibility of occurrence of squalene epoxidase driven triterpene biosynthesis as an alternative biocontrol mechanism in Trichoderma species.

Selection of appropriate isolation method based on morphology of blastocyst for efficient derivation of buffalo embryonic stem cells.

PubMed

Kumar, R; Ahlawat, S P S; Sharma, M; Verma, O P; Sai Kumar, G; Taru Sharma, G

2014-03-01

The efficiency of embryonic stem cell (ESC) derivation from all species except for rodents and primates is very low. There are however, multiple interests in obtaining pluripotent cells from these animals with main expectations in the fields of transgenesis, cloning, regenerative medicine and tissue engineering. Researches are being carried out in laboratories throughout the world to increase the efficiency of ESC isolation for their downstream applications. Thus, the present study was undertaken to study the effect of different isolation methods based on the morphology of blastocyst for efficient derivation of buffalo ESCs. Embryos were produced in vitro through the procedures of maturation, fertilization and culture. Hatched blastocysts or isolated inner cell masses (ICMs) were seeded on mitomycin-C inactivated buffalo fetal fibroblast monolayer for the development of ESC colonies. The ESCs were analyzed for alkaline phosphatase activity, expression of pluripotency markers and karyotypic stability. Primary ESC colonies were obtained after 2-5 days of seeding hatched blastocysts or isolated ICMs on mitomycin-C inactivated feeder layer. Mechanically isolated ICMs attached and formed primary cell colonies more efficiently than ICMs isolated enzymatically. For derivation of ESCs from poorly defined ICMs intact hatched blastocyst culture was the most successful method. Results of this study implied that although ESCs can be obtained using all three methods used in this study, efficiency varies depending upon the morphology of blastocyst and isolation method used. So, appropriate isolation method must be selected depending on the quality of blastocyst for efficient derivation of ESCs.

Characterization of parasporin gene harboring Indian isolates of Bacillus thuringiensis.

PubMed

Lenina, N K; Naveenkumar, A; Sozhavendan, A E; Balakrishnan, N; Balasubramani, V; Udayasuriyan, V

2014-10-01

Bacillus thuringiensis (Bt) is popularly known as insecticidal bacterium. However, non-insecticidal Bt strains are more extensively available in natural environment than the insecticidal ones. Parasporin (PS) is a collection of genealogically heterogeneous Cry proteins synthesized in non-insecticidal isolates of Bt. An important character generally related with PS proteins is their strong cytocidal activity preferentially on human cancer cells of various origins. Identification and characterization of novel parasporin protein which are non-hemolytic and non-insecticidal but having selective anticancer activity raise the possibility of a novel application of Bt in medical field. In the present study, seven new indigenous isolates (T6, T37, T68, T98, T165, T186, and T461) of Bt showed variation in colony morphology, crystal characters and protein profiles with each other. Out of the seven new isolates screened for parasporin (ps) and cry genes, two of the new indigenous isolates (T98 and T186) of Bt showed the presence of ps4 gene. Partial ps4 gene was cloned from the two new isolates and the sequence of partial ps4 gene showed high homology with its holotype ps4Aa1. These two isolates were characterized based on the proteolytic processing of the inclusion proteins and the proteolytic products were found to be comparable to the PS4 reference strain A1470. The two isolates of Bt did not show toxicity toward Spodoptera litura and Helicoverpa armigera. Based on the results of this study, it can be concluded that the isolates T98 and T186 are parasporin producers.

Effect of severe weather events on the shedding of Shiga toxigenic Escherichia coli in slaughter cattle and phenotype of serogroup O157 isolates.

PubMed

Stanford, Kim; Reuter, Tim; Bach, Susan J; Chui, Linda; Ma, Angela; Conrad, Cheyenne C; Tostes, Renata; McAllister, Tim A

2017-09-01

High-event periods (HEPs) occur sporadically when beef carcasses and meat have episodes of acute contamination with Shiga toxin-producing Escherichia coli (STEC). In this study, severe weather events were investigated as catalysts for HEPs based on PCR and isolate prevalence of seven E. coli serogroups in slaughter cattle feces. Winter ambient temperatures with daily means 10.5oC warmer or 12.3°C colder than seasonal norms (-10.4°C) most altered STEC shedding. Fecal samples yielded increased proportions (P < 0.05) of O26 and O157 isolates during winter warm periods, and reduced (P < 0.05) O45 isolates during cold periods compared to samplings during seasonal norms. Based on changing PCR prevalence and isolates collected, O157 was the serogroup most responsive to severe weather events. Consequently, O157 isolates (n = 219) were evaluated for heat resistance, biofilm-forming potential and virulence gene subtypes. Two isolates had heat-resistant phenotypes with thermal death time at 60°C (D60) > 10 min and one also had strong biofilm-forming potential. However, this isolate lacked eae and stx genes. Severe weather can influence STEC shedding, particularly of O157, and could possibly trigger HEPs. However, our data suggest that it is unlikely for isolates to carry virulence genes and possess phenotypes capable of evading post-harvest microbiological interventions. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Isolation, molecular characterization and an artificial infection model for a variant porcine epidemic diarrhea virus strain from Jiangsu Province, China.

PubMed

Zhang, Hewei; Xia, Mingqi; Ju, Decai; Wu, Bai; Ning, Chen; Song, Ni; Feng, Teng; Chen, Feng; Wang, Xin; Wu, Ying; Wang, Wei; Cheng, Shipeng; Jin, Wenjie; Zhang, Shucheng; Zhang, Chunjie; Cheng, Xiangchao; Ding, Ke; Wu, Hua

2017-12-01

Porcine epidemic diarrhea virus (PEDV) is a causative agent of porcine intestinal disease, which causes vomiting, diarrhea, and dehydration in piglets. PEDV is associated with the most severe pathogenesis in one-week-old piglets, with mortality rates reaching 100%. A PEDV strain was isolated from the intestinal tract of diarrheic piglets from a pig farm in Jiangsu Province in March 2016, termed the JS201603 isolate. The isolated virus was confirmed to be PEDV via RT-PCR, electron microscopy, a cytopathic effect assay and sequence analysis. The S and ORF3 genes of the JS201603 isolate were sequenced, revealing that the S gene was associated with a 15-base insertion at 167 nt, 176 - 186 nt, and 427 - 429 nt, as well as a six-base deletion in 487 - 492 nt, indicating that it was a current epidemic variant compared with the classical strain, CV777. No deletion occurred between 245 - 293 nt of the ORF3 gene in the JS201603 isolate compared with the vaccine isolates YY2013 and SQ2014. An experimental infection model indicated that the piglets in the challenge group successively developed diarrhea, exhibiting yellow-colored loose stools with a foul odor. The piglets in the JS201603 isolate challenge group displayed reduced food consumption, lost weight, and in severe cases even died. No abnormalities were observed in the control group. The JS201603 variant isolated in this study contributes to the evolutionary analysis of diarrhea virus. The experimental infection model has established a foundation for further studies on vaccine development.

Characterization of Enterotoxigenic Bacillus cereus sensu lato and Staphylococcus aureus Isolates and Associated Enterotoxin Production Dynamics in Milk or Meat-Based Broth

PubMed Central

Walker-York-Moore, Laura; Moore, Sean C.; Fox, Edward M.

2017-01-01

Bacillus cereus sensu lato species, as well as Staphylococcus aureus, are important pathogenic bacteria which can cause foodborne illness through the production of enterotoxins. This study characterised enterotoxin genes of these species and examined growth and enterotoxin production dynamics of isolates when grown in milk or meat-based broth. All B. cereus s. l. isolates harboured nheA, hblA and entFM toxin genes, with lower prevalence of bceT and hlyII. When grown at 16 °C, toxin production by individual B. cereus s. l. isolates varied depending on the food matrix; toxin was detected at cell densities below 5 log10(CFU/mL). At 16 °C no staphylococcal enterotoxin C (SEC) production was detected by S. aureus isolates, although low levels of SED production was noted. At 30 °C all S. aureus isolates produced detectable enterotoxin in the simulated meat matrix, whereas SEC production was significantly reduced in milk. Relative to B. cereus s. l. toxin production, S. aureus typically required reaching higher cell numbers to produce detectable levels of enterotoxin. Phylogenetic analysis of the sec and sel genes suggested population evolution which correlated with animal host adaptation, with subgroups of bovine isolates or caprine/ovine isolates noted, which were distinct from human isolates. Taken together, this study highlights the marked differences in the production of enterotoxins both associated with different growth matrices themselves, but also in the behaviour of individual strains when exposed to different food matrices. PMID:28714887

Characterization of Enterotoxigenic Bacillus cereus sensu lato and Staphylococcus aureus Isolates and Associated Enterotoxin Production Dynamics in Milk or Meat-Based Broth.

PubMed

Walker-York-Moore, Laura; Moore, Sean C; Fox, Edward M

2017-07-15

Bacillus cereus sensu lato species, as well as Staphylococcus aureus , are important pathogenic bacteria which can cause foodborne illness through the production of enterotoxins. This study characterised enterotoxin genes of these species and examined growth and enterotoxin production dynamics of isolates when grown in milk or meat-based broth. All B. cereus s. l. isolates harboured nheA , hblA and entFM toxin genes, with lower prevalence of bceT and hlyII . When grown at 16 °C, toxin production by individual B. cereus s. l. isolates varied depending on the food matrix; toxin was detected at cell densities below 5 log 10 (CFU/mL). At 16 °C no staphylococcal enterotoxin C (SEC) production was detected by S. aureus isolates, although low levels of SED production was noted. At 30 °C all S. aureus isolates produced detectable enterotoxin in the simulated meat matrix, whereas SEC production was significantly reduced in milk. Relative to B. cereus s. l. toxin production, S. aureus typically required reaching higher cell numbers to produce detectable levels of enterotoxin. Phylogenetic analysis of the sec and sel genes suggested population evolution which correlated with animal host adaptation, with subgroups of bovine isolates or caprine/ovine isolates noted, which were distinct from human isolates. Taken together, this study highlights the marked differences in the production of enterotoxins both associated with different growth matrices themselves, but also in the behaviour of individual strains when exposed to different food matrices.

Establishment of Canine-Derived Giardia duodenalis Isolates in Culture.

PubMed

Tysnes, Kristoffer R; Robertson, Lucy J

2016-06-01

Researchers continue to rely on axenic cultivation of Giardia duodenalis trophozoites in vitro to study the life cycle and host-parasite interactions of G. duodenalis and to develop vaccines and drugs to prevent and treat giardiasis. The majority of in vitro studies of G. duodenalis have used a small subset of isolates, mostly of assemblage A, and these isolates are usually originally isolated from humans. The most commonly used isolate for lab studies is known as WB. Canine giardiasis is a disease of veterinary importance, but it may also be of relevance in zoonotic transmission. Few G. duodenalis isolates from dogs have been adapted to in vitro culture, probably because the methods used are not suitable for the canine-specific genotypes that tend to dominate in most dog populations. In the current study, an experimental approach to cultivating canine-derived isolates of G. duodenalis was attempted by modification of the standard protocol based on physiological differences between the human and canine digestive system. An adapted method is described for improving the rate of in vitro excystation of cysts isolated from dogs by chemically weakening the cyst wall. A new canine-derived assemblage A G. duodenalis isolate was successfully adapted to axenic culture by using this method; the dog apparently had a mixed infection of assemblages A and D, but the assemblage A successfully outcompeted the assemblage D under conditions of in vitro culture. Based on the results, reasons regarding why humans do not seem to be suitable hosts for G. duodenalis in assemblages C and D are discussed.

Design and test of aircraft engine isolators for reduced interior noise

NASA Technical Reports Server (NTRS)

Unruh, J. F.; Scheidt, D. C.

1982-01-01

Improved engine vibration isolation was proposed to be the most weight and cost efficient retrofit structure-borne noise control measure for single engine general aviation aircraft. A study was carried out the objectives: (1) to develop an engine isolator design specification for reduced interior noise transmission, (2) select/design candidate isolators to meet a 15 dB noise reduction design goal, and (3) carry out a proof of concept evaluation test. Analytical model of the engine, vibration isolators and engine mount structure were coupled to an empirical model of the fuselage for noise transmission evaluation. The model was used to develop engine isolator dynamic properties design specification for reduced noise transmission. Candidate isolators ere chosen from available product literature and retrofit to a test aircraft. A laboratory based test procedure was then developed to simulate engine induced noise transmission in the aircraft for a proof of concept evaluation test. Three candidate isolator configurations were evaluated for reduced structure-borne noise transmission relative to the original equipment isolators.

Isolation and Identification of Mushroom Pathogens from Agrocybe aegerita

PubMed Central

Choi, Jang-Nam; Sharma, Praveen K.; Lee, Wang-Hyu

2010-01-01

Agrocybe aegerita is an important mushroom cultivated in Korea, with good feel and a peculiar fragrance. A. aegerita can be cultivated throughout the year using culture bottles but is more susceptible to contamination than other mushrooms. Twenty-two pathogens were isolated from the fruiting bodies and compost of A. aegerita, and seven isolates were isolated from Pleurotus ostreatus to compare with the A. aegerita isolates, collected from Gimje, Iksan, Gunsan of Chonbuk, and Chilgok of Gyeongbuk Province in 2009. These isolates were identified based on morphological and molecular characteristics. Of the 29 isolates, 26 were identified as Trichoderma spp. and the remaining three were Aspergillus spp., Mucor spp., and Penicillium spp. A phylogenetic analysis revealed that the 26 isolates of Trichoderma were divided into four taxa, namely T. harzianum, T. pleuroticola, T. longibrachiatum, and T. atroviride. Among the Trichoderma spp., 16 isolates (55.2%) were identified as T. harzianum, six as T. pleuroticola (20.7%), two as T. longibrachiatum, and the remaining two were T. atroviride. PMID:23956671

Isolation and characterisation of obligately anaerobic, lipolytic bacteria from the rumen of red deer.

PubMed

Jarvis, G N; Strömpl, C; Moore, E R; Thiele, J H

1998-03-01

Two Gram-positive, obligately anaerobic, lipolytic bacteria, isolates LIP4 and LIP5, were obtained from the rumen contents of juvenile red deer. These mesophilic bacterial strains were capable of hydrolysing the neutral lipids, tallow, tripalmitin and oliver oil, into their constituent free long-chain fatty acid and glycerol moieties. The latter compound was dissimilated by both isolates, with isolate LIP4 producing propionate as the predominant product, while isolate LIP5 produced acetate, ethanol and succinate. The lactate-utilising isolate LIP4 grew on a limited range of saccharide substrates including glucose, fructose and ribose, and exhibited an unusual cell wall structure and morphology. The isolate LIP5 grew upon a wider range of saccharides, but was unable to use lactate as a substrate. Based upon phenotypic and 16S rRNA gene sequence analyses, isolate LIP4 clusters with species in the genus Propionibacterium, while isolate LIP5 is a member of clostridial cluster XIVa.

Properties of Cast Films Made from Different Ratios of Whey Protein Isolate, Hydrolysed Whey Protein Isolate and Glycerol

PubMed Central

Schmid, Markus

2013-01-01

Whey protein isolate (WPI)-based cast films are very brittle, due to several chain interactions caused by a large amount of different functional groups. In order to overcome film brittleness, plasticizers, like glycerol, are commonly used. As a result of adding plasticizers, the free volume between the polymer chains increases, leading to higher permeability values. The objective of this study was to investigate the effect of partially substituting glycerol by hydrolysed whey protein isolate (h-WPI) in WPI-based cast films on their mechanical, optical and barrier properties. As recently published by the author, it is proven that increasing the h-WPI content in WPI-based films at constant glycerol concentrations significantly increases film flexibility, while maintaining the barrier properties. The present study considered these facts in order to increase the barrier performance, while maintaining film flexibility. Therefore glycerol was partially replaced by h-WPI in WPI-based cast films. The results clearly indicate that partially replacing glycerol by h-WPI reduces the oxygen permeability and the water vapor transmission rate, while the mechanical properties did not change significantly. Thus, film flexibility was maintained, even though the plasticizer concentration was decreased. PMID:28811434

Leek yellow stripe virus isolates from Brazil form a distant clade based on the P1 gene

USDA-ARS?s Scientific Manuscript database

The complete genomic sequence of a garlic isolate of Leek yellow stripe virus from Brazil (LYSV-MG) has been determined, and phylogenetic comparisons made to LYSV isolates from other parts of the world. In addition, the nucleotide sequence of the 5'UTR and part of the P1 gene of multiple LYSV isolat...

Antioxidant activities of phenolic compounds isolated from the leaves of Macaranga allorobinsonii Whitmore

NASA Astrophysics Data System (ADS)

Darmawan, Akhmad; Fajriah, Sofa; Megawati, Dewijanti, Indah D.; Banjarnahor, Sofna; Yuliani, Tri; Hartati, Sri; Mozef, Tjandrawati; Effendi, Ruslan; Swandiny, Greesty F.

2017-01-01

Two secondary metabolites compounds, gallic acid (1) and methyl gallate (2) have been isolated from the ethyl acetate fraction of the methanol extract of the leaves of Macaranga allorobinsonii Whitmore. Isolation and purification of the secondary metabolite compounds conducted using chromatography methods, and structure elucidation determined based on NMR, mass spectroscopic data and compared with appropriate references.

Use of flow cytometry, fluorescence microscopy, and PCR-based techniques to assess intraspecific and interspecific matings of Armillaria species

Treesearch

Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald; Kathiravetpillai Arumuganathan

2001-01-01

For assessments of intraspecific mating using flow cytometry and fluorescence microscopy, two compatible basidiospore-derived isolates were selected from each of four parental basidiomata of North American Biological Species (NABS) X. The nuclear status in NABS X varied with basidiospore-derived isolates. Nuclei within basidiospore-derived isolates existed as haploids...

Isolation of Tannin-Degrading Lactobacilli from Humans and Fermented Foods

PubMed Central

Osawa, Ro; Kuroiso, Keiko; Goto, Satoshi; Shimizu, Akira

2000-01-01

Lactobacilli with tannase activity were isolated from human feces and fermented foods. A PCR-based taxonomic assay revealed that the isolates belong to Lactobacillus plantarum, L. paraplantarum, and L. pentosus. Additional studies on a range of Lactobacillus species from established culture collections confirmed that this enzymatic activity is a phenotypic property common to these three species. PMID:10877812

Artificial dielectric polarizing-beamsplitter and isolator for the terahertz region.

PubMed

Mendis, Rajind; Nagai, Masaya; Zhang, Wei; Mittleman, Daniel M

2017-07-19

We demonstrate a simple and effective strategy for implementing a polarizing beamsplitter for the terahertz spectral region, based on an artificial dielectric medium that is scalable to a range of desired frequencies. The artificial dielectric medium consists of a uniformly spaced stack of metal plates, which is electromagnetically equivalent to a stacked array of parallel-plate waveguides. The operation of the device relies on both the lowest-order, transverse-electric and transverse-magnetic modes of the parallel-plate waveguide. This is in contrast to previous work that relied solely on the transverse-electric mode. The fabricated polarizing beamsplitter exhibits extinction ratios as high as 42 dB along with insertion losses as low as 0.18 dB. Building on the same idea, we also demonstrate an isolator with non-reciprocal transmission, providing high isolation and low insertion loss at a select design frequency. The performance of our isolator far exceeds that of other experimentally demonstrated terahertz isolators, and indeed, even rivals that of commercially available isolators for optical wavelengths. Because these waveguide-based artificial dielectrics are low loss, inexpensive, and easy to fabricate, this approach offers a promising new route for polarization control of free-space terahertz beams.

Distribution of monoclonal antibody subgroups and sequence-based types among Legionella pneumophila serogroup 1 isolates derived from cooling tower water, bathwater, and soil in Japan.

PubMed

Amemura-Maekawa, Junko; Kikukawa, Kiyomi; Helbig, Jürgen H; Kaneko, Satoko; Suzuki-Hashimoto, Atsuko; Furuhata, Katsunori; Chang, Bin; Murai, Miyo; Ichinose, Masayuki; Ohnishi, Makoto; Kura, Fumiaki

2012-06-01

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat.

Isolation and identification of methylobacterium species from the tap water in hospitals in Japan and their antibiotic susceptibility.

PubMed

Furuhata, Katsunori; Kato, Yuko; Goto, Keiichi; Hara, Motonobu; Yoshida, Shin-ichi; Fukuyama, Masafumi

2006-01-01

Contamination of tap water by Methylobacterium species has become a serious concern in hospitals. This study was planned to examine the distribution of Methylobacterium species inhabiting tap water used in Japanese hospitals and antibiotic sensitivity of the isolates in 2004. Species identification of 58 isolates was performed based on the homology of a partial sequence of 16S rDNA. The dominant Methylobacterium species in hospital water were M. aquaticum and M. fujisawaense. To examine the biochemical properties of these isolates, a carbon source utilization was tested using an API50CH kit. The phenotypic character varied widely, and was not necessarily consistent with the results of phylogenic analysis based on the partial 16S rDNA sequence, suggesting that the biochemical properties are not suitable for identification of Methylobacterium species. The isolates were also subjected to antibiotic sensitivity tests. They were resistant to 8 antibiotics, but highly sensitive to imipenem (MIC90 = 1 microg/ml) and tetracycline (MIC90 = 8 microg/ml). These findings concerning the isolates revealed the presence of Methylobacterium species with resistance to multiple antibiotics in hospital tap water.

Occurrence and characterization of hitherto unknown Streptomyces species in semi-arid soils.

PubMed

Kumar, Surendra; Priya, E; Singh Solanki, Dilip; Sharma, Ruchika; Gehlot, Praveen; Pathak, Rakesh; Singh, S K

2016-09-01

Streptomyces the predominant genus of Actinobacteria and plays an important role in the recycling of soil organic matter and production of important secondary metabolites. The occurrence and diversity assessment of Streptomyces species revealed alkaline and poor nutrient status of soils of semi-arid region of Jodhpur, Rajasthan. The morphological and biochemical characterization of 21 Streptomyces isolates facilitated Genus level identification but were insufficient to designate species. Species designation based on 16S rRNA gene delineated 21 isolates into 14 Streptomyces species. Upon BLAST search, the test isolates exhibited 98 to 100% identities with that of the best aligned sequences of the NCBI database. The GC content of 16S rRNA gene sequences of all the Streptomyces isolates tested ranged from 59.03% to 60.94%. The multiple sequence alignment of all the 21 Streptomyces isolates generated a phylogram with high bootstrap values indicating reliable grouping of isolates based on nucleotide sequence variations by way of insertion, deletion and substitutions and 16S rRNA length polymorphism. Some of the Streptomyces species molecularly identified under present study are reported for the first time from semi-arid region of Jodhpur.

Bus bar electrical feedthrough for electrorefiner system

DOEpatents

Williamson, Mark; Wiedmeyer, Stanley G; Willit, James L; Barnes, Laurel A; Blaskovitz, Robert J

2013-12-03

A bus bar electrical feedthrough for an electrorefiner system may include a retaining plate, electrical isolator, and/or contact block. The retaining plate may include a central opening. The electrical isolator may include a top portion, a base portion, and a slot extending through the top and base portions. The top portion of the electrical isolator may be configured to extend through the central opening of the retaining plate. The contact block may include an upper section, a lower section, and a ridge separating the upper and lower sections. The upper section of the contact block may be configured to extend through the slot of the electrical isolator and the central opening of the retaining plate. Accordingly, relatively high electrical currents may be transferred into a glovebox or hot-cell facility at a relatively low cost and higher amperage capacity without sacrificing atmosphere integrity.

Fault detection and isolation in the challenging Tennessee Eastman process by using image processing techniques.

PubMed

Hajihosseini, Payman; Anzehaee, Mohammad Mousavi; Behnam, Behzad

2018-05-22

The early fault detection and isolation in industrial systems is a critical factor in preventing equipment damage. In the proposed method, instead of using the time signals of sensors, the 2D image obtained by placing these signals next to each other in a matrix has been used; and then a novel fault detection and isolation procedure has been carried out based on image processing techniques. Different features including texture, wavelet transform, mean and standard deviation of the image accompanied with MLP and RBF neural networks based classifiers have been used for this purpose. Obtained results indicate the notable efficacy and success of the proposed method in detecting and isolating faults of the Tennessee Eastman benchmark process and its superiority over previous techniques. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

16S rRNA and Omp31 Gene Based Molecular Characterization of Field Strains of B. melitensis from Aborted Foetus of Goats in India

PubMed Central

Singh, Ajay; Gupta, Vivek Kumar; Kumar, Amit; Singh, Vikas Kumar; Nayakwadi, Shivasharanappa

2013-01-01

Brucellosis is a reemerging infectious zoonotic disease of worldwide importance. In human, it is mainly caused by Brucella melitensis, a natural pathogen for goats. In India, a large number of goats are reared in semi-intensive to intensive system within the close vicinity of human being. At present, there is no vaccination and control strategy for caprine brucellosis in the country. Thus, to formulate an effective control strategy, the status of etiological agent is essential. To cope up with these, the present study was conducted to isolate and identify the prevalent Brucella species in caprine brucellosis in India. The 30 samples (fetal membrane, fetal stomach content and vaginal swabs) collected throughout India from the aborted fetus of goats revealed the isolation of 05 isolates all belonging to Brucella melitensis biovars 3. All the isolates produced amplification products of 1412 and 720 bp in polymerase chain reaction with genus and species specific 16S rRNA and omp31 gene based primers, respectively. Moreover, the amplification of omp31 gene in all the isolates confirmed the presence of immuno dominant outer membrane protein (31 kDa omp) in all the field isolates of B. melitensis in aborted foetus of goats in India. These findings can support the development of omp31 based specific serodiagnostic test as well as vaccine for the control of caprine brucellosis in India. PMID:24453799

Ocular surface infections in northeastern state of malaysia: a 10-year review of bacterial isolates and antimicrobial susceptibility.

PubMed

Rahman, Zaidah A; Harun, Azian; Hasan, Habsah; Mohamed, Zeehaida; Noor, Siti S Md; Deris, Zakuan Z; Ismail, Nabilah; Hassan, Asma S; Ahmad, Fadzhilah; Yaakub, Azhany

2013-09-01

Ocular surface infections that include infections of conjunctiva, adnexa, and cornea have the potential risk of causing blindness within a given population. Empirical antibiotic therapy is usually initiated based on epidemiological data of common causative agents. Thus, the aims of this study were to determine the bacterial agents and their susceptibility patterns of isolates from ocular surface specimens in our hospital. This is a retrospective analysis and records of bacterial isolates from ocular surface specimens in Hospital Universiti Sains Malaysia from January 2001 to December 2010 were examined. Specimens were processed according to standard laboratory procedures. Antimicrobial susceptibility testing was conducted based on Clinical and Laboratory Standards Institute recommendations. Only single, nonrepetitive isolates were included in the analysis. A total of 1,267 isolates were obtained during the study period, which comprised Staphylococcus aureus (n = 299, 23.6%), Pseudomonas aeruginosa (n = 194, 15.3%), Streptococcus pneumoniae (n = 108, 8.5%), Haemophilus influenzae (n = 100, 7.9%), Haemophilus parainfluenzae (n = 84, 6.6%), and Enterobacter spp. (n = 81, 6.4%). Fungi contributed to 4.4% of the total isolates. The antimicrobial susceptibility testing demonstrated that gram-positive bacteria were generally resistant to gentamicin (19%-57%), whereas gram-negative bacteria were resistant to chloramphenicol (27%-58%). Based on the above results, knowledge of the initial Gram stain findings is imperative before the commencement of empirical antibiotic therapy. Therefore, a simple Gram staining for all eye specimens is highly recommended.

Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes.

PubMed

Rivera-Posada, J A; Pratchett, M; Cano-Gomez, A; Arango-Gomez, J D; Owens, L

2011-09-09

We used a polyphasic approach for precise identification of bacterial flora (Vibrionaceae) isolated from crown-of-thorns starfish (COTS) from Lizard Island (Great Barrier Reef, Australia) and Guam (U.S.A., Western Pacific Ocean). Previous 16S rRNA gene phylogenetic analysis was useful to allocate and identify isolates within the Photobacterium, Splendidus and Harveyi clades but failed in the identification of Vibrio harveyi-like isolates. Species of the V harveyi group have almost indistinguishable phenotypes and genotypes, and thus, identification by standard biochemical tests and 16S rRNA gene analysis is commonly inaccurate. Biochemical profiling and sequence analysis of additional topA and mreB housekeeping genes were carried out for definitive identification of 19 bacterial isolates recovered from sick and wild COTS. For 8 isolates, biochemical profiles and topA and mreB gene sequence alignments with the closest relatives (GenBank) confirmed previous 16S rRNA-based identification: V. fortis and Photobacterium eurosenbergii species (from wild COTS), and V natriegens (from diseased COTS). Further phylogenetic analysis based on topA and mreB concatenated sequences served to identify the remaining 11 V harveyi-like isolates: V. owensii and V. rotiferianus (from wild COTS), and V. owensii, V. rotiferianus, and V. harveyi (from diseased COTS). This study further confirms the reliability of topA-mreB gene sequence analysis for identification of these close species, and it reveals a wider distribution range of the potentially pathogenic V. harveyi group.

The antimicrobial susceptibility, biofilm formation and genotypic profiles of Staphylococcus haemolyticus from bloodstream infections

PubMed Central

Silva, Patricia Vollú; Cruz, Raquel Souza; Keim, Luiz Sérgio; de Paula, Geraldo Renato; Carvalho, Bernadete Teixeira Ferreira; Coelho, Leonardo Rocchetto; Carvalho, Maria Cícera da Silva; da Rosa, Joel Mauricio Corrêa; Figueiredo, Agnes Marie Sá; Teixeira, Lenise Arneiro

2013-01-01

We analysed the antimicrobial susceptibility, biofilm formation and genotypic profiles of 27 isolates of Staphylococcus haemolyticus obtained from the blood of 19 patients admitted to a hospital in Rio de Janeiro, Brazil. Our analysis revealed a clinical significance of 36.8% and a multi-resistance rate of 92.6% among these isolates. All but one isolate carried the mecA gene. The staphylococcal cassette chromosome mec type I was the most prevalent mec element detected (67%). Nevertheless, the isolates showed clonal diversity based on pulsed-field gel electrophoresis analysis. The ability to form biofilms was detected in 66% of the isolates studied. Surprisingly, no icaAD genes were found among the biofilm-producing isolates. PMID:24037208

The antimicrobial susceptibility, biofilm formation and genotypic profiles of Staphylococcus haemolyticus from bloodstream infections.

PubMed

Silva, Patricia Vollú; Cruz, Raquel Souza; Keim, Luiz Sérgio; Paula, Geraldo Renato de; Carvalho, Bernadete Teixeira Ferreira; Coelho, Leonardo Rocchetto; Carvalho, Maria Cícera da Silva; Rosa, Joel Mauricio Corrêa da; Figueiredo, Agnes Marie Sá; Teixeira, Lenise Arneiro

2013-09-01

We analysed the antimicrobial susceptibility, biofilm formation and genotypic profiles of 27 isolates of Staphylococcus haemolyticus obtained from the blood of 19 patients admitted to a hospital in Rio de Janeiro, Brazil. Our analysis revealed a clinical significance of 36.8% and a multi-resistance rate of 92.6% among these isolates. All but one isolate carried the mecA gene. The staphylococcal cassette chromosome mec type I was the most prevalent mec element detected (67%). Nevertheless, the isolates showed clonal diversity based on pulsed-field gel electrophoresis analysis. The ability to form biofilms was detected in 66% of the isolates studied. Surprisingly, no icaAD genes were found among the biofilm-producing isolates.

Evaluation of a surface plasmon resonance imaging-based multiplex O-antigen serogrouping for Escherichia coli using eleven major serotypes of Shiga -toxin-producing E. coli.

PubMed

Nakano, Satoshi; Nagao, Miki; Yamasaki, Tomomi; Morimura, Hiroyuki; Hama, Natsuki; Iijima, Yoshio; Shinomiya, Hiroto; Tanaka, Michio; Yamamoto, Masaki; Matsumura, Yasufumi; Miyake, Shiro; Ichiyama, Satoshi

2018-06-01

The early detection of Shiga toxin-producing Escherichia coli (STEC) is important for early diagnosis and preventing the spread of STEC. Although the confirmatory test for STEC should be based on the detection of Shiga toxin using molecular analysis, isolation permits additional characterization of STEC using a variety of methods, including O:H serotyping. The conventional slide agglutination O-antigen serogrouping used in many clinical laboratories is laborious and time-consuming. Surface plasmon resonance (SPR)-based immunosensors are commonly used to investigate a large variety of bio-interactions such as antibody/antigen, peptide/antibody, DNA/DNA, and antibody/bacteria interactions. SPR imaging (SPRi) is characterized by multiplexing capabilities for rapidly screening (approximately 100 to several hundred sensorgrams in parallel) molecules. SPRi-based O-antigen serogrouping method for STEC was recently developed by detecting the interactions between O-antigen-specific antibodies and bacterial cells themselves. The aim of this study was to evaluate its performance for E. coli serogrouping using clinical STEC isolates by comparing the results of slide agglutination tests. We tested a total of 188 isolates, including O26, O45, O91, O103, O111, O115, O121, O128, O145, O157, and O159. The overall sensitivity of SPRi-based O-antigen serogrouping was 98.9%. Only two O157 isolates were misidentified as nontypeable and O121. The detection limits of all serotypes were distributed between 1.1 × 10 6 and 17.6 × 10 6  CFU/ml. Pulsed-field gel electrophoresis (PFGE) revealed the heterogeneity of the examined isolates. In conclusion, SPRi is a useful method for the O-antigen serogrouping of STEC isolates, but the further evaluation of non-O157 minor serogroups is needed. Copyright © 2018 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

A magnetic isolation and pointing system for the astrometric telescope facility

NASA Technical Reports Server (NTRS)

Smith, Marcie; Hibble, William; Wolke, Patrick J.

1993-01-01

The astrometric telescope facility (ATF), a 20-meter telescope designed for long-term detection and observation of planetary systems outside of the solar system, is scheduled to be a major user of the Space Station's payload pointing system (PPS) capabilities. However, because the ATF has such a stringent pointing stability specification (as low as 0.01 arcsec error over the frequency range from 5 to 200 hertz) and requires +/- 180-degree roll rotation around the telescope's line of sight, the ATF's utilization of the PPS requires the addition of a mechanism or mechanisms to enhance the basic PPS capabilities. The results of a study conducted to investigate the ATF pointing performance achievable by the addition of a magnetic isolation and pointing (MIPS) system between the PPS upper gimbal and the ATF, and separately, by the addition of a passive isolation system between the Space Station and the PPS base are presented. In addition, the study produced requirements on magnetic force and gap motion as a function of the level of Space Station disturbance. These results were used to support the definition of a candidate MIPS. Pointing performance results from the study indicate that a MIPS can meet the ATF pointing requirements in the presence of a PPS base transitional acceleration of up to 0.018g, with reasonable restrictions placed on the isolation and pointing bandwidths. By contrast, the passive base isolator system must have an unrealistically low isolation bandwidth on all axes (less than 0.1 hertz) to meet ATF pointing requirements. The candidate MIPS is based on an assumed base translational disturbance of 0.01g. The system fits within the available annular region between the PPS and ATF while meeting power and weight limitations and providing the required payload roll motion. Payload data and power services are provided by noncontacting transfer devices.

Carbapenemase-producing Enterobacteriaceae: a 2-year surveillance in a hospital in Iaşi, Romania.

PubMed

Braun, Sascha D; Dorneanu, Olivia S; Vremeră, Teodora; Reißig, Annett; Monecke, Stefan; Ehricht, Ralf

2016-01-01

Limited information is currently available about the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in Romania. Routine tests of 1,993 clinical isolates at a hospital in Iaşi yielded 46 isolates that were resistant to carbapenems. All 46 isolates were phenotypically and genotypically analyzed using VITEK-2 and DNA microarray-based assays. Isolates were assigned to Klebsiella pneumoniae and Enterobacter cloacae. For 39 isolates, carbapenem resistance was confirmed and 37 harbored at least one carbapenem resistance gene. Two isolates were probably resistant due to AmpC β-lactamases in combination with a porin loss. The overall concordance between detected phenotype and genotype was 95%. Our data show that carbapenemase-producing isolates with different underlying resistance mechanisms are still rare in Iaşi, but the global rise of CPE warrants intensified surveillance.

Deciphering the Origins and Tracking the Evolution of Cholera Epidemics with Whole-Genome-Based Molecular Epidemiology

PubMed Central

Grad, Yonatan H.; Waldor, Matthew K.

2013-01-01

ABSTRACT The devastating Haitian cholera outbreak that began in October 2010 is the first known cholera epidemic in this island nation. Epidemiological and genomic data have provided strong evidence that United Nations security forces from Nepal introduced toxigenic Vibrio cholerae O1, the cause of epidemic cholera, to Haiti shortly before the outbreak arose. However, some have contended that indigenous V. cholerae contributed to the outbreak. In a recent paper (mBio 4:e00398-13, 2013), L. S. Katz et al. explored the nature and rate of changes in this ancient pathogen’s genome during an outbreak, based on whole-genome sequencing of 23 Haitian V. cholerae clinical isolates obtained over a 20-month period. Notably, they detected point mutations, deletions, and inversions but found no insertion of horizontally transmitted DNA, arguing strongly against the idea that autochthonous V. cholerae donated DNA to the outbreak strain. Furthermore, they found that Haitian epidemic V. cholerae isolates were virtually untransformable. Comparative genomic analyses revealed that the Haitian isolates were nearly identical to isolates from Nepal and that the Nepalese-Haitian isolates were distinguishable from isolates circulating elsewhere in the world. Reconstruction of the phylogeny of the Haitian isolates was consistent with a single introduction of V. cholerae to Haiti sometime between late July and late October 2010, dates remarkably concordant with epidemiological observations. In aggregate, this paper provides additional compelling evidence that the V. cholerae strain responsible for the Haitian cholera epidemic came from Nepal and illustrates the power of whole-genome-based analyses for epidemiology, pathogen evolution, and forensics. PMID:24023387

Median infectious dose (ID₅₀) of porcine reproductive and respiratory syndrome virus isolate MN-184 via aerosol exposure.

PubMed

Cutler, Timothy D; Wang, Chong; Hoff, Steven J; Kittawornrat, Apisit; Zimmerman, Jeffrey J

2011-08-05

The median infectious dose (ID(50)) of porcine reproductive and respiratory syndrome (PRRS) virus isolate MN-184 was determined for aerosol exposure. In 7 replicates, 3-week-old pigs (n=58) respired 10l of airborne PRRS virus from a dynamic aerosol toroid (DAT) maintained at -4°C. Thereafter, pigs were housed in isolation and monitored for evidence of infection. Infection occurred at virus concentrations too low to quantify by microinfectivity assays. Therefore, exposure dose was determined using two indirect methods ("calculated" and "theoretical"). "Calculated" virus dose was derived from the concentration of rhodamine B monitored over the exposure sequence. "Theoretical" virus dose was based on the continuous stirred-tank reactor model. The ID(50) estimate was modeled on the proportion of pigs that became infected using the probit and logit link functions for both "calculated" and "theoretical" exposure doses. Based on "calculated" doses, the probit and logit ID(50) estimates were 1 × 10(-0.13)TCID(50) and 1 × 10(-0.14)TCID(50), respectively. Based on "theoretical" doses, the probit and logit ID(50) were 1 × 10(0.26)TCID(50) and 1 × 10(0.24)TCID(50), respectively. For each point estimate, the 95% confidence interval included the other three point estimates. The results indicated that MN-184 was far more infectious than PRRS virus isolate VR-2332, the only other PRRS virus isolate for which ID(50) has been estimated for airborne exposure. Since aerosol ID(50) estimates are available for only these two isolates, it is uncertain whether one or both of these isolates represent the normal range of PRRS virus infectivity by this route. Copyright © 2011 Elsevier B.V. All rights reserved.

PCR-based molecular discrimination of Pandora neoaphidis isolates from related entomopathogenic fungi and development of species-specific diagnostic primers.

PubMed

Tymon, Anna M; Shah, Paresh A; Pell, Judith K

2004-04-01

Studies were performed to assess the genetic variation amongst isolates of the aphid-pathogenic fungus Pandora neoaphidis (syn. Erynia neoaphidis). 37 isolates were examined, from a range of pest and non-pest aphid species, as well as 21 from eight other entomophthoralean species. Universal primers were used to amplify the ITS rDNA regions and all of the species tested produced discrete ITS groups, with the exception of Conidiobolus spp. Neighbour-joining analysis of the ITS2 regions from P. neoaphidis, P. kondoiensis and Zoophthora radicans demonstrated that these three species formed distinct groups with sequence identities of 58-82% between the groups. An ITS size of ca 1,100 bp was diagnostic for P. neoaphidis, while ca 1,450 bp was characteristic of P. kondoiensis. ITS-RFLP analysis failed to yield intraspecific polymorphisms in any of the P. neoaphidis isolates screened, although it was useful in distinguishing between different entomophthoralean species. Some intraspecific variation in the ITS region was detected in a number of isolates of Z. radicans and Conidiobolus spp. We propose that two isolates previously identified as P. neoaphidis based on conidia morphology, are actually P. kondoiensis based on molecular studies. Sequencing analysis of the complete ITS region from P. neoaphidis and P. kondoiensis allowed species-specific primers to be developed for P. neoaphidis and P. kondoiensis. These were used to screen aphids infected in laboratory bioassays and from field-collected samples, without prior isolation of the fungus. The primers are useful tools for quantifying the epizootiology of P. neoaphidis in aphid populations, as well as assessing competitive interactions between these two species.

Genetic Characterization of Listeria monocytogenes Isolates from Industrial and Retail Ready-to-Eat Meat-Based Foods and Their Relationship with Clinical Strains from Human Listeriosis in Portugal.

PubMed

Henriques, A R; Cristino, J Melo; Fraqueza, M J

2017-04-01

Listeria monocytogenes isolates (n = 81) recovered from ready-to-eat meat-based food products (RTEMP) collected in industrial processing plants and retail establishments were genetically characterized for comparison with those from human clinical cases of listeriosis (n = 49). The aim was to assess RTEMP as a possible food source for human infection. L. monocytogenes was detected in 12.5% of the RTEMP samples, and in some cases, counts were above the European food safety criteria. All isolates were assessed by multiplex PCR for serogroup determination and detection of virulence-associated genes inlA, inlB, inlC, inlJ, plcA, hlyA, actA, and iap. Serogroups IIb and IVb dominated in RTEMP and human isolates, and all were positive for the assessed virulence genes. Antibiotic susceptibility testing by the disk diffusion method revealed a low level of resistance among the isolates. Pulsed-field gel electrophoresis (PFGE) of L. monocytogenes isolates, using restriction enzymes ApaI and AscI, revealed genetic variability and differentiated the isolates in five clusters. Although some pulsed-field gel electrophoresis profiles of particular RTEMP and human isolates seemed to be highly related, exhibiting more than 90% similarity, which suggests a possible common source, in most cases the strains were not genetically or temporally matched. The close genetic relatedness of RTEMP and human listeriosis strains stressed the importance of preventive measure implementation throughout the food chain.

Label-free Rapid Viable Enrichment of Circulating Tumor Cell by Photosensitive Polymer-based Microfilter Device.

PubMed

Kang, Yoon-Tae; Doh, Il; Byun, Jiyoung; Chang, Hee Jin; Cho, Young-Ho

2017-01-01

We present a clinical device for simple, rapid, and viable isolation of circulating tumor cells (CTCs) from cancer patient bloods. In spite of the clinical importance of CTCs, the lack of easy and non-biased isolation methods is a big hurdle for implementing CTC into clinical use. The present device made of photosensitive polymer was designed to attach to conventional syringe to isolate the CTCs at minimal resources. Its unique tapered-slits on the filter are capable not only to isolate the cell based on their size and deformability, but also to increase sample flow rate, thus achieving label-free rapid viable CTC isolation. We verified our device performance using 9 different types of cancer cells at the cell concentration from 5 to 100cells/ml, showing that the device capture 77.7% of the CTCs while maintaining their viability of 80.6%. We extended our study using the 18 blood samples from lung, colorectal, pancreatic and renal cancer patients and captured 1-172 CTCs or clustered CTCs by immunofluorescent or immunohistochemical staining. The captured CTCs were also molecularly assayed by RT-PCR with three cancer-associated genes (CK19, EpCAM, and MUC1). Those comprehensive studies proved to use our device for cancer study, thereby inaugurating further in-depth CTC-based clinical researches.

Integration of Magnetic Bead-Based Cell Selection into Complex Isolations

PubMed Central

2018-01-01

Magnetic bead-based analyte capture has emerged as a ubiquitous method in cell isolation, enabling the highly specific capture of target populations through simple magnetic manipulation. To date, no “one-size fits all” magnetic bead has been widely adopted leading to an overwhelming number of commercial beads. Ultimately, the ideal bead is one that not only facilitates cell isolation but also proves compatible with the widest range of downstream applications and analytic endpoints. Despite the diverse offering of sizes, coatings, and conjugation chemistries, few studies exist to benchmark the performance characteristics of different commercially available beads; importantly, these bead characteristics ultimately determine the ability of a bead to integrate into the user’s assay. In this report, we evaluate bead-based cell isolation considerations, approaches, and results across a subset of commercially available magnetic beads (Dynabeads FlowComps, Dynabeads CELLection, GE Healthcare Sera-Mag SpeedBeads streptavidin-blocked magnetic particles, Dynabeads M-270s, Dynabeads M-280s) to compare and contrast both capture-specific traits (i.e., purity, capture efficacy, and contaminant isolations) and endpoint compatibility (i.e., protein localization, fluorescence imaging, and nucleic acid extraction). We identify specific advantages and contexts of use in which distinct bead products may facilitate experimental goals and integrate into downstream applications. PMID:29732449

From brief gaps to very long pauses: temporal isolation does not benefit serial recall.

PubMed

Nimmo, Lisa M; Lewandowsky, Stephan

2005-12-01

Theoretical explanations of short-term memory for serial order can be classified on the basis of whether or not they invoke time as a causal variable. According to time-based accounts, such as temporal distinctiveness theories, there is an intimate link between time and memory. Event-based theories, by contrast, postulate processes such as interference or rehearsal to account for seemingly temporal phenomena in short-term memory. We report an experiment that examined whether extended temporal isolation benefits serial recall performance. Regardless of whether the participants were quiet or performed articulatory suppression during list presentation, temporal isolation did not benefit memory even if items were separated from their neighbors by up to 7 sec. These findings challenge time-based theories of short-term memory.

Molecular epidemiology of Plum pox virus in Japan.

PubMed

Maejima, Kensaku; Himeno, Misako; Komatsu, Ken; Takinami, Yusuke; Hashimoto, Masayoshi; Takahashi, Shuichiro; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2011-05-01

For a molecular epidemiological study based on complete genome sequences, 37 Plum pox virus (PPV) isolates were collected from the Kanto region in Japan. Pair-wise analyses revealed that all 37 Japanese isolates belong to the PPV-D strain, with low genetic diversity (less than 0.8%). In phylogenetic analysis of the PPV-D strain based on complete nucleotide sequences, the relationships of the PPV-D strain were reconstructed with high resolution: at the global level, the American, Canadian, and Japanese isolates formed their own distinct monophyletic clusters, suggesting that the routes of viral entry into these countries were independent; at the local level, the actual transmission histories of PPV were precisely reconstructed with high bootstrap support. This is the first description of the molecular epidemiology of PPV based on complete genome sequences.

In vitro antibiotic susceptibility of Dutch Mycoplasma synoviae field isolates originating from joint lesions and the respiratory tract of commercial poultry.

PubMed

Landman, W J M; Mevius, D J; Veldman, K T; Feberwee, A

2008-08-01

The in vitro susceptibility of 17 Dutch Mycoplasma synoviae isolates from commercial poultry to enrofloxacin, difloxacin, doxycycline, tylosin and tilmicosin was examined. Three isolates originated from joint lesions and 14 were from the respiratory tract. The type strain M. synoviae WVU 1853 was included as a control strain. Antibiotic susceptibility was tested quantitatively using the broth microdilution test. Based on initial and final minimum inhibitory concentration values, all tested isolates were susceptible to doxycycline, tylosin and tilmicosin. Two isolates from the respiratory tract were resistant to enrofloxacin and showed intermediate resistance to difloxacin.

Human isolates of Listeria monocytogenes in Sweden during half a century (1958-2010).

PubMed

Lopez-Valladares, G; Tham, W; Parihar, V Singh; Helmersson, S; Andersson, B; Ivarsson, S; Johansson, C; Ringberg, H; Tjernberg, I; Henriques-Normark, B; Danielsson-Tham, M-L

2014-11-01

Isolates of Listeria monocytogenes (n = 932) isolated in Sweden during 1958-2010 from human patients with invasive listeriosis were characterized by serotyping and pulsed-field gel electrophoresis (PFGE) (AscI). Of the 932 isolates, 183 different PFGE types were identified, of which 83 were each represented by only one isolate. In all, 483 serovar 1/2a isolates were distributed over 114 PFGE types; 90 serovar 1/2b isolates gave 32 PFGE types; 21 serovar 1/2c isolates gave nine PFGE types; three serovar 3b isolates gave one PFGE type; and, 335 serovar 4b isolates gave 31 PFGE types. During the 1980s in Sweden, several serovar 4b cases were associated with the consumption of European raw soft cheese. However, as cheese-production hygiene has improved, the number of 4b cases has decreased. Since 1996, serovar 1/2a has been the dominant L. monocytogenes serovar in human listeriosis in Sweden. Therefore, based on current serovars and PFGE types, an association between human cases of listeriosis and the consumption of vacuum-packed gravad and cold-smoked salmon is suggested.

Engine isolation for structural-borne interior noise reduction in a general aviation aircraft

NASA Technical Reports Server (NTRS)

Unruh, J. F.; Scheidt, D. C.

1981-01-01

Engine vibration isolation for structural-borne interior noise reduction is investigated. A laboratory based test procedure to simulate engine induced structure-borne noise transmission, the testing of a range of candidate isolators for relative performance data, and the development of an analytical model of the transmission phenomena for isolator design evaluation are addressed. The isolator relative performance test data show that the elastomeric isolators do not appear to operate as single degree of freedom systems with respect to noise isolation. Noise isolation beyond 150 Hz levels off and begins to decrease somewhat above 600 Hz. Coupled analytical and empirical models were used to study the structure-borne noise transmission phenomena. Correlation of predicted results with measured data show that (1) the modeling procedures are reasonably accurate for isolator design evaluation, (2) the frequency dependent properties of the isolators must be included in the model if reasonably accurate noise prediction beyond 150 Hz is desired. The experimental and analytical studies were carried out in the frequency range from 10 Hz to 1000 Hz.

Isolation and identification of cellulolytic bacteria from termites gut (Cryptotermes sp.)

NASA Astrophysics Data System (ADS)

Peristiwati; Natamihardja, Y. S.; Herlini, H.

2018-05-01

The energy and environmental crises developed due to a huge amount of cellulosic materials are disposed of as “waste.” Cellulose is the most abundant biopolymer on Earth. The hydrolysis of cellulose to glucose and soluble sugars has thus become a subject of intense research. Termites are one of the most important soil insects that efficiently decompose lignocelluloses with the aid of their associated microbial symbionts to a simpler form of sugars. The steps of this study consisted of cellulose isolation, cellulolytic bacteria isolation and identification. Cellulose degrading bacteria from termite (Cryptotermes sp.) gut flora were isolated, screened and their identification was studied which showed halo zones due to CMC agar. Among 12 isolates of bacteria, six isolates were cellulolytic. MLC-A isolate had shown a maximum in a cellulolytic index (1.32). Each isolate was identified based on standard physical and biochemical tests. Three isolates were identified in the genus of Clostridium, one isolate be placed in the group of Mycobacteriaceae, Lactobacillaceae or Coryneform and the last one in the genus Proteus.

RAPD cluster analysis and chlorate sensitivity of some Indian isolates of Macrophomina phaseolina from sorghum and their relationships with pathogenicity.

PubMed

Das, I K; Fakrudin, B; Arora, D K

2008-01-01

Charcoal rot caused by Macrophomina phaseolina is an economically important disease in sorghum grown during the post rainy season in India. Variations in random amplified polymorphic DNA (RAPD) polymorphisms, chlorate sensitivity and pathogenicity were studied among sorghum isolates of M. phaseolina collected from different parts of India. RAPD data based on 14 random primers of Kit A and C (OPA and OPC) on 20 isolates showed a high degree of polymorphism (98.1%) in different isolates. UPGMA dendrogram on RAPD data produced 7 clusters at the level of 37% similarity. Isolates from the same locations showed a tendency to group closer, substantiating closer genetic relatedness. Sorghum infecting Macrophomina isolates showed a mixed response for sensitivity to potassium chlorate (120 mM). Chlorate-resistant isolates were predominant (>65% of the isolates) over sensitive isolates. Chlorate-sensitive isolates were found to be genetically closer among them than the resistant ones. For the first time it was shown that chlorate sensitivity in Macrophomina had some relations with charcoal rot severity in sorghum.

Correlates of Objective Social Isolation from Family and Friends among Older Adults.

PubMed

Chatters, Linda M; Taylor, Harry Owen; Nicklett, Emily J; Taylor, Robert Joseph

2018-03-03

This study examined the correlates of objective social isolation from extended family members and friends among older adults. The analysis is based on the older adult sub-sample of the National Survey of American Life ( n = 1321). Multinomial logistic regression analyses examined race/ethnicity, demographics, functional health and family and friend network factors as correlates of objective isolation from family and friends. Only 4.47% of respondents were objectively isolated from both their extended family and friends, 10.82% were isolated from their friends, and 7.43% were isolated from their family members. Men were more likely to be objectively isolated from both family and friends and older adults who live with others were significantly more likely to be objectively isolated from their friends. When controlling for subjective social isolation, the two measures of functional health were significantly associated with objective social isolation. In particular, higher levels of self-care impairment decreased the risk of being objectively isolated from friends only, whereas higher mobility impairment was associated with an increased likelihood of being objectively isolated from friends only. Subjective evaluations of social isolation from family and friends were consistently associated with being objectively isolated from family and friends. There were no significant differences between African-Americans, Black Caribbeans and non-Hispanic Whites in objective isolation. These and other findings are discussed in detail.

Correlates of Objective Social Isolation from Family and Friends among Older Adults

PubMed Central

Chatters, Linda M.; Taylor, Harry Owen; Taylor, Robert Joseph

2018-01-01

This study examined the correlates of objective social isolation from extended family members and friends among older adults. The analysis is based on the older adult sub-sample of the National Survey of American Life (n = 1321). Multinomial logistic regression analyses examined race/ethnicity, demographics, functional health and family and friend network factors as correlates of objective isolation from family and friends. Only 4.47% of respondents were objectively isolated from both their extended family and friends, 10.82% were isolated from their friends, and 7.43% were isolated from their family members. Men were more likely to be objectively isolated from both family and friends and older adults who live with others were significantly more likely to be objectively isolated from their friends. When controlling for subjective social isolation, the two measures of functional health were significantly associated with objective social isolation. In particular, higher levels of self-care impairment decreased the risk of being objectively isolated from friends only, whereas higher mobility impairment was associated with an increased likelihood of being objectively isolated from friends only. Subjective evaluations of social isolation from family and friends were consistently associated with being objectively isolated from family and friends. There were no significant differences between African-Americans, Black Caribbeans and non-Hispanic Whites in objective isolation. These and other findings are discussed in detail. PMID:29510504

Species Based Synonymous Codon Usage in Fusion Protein Gene of Newcastle Disease Virus

PubMed Central

Kumar, Chandra Shekhar; Kumar, Sachin

2014-01-01

Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species. PMID:25479071

Scapular dyskinesia: evolution towards a systems-based approach

PubMed Central

Smith, Michael J

2015-01-01

Historically, scapular dyskinesia has been used to describe an isolated clinical entity whereby an abnormality in positioning, movement or function of the scapula is present. Based upon this, treatment approaches have focused on addressing local isolated muscle activity. Recently, however, there has been a progressive move towards viewing the scapula as being part of a wider system of movement that is regulated and controlled by multiple factors, including the wider kinetic chain and individual patient-centred requirements. We therefore propose a paradigm shift whereby scapular dyskinesia is seen not in isolation but is considered within the broader context of patient-centred care and an entire neuromuscular system. PMID:27583003

Prevotella timonensis sp. nov., isolated from a human breast abscess.

PubMed

Glazunova, Olga O; Launay, Thierry; Raoult, Didier; Roux, Véronique

2007-04-01

Gram-negative anaerobic rods were isolated from a human breast abscess. Based on genotypic and phenotypic characteristics, the novel strain belonged to the genus Prevotella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that it was closely related to Prevotella buccalis (94 % 16S rRNA gene sequence similarity), Prevotella salivae (90 %) and Prevotella oris (89.1 %). The major cellular fatty acid was C(14 : 0) (19.5 %). The new isolate represents a novel species in the genus Prevotella, for which the name Prevotella timonensis sp. nov. is proposed. The type strain is strain 4401737(T) (=CIP 108522(T)=CCUG 50105(T)).

Analysis of infant isolates of Bifidobacterium breve by comparative genome hybridization indicates the existence of new subspecies with marked infant specificity.

PubMed

Boesten, Rolf; Schuren, Frank; Wind, Richèle D; Knol, Jan; de Vos, Willem M

2011-09-01

A total of 20 Bifidobacterium strains were isolated from fecal samples of 4 breast- and bottle-fed infants and all were characterized as Bifidobacterium breve based on 16S rRNA gene sequence and metabolic analysis. These isolates were further characterized and compared to the type strains of B. breve and 7 other Bifidobacterium spp. by comparative genome hybridization. For this purpose, we constructed and used a DNA-based microarray containing over 2000 randomly cloned DNA fragments from B. breve type strain LMG13208. This molecular analysis revealed a high degree of genomic variation between the isolated strains and allowed the vast majority to be grouped into 4 clusters. One cluster contained a single isolate that was virtually indistinguishable from the B. breve type strain. The 3 other clusters included 19 B. breve strains that differed considerably from all type strains. Remarkably, each of the 4 clusters included strains that were isolated from a single infant, indicating that a niche adaptation may contribute to variation within the B. breve species. Based on genomic hybridization data, the new B. breve isolates were estimated to contain approximately 60-90% of the genes of the B. breve type strain, attesting to the existence of various subspecies within the species B. breve. Further bioinformatic analysis identified several hundred diagnostic clones specific to the genomic clustering of the B. breve isolates. Molecular analysis of representatives of these revealed that annotated genes from the conserved B. breve core encoded mainly housekeeping functions, while the strain-specific genes were predicted to code for functions related to life style, such as carbohydrate metabolism and transport. This is compatible with genetic adaptation of the strains to their niche, a combination of infants and diet. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Wieme, Anneleen D; Spitaels, Freek; Aerts, Maarten; De Bruyne, Katrien; Van Landschoot, Anita; Vandamme, Peter

2014-08-18

Applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of beer-spoilage bacteria was examined. To achieve this, an extensive identification database was constructed comprising more than 4200 mass spectra, including biological and technical replicates derived from 273 acetic acid bacteria (AAB) and lactic acid bacteria (LAB), covering a total of 52 species, grown on at least three growth media. Sequence analysis of protein coding genes was used to verify aberrant MALDI-TOF MS identification results and confirmed the earlier misidentification of 34 AAB and LAB strains. In total, 348 isolates were collected from culture media inoculated with 14 spoiled beer and brewery samples. Peak-based numerical analysis of MALDI-TOF MS spectra allowed a straightforward species identification of 327 (94.0%) isolates. The remaining isolates clustered separately and were assigned through sequence analysis of protein coding genes either to species not known as beer-spoilage bacteria, and thus not present in the database, or to novel AAB species. An alternative, classifier-based approach for the identification of spoilage bacteria was evaluated by combining the identification results obtained through peak-based cluster analysis and sequence analysis of protein coding genes as a standard. In total, 263 out of 348 isolates (75.6%) were correctly identified at species level and 24 isolates (6.9%) were misidentified. In addition, the identification results of 50 isolates (14.4%) were considered unreliable, and 11 isolates (3.2%) could not be identified. The present study demonstrated that MALDI-TOF MS is well-suited for the rapid, high-throughput and accurate identification of bacteria isolated from spoiled beer and brewery samples, which makes the technique appropriate for routine microbial quality control in the brewing industry. Copyright © 2014 Elsevier B.V. All rights reserved.

Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014.

PubMed

Becker, Laura; Kaase, Martin; Pfeifer, Yvonne; Fuchs, Stephan; Reuss, Annicka; von Laer, Anja; Sin, Muna Abu; Korte-Berwanger, Miriam; Gatermann, Sören; Werner, Guido

2018-01-01

By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/ cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae. NGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of bla OXA-48 via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany. Our study results suggest prevalence of "classical" K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota.

PubMed

Jami, Mansooreh; Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J

2015-06-01

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated biosynthetic genes, one-fourth of them harbours more than four. This study demonstrates the significant diversity of Actinobacteria in the fish gut microbiota and it's potential to produce biologically active compounds. Copyright © 2015 Elsevier GmbH. All rights reserved.

Molecular analysis of Leptospira spp. isolated from humans by restriction fragment length polymorphism, real-time PCR and pulsed-field gel electrophoresis.

PubMed

Turk, Nenad; Milas, Zoran; Mojcec, Vesna; Ruzic-Sabljic, Eva; Staresina, Vilim; Stritof, Zrinka; Habus, Josipa; Postic, Daniele

2009-11-01

A total of 17 Leptospira clinical strains isolated from humans in Croatia were serologically and genetically analysed. For serovar identification, the microscopic agglutination test (MAT) and pulsed-field gel electrophoresis (PFGE) were used. To identify isolates on genomic species level, PCR-based restriction fragment length polymorphism (RFLP) and real-time PCR were performed. MAT revealed the following serogroup affinities: Grippotyphosa (seven isolates), Icterohaemorrhagiae (eight isolates) and Javanica (two isolates). RFLP of PCR products from a 331-bp-long fragment of rrs (16S rRNA gene) digested with endonucleases MnlI and DdeI and real-time PCR revealed three Leptospira genomic species. Grippotyphosa isolates belonged to Leptospira kirschneri, Icterohaemorrhagiae isolates to Leptospira interrogans and Javanica isolates to Leptospira borgpetersenii. Genomic DNA from 17 leptospiral isolates was digested with NotI and SgrAI restriction enzymes and analysed by PFGE. Results showed that seven isolates have the same binding pattern to serovar Grippotyphosa, eight isolates to serovar Icterohaemorrhagiae and two isolates to serovar Poi. Results demonstrate the diversity of leptospires circulating in Croatia. We point out the usefulness of a combination of PFGE, RFLP and real-time PCR as appropriate molecular methods in molecular analysis of leptospires.

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

PubMed Central

Baig, Abiyad; Weinert, Lucy A.; Peters, Sarah E.; Howell, Kate J.; Chaudhuri, Roy R.; Wang, Jinhong; Holden, Matthew T. G.; Parkhill, Julian; Langford, Paul R.; Rycroft, Andrew N.; Wren, Brendan W.; Tucker, Alexander W.; Maskell, Duncan J.

2015-01-01

Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species. PMID:26583006

Circulation of Highly Drug-Resistant Clostridium difficile Ribotypes 027 and 001 in Two Tertiary-Care Hospitals in Mexico.

PubMed

Martínez-Meléndez, Adrián; Tijerina-Rodríguez, Laura; Morfin-Otero, Rayo; Camacho-Ortíz, Adrián; Villarreal-Treviño, Licet; Sánchez-Alanís, Hugo; Rodríguez-Noriega, Eduardo; Baines, Simon D; Flores-Treviño, Samantha; Maldonado-Garza, Héctor Jesús; Garza-González, Elvira

2018-05-01

To assess drug susceptibility and characterize Clostridium difficile ribotypes in isolates from two tertiary-care hospitals in Mexico. Isolates were evaluated for genotyping, antimicrobial susceptibility testing and detection of mutations associated with drug resistance. PCR ribotyping was performed using a combination of gel-based and capillary electrophoresis-based approaches. MIC 50 and MIC 90 were ≥128 mg/L for ciprofloxacin, erythromycin, clindamycin, and rifampicin. There was no reduced susceptibility to metronidazole or tetracycline; however, reduced susceptibility to vancomycin (≥4 mg/L) and fidaxomicin (≥2 mg/L) was detected in 50 (40.3%) and 4 (3.2%) isolates, respectively. Furthermore, the rpoB Arg505Lys mutation was more frequently detected in isolates with high minimum inhibitory concentration (MIC) to rifampicin (≥32 mg/L) (OR = 52.5; 95% CI = 5.17-532.6; p < 0.000). Of the 124 C. difficile isolates recovered, 84 (66.7%) were of ribotype 027, 18 (14.5%) of ribotype 001, and the remainder were other ribotypes (353, 255, 220, 208, 176, 106, 076, 020, 019, 017, 014, 012, 003, and 002). Ribotypes 027 and 001 were the most frequent C. difficile isolates recovered in this study, and demonstrated higher MICs. Furthermore, we found four isolates with reduced susceptibility to fidaxomicin, raising a concern since this drug is currently unavailable in Mexican Hospitals.

Enterobacter mori sp. nov., associated with bacterial wilt on Morus alba L.

PubMed

Zhu, Bo; Lou, Miao-Miao; Xie, Guan-Lin; Wang, Guo-Fen; Zhou, Qin; Wang, Fang; Fang, Yuan; Su, Ting; Li, Bin; Duan, Yong-Pin

2011-11-01

Two isolates of mulberry-pathogenic bacteria isolated from diseased mulberry roots were investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strains R18-2(T) and R3-3 to the genus Enterobacter, with Enterobacter asburiae, E. amnigenus, E. cancerogenus, E. cloacae subsp. cloacae, E. cloacae subsp. dissolvens and E. nimipressuralis as their closest relatives. Cells of the isolates were Gram-negative, facultatively anaerobic rods, 0.3-1.0 µm wide and 0.8-2.0 µm long, with peritrichous flagella, showing a DNA G+C content of 55.1 ± 0.5 mol%. Calculation of a similarity index based on phenotypic features and fatty acid methyl ester (FAME) analysis suggested that these isolates are members of E. cancerogenus or E. asburiae or a closely related species. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by the presence of lysine decarboxylase activity and their ability to utilize d-arabitol. DNA-DNA relatedness also distinguished the two isolates from phylogenetically closely related Enterobacter strains. Based on these data, it is proposed that the isolates represent a novel species of the genus Enterobacter, named Enterobacter mori sp. nov. The type strain is R18-2(T) ( = CGMCC 1.10322(T) = LMG 25706(T)).

Analysis of Chromobacterium sp. natural isolates from different Brazilian ecosystems

PubMed Central

Lima-Bittencourt, Cláudia I; Astolfi-Filho, Spartaco; Chartone-Souza, Edmar; Santos, Fabrício R; Nascimento, Andréa MA

2007-01-01

Background Chromobacterium violaceum is a free-living bacterium able to survive under diverse environmental conditions. In this study we evaluate the genetic and physiological diversity of Chromobacterium sp. isolates from three Brazilian ecosystems: Brazilian Savannah (Cerrado), Atlantic Rain Forest and Amazon Rain Forest. We have analyzed the diversity with molecular approaches (16S rRNA gene sequences and amplified ribosomal DNA restriction analysis) and phenotypic surveys of antibiotic resistance and biochemistry profiles. Results In general, the clusters based on physiological profiles included isolates from two or more geographical locations indicating that they are not restricted to a single ecosystem. The isolates from Brazilian Savannah presented greater physiologic diversity and their biochemical profile was the most variable of all groupings. The isolates recovered from Amazon and Atlantic Rain Forests presented the most similar biochemical characteristics to the Chromobacterium violaceum ATCC 12472 strain. Clusters based on biochemical profiles were congruent with clusters obtained by the 16S rRNA gene tree. According to the phylogenetic analyses, isolates from the Amazon Rain Forest and Savannah displayed a closer relationship to the Chromobacterium violaceum ATCC 12472. Furthermore, 16S rRNA gene tree revealed a good correlation between phylogenetic clustering and geographic origin. Conclusion The physiological analyses clearly demonstrate the high biochemical versatility found in the C. violaceum genome and molecular methods allowed to detect the intra and inter-population diversity of isolates from three Brazilian ecosystems. PMID:17584942

Phylogenetic Identification of Fungi Isolated from the Marine Sponge Tethya aurantium and Identification of Their Secondary Metabolites

PubMed Central

Wiese, Jutta; Ohlendorf, Birgit; Blümel, Martina; Schmaljohann, Rolf; Imhoff, Johannes F.

2011-01-01

Fungi associated with the marine sponge Tethya aurantium were isolated and identified by morphological criteria and phylogenetic analyses based on internal transcribed spacer (ITS) regions. They were evaluated with regard to their secondary metabolite profiles. Among the 81 isolates which were characterized, members of 21 genera were identified. Some genera like Acremonium, Aspergillus, Fusarium, Penicillium, Phoma, and Trichoderma are quite common, but we also isolated strains belonging to genera like Botryosphaeria, Epicoccum, Parasphaeosphaeria, and Tritirachium which have rarely been reported from sponges. Members affiliated to the genera Bartalinia and Volutella as well as to a presumably new Phoma species were first isolated from a sponge in this study. On the basis of their classification, strains were selected for analysis of their ability to produce natural products. In addition to a number of known compounds, several new natural products were identified. The scopularides and sorbifuranones have been described elsewhere. We have isolated four additional substances which have not been described so far. The new metabolite cillifuranone (1) was isolated from Penicillium chrysogenum strain LF066. The structure of cillifuranone (1) was elucidated based on 1D and 2D NMR analysis and turned out to be a previously postulated intermediate in sorbifuranone biosynthesis. Only minor antibiotic bioactivities of this compound were found so far. PMID:21731550

Predicting Virulence of Aeromonas Isolates Based-on Changes in Transcription of c-jun and c-fos in Human Tissue Culture Cells

EPA Science Inventory

Aims: To assess virulence of Aeromonas isolates based on the change in regulation of c-jun and c-fos in the human intestinal tissue culture cell line Caco-2. Methods and Results: Aeromonas cells were added to Caco-2 cells at approximately a one to one ratio. After 1, 2 and 3 ...

Isolation of histamine-producing Lactobacillus buchneri from Swiss cheese implicated in a food poisoning outbreak.

PubMed Central

Sumner, S S; Speckhard, M W; Somers, E B; Taylor, S L

1985-01-01

A histamine-producing strain of Lactobacillus buchneri was isolated from Swiss cheese that had been implicated in an outbreak of histamine poisoning. It produced up to 4,070 nmol of histamine per ml in MRS broth supplemented with 0.1% histidine. The identification of this isolate was based on its biochemical, bacteriological, and DNA characterizations. PMID:4083875

Matrix isolation sublimation: An apparatus for producing cryogenic beams of atoms and molecules

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

Sacramento, R. L.; Alves, B. X.; Silva, B. A.

2015-07-15

We describe the apparatus to generate cryogenic beams of atoms and molecules based on matrix isolation sublimation. Isolation matrices of Ne and H{sub 2} are hosts for atomic and molecular species which are sublimated into vacuum at cryogenic temperatures. The resulting cryogenic beams are used for high-resolution laser spectroscopy. The technique also aims at loading atomic and molecular traps.

Phytochemical investigation and hair growth studies on the rhizomes of Nardostachys jatamansi DC

PubMed Central

Gottumukkala, Venkateswara Rao; Annamalai, Tiruganasambandham; Mukhopadhyay, Triptikumar

2011-01-01

Nardostachys jatamansi DC rhizomes were subjected to extraction, fractionation, and isolation of terpenoid compounds. Three terpenoid compounds were isolated which are nardal, jatamansic acid, and nardin. These compounds were identified based on physical and spectral data (UV, IR,1H and13C NMR, 2D NMR, Mass) and comparison with authentic compounds. The crude extract, fractions, and two of the isolated compounds were tested for their hair growth activity. The hair growth studies showed good activities for the extract, fraction, and the isolated compounds. PMID:21716625

[Isolation of C. pyloridis from children].

PubMed

Spirina, T S; Bokser, G V; Safonova, T B; Taranenko, L A; Levitskaia, S V

1989-01-01

The authors analyze the findings of gastroduodenal biopsies in 25 children aged 6 to 15 years suffering from mucosal inflammations and functional abnormalities of the upper portions of the digestive tract. Chocolate agar with various bases, one of which has been suggested by the authors, has been used for the isolation of C. pyloridis. Five cultures have been isolated. Microscopic examinations and biochemical identification of the isolates have lead the authors to a conclusion that campylobacter infections of the upper digestive tract may be diagnosed with certainty only after a comprehensive bacteriologic examination.

Differentiation among isolates of prunus necrotic ringspot virus by transcript conformation polymorphism.

PubMed

Rosner, A; Maslenin, L; Spiegel, S

1998-09-01

A method based on differences in electrophoretic mobility of RNA transcripts made from polymerase chain reaction (PCR) products was used for differentiation among virus isolates. A T7 RNA polymerase promoter was attached to amplified prunus necrotic ringspot virus (PNRSV) sequences by PCR. The PCR products then served as a template for transcription. Single-stranded transcripts originated from different PNRSV isolates varied in electrophoretic mobility in polyacrylamide gels, presumably because of transcript conformation polymorphism (TCP). This procedure was applied for the differentiation of PNRSV isolates.

Advanced BCD technology with vertical DMOS based on a semi-insulation structure

NASA Astrophysics Data System (ADS)

Kui, Ma; Xinghua, Fu; Jiexin, Lin; Fashun, Yang

2016-07-01

A new semi-insulation structure in which one isolated island is connected to the substrate was proposed. Based on this semi-insulation structure, an advanced BCD technology which can integrate a vertical device without extra internal interconnection structure was presented. The manufacturing of the new semi-insulation structure employed multi-epitaxy and selectively multi-doping. Isolated islands are insulated with the substrate by reverse-biased PN junctions. Adjacent isolated islands are insulated by isolation wall or deep dielectric trenches. The proposed semi-insulation structure and devices fixed in it were simulated through two-dimensional numerical computer simulators. Based on the new BCD technology, a smart power integrated circuit was designed and fabricated. The simulated and tested results of Vertical DMOS, MOSFETs, BJTs, resistors and diodes indicated that the proposed semi-insulation structure is reasonable and the advanced BCD technology is validated. Project supported by the National Natural Science Foundation of China (No. 61464002), the Science and Technology Fund of Guizhou Province (No. Qian Ke He J Zi [2014]2066), and the Dr. Fund of Guizhou University (No. Gui Da Ren Ji He Zi (2013)20Hao).

Molecular epidemiological investigation of velogenic Newcastle disease viruses from village chickens in Cambodia.

PubMed

Choi, Kang-Seuk; Kye, Soo-Jeong; Kim, Ji-Ye; Damasco, Vanessa R; Sorn, San; Lee, Youn-Jeong; Choi, Jun-Gu; Kang, Hyun-Mi; Kim, Kwang-Il; Song, Byung-Min; Lee, Hee-Soo

2013-10-01

Three isolates of Newcastle disease virus (NDV) were isolated from tracheal samples of dead village chickens in two provinces (Phnom Penh and Kampong Cham) in Cambodia during 2011-2012. All of these Cambodian NDV isolates were categorized as velogenic pathotype, based on in vivo pathogenicity tests and F cleavage site motif sequence ((112)RRRKRF(117)). The phylogenetic analysis and the evolutionary distances based on the sequences of the F gene revealed that all the three field isolates of NDV from Cambodia form a distinct cluster (VIIh) together with three Indonesian strains and were assigned to the genotype VII within the class II. Further phylogenetic analysis based on the hyper-variable region of the F gene revealed that some of NDV strains from Malaysia since the mid-2000s were also classified into the VIIh virus. This indicates that the VIIh NDVs are spreading through Southeast Asia. The present investigation, therefore, emphasizes the importance of further surveillance of NDV in neighboring countries as well as throughout Southeast Asia to contain further spreading of these VIIh viruses.

False star detection and isolation during star tracking based on improved chi-square tests.

PubMed

Zhang, Hao; Niu, Yanxiong; Lu, Jiazhen; Yang, Yanqiang; Su, Guohua

2017-08-01

The star sensor is a precise attitude measurement device for a spacecraft. Star tracking is the main and key working mode for a star sensor. However, during star tracking, false stars become an inevitable interference for star sensor applications, which may result in declined measurement accuracy. A false star detection and isolation algorithm in star tracking based on improved chi-square tests is proposed in this paper. Two estimations are established based on a Kalman filter and a priori information, respectively. The false star detection is operated through adopting the global state chi-square test in a Kalman filter. The false star isolation is achieved using a local state chi-square test. Semi-physical experiments under different trajectories with various false stars are designed for verification. Experiment results show that various false stars can be detected and isolated from navigation stars during star tracking, and the attitude measurement accuracy is hardly influenced by false stars. The proposed algorithm is proved to have an excellent performance in terms of speed, stability, and robustness.

Identification of Mucorales From Clinical Specimens: A 4-Year Experience in a Single Institution

PubMed Central

Yang, Mina; Lee, Jang Ho; Kim, Young-Kwon; Ki, Chang-Seok

2016-01-01

Mucormycosis, a fatal opportunistic infection in immunocompromised hosts, is caused by fungi belonging to the order Mucorales. Early diagnosis based on exact identification and multidisciplinary treatments is critical. However, identification of Mucorales fungi is difficult and often delayed, resulting in poor prognosis. This study aimed to compare the results of phenotypic and molecular identification of 12 Mucorales isolates collected from 4-yr-accumulated data. All isolates were identified on the basis of phenotypic characteristics such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing were performed to target internal transcribed spacer (ITS) and/or D1/D2 regions. Target DNA sequencing identified five Lichtheimia isolates, two Rhizopus microsporus isolates, two Rhizomucor pusillus isolates, one Cunninghamella bertholletiae isolate, one Mucor fragilis isolate, and one Syncephalastrum racemosum isolate. Five of the 12 (41.7%) isolates were incorrectly identified on the basis of phenotypic identification. DNA sequencing showed that of these five isolates, two were Lichtheimia isolates, one was Mucor isolate, one was Rhizomucor isolate, and one was Rhizopus microspores. All the isolates were identified at the species level by ITS and/or D1/D2 analyses. Phenotypic differentiation and identification of Mucorales is difficult because different Mucorales share similar morphology. Our results indicate that the molecular methods employed in this study are valuable for identifying Mucorales. PMID:26522761

Identification of mucorales from clinical specimens: a 4-year experience in a single institution.

PubMed

Yang, Mina; Lee, Jang Ho; Kim, Young Kwon; Ki, Chang Seok; Huh, Hee Jae; Lee, Nam Yong

2016-01-01

Mucormycosis, a fatal opportunistic infection in immunocompromised hosts, is caused by fungi belonging to the order Mucorales. Early diagnosis based on exact identification and multidisciplinary treatments is critical. However, identification of Mucorales fungi is difficult and often delayed, resulting in poor prognosis. This study aimed to compare the results of phenotypic and molecular identification of 12 Mucorales isolates collected from 4-yr-accumulated data. All isolates were identified on the basis of phenotypic characteristics such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing were performed to target internal transcribed spacer (ITS) and/or D1/D2 regions. Target DNA sequencing identified five Lichtheimia isolates, two Rhizopus microsporus isolates, two Rhizomucor pusillus isolates, one Cunninghamella bertholletiae isolate, one Mucor fragilis isolate, and one Syncephalastrum racemosum isolate. Five of the 12 (41.7%) isolates were incorrectly identified on the basis of phenotypic identification. DNA sequencing showed that of these five isolates, two were Lichtheimia isolates, one was Mucor isolate, one was Rhizomucor isolate, and one was Rhizopus microspores. All the isolates were identified at the species level by ITS and/or D1/D2 analyses. Phenotypic differentiation and identification of Mucorales is difficult because different Mucorales share similar morphology. Our results indicate that the molecular methods employed in this study are valuable for identifying Mucorales.

The Effect of Information Communication Technology Interventions on Reducing Social Isolation in the Elderly: A Systematic Review.

PubMed

Chen, Yi-Ru Regina; Schulz, Peter J

2016-01-28

The aging of the population is an inexorable change that challenges governments and societies in every developed country. Based on clinical and empirical data, social isolation is found to be prevalent among elderly people, and it has negative consequences on the elderly's psychological and physical health. Targeting social isolation has become a focus area for policy and practice. Evidence indicates that contemporary information and communication technologies (ICT) have the potential to prevent or reduce the social isolation of elderly people via various mechanisms. This systematic review explored the effects of ICT interventions on reducing social isolation of the elderly. Relevant electronic databases (PsycINFO, PubMed, MEDLINE, EBSCO, SSCI, Communication Studies: a SAGE Full-Text Collection, Communication & Mass Media Complete, Association for Computing Machinery (ACM) Digital Library, and IEEE Xplore) were systematically searched using a unified strategy to identify quantitative and qualitative studies on the effectiveness of ICT-mediated social isolation interventions for elderly people published in English between 2002 and 2015. Narrative synthesis was performed to interpret the results of the identified studies, and their quality was also appraised. Twenty-five publications were included in the review. Four of them were evaluated as rigorous research. Most studies measured the effectiveness of ICT by measuring specific dimensions rather than social isolation in general. ICT use was consistently found to affect social support, social connectedness, and social isolation in general positively. The results for loneliness were inconclusive. Even though most were positive, some studies found a nonsignificant or negative impact. More importantly, the positive effect of ICT use on social connectedness and social support seemed to be short-term and did not last for more than six months after the intervention. The results for self-esteem and control over one's life were consistent but generally nonsignificant. ICT was found to alleviate the elderly's social isolation through four mechanisms: connecting to the outside world, gaining social support, engaging in activities of interests, and boosting self-confidence. More well-designed studies that contain a minimum risk of research bias are needed to draw conclusions on the effectiveness of ICT interventions for elderly people in reducing their perceived social isolation as a multidimensional concept. The results of this review suggest that ICT could be an effective tool to tackle social isolation among the elderly. However, it is not suitable for every senior alike. Future research should identify who among elderly people can most benefit from ICT use in reducing social isolation. Research on other types of ICT (eg, mobile phone-based instant messaging apps) should be conducted to promote understanding and practice of ICT-based social-isolation interventions for elderly people.

The Effect of Information Communication Technology Interventions on Reducing Social Isolation in the Elderly: A Systematic Review

PubMed Central

Schulz, Peter J

2016-01-01

Background The aging of the population is an inexorable change that challenges governments and societies in every developed country. Based on clinical and empirical data, social isolation is found to be prevalent among elderly people, and it has negative consequences on the elderly’s psychological and physical health. Targeting social isolation has become a focus area for policy and practice. Evidence indicates that contemporary information and communication technologies (ICT) have the potential to prevent or reduce the social isolation of elderly people via various mechanisms. Objective This systematic review explored the effects of ICT interventions on reducing social isolation of the elderly. Methods Relevant electronic databases (PsycINFO, PubMed, MEDLINE, EBSCO, SSCI, Communication Studies: a SAGE Full-Text Collection, Communication & Mass Media Complete, Association for Computing Machinery (ACM) Digital Library, and IEEE Xplore) were systematically searched using a unified strategy to identify quantitative and qualitative studies on the effectiveness of ICT-mediated social isolation interventions for elderly people published in English between 2002 and 2015. Narrative synthesis was performed to interpret the results of the identified studies, and their quality was also appraised. Results Twenty-five publications were included in the review. Four of them were evaluated as rigorous research. Most studies measured the effectiveness of ICT by measuring specific dimensions rather than social isolation in general. ICT use was consistently found to affect social support, social connectedness, and social isolation in general positively. The results for loneliness were inconclusive. Even though most were positive, some studies found a nonsignificant or negative impact. More importantly, the positive effect of ICT use on social connectedness and social support seemed to be short-term and did not last for more than six months after the intervention. The results for self-esteem and control over one’s life were consistent but generally nonsignificant. ICT was found to alleviate the elderly’s social isolation through four mechanisms: connecting to the outside world, gaining social support, engaging in activities of interests, and boosting self-confidence. Conclusions More well-designed studies that contain a minimum risk of research bias are needed to draw conclusions on the effectiveness of ICT interventions for elderly people in reducing their perceived social isolation as a multidimensional concept. The results of this review suggest that ICT could be an effective tool to tackle social isolation among the elderly. However, it is not suitable for every senior alike. Future research should identify who among elderly people can most benefit from ICT use in reducing social isolation. Research on other types of ICT (eg, mobile phone–based instant messaging apps) should be conducted to promote understanding and practice of ICT-based social-isolation interventions for elderly people. PMID:26822073

Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri

PubMed Central

2009-01-01

Background Shigella flexneri is one of the causative agents of shigellosis, a major cause of childhood mortality in developing countries. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related bacterial isolates for investigation of disease outbreaks and provide information for establishing phylogenetic patterns among isolates. The present study aimed to develop an MLVA method for S. flexneri and the VNTR loci identified were tested on 242 S. flexneri isolates to evaluate their variability in various serotypes. The isolates were also analyzed by pulsed-field gel electrophoresis (PFGE) to compare the discriminatory power and to evaluate the usefulness of MLVA as a tool for phylogenetic analysis of S. flexneri. Results Thirty-six VNTR loci were identified by exploring the repeat sequence loci in genomic sequences of Shigella species and by testing the loci on nine isolates of different subserotypes. The VNTR loci in different serotype groups differed greatly in their variability. The discriminatory power of an MLVA assay based on four most variable VNTR loci was higher, though not significantly, than PFGE for the total isolates, a panel of 2a isolates, which were relatively diverse, and a panel of 4a/Y isolates, which were closely-related. Phylogenetic groupings based on PFGE patterns and MLVA profiles were considerably concordant. The genetic relationships among the isolates were correlated with serotypes. The phylogenetic trees constructed using PFGE patterns and MLVA profiles presented two distinct clusters for the isolates of serotype 3 and one distinct cluster for each of the serotype groups, 1a/1b/NT, 2a/2b/X/NT, 4a/Y, and 6. Isolates that had different serotypes but had closer genetic relatedness than those with the same serotype were observed between serotype Y and subserotype 4a, serotype X and subserotype 2b, subserotype 1a and 1b, and subserotype 3a and 3b. Conclusions The 36 VNTR loci identified exhibited considerably different degrees of variability among S. flexneri serotype groups. VNTR locus could be highly variable in a serotype but invariable in others. MLVA assay based on four highly variable loci could display a comparable resolving power to PFGE in discriminating isolates. MLVA is also a prominent molecular tool for phylogenetic analysis of S. flexneri; the resulting data are beneficial to establish clear clonal patterns among different serotype groups and to discern clonal groups among isolates within the same serotype. As highly variable VNTR loci could be serotype-specific, a common MLVA protocol that consists of only a small set of loci, for example four to eight loci, and that provides high resolving power to all S. flexneri serotypes may not be obtainable. PMID:20042119

Genetic relatedness of Trichoderma isolates antagonistic against Fusarium oxysporum f.sp. dianthi inflicting carnation wilt.

PubMed

Shanmugam, V; Sharma, Vivek; Ananthapadmanaban

2008-01-01

Twenty-eight isolates of Trichoderma belonging to four different species were screened in vitro for their antagonistic ability against Fusarium oxysporum f.sp. dianthi causing carnation wilt. Three different levels of antagonism observed in dual plate assay were further confirmed by cell-free culture filtrate experiments. Isolates showing class I level of antagonism produced maximum lytic enzymes, chitinases and beta-1,3-glucanases. Genetic variability of 25 selected isolates was assessed by random amplified polymorphic DNA technique and the amplified products were correlated for their level of antagonism. Unweighed pair-group method with arithmetical averages cluster analysis revealed prominent inter-and intraspecific genetic variation among the isolates. Based on their genetic relationship, the isolates were mainly distributed into 3 major groups representing T. atroviride, T. pseudokoningii and T. harzianum, with 20-35% interspecific dissimilarity. However, the polymorphism shown by the isolates did not correlate to their level of antagonism.

The neuroendocrinology of social isolation.

PubMed

Cacioppo, John T; Cacioppo, Stephanie; Capitanio, John P; Cole, Steven W

2015-01-03

Social isolation has been recognized as a major risk factor for morbidity and mortality in humans for more than a quarter of a century. Although the focus of research has been on objective social roles and health behavior, the brain is the key organ for forming, monitoring, maintaining, repairing, and replacing salutary connections with others. Accordingly, population-based longitudinal research indicates that perceived social isolation (loneliness) is a risk factor for morbidity and mortality independent of objective social isolation and health behavior. Human and animal investigations of neuroendocrine stress mechanisms that may be involved suggest that (a) chronic social isolation increases the activation of the hypothalamic pituitary adrenocortical axis, and (b) these effects are more dependent on the disruption of a social bond between a significant pair than objective isolation per se. The relational factors and neuroendocrine, neurobiological, and genetic mechanisms that may contribute to the association between perceived isolation and mortality are reviewed.

Rise of CC398 Lineage of Staphylococcus aureus among Infective Endocarditis Isolates Revealed by Two Consecutive Population-Based Studies in France

PubMed Central

Tristan, Anne; Rasigade, Jean-Philippe; Ruizendaal, Esmée; Laurent, Frédéric; Bes, Michèle; Meugnier, Hélène; Lina, Gérard; Etienne, Jerome; Celard, Marie; Tattevin, Pierre; Monecke, Stefan; Le Moing, Vincent; Vandenesch, François

2012-01-01

Staphylococcus aureus isolates from two prospective studies on infective endocarditis (IE) conducted in 1999 and 2008 and isolated from non-IE bacteremia collected in 2006 were spa-typed and their virulence factors were analyzed with a microarray. Both populations were genetically diverse, with no virulence factors or genotypes significantly more associated with the IE isolates compared with the non-IE isolates. The population structure of the IE isolates did not change much between 1999 and 2008, with the exception of the appearance of CC398 methicillin-susceptible Staphylococcus aureus (MSSA) isolates responsible for 5.6% of all cases in 2008. In 1999, this lineage was responsible for no cases. The increasing prevalence of S. aureus in IE is apparently not the result of a major change in staphylococcal population structure over time, with the exception of the emerging CC398 MSSA lineage. PMID:23272091

The Neuroendocrinology of Social Isolation

PubMed Central

Cacioppo, John T.; Cacioppo, Stephanie; Capitanio, John P.; Cole, Steven W.

2016-01-01

Social isolation has been recognized as a major risk factor for morbidity and mortality in humans for more than a quarter of a century. Although the focus of research has been on objective social roles and health behavior, the brain is the key organ for forming, monitoring, maintaining, repairing, and replacing salutary connections with others. Accordingly, population-based longitudinal research indicates that perceived social isolation (loneliness) is a risk factor for morbidity and mortality independent of objective social isolation and health behavior. Human and animal investigations of neuroendocrine stress mechanisms that may be involved suggest that (a) chronic social isolation increases the activation of the hypothalamic pituitary adrenocortical axis, and (b) these effects are more dependent on the disruption of a social bond between a significant pair than objective isolation per se. The relational factors and neuroendocrine, neurobiological, and genetic mechanisms that may contribute to the association between perceived isolation and mortality are reviewed. PMID:25148851

Characterization of apple stem grooving virus and apple chlorotic leaf spot virus identified in a crab apple tree.

PubMed

Li, Yongqiang; Deng, Congliang; Bian, Yong; Zhao, Xiaoli; Zhou, Qi

2017-04-01

Apple stem grooving virus (ASGV), apple chlorotic leaf spot virus (ACLSV), and prunus necrotic ringspot virus (PNRSV) were identified in a crab apple tree by small RNA deep sequencing. The complete genome sequence of ACLSV isolate BJ (ACLSV-BJ) was 7554 nucleotides and shared 67.0%-83.0% nucleotide sequence identity with other ACLSV isolates. A phylogenetic tree based on the complete genome sequence of all available ACLSV isolates showed that ACLSV-BJ clustered with the isolates SY01 from hawthorn, MO5 from apple, and JB, KMS and YH from pear. The complete nucleotide sequence of ASGV-BJ was 6509 nucleotides (nt) long and shared 78.2%-80.7% nucleotide sequence identity with other isolates. ASGV-BJ and the isolate ASGV_kfp clustered together in the phylogenetic tree as an independent clade. Recombination analysis showed that isolate ASGV-BJ was a naturally occurring recombinant.

Genetic heterogeneity of the dnaK gene locus including transcription terminator region (TTR) in Campylobacter lari.

PubMed

Shitara, M; Tsuboi, Y; Sekizuka, T; Tazumi, A; Moorei, J E; Millar, B C; Taneike, I; Matsuda, M

2008-01-01

Nucleotide sequences of approximately 3.1 kbp consisting of the full-length open reading frame (ORF) for grpE, a non-coding (NC) region and a putative ORF for the full-length dnaK gene (1860 bp) were identified from a urease-positive thermophilic Campylobacter (UPTC) CF89-12 isolate. Then, following the construction of a new degenerate polymerase chain reaction (PCR) primer pair for amplification of the dnaK structural gene, including the transcription terminator region of C. lari isolates, the dnaK region was amplified successfully, TA-cloned and sequenced in nine C. lari isolates. The dnaK gene sequences commenced with an ATG and terminated with a TAA in all 10 isolates, including CF89-12. In addition, the putative ORFs for the dnaK gene locus from seven UPTC isolates consisted of 1860 bases, and the four urease-negative (UN) C. lari isolates included C. lari RM2100 reference strain 1866. Interestingly, different probable ribosome binding sites and hypothetically intrinsic p-independent terminator structures were identified between the seven UPTC and four UN C. lari isolates, respectively. Moreover, it is interesting to note that 20 out of a total of 28 polymorphic sites occurred among amino acid sequences of the dnaK ORF from 11 C. lari isolates, identified to be alternatively UPTC-specific or UN C. lari-specific. In the neighbour-joining tree based on the nucleotide sequence information of the dnaK gene, C. lari forms two major distinct clusters consisting of UPTC and UN C. lari isolates, respectively, with UN C. lari being more closely related to other thermophilic campylobacters than to UPTC.

Sweetened ethanol drinking during social isolation: enhanced intake, resistance to genetic heterogeneity and the emergence of a distinctive drinking pattern in adolescent mice.

PubMed

Panksepp, J B; Rodriguez, E D; Ryabinin, A E

2017-03-01

With its ease of availability during adolescence, sweetened ethanol ('alcopops') is consumed within many contexts. We asked here whether genetically based differences in social motivation are associated with how the adolescent social environment impacts voluntary ethanol intake. Mice with previously described differences in sociability (BALB/cJ, C57BL/6J, FVB/NJ and MSM/MsJ strains) were weaned into isolation or same-sex pairs (postnatal day, PD, 21), and then given continuous access to two fluids on PDs 34-45: one containing water and the other containing an ascending series of saccharin-sweetened ethanol (3-6-10%). Prior to the introduction of ethanol (PDs 30-33), increased water and food intake was detected in some of the isolation-reared groups, and controls indicated that isolated mice also consumed more 'saccharin-only' solution. Voluntary drinking of 'ethanol-only' was also higher in a subset of the isolated groups on PDs 46-49. However, sweetened ethanol intake was increased in all isolated strain × sex combinations irrespective of genotype. Surprisingly, blood ethanol concentration (BEC) was not different between these isolate and socially housed groups 4 h into the dark phase. Using lickometer-based measures of intake in FVB mice, we identified that a predominance of increased drinking during isolation transpired outside of the typical circadian consumption peak, occurring ≈8.5 h into the dark phase, with an associated difference in BEC. These findings collectively indicate that isolate housing leads to increased consumption of rewarding substances in adolescent mice independent of their genotype, and that for ethanol this may be because of when individuals drink during the circadian cycle. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Emergence of multidrug-resistant Proteus mirabilis in a long-term care facility in Croatia.

PubMed

Bedenić, Branka; Firis, Nataša; Elveđi-Gašparović, Vesna; Krilanović, Marija; Matanović, Krešimir; Štimac, Iva; Luxner, Josefa; Vraneš, Jasmina; Meštrović, Tomislav; Zarfel, Gernot; Grisold, Andrea

2016-06-01

An increased frequency of Proteus mirabilis isolates resistant to expanded-spectrum cephalosporins was observed recently in a long-term care facility in Zagreb (Godan). The aim of this study was the molecular characterization of resistance mechanisms to new cephalosporins in P. mirabilis isolates from this nursing home. Thirty-eight isolates collected from 2013-2015 showing reduced susceptibility to ceftazidime were investigated. Antibiotic susceptibilities were determined by broth microdilution method. Inhibitor-based tests were performed to detect extended-spectrum (ESBLs) and AmpC β-lactamases. AmpC β-lactamases were characterized by polymerase chain reaction (PCR) followed by sequencing of bla ampC genes. Quinolone resistance determinants (qnr genes) were characterized by PCR. Genotyping of the isolates was performed by repetitive element sequence (rep)-PCR and pulsed-field gel electrophoresis (PFGE). Presence of an AmpC β-lactamase was confirmed in all isolates by combined-disk test with phenylboronic acid. All isolates were resistant to amoxicillin alone and combined with clavulanate, cefotaxime, ceftriaxone, cefoxitin, and ciprofloxacin; but susceptible to cefepime, imipenem, and meropenem. PCR followed by sequencing using primers targeting bla ampc genes revealed CMY-16 β-lactamase in all but one strain. Bla cmy-16 was carried by a non-conjugative plasmid which did not belong to any known plasmid-based replicon typing (PBRT) group. Rep-PCR identified one large clone consisting of 15 isolates, three pairs or related isolates, one triplet, and four singletons. PFGE confirmed the clonality of the isolates. This is the first report of multidrug resistant P. mirabilis in a nursing home in Croatia. Cephalosporin resistance was due to plasmid-mediated AmpC β-lactamase CMY-16.

Selective isolation of magnetic nanoparticle-mediated heterogeneity subpopulation of circulating tumor cells using magnetic gradient based microfluidic system.

PubMed

Kwak, Bongseop; Lee, Jaehun; Lee, Dongkyu; Lee, Kangho; Kwon, Ohwon; Kang, Shinwon; Kim, Youngwoo

2017-02-15

Relocation mechanisms of the circulating tumor cells (CTCs) from the primary site to the secondary site through the blood vessel network cause tumor metastasis. Despite of the importance to diagnose the cancer metastasis by CTCs, still it is formidable challenge to use in the clinical purpose because of the rarity and the heterogeneity of CTCs in the cancer patient's peripheral blood sample. In this study we have developed magnetic force gradient based microfluidic chip (Mag-Gradient Chip) for isolating the total number of CTCs in the sample and characterizing the state of CTCs simultaneously with respect to the epithelial cell adhesion molecule (EpCAM) expression level. We have synthesized magnetic nanoparticles (MNPs) using hydrothermal method and functionalized anti-EpCAM on their surface for the specific binding with CTCs. The Mag-Gradient Chip designed to isolate and classify the CTCs by isolating at the different location in the chip using magnetic force differences depending on the EpCAM expression level. We observed 95.7% of EpCAM positive and 79.3% of EpCAM negative CTCs isolated in the Mag-Gradient Chip. At the same time, the 71.3% of isolated EpCAM positive CTCs were isolated at the first half area whereas the 76.9% of EpCAM negative CTCs were collected at the latter half area. The Mag-Gradient Chip can isolate the 3ml of heterogeneous CTCs sample in 1h with high isolating yield. The EpCAM expression level dose not means essential condition of the metastatic CTCs, but the Mag-Gradient Chip can shorten the date to diagnose the cancer metastasis in clinic. Copyright © 2016 Elsevier B.V. All rights reserved.

Using magnetic resonance imaging to determine the compartmental prevalence of knee joint structural damage.

PubMed

Stefanik, J J; Niu, J; Gross, K D; Roemer, F W; Guermazi, A; Felson, D T

2013-05-01

To describe the prevalence of magnetic resonance imaging (MRI) detected structural damage in the patellofemoral joint (PFJ) and tibiofemoral joint (TFJ) in a population-based cohort. A secondary aim was to evaluate the patterns of compartmental involvement in knees with pain, between men and women, and in different age and body mass index (BMI) categories. We studied 970 knees, one knee per subject, from the Framingham Osteoarthritis Study, a population-based cohort study of persons 51-92 years old. Cartilage damage and bone marrow lesions (BMLs) were assessed using the Whole Organ Magnetic Resonance Imaging Score (WORMS). The prevalence of isolated PFJ, isolated TFJ, and mixed structural damage was determined using the following definitions: any cartilage damage, full thickness cartilage loss, any BML, and the combination of full thickness cartilage loss with any BML. The mean age and BMI was 63.4 years and 28.6 m/kg(2), respectively; 57% were female. Isolated PFJ damage occurred in 15-20% of knees and isolated TFJ damage occurred in 8-17% of knees depending on the definition used. The prevalence of isolated PFJ damage was greater than isolated TFJ damage using all definitions except the any BML definition. This pattern was similar between genders and among age and BMI categories. In those with knee pain, isolated PFJ was at least as common as TFJ damage depending on the definition used. Using MRI to assess knee joint structural damage, isolated PFJ damage was at least as common as, if not more common than, isolated TFJ damage. Copyright © 2013 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

In vitro antagonistic activity, plant growth promoting traits and phylogenetic affiliation of rhizobacteria associated with wild plants grown in arid soil.

PubMed

El-Sayed, Wael S; Akhkha, Abdellah; El-Naggar, Moustafa Y; Elbadry, Medhat

2014-01-01

The role of plant growth-promoting rhizobacteria (PGPR) in adaptation of plants in extreme environments is not yet completely understood. For this study native bacteria were isolated from rhizospeheric arid soils and evaluated for both growth-promoting abilities and antagonistic potential against phytopathogenic fungi and nematodes. The phylogentic affiliation of these representative isolates was also characterized. Rhizobacteria associated with 11 wild plant species from the arid soil of Almadinah Almunawarah, Kingdom of Saudi Arabia (KSA) were investigated. From a total of 531 isolates, only 66 bacterial isolates were selected based on their ability to inhibit Fusarium oxysporum, and Sclerotinia sclerotiorum. The selected isolates were screened in vitro for activities related to plant nutrition and plant growth regulation as well as for antifungal and nematicidal traits. Isolated bacteria were found to exhibit capabilities in fix atmospheric nitrogen, produce ammonia, indoleacetic acid (IAA), siderophores, solubilize phosphate and zinc, and showed an antagonistic potential against some phytopathogenic fungi and one nematode species (Meloidogyne incognita) to various extent. Isolates were ranked by their potential ability to function as PGPR. The 66 isolates were genotyped using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. The taxonomic composition of the representative genotypes from both rhizosphere and rhizoplane comprised Bacillus, Enterobacter and Pseudomonas. Out of the 10 genotypes, three strains designated as PHP03, CCP05, and TAP02 might be regarded as novel strains based on their low similarity percentages and high bootstrap values. The present study clearly identified specific traits in the isolated rhizobacteria, which make them good candidates as PGPR and might contribute to plant adaption to arid environments. Application of such results in agricultural fields may improve and enhance plant growth in arid soils.

Identification of Mycobacterium spp. of veterinary importance using rpoB gene sequencing

PubMed Central

2011-01-01

Background Studies conducted on Mycobacterium spp. isolated from human patients indicate that sequencing of a 711 bp portion of the rpoB gene can be useful in assigning a species identity, particularly for members of the Mycobacterium avium complex (MAC). Given that MAC are important pathogens in livestock, companion animals, and zoo/exotic animals, we were interested in evaluating the use of rpoB sequencing for identification of Mycobacterium isolates of veterinary origin. Results A total of 386 isolates, collected over 2008 - June 2011 from 378 animals (amphibians, reptiles, birds, and mammals) underwent PCR and sequencing of a ~ 711 bp portion of the rpoB gene; 310 isolates (80%) were identified to the species level based on similarity at ≥ 98% with a reference sequence. The remaining 76 isolates (20%) displayed < 98% similarity with reference sequences and were assigned to a clade based on their location in a neighbor-joining tree containing reference sequences. For a subset of 236 isolates that received both 16S rRNA and rpoB sequencing, 167 (70%) displayed a similar species/clade assignation for both sequencing methods. For the remaining 69 isolates, species/clade identities were different with each sequencing method. Mycobacterium avium subsp. hominissuis was the species most frequently isolated from specimens from pigs, cervids, companion animals, cattle, and exotic/zoo animals. Conclusions rpoB sequencing proved useful in identifying Mycobacterium isolates of veterinary origin to clade, species, or subspecies levels, particularly for assemblages (such as the MAC) where 16S rRNA sequencing alone is not adequate to demarcate these taxa. rpoB sequencing can represent a cost-effective identification tool suitable for routine use in the veterinary diagnostic laboratory. PMID:22118247

Genetic variation among Flavobacterium psychrophilum isolates from wild and farmed salmonids in Norway and Chile.

PubMed

Apablaza, P; Løland, A D; Brevik, Ø J; Ilardi, P; Battaglia, J; Nylund, A

2013-04-01

To aim of the study was to describe the genetic relationship between isolates of Flavobacterium psychrophilum with a main emphasis of samples from Chile and Norway. The isolates have been obtained from farmed salmonids in Norway and Chile, and from wild salmonids in Norway, but isolates from North America and European countries are also included in the analysis. The study is based on phylogenetic analysis of 16S rRNA and seven housekeeping genes (HG), gyrB, atpA, dnaK, trpB, fumC, murG and tuf, and the use of a multilocus sequence typing (MLST) system, based on nucleotide polymorphism in the HG, as an alternative to the phylogenies. The variation within the selected genes was limited, and the phylogenetic analysis gave little resolution between the isolates. The MLST gave a much better resolution resulting in 53 sequence types where the same sequences types could be found in Chile, North America and European countries, and in different host species. Multilocus sequence typing give a relatively good separation of different isolates of Fl. psychrophilum and show that there are no distinct geographical or host-specific isolates in the studied material from Chile, North America and Europe. Nor was it possible to separate between isolates from ulcers and systemic infections vs isolates from the surface of healthy salmonids. This study shows a wide geographical distribution of Fl. psychrophilum, indicating that the bacterium has a large potential for transmission over long distances, and between different salmonid hosts species. This knowledge will be important for future management of salmonids diseases connected to Fl. psychrophilum. © 2013 The Society for Applied Microbiology.

Genetic Relatedness of Clostridium difficile Isolates from Various Origins Determined by Triple-Locus Sequence Analysis Based on Toxin Regulatory Genes tcdC, tcdR, and cdtR▿

PubMed Central

Bouvet, Philippe J. M.; Popoff, Michel R.

2008-01-01

A triple-locus nucleotide sequence analysis based on toxin regulatory genes tcdC, tcdR and cdtR was initiated to assess the sequence variability of these genes among Clostridium difficile isolates and to study the genetic relatedness between isolates. A preliminary investigation of the variability of the tcdC gene was done with 57 clinical and veterinary isolates. Twenty-three isolates representing nine main clusters were selected for tcdC, tcdR, and cdtR analysis. The numbers of alleles found for tcdC, tcdR and cdtR were nine, six, and five, respectively. All strains possessed the cdtR gene except toxin A-negative toxin B-positive variants. All but one binary toxin CDT-positive isolate harbored a deletion (>1 bp) in the tcdC gene. The combined analyses of the three genes allowed us to distinguish five lineages correlated with the different types of deletion in tcdC, i.e., 18 bp (associated or not with a deletion at position 117), 36 bp, 39 bp, and 54 bp, and with the wild-type tcdC (no deletion). The tcdR and tcdC genes, though located within the same pathogenicity locus, were found to have evolved separately. Coevolution of the three genes was noted only with strains harboring a 39-bp or a 54-bp deletion in tcdC that formed two homogeneous, separate divergent clusters. Our study supported the existence of the known clones (PCR ribotype 027 isolates and toxin A-negative toxin B-positive C. difficile variants) and evidence for clonality of isolates with a 39-bp deletion (toxinotype V, PCR ribotype 078) that are frequently isolated worldwide from human infections and from food animals. PMID:18832125

Isolation and purification of rabbit mesenchymal stem cells using an optimized protocol.

PubMed

Lin, Chunbo; Shen, Maorong; Chen, Weiping; Li, Xiaofeng; Luo, Daoming; Cai, Jinhong; Yang, Yuan

2015-11-01

Mesenchymal stem cells were first isolated and grown in vitro by Friedenstein over 40 yr ago; however, their isolation remains challenging as they lack unique markers for identification and are present in very small quantities in mesenchymal tissues and bone marrow. Using whole marrow samples, common methods for mesenchymal stem cell isolation are the adhesion method and density gradient fractionation. The whole marrow sample adhesion method still results in the nonspecific isolation of mononuclear cells, and activation and/or potential loss of target cells. Density gradient fractionation methods are complicated, and may result in contamination with toxic substances that affect cell viability. In the present study, we developed an optimized protocol for the isolation and purification of mesenchymal stem cells based on the principles of hypotonic lysis and natural sedimentation.

High-Voltage Isolation Transformer

NASA Technical Reports Server (NTRS)

Clatterbuck, C. H.; Ruitberg, A. P.

1985-01-01

Arcing and field-included surface erosion reduced by electrostatic shields around windings and ferromagnetic core of 80-kilovolt isolation transformer. Fabricated from high-resistivity polyurethane-based material brushed on critical surfaces, shields maintained at approximately half potential difference of windings.

46. Communication equipment room, shock isolator air compressor at right, ...

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

46. Communication equipment room, shock isolator air compressor at right, looking northeast - Ellsworth Air Force Base, Delta Flight, Launch Control Facility, County Road CS23A, North of Exit 127, Interior, Jackson County, SD

Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

PubMed Central

Kruhøffer, Mogens; Dyrskjøt, Lars; Voss, Thorsten; Lindberg, Raija L.P.; Wyrich, Ralf; Thykjaer, Thomas; Orntoft, Torben F.

2007-01-01

We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated microRNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis. PMID:17690207

Identification of Colletotrichum spp. isolated from strawberry in Zhejiang Province and Shanghai City, China*

PubMed Central

Xie, Liu; Zhang, Jing-ze; Wan, Yao; Hu, Dong-wei

2010-01-01

Strawberry anthracnose, caused by Colletotrichum spp., is a major disease of cultivated strawberry. This study identifies 31 isolates of Colletotrichum spp. which cause strawberry anthracnose in Zhejiang Province and Shanghai City, China. Eleven isolates were identified as C. acutatum, 10 as C. gloeosporioides and 10 as C. fragariae based on morphological characteristics, phylogenetic and sequence analyses. Species-specific polymerase chain reaction (PCR) and enzyme digestion further confirmed the identification of the Colletotrichum spp., demonstrating that these three species are currently the causal agents of strawberry anthracnose in the studied regions. Based on analysis of rDNA internal transcribed spacers (ITS) sequences, sequences of all C. acutatum were identical, and little genetic variability was observed between C. fragariae and C. gloeosporioides. However, the conservative nature of the MvnI specific site from isolates of C. gloeosporioides was confirmed, and this site could be used to differentiate C. gloeosporioides from C. fragariae. PMID:20043353

Isolation and characterization of fatty acid methyl ester (FAME)-producing Streptomyces sp. S161 from sheep (Ovis aries) faeces.

PubMed

Lu, Y; Wang, J; Deng, Z; Wu, H; Deng, Q; Tan, H; Cao, L

2013-09-01

An actinomycete producing oil-like mixtures was isolated and characterized. The strain was isolated from sheep faeces and identified as Streptomyces sp. S161 based on 16S rRNA gene sequence analysis. The strain showed cellulase and xylanase activities. The (1) H nuclear magnetic resonance (NMR) spectra of the mixtures showed that the mixtures were composed of fatty acid methyl esters (52·5), triglycerides (13·7) and monoglycerides (9·1) (mol.%). Based on the gas chromatography-mass spectrometry (GC-MS) analysis, the fatty acid methyl esters were mainly composed of C14-C16 long-chain fatty acids. The results indicated that Streptomyces sp. S161 could produce fatty acid methyl esters (FAME) directly from starch. To our knowledge, this is the first isolated strain that can produce biodiesel (FAME) directly from starch. © 2013 The Society for Applied Microbiology.

Cooperative solution in the synthesis of multidegree-of-freedom shock isolation systems

NASA Astrophysics Data System (ADS)

Hati, S. K.; Rao, S. S.

1983-01-01

It is noted that there are essentially two major criteria in the synthesis of shock isolation stems. One is related to the minimization of the relative displacement between the main mass (which is to be isolated from vibration) and the base (where disturbance is given); the other concerns the minimization of force transmitted to the main mass. From the available literature, it is observed that nearly all the investigators have considered the design problem by treating one of these factors as the objective and the other as a constraint. This problem is treated here as a multicriteria optimization problem, and the trade-off between the two objectives is determined by using a game theory approach. The synthesis of a multidegree-of-freedom shock isolation system under a sinusoidal base disturbance is given as an example problem to illustrate the theory.

Preparation and Respirometric Assessment of Mitochondria Isolated from Skeletal Muscle Tissue Obtained by Percutaneous Needle Biopsy

PubMed Central

Bharadwaj, Manish S.; Tyrrell, Daniel J.; Lyles, Mary F.; Demons, Jamehl L.; Rogers, George W.; Molina, Anthony J. A.

2015-01-01

Respirometric profiling of isolated mitochondria is commonly used to investigate electron transport chain function. We describe a method for obtaining samples of human Vastus lateralis, isolating mitochondria from minimal amounts of skeletal muscle tissue, and plate based respirometric profiling using an extracellular flux (XF) analyzer. Comparison of respirometric profiles obtained using 1.0, 2.5 and 5.0 μg of mitochondria indicate that 1.0 μg is sufficient to measure respiration and that 5.0 μg provides most consistent results based on comparison of standard errors. Western blot analysis of isolated mitochondria for mitochondrial marker COX IV and non-mitochondrial tissue marker GAPDH indicate that there is limited non-mitochondrial contamination using this protocol. The ability to study mitochondrial respirometry in as little as 20 mg of muscle tissue allows users to utilize individual biopsies for multiple study endpoints in clinical research projects. PMID:25741892

Social isolation and loneliness among older people: issues and future challenges in community and residential settings.

PubMed

Grenade, Linda; Boldy, Duncan

2008-08-01

Although often associated with older age, loneliness and social isolation are not well understood in terms of their prevalence, risk and protective factors. Evidence suggests that only a minority of community-dwelling older people are "severely" lonely or isolated, however a number of factors need to be considered to fully understand the extent and significance of the problem. Community-based studies have identified a variety of risk factors for loneliness/isolation including widowhood, no (surviving) children, living alone, deteriorating health, and life events (eg, loss and bereavement). Having a confidant has been identified as a protective factor for loneliness. However, evidence is often unclear or inconclusive, especially within residential settings. We identified the need to conduct more residential care-focused research; the importance of addressing a variety of methodological concerns; and the need for practitioners to develop intervention programs that are appropriately targeted, evidence-based and evaluated.

Connecting Socially Isolated Older Rural Adults with Older Volunteers through Expressive Arts.

PubMed

MacLeod, Ann; Skinner, Mark W; Wilkinson, Fay; Reid, Heather

2016-03-01

Employing a participatory arts-based research approach, we examined an innovative program from rural Ontario, Canada, designed to address social isolation among older people. Older socially isolated adults were matched to trained volunteers, where in dyads, the eight pairs created expressive art in their home setting over the course of 10 home visits. With thematic and narrative inquiry, we analysed the experiences and perceptions of the program leader, older participants, and older volunteers via their artistic creations, weekly logs, evaluations, and field notes. The findings reveal a successful intervention that positively influenced the well-being of older adult participants and older volunteers, especially in regards to relationships, personal development, and creating meaning as well as extending the intervention's impact beyond the program's duration. We also discuss opportunities for similar programs to inform policy and enable positive community-based health and social service responses to rural social isolation.

Molecular characterization of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the countries of the Gulf cooperation council: dominance of OXA-48 and NDM producers.

PubMed

Zowawi, Hosam M; Sartor, Anna L; Balkhy, Hanan H; Walsh, Timothy R; Al Johani, Sameera M; AlJindan, Reem Y; Alfaresi, Mubarak; Ibrahim, Emad; Al-Jardani, Amina; Al-Abri, Seif; Al Salman, Jameela; Dashti, Ali A; Kutbi, Abdullah H; Schlebusch, Sanmarié; Sidjabat, Hanna E; Paterson, David L

2014-06-01

The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Enterobacteriaceae (CRE) were determined in hospitals in the countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic-resistant genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Sixty-two isolates which screened positive for potential carbapenemase production were assessed, and 45 were found to produce carbapenemase. The most common carbapenemases were of the OXA-48 (35 isolates) and NDM (16 isolates) types; 6 isolates were found to coproduce the OXA-48 and NDM types. No KPC-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with seven clusters of clonally related Klebsiella pneumoniae. Awareness of CRE in GCC countries has important implications for controlling the spread of CRE in the Middle East and in hospitals accommodating patients transferred from the region. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Molecular characterization of Indian rabies virus isolates by partial sequencing of nucleoprotein (N) and phosphoprotein (P) genes.

PubMed

Reddy, G B Manjunatha; Singh, R; Singh, R P; Singh, K P; Gupta, P K; Mahadevan, Anita; Desai, Anita; Shankar, S K; Ramakrishnan, M A; Verma, Rishendra

2011-08-01

Rabies is endemic and an important zoonosis in India. There are very few reports available on molecular epidemiology of rabies virus of Indian origin. In this study to know the dynamics of rabies virus, a total of 41 rabies positive brain samples from dogs, cats, domestic animals, wildlife, and humans from 11 states were subjected to RT-PCR amplification of N gene between nucleotide N521-N1262 (742 bp) and P gene between nucleotide P239-P750 (512 bp). The N gene could be amplified from 30, while P gene from 41 samples, using specific sets of primers. The N gene-based phylogenetic analysis indicated that all Indian virus isolates are genetically closely related with a single cluster under arctic/arctic-like viruses. However, two distinct clusters were realized in P gene-based phylogeny viz., Rabies virus isolates of Punjab and Rabies virus isolates of remaining parts of India (other than Punjab). All the Indian rabies virus isolates were closely related to geography (>95% homology), but not to host species.

16S rRNA-Based Identification of a Glucan-Hyperproducing Weissella confusa

PubMed Central

Shukla, Shraddha; Goyal, Arun

2011-01-01

A gram-positive, nonmotile, irregular, short, rod-shaped new strain of Weissella confusa bacterium was isolated from fermented cabbage. The isolate was physiologically and biochemically characterised. The 16S rDNA was amplified by polymerase chain reaction (PCR). The isolate was identified as Weissella confusa (GenBank accession number: GU138518.1) based on nucleotide homology and phylogenetic analysis. The isolate produces glucansucrase when grown in sucrose-supplemented culture medium which catalyses glucan formation. This novel isolate possesses high capacity of industrial use due to its high productivity of glucan (34 mg/mL) as compared to other strains reported. The optimum temperature for glucansucrase production was 25°C. The shaking condition gave an enzyme activity of 6.1 U/mL which was 1.5 times higher than that given by static condition (4.1 U/mL). The temperature 35°C, pH 5.4, and ionic strength 10–20 mM were optimum for enzyme assay. This investigation unraveled the abundance of industrially valuable microflora of the north east India. PMID:21603260

Astrometric Telescope Facility isolation and pointing study

NASA Technical Reports Server (NTRS)

Hibble, William; Allen, Terry; Jackson, Louis; Medbery, James; Self, Richard

1988-01-01

The Astrometric Telescope Facility (ATF), an optical telescope designed to detect extrasolar planetary systems, is scheduled to be a major user of the Space Station's Payload Pointing System (PPS). However, because the ATF has such a stringent pointing stability specification and requires + or - 180 deg roll about its line of sight, mechanisms to enhance the basic PPS capability are required. The ATF pointing performance achievable by the addition of a magnetic isolation and pointing system (MIPS) between the PPS upper gimbal and the ATF, and separately, by the addition of a passive isolation system between the Space Station and the PPS base was investigated. The candidate MIPS can meet the ATF requirements in the presence of a 0.01 g disturbance. It fits within the available annular region between the PPS and the ATF while meeting power and weight limitations and providing the required roll motion, payload data and power services. By contrast, the passive base isolator system must have an unrealistically low isolation bandwidth on all axes to meet ATF pointing requirements and does not provide roll about the line of sight.

Isolation and identification of bacterial pathogen from mastitis milk in Central Java Indonesia

NASA Astrophysics Data System (ADS)

Harjanti, D. W.; Ciptaningtyas, R.; Wahyono, F.; Setiatin, ET

2018-01-01

Mastitis is a multi-etiologic disease of the mammary gland characterized mainly by reduction in milk production and milk quality due to intramammary infection by pathogenic bacteria. Nearly 83% of lactating dairy cows in Indonesia are infected with mastitis in various inflammation degrees. This study was conducted to isolate and identify the pathogen in milk collected from mastitis-infected dairy cows. The study was carried out in ten smallholder dairy farms in Central Java Indonesia based on animal examination, California mastitis test, isolation bacterial pathogens, Gram staining, Catalase and Coagulase test, and identification of bacteria species using Vitek. Bacteriological examination of milk samples revealed 15 isolates where Streptococcus was predominant species (73.3%) and the coagulase negative Staphylococcus species was identified at the least bacteria (26.7%). The Streptococcus bacteria found were Streptococcus uberis (2 isolates), Streptococcus sanguinis(6 isolates), Streptococcus dysgalactiaessp dysgalactiae(1 isolate) , Streptococcus mitis (1 isolate) and Streptococcus agalactiae (1 isolate). The Staphylococcus isolates comprising of Staphylococcus simulans (1 isolate) and Staphylococcus chromogens (3 isolates). Contamination of raw milkwith pathogenic bacteria can cause outbreaks of human disease (milk borne disease). Thus, proper milk processing method that couldinhibit the growth or kill these pathogenic bacteria is important to ensure the safety of milk and milk products.

Antagonistic activity of isolated lactic acid bacteria from Pliek U against gram-negative bacteria Escherichia coli ATCC 25922

NASA Astrophysics Data System (ADS)

Kiti, A. A.; Jamilah, I.; Rusmarilin, H.

2017-09-01

Lactic acid bacteria (LAB) is one group of microbes that has many benefits, notably in food and health industries sector. LAB plays an important role in food fermentation and it has bacteriostatic effect against the growth of pathogenic microorganisms. The research related LAB continued to be done to increase the diversity of potential isolates derived from nature which is indigenous bacteria for biotechnological purposes. This study was aimed to isolate and characterize LAB derived from pliek u sample and to examine the potency to inhibits Escherichia coli ATCC 25922 bacteria growth. A total of 5 isolates were isolated and based on morphological and physiological characteristics of the fifth bacteria, they are allegedly belonging to the genus Bacillus. Result of antagonistic test showed that the five isolates could inhibits the growth of E. coli ATCC 25922. The highest inhibition zone is 8.5 mm was shown by isolates NQ2, while the lowest inhibition is 1.5 mm was shown by isolates NQ3.

A Stewart isolator with high-static-low-dynamic stiffness struts based on negative stiffness magnetic springs

NASA Astrophysics Data System (ADS)

Zheng, Yisheng; Li, Qingpin; Yan, Bo; Luo, Yajun; Zhang, Xinong

2018-05-01

In order to improve the isolation performance of passive Stewart platforms, the negative stiffness magnetic spring (NSMS) is employed to construct high static low dynamic stiffness (HSLDS) struts. With the NSMS, the resonance frequencies of the platform can be reduced effectively without deteriorating its load bearing capacity. The model of the Stewart isolation platform with HSLDS struts is presented and the stiffness characteristic of its struts is studied firstly. Then the nonlinear dynamic model of the platform including both geometry nonlinearity and stiffness nonlinearity is established; and its simplified dynamic model is derived under the condition of small vibration. The effect of nonlinearity on the isolation performance is also evaluated. Finally, a prototype is built and the isolation performance is tested. Both simulated and experimental results demonstrate that, by using the NSMS, the resonance frequencies of the Stewart isolator are reduced and the isolation performance in all six directions is improved: the isolation frequency band is increased and extended to a lower-frequency level.

A Sub-Hertz, Low-Frequency Vibration Isolation Platform

NASA Technical Reports Server (NTRS)

Ortiz, Gerardo, G.; Farr, William H.; Sannibale, Virginio

2011-01-01

One of the major technical problems deep-space optical communication (DSOC) systems need to solve is the isolation of the optical terminal from vibrations produced by the spacecraft navigational control system and by the moving parts of onboard instruments. Even under these vibration perturbations, the DSOC transceivers (telescopes) need to be pointed l000 fs of times more accurately than an RF communication system (parabolic antennas). Mechanical resonators have been extensively used to provide vibration isolation for groundbased, airborne, and spaceborne payloads. The effectiveness of these isolation systems is determined mainly by the ability of designing a mechanical oscillator with the lowest possible resonant frequency. The Low-Frequency Vibration Isolation Platform (LFVIP), developed during this effort, aims to reduce the resonant frequency of the mechanical oscillators into the sub-Hertz region in order to maximize the passive isolation afforded by the 40 dB/decade roll-off response of the resonator. The LFVIP also provides tip/tilt functionality for acquisition and tracking of a beacon signal. An active control system is used for platform positioning and for dampening of the mechanical oscillator. The basic idea in the design of the isolation platform is to use a passive isolation strut with an approximately equal to 100-mHz resonance frequency. This will extend the isolation range to lower frequencies. The harmonic oscillator is a second-order lowpass filter for mechanical disturbances. The resonance quality depends on the dissipation mechanisms, which are mainly hysteretic because of the low resonant frequency and the absence of any viscous medium. The LFVIP system is configured using the well-established Stewart Platform, which consists of a top platform connected to a base with six extensible struts (see figure). The struts are attached to the base and to the platform via universal joints, which permit the extension and contraction of the struts. The struts ends are connected in pairs to the base and to the platform, forming an octahedron. The six struts provide the vibration isolation due to the properties of mechanical oscillators that behave as second-order lowpass filters for frequencies above the resonance. At high frequency, the ideal second-order low-pass filter response is spoiled by the distributed mass and the internal modes of membrane and of the platform with its payload.

Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12.

PubMed

Li, Tonghui; Wen, Jianqiang; Zhang, Yaling; Correll, James; Wang, Ling; Pan, Qinghua

2018-05-31

Pathogen avirulence (Avr) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-populated genetic map is available. An updated, SSR-based physical map of the rice blast pathogen Magnaporthe oryzae (Mo) has been constructed based on 116 of the 120 SSRs used to assemble the last map, along with 18 newly developed ones. A comparison between the two versions of the map has revealed an altered marker content and order within most of the Mo chromosomes. The avirulence gene AvrPi12 was mapped in a population of 219 progeny derived from a cross between the two Mo isolates CHL42 and CHL357. A bulked segregant analysis indicated that the gene was located on chromosome 6, a conclusion borne out by an analysis of the pattern of segregation shown by individual isolates. Six additional PCR-based markers were developed to improve the map resolution in the key region. AvrPi12 was finally located within the sub-telomeric region of chromosome 6, distal to the SSR locus LSM6-5. The improved SSR-based linkage map should be useful as a platform for gene mapping and isolation in Mo. It was used to establish the location of AvrPi12, thereby providing a starting point for its positional cloning.

Polymorphic butterfly reveals the missing link in ecological speciation.

PubMed

Chamberlain, Nicola L; Hill, Ryan I; Kapan, Durrell D; Gilbert, Lawrence E; Kronforst, Marcus R

2009-11-06

Ecological speciation occurs when ecologically based, divergent selection causes the evolution of reproductive isolation. There are many empirical examples of this process; however, there exists a poorly characterized stage during which the traits that distinguish species ecologically and reproductively segregate in a single population. By using a combination of genetic mapping, mate-choice experiments, field observations, and population genetics, we studied a butterfly population with a mimetic wing color polymorphism and found that the butterflies exhibited partial, color-based, assortative mate preference. These traits represent the divergent, ecologically based signal and preference components of sexual isolation that usually distinguish incipient and sibling species. The association between behavior and recognition trait in a single population may enhance the probability of speciation and provides an example of the missing link between an interbreeding population and isolated species.

Isolation and characterization of a novel Rickettsia species (Rickettsia asembonensis sp. nov.) obtained from cat fleas (Ctenocephalides felis).

PubMed

Maina, Alice N; Luce-Fedrow, Alison; Omulo, Sylvia; Hang, Jun; Chan, Teik-Chye; Ade, Fredrick; Jima, Dereje D; Ogola, Eric; Ge, Hong; Breiman, Robert F; Njenga, Moses K; Richards, Allen L

2016-11-01

A novel rickettsial agent, 'Candidatus Rickettsia asembonensis' strain NMRCiiT, was isolated from cat fleas, Ctenocephalides felis, from Kenya. Genotypic characterization of the new isolate based on sequence analysis of five rickettsial genes, rrs, gltA, ompA, ompB and sca4, indicated that this isolate clustered with Rickettsia felis URRWXCal2. The degree of nucleotide similarity demonstrated that isolate NMRCiiT belongs within the genus Rickettsia and fulfils the criteria for classification as a representative of a novel species. The name Rickettsia asembonensis sp. nov. is proposed, with NMRCiiT (=DSM 100172T=CDC CRIRC RAS001T=ATCC VR-1827T) as the type strain.

Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region.

PubMed

Debruyne, Lies; Broman, Tina; Bergström, Sven; Olsen, Björn; On, Stephen L W; Vandamme, Peter

2010-04-01

Six Gram-stain-negative, spiral-shaped, microaerobic isolates were obtained during a sampling from wild birds in the sub-Antarctic region. Based on initial observations, these isolates were classified as Campylobacter lari-like. The isolates were further characterized by whole-cell protein and amplified fragment length polymorphism (AFLP) analysis, which revealed that they were distinct from C. lari and all other known species of the genus Campylobacter. Here, we present comprehensive phylogenetic, genomic and phenotypic evidence that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter subantarcticus sp. nov. is proposed. The type strain is R-3023(T) (=LMG 24377(T) =CCUG 38513(T)).

A modified culture-based study of bacterial community composition in a tannery wastewater treatment plant.

PubMed

Desta, Adey F; Dalhammer, Gunnel; Kittuva, Gunatrana R

2010-01-01

Though culture-independent methods have been used in preference to traditional isolation techniques for characterization of microbial community of wastewater treatment plants, it is difficult to widely apply this approach in resource-poor countries. The present study aimed to develop a test to identify the culturable portion of bacterial community in a high-strength wastewater. Wastewater samples were collected from nitrification-denitrification and settling tanks of the treatment plant of Elmo Leather AB tannery located in Borås, Sweden. After cultivating on nutrient agar with the optimal dilution (10⁻²), phenotypic and biochemical identification of the bacteria were done with colony morphology, Gram reaction, growth on MacConkey, phenylethanol media, triple sugar Iron agar slants, catalase and oxidase tests. Biochemical grouping of the isolates was done based on their test results for MacConkey, phenylethanol media, triple sugar Iron agar and oxidase test reaction. From the biochemical groups, isolates were randomly selected for API test and 16SrRNA gene sequencing. The isolates from the denitrification, nitrification tank were identified to be Paracoccus denitrificans (67%), Azoarcus spp (3%) and Spingomonas wittichii (1%). From the settling tank, Paracoccus denitrificans (22%), Corynebacterium freneyi (20%) and Bacillus cereus (1%) were identified. The grouping based on biochemical test results as well as the identification based on sequencing has shown coherence except for discrepancies with the API test. The preliminary implications of the grouping based on culture-based characteristics and its potential application for resource-limited environmental microbial studies is discussed.

Fitness and Competitive Ability of Botrytis cinerea Isolates with Resistance to Multiple Chemical Classes of Fungicides.

PubMed

Chen, S N; Luo, C X; Hu, M J; Schnabel, G

2016-09-01

Resistance to multiple chemical classes of fungicides in Botrytis cinerea isolates from eastern United States strawberry fields is common and strategies to control them are needed. In this study, we compared fitness and competitive ability of eight sensitive isolates (S), eight isolates resistant to five or six chemical classes of fungicides but not to phenylpyrroles (5CCR), and eight isolates resistant to six or seven chemical classes including phenylpyrroles (6CCR/MDR1h). The latter included the MDR1h phenotype due to overexpression of atrB based on Δ497V/L in mrr1. The 6CCR/MDR1h isolates grew more slowly at 4°C on potato dextrose agar, and both 5CCR and 6CCR/MDR1h isolates were hypersensitive to osmotic stress compared with S isolates. In contrast, no differences were found in oxidative sensitivity, aggressiveness, and spore production in vivo, and sclerotia production and viability in vitro. In competition experiments, the 5CCR and 6CCR/MDR1h isolates were both outcompeted by S isolates and 6CCR/MDR1h isolates were outcompeted by 5CCR isolates in the absence of fungicide pressure. Under selective pressure of a fludioxonil/pyraclostrobin rotation, the 6CCR/MDR1h isolates dominated after coinoculation with 5CCR and S isolates. The competitive disadvantage of 5CCR and especially 6CCR/MDR1h isolates suggest that, in the absence of fungicide selection pressure, S isolates may reduce inoculum potential of multifungicide-resistant isolates under field conditions.

Whole genome sequencing of Mycobacterium bovis to obtain molecular fingerprints in human and cattle isolates from Baja California, Mexico.

PubMed

Sandoval-Azuara, Sarai Estrella; Muñiz-Salazar, Raquel; Perea-Jacobo, Ricardo; Robbe-Austerman, Suelee; Perera-Ortiz, Alejandro; López-Valencia, Gilberto; Bravo, Doris M; Sanchez-Flores, Alejandro; Miranda-Guzmán, Daniela; Flores-López, Carlos Alberto; Zenteno-Cuevas, Roberto; Laniado-Laborín, Rafael; de la Cruz, Fabiola Lafarga; Stuber, Tod P

2017-10-01

To determine genetic diversity by comparing the whole genome sequences of cattle and human Mycobacterium bovis isolates from Baja California. A whole genome sequencing strategy was used to obtain the molecular fingerprints of 172 isolates of M. bovis obtained from Baja California, Mexico; 155 isolates were from cattle and 17 isolates were from humans. Spoligotypes were characterized in silico and single nucleotide polymorphism (SNP) differences between the isolates were evaluated. A total of 12 M. bovis spoligotype patterns were identified in cattle and humans. Two predominant spoligotypes patterns were seen in both cattle and humans: SB0145 and SB1040. The SB0145 spoligotype represented 59% of cattle isolates (n=91) and 65% of human isolates (n=11), while the SB1040 spoligotype represented 30% of cattle isolates (n=47) and 30% of human isolates (n=5). When evaluating SNP differences, the human isolates were intimately intertwined with the cattle isolates. All isolates from humans had spoligotype patterns that matched those observed in the cattle isolates, and all human isolates shared common ancestors with cattle in Baja California based on SNP analysis. This suggests that most human tuberculosis caused by M. bovis in Baja California is derived from M. bovis circulating in Baja California cattle. These results reinforce the importance of bovine tuberculosis surveillance and control in this region. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Molecular typing of Vibrio parahaemolyticus strains isolated from the Philippines by PCR-based methods.

PubMed

Maluping, R P; Ravelo, C; Lavilla-Pitogo, C R; Krovacek, K; Romalde, J L

2005-01-01

The main aim of the present study was to use three PCR-based techniques for the analysis of genetic variability among Vibrio parahaemolyticus strains isolated from the Philippines. Seventeen strains of V. parahaemolyticus isolated from shrimps (Penaeus monodon) and from the environments where these shrimps are being cultivated were analysed by random amplified polymorphic DNA PCR (RAPD-PCR), enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) and repetitive extragenic palindromic PCR (REP-PCR). The results of this work have demonstrated genetic variability within the V. parahaemolyticus strains that were isolated from the Philippines. In addition, RAPD, ERIC and REP-PCR are suitable rapid typing methods for V. parahaemolyticus. All three methods have good discriminative ability and can be used as a rapid means of comparing V. parahaemolyticus strains for epidemiological investigation. Based on the results of this study, we could say that REP-PCR is inferior to RAPD and ERIC-PCR owing to the fact that it is less reproducible. Moreover, the REP-PCR analysis yielded a relatively small number of products. This may suggests that the REP sequences may not be widely distributed in the V. parahaemolyticus genome. Genetic variability within V. parahaemolyticus strains isolated in the Philippines has been demonstrated. The presence of ERIC and REP sequences in the genome of this bacterial species was confirmed. The RAPD, ERIC and REP-PCR techniques are useful methods for molecular typing of V. parahaemolyticus strains. To our knowledge this is the first study of this kind carried out on V. parahaemolyticus strains isolated from the Philippines.

Antimicrobial Susceptibility of Campylobacter Cuniculorum Isolated from Rabbits Reared in Intensive and Rural Farms

PubMed Central

Piva, Silvia; Florio, Daniela; Mion, Domenico; Zanoni, Renato Giulio

2016-01-01

The present study aimed to investigate the antimicrobial susceptibility in Campylobacter cuniculorum. To do so, 29 isolates from rabbits reared in 18 intensive and 11 rural farms not epidemiologically correlated were tested. Minimum inhibitory concentration of 8 antimicrobial agents was determined using the agar dilution method recommended by the Clinical and Laboratory Standards Institute (Wayne, PA, USA), modified – for what supplements in the base medium and incubation conditions concern – for C. cuniculorum isolates. The isolates obtained from rural farming resulted susceptible to all the antimicrobial agents tested, with the exception of one isolate resistant to nalidixic acid. All the isolates obtained from intensively farmed rabbits were sensitive to chloramphenicol and ampicillin; 16 isolates were resistant to tetracycline; 15 to nalidixic acid and erythromycin; 13 and 10 isolates to ciprofloxacin and enrofloxacin, respectively; and only 1 to gentamicin. The resistance of several isolates to macrolides and fluoroquinolones, which are the drugs of choice in treatment of human campylobacteriosis, could pose a risk to human health if a pathogenic role of C. cuniculorum was demonstrated. PMID:27853713

Identification and Characterization of Benzimidazole Resistance in Monilinia fructicola from Stone Fruit Orchards in California

PubMed Central

Ma, Zhonghua; Yoshimura, Michael A.; Michailides, Themis J.

2003-01-01

Low and high levels of resistance to the benzimidazole fungicides benomyl and thiophanate-methyl were observed in field isolates of Monilinia fructicola, which is the causative agent of brown rot of stone fruit. Isolates that had low levels of resistance (hereafter referred to as LR isolates) and high levels of resistance (hereafter referred to as HR isolates) were also cold and heat sensitive, respectively. Results from microsatellite DNA fingerprints showed that genetic identities among the populations of sensitive (S), LR, and HR isolates were very high (>0.96). Analysis of DNA sequences of the β-tubulin gene showed that the LR isolates had a point mutation at codon 6, causing a replacement of the amino acid histidine by tyrosine. Codon 198, which encodes a glutamic acid in S and LR isolates, was converted to a codon for alanine in HR isolates. Based on these point mutations in the β-tubulin gene, allele-specific PCR assays were developed for rapid detection of benzimidazole-resistant isolates of M. fructicola from stone fruit. PMID:14660360

Resistance to Extended-Spectrum β-Lactamases in Salmonella from a Broiler Supply Chain

PubMed Central

Gelinski, Jane Mary Lafayette Neves; Bombassaro, Amanda; Baratto, César Milton; Vicente, Vânia Aparecida

2014-01-01

The prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae varies worldwide, however, the incidence of ESBL-producing environmental Salmonella isolates is increasing. Salmonella is still one of the most important pathogens that occur in the poultry supply chain. Therefore, this study analyzed the susceptibility of Salmonella isolates collected from a poultry supply chain to β-lactam antibiotics, and examined the phenotypes of the isolates based on enzyme-inducible AmpC β-lactamase analysis. All analysis of the putative positive isolates in the current study confirmed that 27.02% (77/285 analysis) of all ESBL tests realized with the isolates produced a profile of resistance consistent with β-lactamase production. All isolates of S. Minnesota serotype had ESBL phenotype. Aztreonam resistance was the least common amongst the Salmonella isolates, followed by ceftazidime. The presence of inducible chromosomal ESBL was detected in 14 different isolates of the 19 serotypes investigated. These results are very indicatives of the presence of ESBL genes in Salmonella isolates from a broiler supply chain, reaffirming the growing global problem of ESBL resistance. PMID:25402566

Isolation, characterization, and diversity of novel radiotolerant carotenoid-producing bacteria.

PubMed

Asker, Dalal; Awad, Tarek S; Beppu, Teruhiko; Ueda, Kenji

2012-01-01

Carotenoids are natural pigments that exhibit many biological functions, such as antioxidants (i.e., promote oxidative stress resistance), membrane stabilizers, and precursors for vitamin A. The link between these biological activities and many health benefits (e.g., anticarcinogenic activity, prevention of chronic diseases, etc.) has raised the interest of several industrial sectors, especially in the cosmetics and pharmaceutical industries. The use of microorganisms in biotechnology to produce carotenoids is favorable by consumer and can help meet the growing demand for these bioactive compounds in the food, feed, and pharmaceutical industries. This methodological chapter details the development of a rapid and selective screening method for isolation and identification of carotenoid-producing microorganisms based on UV treatment, sequencing analysis of 16S rRNA genes, and carotenoids' analysis using rapid and effective High-Performance Liquid Chromatography-Diodearray-MS methods. The results of a comprehensive 16S rRNA gene-based phylogenetic analysis revealed a diversity of carotenoid-producing microorganisms (104 isolates) that were isolated at a high frequency from water samples collected at Misasa (Tottori, Japan), a region known for its high natural radioactivity content. These carotenoid-producing isolates were classified into 38 different species belonging to 7 bacterial classes (Flavobacteria, Sphingobacteria, α-Proteobacteria, γ-Proteobacteria, Deinococci, Actinobacteria, and Bacilli). The carotenoids produced by the isolates were zeaxanthin (6 strains), dihydroxyastaxanthin (24 strains), astaxanthin (27 strains), canthaxanthin (10 strains), and unidentified molecular species that were produced by the isolates related to Deinococcus, Exiguobacterium, and Flectobacillus. Here, we describe the methods used to isolate and classify these microorganisms.

Fabrication and investigation on field-dependent properties of natural rubber based magneto-rheological elastomer isolator

NASA Astrophysics Data System (ADS)

Ain Abd Wahab, Nurul; Amri Mazlan, Saiful; Ubaidillah; Kamaruddin, Shamsul; Intan Nik Ismail, Nik; Choi, Seung-Bok; Haziq Rostam Sharif, Amirul

2016-10-01

This study presents a laminated magnetorheological elastomer (MRE) isolator which applies to vibration control in practice. The proposed isolator is fabricated with multilayer MRE sheets associated with the natural rubber (NR) as a matrix, and steel plates. The fabricated MRE isolator is then magnetically analysed to achieve high magnetic field intensity which can produce high damping force required for effective vibration control. Subsequently, the NR-based MRE specimen is tested to identify the field-dependent rheological properties such as storage modulus with 60 weight percentage of carbonyl iron particles. It is shown from this test that the MR effect of MRE specimen is quantified to reach up to 120% at 0.8 T. Following the design stage, the electromagnetic simulation using the finite element method magnetic (FEMM) software is carried out for analysing the magnetic flux distribution in the laminated MRE isolator. The laminated MRE isolator is then examined to a series of compression for static and dynamic test under various applied currents using the dynamic fatigue machine and biaxial dynamic testing machine. It is shown that the static compression force is increased by 14.5% under strong magnetic field compared to its off-state. Meanwhile, the dynamic compression test results show that the force increase of the laminated MRE isolator is up to 16% and 7% for low and high frequency respectively. From the results presented in this work, it is demonstrated that the full-scale concept of the MRE isolator can be one of the potential candidates for vibration control applications by tunability of the dynamic stiffness.

Biodegradable soy protein isolate-based materials: a review.

PubMed

Song, Fei; Tang, Dao-Lu; Wang, Xiu-Li; Wang, Yu-Zhong

2011-10-10

Recently, there is an increasing interest of using bio-based polymers instead of conventional petroleum-based polymers to fabricate biodegradable materials. Soy protein isolate (SPI), a protein with reproducible resource, good biocompatibility, biodegradability, and processability, has a significant potential in the food industry, agriculture, bioscience, and biotechnology. Up to now, several technologies have been applied to prepare SPI-based materials with equivalent or superior physical and mechanical properties compared with petroleum-based materials. The aim of this review is focused on discussion of the advantages and limitations of native SPI as well as the bulk and surface modification strategies for SPI. Moreover, some applications of SPI-based materials, especially for food preservation and packaging technology, were discussed.

In Vitro and In Vivo Plant Growth Promoting Activities and DNA Fingerprinting of Antagonistic Endophytic Actinomycetes Associates with Medicinal Plants.

PubMed

Passari, Ajit Kumar; Mishra, Vineet Kumar; Gupta, Vijai Kumar; Yadav, Mukesh Kumar; Saikia, Ratul; Singh, Bhim Pratap

2015-01-01

Endophytic actinomycetes have shown unique plant growth promoting as well as antagonistic activity against fungal phytopathogens. In the present study forty-two endophytic actinomycetes recovered from medicinal plants were evaluated for their antagonistic potential and plant growth-promoting abilities. Twenty-two isolates which showed the inhibitory activity against at least one pathogen were subsequently tested for their plant-growth promoting activities and were compared genotypically using DNA based fingerprinting, including enterobacterial repetitive intergenic consensus (ERIC) and BOX repetitive elements. Genetic relatedness based on both ERIC and BOX-PCR generates specific patterns corresponding to particular genotypes. Exponentially grown antagonistic isolates were used to evaluate phosphate solubilization, siderophores, HCN, ammonia, chitinase, indole-3-acetic acid production, as well as antifungal activities. Out of 22 isolates, the amount of indole-3-acetic acid (IAA) ranging between 10-32 μg/ml was produced by 20 isolates and all isolates were positive for ammonia production ranging between 5.2 to 54 mg/ml. Among 22 isolates tested, the amount of hydroxamate-type siderophores were produced by 16 isolates ranging between 5.2 to 36.4 μg/ml, while catechols-type siderophores produced by 5 isolates ranging from 3.2 to 5.4 μg/ml. Fourteen isolates showed the solubilisation of inorganic phosphorous ranging from 3.2 to 32.6 mg/100ml. Chitinase and HCN production was shown by 19 and 15 different isolates, respectively. In addition, genes of indole acetic acid (iaaM) and chitinase (chiC) were successively amplified from 20 and 19 isolates respectively. The two potential strains Streptomyces sp. (BPSAC34) and Leifsonia xyli (BPSAC24) were tested in vivo and improved a range of growth parameters in chilli (Capsicum annuum L.) under greenhouse conditions. This study is the first published report that actinomycetes can be isolated as endophytes from within these plants and were shown to have antagonistic and plant growth promoting abilities. These results clearly suggest the possibility of using endophytic actinomycetes as bioinoculant for plant growth promotion, nutrient mobilization or as biocontrol agent against fungal phytopathogens for sustainable agriculture.

Hollow-cylinder waveguide isolators for use at millimeter wavelengths

NASA Technical Reports Server (NTRS)

Kanda, M.; May, W. G.

1974-01-01

A semiconductor waveguide isolator consisting of a hollow column of a semiconductor mounted coaxially is considered in a circular waveguide in a longitudinal dc magnetic field. An elementary and physical analysis based on the excitation of plane waves in the guide and a more rigorous mode matching analysis are presented. These theoretical predictions are compared with experimental results for an InSb isolator at 94GHz and 75 K.

The investigation of probiotic potential of lactic acid bacteria isolated from traditional Mongolian dairy products.

PubMed

Takeda, Shiro; Yamasaki, Keiko; Takeshita, Masahiko; Kikuchi, Yukiharu; Tsend-Ayush, Chuluunbat; Dashnyam, Bumbein; Ahhmed, Abdulatef M; Kawahara, Satoshi; Muguruma, Michio

2011-08-01

The aims of this study were to investigate the diversity of lactic acid bacteria (LAB) isolated from traditional Mongolian dairy products, and to estimate the probiotic potential of the isolated strains. We collected 66 samples of the traditional Mongolian dairy products tarag (n = 45), airag (n = 7), aaruul (n = 8), byasulag (n = 1) and eezgii (n = 5), from which 543 LAB strains were isolated and identified based on 16S ribosomal DNA sequence. The predominant species of those products were Lactobacillus (L.) delbrueckii ssp. bulgaricus, L. helveticus, L. fermentum, L. delbrueckii ssp. lactis and Lactococcus lactis ssp. lactis. However, we could not detect any LAB strains from eezgii. All LAB isolates were screened for tolerance to low pH and to bile acid, gas production from glucose, and adherence to Caco-2 cells. In vitro, we found 10 strains possess probiotic properties, and almost identified them as L. plantarum or L. paracasei subspecies, based on 16S ribosomal DNA and carbohydrate fermentation pattern. These strains were differentiated from each other individually by randomly amplified polymorphic DNA analysis. Additionally, it was notable that 6/10 strains were isolated from camel milk tarag from the Dornogovi province. 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

Effectiveness of Needleless Vial Adaptors and Blunt Cannulas for Drug Administration in a Microgravity Environment

NASA Technical Reports Server (NTRS)

Hailey, M.; Bayuse, T.

2010-01-01

Fluid Isolation in the medication vial: Air/ fluid isolation maneuvers were used to move the medication to the septum end of vial. This isolation may be achieved in multiple ways based on the experience of the astronaut with fluid management in microgravity. If vial adaptors/blunt cannula or syringe assembly is inserted into the to vial before fluid isolation commences, the stability of this assembly should be considered in an effort to limit the risk of "slinging off" of the vial during isolation. Alternatively, fluid isolation can be performed prior to attaching the syringe/vial adaptor assembly. Terrestrial practices for medication withdrawal from a nonvented vial require injection of an equivalent amount of air as the expected medication volume prior to withdrawing liquid. In microgravity, this action is still valid, however the injection of additional air into the vial creates a multitude of micro bubbles and increases the volume of medication mixed with air that then must be withdrawn to achieve the desired drug volume in syringe. This practice is more likely to be required when using vials >30ml in size and injection volumes >10mL. It is felt that based on the microgravity flight, the practice of air injection is more of a hindrance than help.

Genetic Diversity of Blumeria graminis f. sp. hordei in Central Europe and Its Comparison with Australian Population

PubMed Central

Komínková, Eva; Dreiseitl, Antonín; Malečková, Eva; Doležel, Jaroslav

2016-01-01

Population surveys of Blumeria graminis f. sp. hordei (Bgh), a causal agent of more than 50% of barley fungal infections in the Czech Republic, have been traditionally based on virulence tests, at times supplemented with non-specific Restriction fragment length polymorphism or Random amplified polymorphic DNA markers. A genomic sequence of Bgh, which has become available recently, enables identification of potential markers suitable for population genetics studies. Two major strategies relying on transposable elements and microsatellites were employed in this work to develop a set of Repeat junction markers, Single sequence repeat and Single nucleotide polymorphism markers. A resolution power of the new panel of markers comprising 33 polymorphisms was demonstrated by a phylogenetic analysis of 158 Bgh isolates. A core set of 97 Czech isolates was compared to a set 50 Australian isolates on the background of 11 diverse isolates collected throughout the world. 73.2% of Czech isolates were found to be genetically unique. An extreme diversity of this collection was in strong contrast with the uniformity of the Australian one. This work paves the way for studies of population structure and dynamics based on genetic variability among different Bgh isolates originating from geographically limited regions. PMID:27875588

Sequence-based characterization of  Listeria monocytogenes  strains isolated from domestic retail meat in the Tokyo metropolitan area of Japan.

PubMed

Yoshikawa, Yuko; Ochiai, Yoshitsugu; Mochizuki, Mariko; Takano, Takashi; Hondo, Ryo; Ueda, Fukiko

2018-05-31

To assess the level of Listeria monocytogenes contamination of domestic retail meat in Tokyo, Japan, we compared isolates from 2004 to 2007 with those isolated before 2003. The overall prevalence of L. monocytogenes among these samples significantly diminished over time (1998-2003, 28.0%; 2004-2007, 17.6%) reflecting a significant decrease in the frequency of contamination of beef. Serotype 1/2a was isolated most frequently, reflecting a change in the predominant serotype in pork from 1/2c to 1/2a. We performed a simple genetic subtyping method based on three genes, iap, sigB, and actA, as well as traditional multilocus sequence typing to classify the allele types (ATs). No extensive variation among sequence types was detected; however, increased genetic diversity among the ATs of the three genes in the 2004-2007 isolates was evident. We identified AT 26 of the iap gene, not previously reported in Japanese isolates, and six ATs of the sigB gene, including four with nonsense mutations not currently registered in L. monocytogenes DNA databases. sigB is an evolutionally conserved gene that plays a role in the stress response. Our results indicate that the sigB gene may be relatively unstable among L. monocytogenes strains circulating in Japan.

Distribution of Monoclonal Antibody Subgroups and Sequence-Based Types among Legionella pneumophila Serogroup 1 Isolates Derived from Cooling Tower Water, Bathwater, and Soil in Japan

PubMed Central

Kikukawa, Kiyomi; Helbig, Jürgen H.; Kaneko, Satoko; Suzuki-Hashimoto, Atsuko; Furuhata, Katsunori; Chang, Bin; Murai, Miyo; Ichinose, Masayuki; Ohnishi, Makoto; Kura, Fumiaki

2012-01-01

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat. PMID:22492442

State observers and Kalman filtering for high performance vibration isolation systems.

PubMed

Beker, M G; Bertolini, A; van den Brand, J F J; Bulten, H J; Hennes, E; Rabeling, D S

2014-03-01

There is a strong scientific case for the study of gravitational waves at or below the lower end of current detection bands. To take advantage of this scientific benefit, future generations of ground based gravitational wave detectors will need to expand the limit of their detection bands towards lower frequencies. Seismic motion presents a major challenge at these frequencies and vibration isolation systems will play a crucial role in achieving the desired low-frequency sensitivity. A compact vibration isolation system designed to isolate in-vacuum optical benches for Advanced Virgo will be introduced and measurements on this system are used to present its performance. All high performance isolation systems employ an active feedback control system to reduce the residual motion of their suspended payloads. The development of novel control schemes is needed to improve the performance beyond what is currently feasible. Here, we present a multi-channel feedback approach that is novel to the field. It utilizes a linear quadratic regulator in combination with a Kalman state observer and is shown to provide effective suppression of residual motion of the suspended payload. The application of state observer based feedback control for vibration isolation will be demonstrated with measurement results from the Advanced Virgo optical bench suspension system.

Cross-reactions in specific Brachyspira spp. PCR assays caused by "Brachyspira hampsonii" isolates: implications for detection.

PubMed

Aller-Morán, Luis M; Martínez-Lobo, F Javier; Rubio, Pedro; Carvajal, Ana

2016-11-01

An emerging novel spirochete in swine, provisionally designated "Brachyspira hampsonii," has been detected worldwide. It has been associated with swine dysentery and cannot be differentiated from B. hyodysenteriae, the classical etiologic agent of this disease, using standard phenotypic methods. We evaluated cross-reactions of "B. hampsonii" isolates recovered from avian species in some of the currently available species-specific polymerase chain reaction (PCR) assays for the identification of swine Brachyspira species. Ten avian "B. hampsonii" isolates recovered from wild waterfowl were used. No false-positive results were recorded with a B. pilosicoli-specific PCR based on the amplification of a fragment of the 16S rRNA gene. However, the percentage of false-positive results varied, with a range of 10-80%, in the evaluated B. hyodysenteriae-specific assays based on the amplification of the 23S rRNA, nox, and tlyA genes. Similarly, results of the B. intermedia-specific PCR assays yielded poor specificity, with up to 80% of the "B. hampsonii" isolates tested giving false-positive results. Finally, 2 "B. hampsonii" avian isolates yielded a positive result in a B. innocens- and B. murdochii-specific PCR. This result should be interpreted very cautiously as these 2 isolates could represent a recombinant genotype. © 2016 The Author(s).

78 FR 4469 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses and Combined Licenses...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-22

... controverted. In addition, the requestor/petitioner shall provide a brief explanation of the bases for the... pressurizer PORV block valves provide isolation for a postulated stuck-open or leaking PORV. Isolation is...

Comparison between rpoB and 16S rRNA Gene Sequencing for Molecular Identification of 168 Clinical Isolates of Corynebacterium

PubMed Central

Khamis, Atieh; Raoult, Didier; La Scola, Bernard

2005-01-01

Higher proportions (91%) of 168 corynebacterial isolates were positively identified by partial rpoB gene determination than by that based on 16S rRNA gene sequences. This method is thus a simple, molecular-analysis-based method for identification of corynebacteria, but it should be used in conjunction with other tests for definitive identification. PMID:15815024

Clustering of Tuberculosis Cases Based on Variable-Number Tandem-Repeat Typing in Relation to the Population Structure of Mycobacterium tuberculosis in the Netherlands

PubMed Central

Sloot, Rosa; Borgdorff, Martien W.; de Beer, Jessica L.; van Ingen, Jakko; Supply, Philip

2013-01-01

The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmission is overestimated if based on identical VNTR patterns. PMID:23658260

Determination of minimum inhibitory concentrations of itraconazole, terbinafine and ketoconazole against dermatophyte species by broth microdilution method.

PubMed

Bhatia, V K; Sharma, P C

2015-01-01

Various antifungal agents both topical and systemic have been introduced into clinical practice for effectively treating dermatophytic conditions. Dermatophytosis is the infection of keratinised tissues caused by fungal species of genera Trichophyton, Epidermophyton and Microsporum, commonly known as dermatophytes affecting 20-25% of the world's population. The present study aims at determining the susceptibility patterns of dermatophyte species recovered from superficial mycoses of human patients in Himachal Pradesh to antifungal agents; itraconazole, terbinafine and ketoconazole. The study also aims at determining the minimum inhibitory concentrations (MICs) of these agents following the recommended protocol of Clinical and Laboratory Standards Institute (CLSI) (M38-A2). A total of 53 isolates of dermatophytes (T. mentagrophyte-34 in no., T. rubrum-18 and M. gypseum-1) recovered from the superficial mycoses were examined. Broth microdilution method M38-A2 approved protocol of CLSI (2008) for filamentous fungi was followed for determining the susceptibility of dermatophyte species. T. mentagrophyte isolates were found more susceptible to both itraconazole and ketoconazole as compared to terbinafine (MIC50: 0.125 µg/ml for itraconazole, 0.0625 µg/ml for ketoconazole and 0.5 µg/ml for terbinafine). Three isolates of T. mentagrophytes (VBS-5, VBSo-3 and VBSo-73) and one isolate of T. rubrum (VBPo-9) had higher MIC values of itraconazole (1 µg/ml). Similarly, the higher MIC values of ketoconazole were observed in case of only three isolates of T. mentagrophyte (VBSo-30 = 2 µg/ml; VBSo-44, VBM-2 = 1 µg/ml). The comparative analysis of the three antifungal drugs based on t-test revealed that 'itraconazole and terbinafine' and 'terbinafine and ketoconazole' were found independent based on the P < 0.005 in case of T. mentagrophyte isolates. In case of T. rubrum, the similarity existed between MIC values of 'itraconazole and ketoconazole' and 'terbinafine and ketoconazole'. The MIC values observed in the present study based on standard protocol M38-A2 of CLSI 2008 might serve as reference for further studies covering large number of isolates from different geographic regions of the state. Such studies might reflect on the acquisition of drug resistance among isolates of dermatophyte species based on MIC values.

Real-Time Model-Based Leak-Through Detection within Cryogenic Flow Systems

NASA Technical Reports Server (NTRS)

Walker, M.; Figueroa, F.

2015-01-01

The timely detection of leaks within cryogenic fuel replenishment systems is of significant importance to operators on account of the safety and economic impacts associated with material loss and operational inefficiencies. Associated loss in control of pressure also effects the stability and ability to control the phase of cryogenic fluids during replenishment operations. Current research dedicated to providing Prognostics and Health Management (PHM) coverage of such cryogenic replenishment systems has focused on the detection of leaks to atmosphere involving relatively simple model-based diagnostic approaches that, while effective, are unable to isolate the fault to specific piping system components. The authors have extended this research to focus on the detection of leaks through closed valves that are intended to isolate sections of the piping system from the flow and pressurization of cryogenic fluids. The described approach employs model-based detection of leak-through conditions based on correlations of pressure changes across isolation valves and attempts to isolate the faults to specific valves. Implementation of this capability is enabled by knowledge and information embedded in the domain model of the system. The approach has been used effectively to detect such leak-through faults during cryogenic operational testing at the Cryogenic Testbed at NASA's Kennedy Space Center.

Disinfectant Susceptibility Profiling of Glutaraldehyde-Resistant Nontuberculous Mycobacteria.

PubMed

Burgess, Winona; Margolis, Alyssa; Gibbs, Sara; Duarte, Rafael Silva; Jackson, Mary

2017-07-01

OBJECTIVE Activated alkaline glutaraldehyde (GTA) remains one of the most widely used high-level disinfectants worldwide. However, several reports have highlighted the potential for nontuberculous mycobacteria to develop high-level resistance to this product. Because aldehyde resistance may lead to cross-resistance to other biocides, we investigated the susceptibility profile of GTA-resistant Mycobacterium chelonae and M. abscessus isolates to various disinfectant chemistries. METHODS High-level disinfectants commonly used in the reprocessing of endoscopes and other heat-sensitive, semicritical medical equipment, including different formulations of aldehyde-based products and oxidizing agents, were tested against 10 slow- and fast-growing, GTA-susceptible and GTA-resistant, Mycobacterium isolates in suspension tests and carrier tests at different temperatures. RESULTS While peracetic acid- and hydrogen peroxide-based disinfectants (S40, Resert XL, Reliance DG) efficiently killed all of the Mycobacterium isolates, GTA- and ortho-phthalaldehyde-based products (ie, Cidex, Aldahol, Cidex OPA) showed variable efficacy against GTA-resistant strains despite the ability of some formulations (Aldahol) to overcome the resistance of some of these isolates, especially when the temperature was increased from 20°C to 25°C. CONCLUSIONS Application permitting, oxidizing chemistries may provide a safe alternative to aldehyde-based products, particularly in GTA-resistant mycobacterial outbreaks. Infect Control Hosp Epidemiol 2017;38:784-791.

A cluster of culture positive gonococcal infections but with false negative cppB gene based PCR.

PubMed

Lum, G; Freeman, K; Nguyen, N L; Limnios, E A; Tabrizi, S N; Carter, I; Chambers, I W; Whiley, D M; Sloots, T P; Garland, S M; Tapsall, J W

2005-10-01

To describe the prevalence and characteristics of isolates of Neisseria gonorrhoeae grown from urine samples that produced negative results with nucleic acid amplification assays (NAA) targeting the cppB gene. An initial cluster of culture positive, but cppB gene based NAA negative, gonococcal infections was recognised. Urine samples and suspensions of gonococci isolated over 9 months in the Northern Territory of Australia were examined using cppB gene based and other non-cppB gene based NAA. The gonococcal isolates were phenotyped by determining the auxotype/serovar (A/S) class and genotyped by pulsed field gel electrophoresis (PFGE). 14 (9.8%) of 143 gonococci isolated were of A/S class Pro(-/)Brpyut, indistinguishable on PFGE and negative in cppB gene based, but not other, NAA. This cluster represents a temporal and geographic expansion of a gonococcal subtype lacking the cppB gene with consequent loss of sensitivity of NAA dependent on amplification of this target. Gonococci lacking the cppB gene have in the past been more commonly associated with the PAU-/PCU- auxotype, a gonococcal subtype hitherto infrequently encountered in Australia. NAA based on the cppB gene as a target may produce false positive as well as false negative NAA. This suggests that unless there is continuing comparison with culture to show their utility, cppB gene based NAA should be regarded as suboptimal for use either as a diagnostic or supplemental assay for diagnosis of gonorrhoea, and NAA with alternative amplification targets should be substituted.

Stacked dielectric elastomer actuator (SDEA): casting process, modeling and active vibration isolation

NASA Astrophysics Data System (ADS)

Li, Zhuoyuan; Sheng, Meiping; Wang, Minqing; Dong, Pengfei; Li, Bo; Chen, Hualing

2018-07-01

In this paper, a novel fabrication process of stacked dielectric elastomer actuator (SDEA) is developed based on casting process and elastomeric electrode. The so-fabricated SDEA benefits the advantages of homogenous and reproducible properties as well as little performance degradation after one-year use. A coupling model of SDEA is established by taking into consideration of the elastomeric electrode and the calculated results agree with the experiments. Based on the model, we attain the method to optimize the SDEA’s parameters. Finally, the SDEA is used as an isolator in active vibration isolation system to verify the feasibility in dynamic application. And the experiment results show a great prospect for SDEA in such application.

Design of vibration isolation systems using multiobjective optimization techniques

NASA Technical Reports Server (NTRS)

Rao, S. S.

1984-01-01

The design of vibration isolation systems is considered using multicriteria optimization techniques. The integrated values of the square of the force transmitted to the main mass and the square of the relative displacement between the main mass and the base are taken as the performance indices. The design of a three degrees-of-freedom isolation system with an exponentially decaying type of base disturbance is considered for illustration. Numerical results are obtained using the global criterion, utility function, bounded objective, lexicographic, goal programming, goal attainment and game theory methods. It is found that the game theory approach is superior in finding a better optimum solution with proper balance of the various objective functions.

In vitro algaecide effect of sodium hypochlorite and iodine based antiseptics on Prototheca zopfii strains isolated from bovine milk.

PubMed

Salerno, Tatiana; Ribeiro, Márcio Garcia; Langoni, Hélio; Siqueira, Amanda Keller; Costa, Elizabeth Oliveira da; Melville, Priscilla Anne; Bueno, Válter Ferreira Félix; Yamamura, Aline Artioli Machado; Roesler, Uwe; da Silva, Aristeu Vieira

2010-04-01

Prototheca zopfii has been considered one of the most important causes of environmental mastitis in Brazil. These algae are refractory to conventional therapy and cause great damage to the mammary gland. The present study evaluated the in vitro algaecide effect of sodium hypochlorite and iodine based antiseptics on 27 P. zopfii strains isolated from the milk of cattle. Low concentrations of sodium hypochlorite (0.0390625-0.15625%) and iodine (0.15625-0.625%) were effective against the isolates. These antiseptics may be recommended for hygiene routines, pre and postdipping and cauterization of bovine mammary glands infected by P. zopfii. Copyright 2009 Elsevier Ltd. All rights reserved.

Microgravity Isolation Control System Design Via High-Order Sliding Mode Control

NASA Technical Reports Server (NTRS)

Shkolnikov, Ilya; Shtessel, Yuri; Whorton, Mark S.; Jackson, Mark

2000-01-01

Vibration isolation control system design for a microgravity experiment mount is considered. The controller design based on dynamic sliding manifold (DSM) technique is proposed to attenuate the accelerations transmitted to an isolated experiment mount either from a vibrating base or directly generated by the experiment, as well as to stabilize the internal dynamics of this nonminimum phase plant. An auxiliary DSM is employed to maintain the high-order sliding mode on the primary sliding manifold in the presence of uncertain actuator dynamics of second order. The primary DSM is designed for the closed-loop system in sliding mode to be a filter with given characteristics with respect to the input external disturbances.

Folic Acid Targeting for Efficient Isolation and Detection of Ovarian Cancer CTCs from Human Whole Blood Based on Two-Step Binding Strategy.

PubMed

Nie, Liju; Li, Fulai; Huang, Xiaolin; Aguilar, Zoraida P; Wang, Yongqiang Andrew; Xiong, Yonghua; Fu, Fen; Xu, Hengyi

2018-04-25

Studies regarding circulating tumor cells (CTCs) have great significance for cancer prognosis, treatment monitoring, and metastasis diagnosis. However, due to their extremely low concentration in peripheral blood, isolation and enrichment of CTCs are the key steps for early detection. To this end, targeting the folic acid receptors (FRs) on the CTC surface for capture with folic acid (FA) using bovine serum albumin (BSA)-tether for multibiotin enhancement in combination with streptavidin-coated magnetic nanoparticles (MNPs-SA) was developed for ovarian cancer CTC isolation. The streptavidin-biotin-system-mediated two-step binding strategy was shown to capture CTCs from whole blood efficiently without the need for a pretreatment process. The optimized parameters for this system exhibited an average capture efficiency of 80%, which was 25% higher than that of FA-decorated magnetic nanoparticles based on the one-step CTC separation method. Moreover, the isolated cells remained highly viable and were cultured directly without detachment from the MNPs-SA-biotin-CTC complex. Furthermore, when the system was applied for the isolation and detection of CTCs in ovarian cancer patients' peripheral blood samples, it exhibited an 80% correlation with clinical diagnostic criteria. The results indicated that FA targeting, in combination with BSA-based multibiotin enhancement magnetic nanoparticle separation, is a promising tool for CTC enrichment and detection of early-stage ovarian cancer.

Isolation of phage-display library-derived scFv antibody specific to Listeria monocytogenes by a novel immobilized method.

PubMed

Nguyen, X-H; Trinh, T-L; Vu, T-B-H; Le, Q-H; To, K-A

2018-02-01

To select Listeria monocytogenes-specific single-chain fragment variable (scFv) antibodies from a phage-display library by a novel simple and cost-effective immobilization method. Light expanded clay aggregate (LECA) was used as biomass support matrix for biopanning of a phage-display library to select L. monocytogenes-specific scFv antibody. Four rounds of positive selection against LECA-immobilized L. monocytogenes and an additional subtractive panning against Listeria innocua were performed. The phage clones selected using this panning scheme and LECA-based immobilization method exhibited the ability to bind L. monocytogenes without cross-reactivity toward 10 other non-L. monocytogenes bacteria. One of the selected phage clones was able to specifically recognize three major pathogenic serotypes (1/2a, 1/2b and 4b) of L. monocytogenes and 11 tested L. monocytogenes strains isolated from foods. The LECA-based immobilization method is applicable for isolating species-specific anti-L. monocytogenes scFv antibodies by phage display. The isolated scFv antibody has potential use in development of immunoassay-based methods for rapid detection of L. monocytogenes in food and environmental samples. In addition, the LECA immobilization method described here could feasibly be employed to isolate specific monoclonal antibodies against any given species of pathogenic bacteria from phage-display libraries. © 2017 The Society for Applied Microbiology.

Diversity of Cronobacter spp. isolates from the vegetables in the middle-east coastline of China.

PubMed

Chen, Wanyi; Yang, Jielin; You, Chunping; Liu, Zhenmin

2016-06-01

Cronobacter spp. has caused life-threatening neonatal infections mainly resulted from consumption of contaminated powdered infant formula. A total of 102 vegetable samples from retail markets were evaluated for the presence of Cronobacter spp. Thirty-five presumptive Cronobacter isolates were isolated and identified using API 20E and 16S rDNA sequencing analyses. All isolates and type strains were characterized using enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and genetic profiles of cluster analysis from this molecular typing test clearly showed that there were differences among isolates from different vegetables. A polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) based on the amplification of the gyrB gene (1258 bp) was developed to differentiate among Cronobacter species. A new PCR-RFLP assay based on the amplification of the gyrB gene using Alu I and Hinf I endonuclease combination is established and it has been confirmed an accurate and rapid subtyping method to differentiate Cronobacter species. Sequence analysis of the gyrB gene was proven to be suitable for the phylogenetic analysis of the Cronobacter strains, which has much better resolution based on SNPs in the identification of Cronobacter species specificity than PCR-RFLP and ERIC-PCR. Our study further confirmed that vegetables are one of the most common habitats or sources of Cronobacter spp. contamination in the middle-east coastline of China.

Parameter optimization of an inerter-based isolator for passive vibration control of Michelangelo's Rondanini Pietà

NASA Astrophysics Data System (ADS)

Siami, A.; Karimi, H. R.; Cigada, A.; Zappa, E.; Sabbioni, E.

2018-01-01

Preserving cultural heritage against earthquake and ambient vibrations can be an attractive topic in the field of vibration control. This paper proposes a passive vibration isolator methodology based on inerters for improving the performance of the isolation system of the famous statue of Michelangelo Buonarroti Pietà Rondanini. More specifically, a five-degree-of-freedom (5DOF) model of the statue and the anti-seismic and anti-vibration base is presented and experimentally validated. The parameters of this model are tuned according to the experimental tests performed on the assembly of the isolator and the structure. Then, the developed model is used to investigate the impact of actuation devices such as tuned mass-damper (TMD) and tuned mass-damper-inerter (TMDI) in vibration reduction of the structure. The effect of implementation of TMDI on the 5DOF model is shown based on physical limitations of the system parameters. Simulation results are provided to illustrate effectiveness of the passive element of TMDI in reduction of the vibration transmitted to the statue in vertical direction. Moreover, the optimal design parameters of the passive system such as frequency and damping coefficient will be calculated using two different performance indexes. The obtained optimal parameters have been evaluated by using two different optimization algorithms: the sequential quadratic programming method and the Firefly algorithm. The results prove significant reduction in the transmitted vibration to the structure in the presence of the proposed tuned TMDI, without imposing a large amount of mass or modification to the structure of the isolator.

Discrimination of multilocus sequence typing-based Campylobacter jejuni subgroups by MALDI-TOF mass spectrometry.

PubMed

Zautner, Andreas Erich; Masanta, Wycliffe Omurwa; Tareen, Abdul Malik; Weig, Michael; Lugert, Raimond; Groß, Uwe; Bader, Oliver

2013-11-07

Campylobacter jejuni, the most common bacterial pathogen causing gastroenteritis, shows a wide genetic diversity. Previously, we demonstrated by the combination of multi locus sequence typing (MLST)-based UPGMA-clustering and analysis of 16 genetic markers that twelve different C. jejuni subgroups can be distinguished. Among these are two prominent subgroups. The first subgroup contains the majority of hyperinvasive strains and is characterized by a dimeric form of the chemotaxis-receptor Tlp7(m+c). The second has an extended amino acid metabolism and is characterized by the presence of a periplasmic asparaginase (ansB) and gamma-glutamyl-transpeptidase (ggt). Phyloproteomic principal component analysis (PCA) hierarchical clustering of MALDI-TOF based intact cell mass spectrometry (ICMS) spectra was able to group particular C. jejuni subgroups of phylogenetic related isolates in distinct clusters. Especially the aforementioned Tlp7(m+c)(+) and ansB+/ ggt+ subgroups could be discriminated by PCA. Overlay of ICMS spectra of all isolates led to the identification of characteristic biomarker ions for these specific C. jejuni subgroups. Thus, mass peak shifts can be used to identify the C. jejuni subgroup with an extended amino acid metabolism. Although the PCA hierarchical clustering of ICMS-spectra groups the tested isolates into a different order as compared to MLST-based UPGMA-clustering, the isolates of the indicator-groups form predominantly coherent clusters. These clusters reflect phenotypic aspects better than phylogenetic clustering, indicating that the genes corresponding to the biomarker ions are phylogenetically coupled to the tested marker genes. Thus, PCA clustering could be an additional tool for analyzing the relatedness of bacterial isolates.

Selection of indigenous Lactobacillus paracasei CD4 and Lactobacillus gastricus BTM 7 as probiotic: assessment of traits combined with principal component analysis.

PubMed

Sharma, K; Mahajan, R; Attri, S; Goel, G

2017-05-01

The population of the Himalayan region is known to consume a variety of fermented and nonfermented foods and as a result they have been benefited in terms of overall health, because of the associated beneficial microbes. Therefore, the focus of the present study was to identify new strains of lactic acid bacteria (LAB) from dairy products such as milk (cow, goat, buffalo) and fermented products (curd and buttermilk) with properties suitable for use as probiotic cultures. A total of 75 isolates tentatively identified as LAB from 100 samples were initially screened for production of β-haemolysin as indicators of virulence which resulted in 38 isolates with no haemolytic activity. Further subtractive screening based on resistance to gastrointestinal tract barriers (acid and bile salts) resulted in the selection of the eight most promising strains. All these eight strains were resistant to pH 2·0, 1% bile concentration and pancreatin (1 mg l -1 ). Among the eight isolates, three isolates were identified as Brevibacillus thermoruber and the others as Brevibacillus aydinogluensis, Lactobacillus gastricus, L. paracasei, Enterococcus sp. Weisella confusa based on 16S rDNA region. Among these isolates, L. paracasei CD4 and L. gastricus BTM7 indicated maximum tolerance to simulated gastric environment. Both the isolates possessed highest score for cell surface hydrophobicity, cell autoaggregation, adherence to Caco-2 cell lines and antimicrobial activity against clinical isolates of Escherichia coli and Shigella sp. comparable to standard strain of Lactobacillus rhamnosus GG. Further principal component analysis and clustering analysis based on Euclidean Similarity index of probiotic characters revealed that L. paracasei strain CD4 and L. gastricus strain BTM7 were placed closest to reference strain L. rhamnosus GG and were therefore identified as most promising probiotic candidate cultures. These characteristics suggest that these strains could be excellent candidates for probiotics. Milk-based products serve as reservoir for bacterial species with probiotic attributes. © 2017 The Society for Applied Microbiology.

Comparative analysis of virulence and resistance profiles of Salmonella Enteritidis isolates from poultry meat and foodborne outbreaks in northern Jordan

PubMed Central

Jaradat, Ziad W; Abedel Hafiz, Leena; Ababneh, Mustafa M; Ababneh, Qotaibah O; Al Mousa, Waseem; Al-Nabulsi, Anas; Osaili, Tareq M; Holley, Richard

2014-01-01

This study was conducted to isolate Salmonella Enteritidis from poultry samples and compare their virulence and antibiotic resistance profiles to S. Enteritidis isolated from outbreaks in northern Jordan. Two hundred presumptive isolates were obtained from 302 raw poultry samples and were subjected to further analysis and confirmation. A phylogenic tree based on 16S rRNA sequencing was constructed and selected isolates representing each cluster were further studied for their virulence in normal adult Swiss white mice. The most virulent strains were isolated from poultry samples and had an LD50 of 1.55 × 105 CFU, while some of the outbreak isolates were avirulent in mice. Antibiotic resistance profiling revealed that the isolates were resistant to seven of eight antibiotics screened with each isolate resistant to multiple antibiotics (from two to six). Of the poultry isolates, 100%, 88.9%, 77.8%, 66.7%, and 50% showed resistance to nalidixic acid, ciprofloxacin, ampicillin, cephalothin, and cefoperazone, respectively. Two outbreak isolates were sensitive to all tested antibiotics, while 71.4% were resistant to cefoperazone and only 28.6% showed resistance to nalidixic acid. Salmonella outbreak isolates were genetically related to poultry isolates as inferred from the 16S rRNA sequencing, yet were phenotypically different. Although outbreak strains were similar to poultry isolates, when tested in the mouse model, some of the outbreak isolates were highly virulent while others were avirulent. This might be due to a variation in susceptibility of the mouse to different S. Enteritidis isolates. PMID:24780883

Evaluation of serum extracellular vesicle isolation methods for profiling miRNAs by next-generation sequencing

PubMed Central

Kotschote, Stefan; Bonin, Michael

2018-01-01

ABSTRACT Extracellular vesicles (EVs) are intercellular communicators with key functions in physiological and pathological processes and have recently garnered interest because of their diagnostic and therapeutic potential. The past decade has brought about the development and commercialization of a wide array of methods to isolate EVs from serum. Which subpopulations of EVs are captured strongly depends on the isolation method, which in turn determines how suitable resulting samples are for various downstream applications. To help clinicians and scientists choose the most appropriate approach for their experiments, isolation methods need to be comparatively characterized. Few attempts have been made to comprehensively analyse vesicular microRNAs (miRNAs) in patient biofluids for biomarker studies. To address this discrepancy, we set out to benchmark the performance of several isolation principles for serum EVs in healthy individuals and critically ill patients. Here, we compared five different methods of EV isolation in combination with two RNA extraction methods regarding their suitability for biomarker discovery-focused miRNA sequencing as well as biological characteristics of captured vesicles. Our findings reveal striking method-specific differences in both the properties of isolated vesicles and the ability of associated miRNAs to serve in biomarker research. While isolation by precipitation and membrane affinity was highly suitable for miRNA-based biomarker discovery, methods based on size-exclusion chromatography failed to separate patients from healthy volunteers. Isolated vesicles differed in size, quantity, purity and composition, indicating that each method captured distinctive populations of EVs as well as additional contaminants. Even though the focus of this work was on transcriptomic profiling of EV-miRNAs, our insights also apply to additional areas of research. We provide guidance for navigating the multitude of EV isolation methods available today and help researchers and clinicians make an informed choice about which strategy to use for experiments involving critically ill patients. PMID:29887978

Evaluation of serum extracellular vesicle isolation methods for profiling miRNAs by next-generation sequencing.

PubMed

Buschmann, Dominik; Kirchner, Benedikt; Hermann, Stefanie; Märte, Melanie; Wurmser, Christine; Brandes, Florian; Kotschote, Stefan; Bonin, Michael; Steinlein, Ortrud K; Pfaffl, Michael W; Schelling, Gustav; Reithmair, Marlene

2018-01-01

Extracellular vesicles (EVs) are intercellular communicators with key functions in physiological and pathological processes and have recently garnered interest because of their diagnostic and therapeutic potential. The past decade has brought about the development and commercialization of a wide array of methods to isolate EVs from serum. Which subpopulations of EVs are captured strongly depends on the isolation method, which in turn determines how suitable resulting samples are for various downstream applications. To help clinicians and scientists choose the most appropriate approach for their experiments, isolation methods need to be comparatively characterized. Few attempts have been made to comprehensively analyse vesicular microRNAs (miRNAs) in patient biofluids for biomarker studies. To address this discrepancy, we set out to benchmark the performance of several isolation principles for serum EVs in healthy individuals and critically ill patients. Here, we compared five different methods of EV isolation in combination with two RNA extraction methods regarding their suitability for biomarker discovery-focused miRNA sequencing as well as biological characteristics of captured vesicles. Our findings reveal striking method-specific differences in both the properties of isolated vesicles and the ability of associated miRNAs to serve in biomarker research. While isolation by precipitation and membrane affinity was highly suitable for miRNA-based biomarker discovery, methods based on size-exclusion chromatography failed to separate patients from healthy volunteers. Isolated vesicles differed in size, quantity, purity and composition, indicating that each method captured distinctive populations of EVs as well as additional contaminants. Even though the focus of this work was on transcriptomic profiling of EV-miRNAs, our insights also apply to additional areas of research. We provide guidance for navigating the multitude of EV isolation methods available today and help researchers and clinicians make an informed choice about which strategy to use for experiments involving critically ill patients.

High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform.

PubMed

Trembizki, Ella; Smith, Helen; Lahra, Monica M; Chen, Marcus; Donovan, Basil; Fairley, Christopher K; Guy, Rebecca; Kaldor, John; Regan, David; Ward, James; Nissen, Michael D; Sloots, Theo P; Whiley, David M

2014-06-01

Neisseria gonorrhoeae antimicrobial resistance (AMR) is a global problem heightened by emerging resistance to ceftriaxone. Appropriate molecular typing methods are important for understanding the emergence and spread of N. gonorrhoeae AMR. We report on the development, validation and testing of a Sequenom MassARRAY iPLEX method for multilocus sequence typing (MLST)-style genotyping of N. gonorrhoeae isolates. An iPLEX MassARRAY method (iPLEX14SNP) was developed targeting 14 informative gonococcal single nucleotide polymorphisms (SNPs) previously shown to predict MLST types. The method was initially validated using 24 N. gonorrhoeae control isolates and was then applied to 397 test isolates collected throughout Queensland, Australia in the first half of 2012. The iPLEX14SNP method provided 100% accuracy for the control isolates, correctly identifying all 14 SNPs for all 24 isolates (336/336). For the 397 test isolates, the iPLEX14SNP assigned results for 5461 of the possible 5558 SNPs (SNP call rate 98.25%), with complete 14 SNP profiles obtained for 364 isolates. Based on the complete SNP profile data, there were 49 different sequence types identified in Queensland, with 11 of the 49 SNP profiles accounting for the majority (n = 280; 77%) of isolates. AMR was dominated by several geographically clustered sequence types. Using the iPLEX14SNP method, up to 384 isolates could be tested within 1 working day for less than Aus$10 per isolate. The iPLEX14SNP offers an accurate and high-throughput method for the MLST-style genotyping of N. gonorrhoeae and may prove particularly useful for large-scale studies investigating the emergence and spread of gonococcal AMR. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Explaining the trade-growth link: Assessing diffusion-based and structure-based models of exchange.

PubMed

Clark, Rob; Mahutga, Matthew C

2013-03-01

International development scholars advance contrasting theoretical explanations for the hypothesized link between trade and growth. Diffusion-based models suggest that trade with integrated partners provides states with greater access to technical knowledge. Structure-based models propose that trading with isolated partners produces a bargaining advantage. In this study, we adjudicate between these competing visions by applying Bonacich's (1987) measure of power centrality to the international trade network. We manipulate the procedure's "attenuation factor" (β) such that a state's trade centrality can be enhanced when a state is connected to either central or isolated partners. Drawing from a sample of 101 states during the 1980-2000 period, we use difference-of-logs models to assess the impact of trade centrality on economic growth net of controls. We find that the positive relationship between trade centrality and growth peaks when states trade with isolated partners in the periphery. Copyright © 2012 Elsevier Inc. All rights reserved.

Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

PubMed Central

Rasigade, Jean-Philippe; Barbier, Maxime; Dumitrescu, Oana; Pichat, Catherine; Carret, Gérard; Ronnaux-Baron, Anne-Sophie; Blasquez, Ghislaine; Godin-Benhaim, Christine; Boisset, Sandrine; Carricajo, Anne; Jacomo, Véronique; Fredenucci, Isabelle; Pérouse de Montclos, Michèle; Flandrois, Jean-Pierre; Ader, Florence; Supply, Philip; Lina, Gérard; Wirth, Thierry

2017-01-01

The transmission dynamics of tuberculosis involves complex interactions of socio-economic and, possibly, microbiological factors. We describe an analytical framework to infer factors of epidemic success based on the joint analysis of epidemiological, clinical and pathogen genetic data. We derive isolate-specific, genetic distance-based estimates of epidemic success, and we represent success-related time-dependent concepts, namely epidemicity and endemicity, by restricting analysis to specific time scales. The method is applied to analyze a surveillance-based cohort of 1,641 tuberculosis patients with minisatellite-based isolate genotypes. Known predictors of isolate endemicity (older age, native status) and epidemicity (younger age, sputum smear positivity) were identified with high confidence (P < 0.001). Long-term epidemic success also correlated with the ability of Euro-American and Beijing MTBC lineages to cause active pulmonary infection, independent of patient age and country of origin. Our results demonstrate how important insights into the transmission dynamics of tuberculosis can be gained from active surveillance data. PMID:28349973

Genetic Characterization of Soybean Rhizobia Isolated from Different Ecological Zones in North-Eastern Afghanistan.

PubMed

Habibi, Safiullah; Ayubi, Abdul Ghani; Ohkama-Ohtsu, Naoko; Sekimoto, Hitoshi; Yokoyama, Tadashi

2017-03-31

Seventy rhizobial isolates were obtained from the root nodules of two soybean (Glycine max) cultivars: Japanese cultivar Enrei and USA cultivar Stine3300, which were inoculated with different soil samples from Afghanistan. In order to study the genetic properties of the isolates, the DNA sequences of the 16S rRNA gene and symbiotic genes (nodD1 and nifD) were elucidated. Furthermore, the isolates were inoculated into the roots of two soybean cultivars, and root nodule numbers and nitrogen fixation abilities were subsequently evaluated in order to assess symbiotic performance. Based on 16S rRNA gene sequences, the Afghanistan isolates obtained from soybean root nodules were classified into two genera, Bradyrhizobium and Ensifer. Bradyrhizobium isolates accounted for 54.3% (38) of the isolates, and these isolates had a close relationship with Bradyrhizobium liaoningense and B. yuanmingense. Five out of the 38 Bradyrhizobium isolates showed a novel lineage for B. liaoningense and B. yuanmingense. Thirty-two out of the 70 isolates were identified as Ensifer fredii. An Ensifer isolate had identical nodD1 and nifD sequences to those in B. yuanmingense. This result indicated that the horizontal gene transfer of symbiotic genes occurred from Bradyrhizobium to Ensifer in Afghanistan soil. The symbiotic performance of the 14 tested isolates from the root nodules of the two soybean cultivars indicated that Bradyrhizobium isolates exhibited stronger acetylene reduction activities than Ensifer isolates. This is the first study to genetically characterize soybean-nodulating rhizobia in Afghanistan soil.

Assessing Social Isolation: Pilot Testing Different Methods.

PubMed

Taylor, Harry Owen; Herbers, Stephanie; Talisman, Samuel; Morrow-Howell, Nancy

2016-04-01

Social isolation is a significant public health problem among many older adults; however, most of the empirical knowledge about isolation derives from community-based samples. There has been less attention given to isolation in senior housing communities. The objectives of this pilot study were to test two methods to identify socially isolated residents in low-income senior housing and compare findings about the extent of isolation from these two methods. The first method, self-report by residents, included 47 out of 135 residents who completed in-person interviews. To determine self-report isolation, residents completed the Lubben Social Network Scale 6 (LSNS-6). The second method involved a staff member who reported the extent of isolation on all 135 residents via an online survey. Results indicated that 26% of residents who were interviewed were deemed socially isolated by the LSNS-6. Staff members rated 12% of residents as having some or a lot of isolation. In comparing the two methods, staff members rated 2% of interviewed residents as having a lot of isolation. The combination of self-report and staff report could be more informative than just self-report alone, particularly when participation rates are low. However, researchers should be aware of the potential discrepancy between these two methods.

Ground Isolation Circuit for Isolating a Transmission Line from Ground Interference

NASA Technical Reports Server (NTRS)

Davidson, Craig A. (Inventor)

1996-01-01

This invention relates generally to a system for isolating ground interference from a transmission line, e.g., a ground isolation circuit for isolating a wideband transmission signal (such as a video signal) from ground by modulating the base signal on a carrier signal to permit the transmission signal to be isolated. In one embodiment, the circuit includes a pair of matched mixer circuits, each of which receives a carrier signal from the same oscillator circuit. The first mixer circuit also receives the baseband signal input, after appropriate conditioning, and modulates the baseband signal onto the carrier signal. In a preferred embodiment the carrier signal has a predetermined frequency which is at least two times the frequency of the baseband signal. The modulated signal (which can comprise an rf signal) is transmitted via an rf transmission line to the second mixer, which demodulates the rf signal to recover the baseband signal. Each port of the mixer connects to an isolation transformer to ensure isolation from ground interference. The circuit is considered to be of commercial value in that it can provide isolation between transmitting and receiving circuits, e.g., ground isolation for television circuits or high frequency transmitters, without the need for video transformers or optical isolators, thereby reducing the complexity, power consumption, and weight of the system.

In vitro interaction of actinomycetes isolates with Aspergillus flavus: impact on aflatoxins B1 and B2 production.

PubMed

Verheecke, C; Liboz, T; Darriet, M; Sabaou, N; Mathieu, F

2014-06-01

This work aimed to study the interaction between Actinomycetal isolates and Aspergillus flavus to promote mutual antagonism in contact. Thirty-seven soilborn Streptomyces spp. isolates were chosen as potential candidates. After a 10-day in vitro co-incubation period, 27 isolates respond to the criteria, that is, mutual antagonism in contact. Further aflatoxins B1 and B2 analysis revealed that those 27 isolates reduced aflatoxin B1 residual concentration from 38·6 to 4·4%, depending on the isolate. We selected 12 isolates and tested their capacity to reduce AFB1 in pure culture to start identifying the mechanisms involved in its reduction. AFB1 was reduced by eight isolates. The remaining AFB1 concentration varied between 82·2 and 15·6%. These findings led us to suggest that these eight isolates could be used as biocontrol agents against AFB1 and B2 with low risk of impacting the natural microbial equilibrium. Interaction between Aspergillus flavus and Actinomycetes isolates was conducted in vitro. Actinomycetes isolates having a mutual antagonism in contact with A. flavus were chosen for further aflatoxins production study. This is a new approach based to develop biocontrol against aflatoxins accumulation in maize while respecting natural microbial equilibrium. © 2014 The Society for Applied Microbiology.

The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.

PubMed

Sailaja, B; Anjum, Najreen; Patil, Yogesh K; Agarwal, Surekha; Malathi, P; Krishnaveni, D; Balachandran, S M; Viraktamath, B C; Mangrauthia, Satendra K

2013-12-01

In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95% to east Indian isolates and 90% to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5' end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.

Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India.

PubMed

Hussain, Arif; Ranjan, Amit; Nandanwar, Nishant; Babbar, Anshu; Jadhav, Savita; Ahmed, Niyaz

2014-12-01

In view of the epidemiological success of CTX-M-15-producing lineages of Escherichia coli and particularly of sequence type 131 (ST131), it is of significant interest to explore its prevalence in countries such as India and to determine if antibiotic resistance, virulence, metabolic potential, and/or the genetic architecture of the ST131 isolates differ from those of non-ST131 isolates. A collection of 126 E. coli isolates comprising 43 ST131 E. coli, 40 non-ST131 E. coli, and 43 fecal E. coli isolates collected from a tertiary care hospital in India was analyzed. These isolates were subjected to enterobacterial repetitive intergenic consensus (ERIC)-based fingerprinting, O typing, phylogenetic grouping, antibiotic sensitivity testing, and virulence and antimicrobial resistance gene (VAG) detection. Representative isolates from this collection were also analyzed by multilocus sequence typing (MLST), conjugation, metabolic profiling, biofilm production assay, and zebra fish lethality assay. All of the 43 ST131 E. coli isolates were exclusively associated with phylogenetic group B2 (100%), while most of the clinical non-ST131 and stool non-ST131 E. coli isolates were affiliated with the B2 (38%) and A (58%) phylogenetic groups, respectively. Significantly greater proportions of ST131 isolates (58%) than non-ST131 isolates (clinical and stool E. coli isolates, 5% each) were technically identified to be extraintestinal pathogenic E. coli (ExPEC). The clinical ST131, clinical non-ST131, and stool non-ST131 E. coli isolates exhibited high rates of multidrug resistance (95%, 91%, and 91%, respectively), extended-spectrum-β-lactamase (ESBL) production (86%, 83%, and 91%, respectively), and metallo-β-lactamase (MBL) production (28%, 33%, and 0%, respectively). CTX-M-15 was strongly linked with ESBL production in ST131 isolates (93%), whereas CTX-M-15 plus TEM were present in clinical and stool non-ST131 E. coli isolates. Using MLST, we confirmed the presence of two NDM-1-positive ST131 E. coli isolates. The aggregate bioscores (metabolite utilization) for ST131, clinical non-ST131, and stool non-ST131 E. coli isolates were 53%, 52%, and 49%, respectively. The ST131 isolates were moderate biofilm producers and were more highly virulent in zebra fish than non-ST131 isolates. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, and this was subsequently followed by the genetic similarity of clinical non-ST131 and stool non-ST131 E. coli strains. In conclusion, our data provide novel insights into aspects of the fitness advantage of E. coli lineage ST131 and suggest that a number of factors are likely involved in the worldwide dissemination of and infections due to ST131 E. coli isolates. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

DIFFERENTIATING HUMAN FROM ANIMAL ISOLATES OF CRYPTOSPORIDIUM PARVUM

EPA Science Inventory

We analyzed 9s Cryptosporidium parvum isolates from humans and animals by a polymerase chain reaction/restriction fragment length polymorphism method based on the thrombospondin-related anonymous protein 2 gene sequence. Used as a molecular marker, this method can differentiate ...

Serological Relationships Among Feline Caliciviruses

PubMed Central

Povey, R. C.

1974-01-01

A total of 46 strains of feline calicivirus isolates from the United Kingdom, United States, Australia, and New Zealand were used in an investigation of their serological relationships based on the serum neutralization test. Although demonstrable antigenic variation exists between these isolates, it is shown that significant in vitro cross-activity exists between all these isolates to greater or lesser extent. All isolates tested may be regarded as serological variants of a single serotype of feline calicivirus. It is postulated that this relationship would provide for considerable cross-protection during successive exposures of cats to various feline caliciviruses. PMID:4435957

Low frequency vibration isolation technology for microgravity space experiments

NASA Technical Reports Server (NTRS)

Grodsinsky, Carlos M.; Brown, Gerald V.

1989-01-01

The dynamic acceleration environment observed on Space Shuttle flights to date and predicted for the Space Station has complicated the analysis of prior microgravity experiments and prompted concern for the viability of proposed space experiments requiring long-term, low-g environments. Isolation systems capable of providing significant improvements in this environment exist, but have not been demonstrated in flight configurations. This paper presents a summary of the theoretical evaluation for two one degree-of-freedom (DOF) active magnetic isolators and their predicted response to both direct and base excitations, that can be used to isolate acceleration sensitive microgravity space experiments.

Isolating Escherichia coli strains for recombinant protein production.

PubMed

Schlegel, Susan; Genevaux, Pierre; de Gier, Jan-Willem

2017-03-01

Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.

Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India.

PubMed

Qumar, Shamsul; Majid, Mohammad; Kumar, Narender; Tiwari, Sumeet K; Semmler, Torsten; Devi, Savita; Baddam, Ramani; Hussain, Arif; Shaik, Sabiha; Ahmed, Niyaz

2017-01-01

Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates. Taken together, these observations provide significant baseline data for functional molecular infection epidemiology of nonpyloric Helicobacter species such as H. pullorum by unraveling their evolution in chickens and their possible zoonotic transmission to humans. Globally, the poultry industry is expanding with an ever-growing consumer base for chicken meat. Given this, food-associated transmission of multidrug-resistant bacteria represents an important health care issue. Our study involves a critical baseline approach directed at genome sequence-based epidemiology and transmission dynamics of H. pullorum, a poultry pathogen having established zoonotic potential. We believe our studies would facilitate the development of surveillance systems that ensure the safety of food for humans and guide public health policies related to the use of antibiotics in animal feed in countries such as India. We sequenced 11 new genomes of H. pullorum as a part of this study. These genomes would provide much value in addition to the ongoing comparative genomic studies of helicobacters. Copyright © 2016 American Society for Microbiology.

A high voltage dielectrically isolated smart power technology based on silicon direct bonding

NASA Astrophysics Data System (ADS)

Macary, Veronique

1992-09-01

The feasibility of a dielectrically isolated technology based on the silicon direct bonding technique, for high voltage smart power applications in the 1000 to 1550 V/1 to 20 A range, where a vertical power switch is necessary, is investigated and demonstrated. Static and dynamic isolation of the low voltage circuitry integrated beside the vertical power transistor is the main concern of this family of circuits. The dielectric isolation offers better protection to the low voltage part than does the junction isolation, because of the elimination of the parasitic bipolar transistor inherent to the latter isolation technique. Silicon direct bonding provides a cost effective way to obtain a buried oxide isolation layer. In addition, the application requires a Si/Si bonded area in the active region of the vertical power switch. Strong influence of the prebonding cleaning in the electrical characteristics of the Si/Si interface is pointed out, and presence of crystalline defects is assumed to be at the origin of electrical failures. The main problems of silicon direct bonding process compatibility with standard processes were overcome, and a complete process flow, including the simultaneous integration of a vertical power bipolar transistor together with a bipolar control circuitry, was validated. Using a peripheral biased ring is shown to provide an easy way to optimize high voltage termination for the smart power circuit, while adding a non-additional technological step. This technique was studied by dimensional electrical simulations (BIDIM2 software), as well as analytically computed.

Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

PubMed Central

Martos, Laura; Fernández-Pardo, Álvaro; Oto, Julia; Medina, Pilar; España, Francisco; Navarro, Silvia

2017-01-01

microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs. In all microRNAs analyzed, the addition of yeast RNA as a carrier in the different isolation protocols used gave lower raw Cq values, indicating higher microRNA recovery. Moreover, this increase in microRNAs recovery was dependent on their own relative abundance in the sample, their GC content and the free-energy of their own most stable secondary structure. Furthermore, the normalization of microRNA levels by an endogenous microRNA is more reliable than the normalization by plasma volume, as it reduced the difference in microRNA fold abundance between the different isolation protocols evaluated. Our thorough study indicates that a standardization of pre- and analytical conditions is necessary to obtain reproducible inter-laboratory results in plasma microRNA studies. PMID:29077772

High-Throughput, Motility-Based Sorter for Microswimmers such as C. elegans

PubMed Central

Yuan, Jinzhou; Zhou, Jessie; Raizen, David M.; Bau, Haim H.

2015-01-01

Animal motility varies with genotype, disease, aging, and environmental conditions. In many studies, it is desirable to carry out high throughput motility-based sorting to isolate rare animals for, among other things, forward genetic screens to identify genetic pathways that regulate phenotypes of interest. Many commonly used screening processes are labor-intensive, lack sensitivity, and require extensive investigator training. Here, we describe a sensitive, high throughput, automated, motility-based method for sorting nematodes. Our method is implemented in a simple microfluidic device capable of sorting thousands of animals per hour per module, and is amenable to parallelism. The device successfully enriches for known C. elegans motility mutants. Furthermore, using this device, we isolate low-abundance mutants capable of suppressing the somnogenic effects of the flp-13 gene, which regulates C. elegans sleep. By performing genetic complementation tests, we demonstrate that our motility-based sorting device efficiently isolates mutants for the same gene identified by tedious visual inspection of behavior on an agar surface. Therefore, our motility-based sorter is capable of performing high throughput gene discovery approaches to investigate fundamental biological processes. PMID:26008643

First report of the Armillaria root disease pathogen, Armillaria sinapina, on subalpine fir (Abies lasiocarpa) and quaking aspen (Populus tremuloides) in Colorado

Treesearch

K. S. Burns; J. W. Hanna; Ned Klopfenstein; M.-S. Kim

2016-01-01

In July 2014, mycelial fans (isolates CO104F, CO106F, and CO108F) of Armillaria sp. were collected from forest trees in Colorado. These isolates were all identified as A. sinapina based on a somatic pairing test against 18 tester isolates representing six North American Armillaria spp. and nucleotide sequences of the translation elongation factor 1alpha (tef-...

Symptom development in response to combined infection of in vitro grown Lilium longiflorum with the root lesion nematode Pratylenchus penetrans and soilborne fungi collected from diseased roots of field-grown lilies

USDA-ARS?s Scientific Manuscript database

Eight fungal isolates (ELRF 1-8) were isolated from necrotic roots of Lilium longiflorum cv. Nellie White (Easter lily) grown in a field in the U.S. Pacific Northwest. The eight fungal isolates were identified by sequencing and molecular phylogenetic analyses based on their ITS rDNA region. Five iso...

Non-Tuberculous Mycobacteria. An Emerging Threat?

PubMed

Martínez González, Susana; Cano Cortés, Arantxa; Sota Yoldi, Luis Alfonso; García García, José María; Alba Álvarez, Luz María; Palacios Gutiérrez, Juan José

2017-10-01

Non-tuberculous mycobacteria (NTM) isolates are becoming more common. The main objective of our study was to establish the number and diversity of NTM species in our region and their distribution according to the source sample, age and gender of the patients, and to analyse clinically significant isolates. Prospective study of all NTM isolated in Asturias from 2005 to 2012. Samples were processed following internationally accepted guidelines. Statistical analysis was based on Fisher's exact test for 2×2 contingency tables. A total of 3,284 mycobacteria were isolated: 1,499 Mycobacterium tuberculosis complex (MTB) and 1,785 NTM.During the study, NTM isolation rates increased while MTB isolation decreased. NTM were more frequent in men (P<.001). M.gordonae was the most frequently isolated species but did not cause disease in any case. NTM isolates from 212 patients were associated with clinically significant disease (17.1%). M.kansasii and M.avium were most commonly associated with disease. The number of M.kansasii isolates from men was statistically significant (P<.01). In our study, NTM isolates increased by 35%, compared with a 21% decline in cases of MTB. Both isolation of NTM and clinically significant cases were more common in men. Only 17.1% of NTM isolates were associated with disease, most commonly M.avium complex and M.kansasii. Copyright © 2017 SEPAR. Publicado por Elsevier España, S.L.U. All rights reserved.

Rational Autologous Cell Sources For Therapy of Heart Failure - Vehicles and Targets For Gene and RNA Therapies.

PubMed

Lampinen, Milla; Vento, Antti; Laurikka, Jari; Nystedt, Johanna; Mervaala, Eero; Harjula, Ari; Kankuri, Esko

2016-01-01

This review focuses on the possibilities for intraoperative processing and isolation of autologous cells, particularly atrial appendage-derived cells (AADCs) and cellular micrografts, and their straightforward use in cell transplantation for heart failure therapy. We review the potential of autologous tissues to serve as sources for cell therapy and consider especially those tissues that are used in surgery but from which the excess is currently discarded as surgical waste. We compare the inculture expanded cells to the freshly isolated ones in terms of evidence-based cost-efficacy and their usability as gene- and RNA therapy vehicles. We also review how financial and authority-based decisions and restrictions sculpt the landscape for patients to participate in academic-based trials. Finally, we provide an insight example into AADCs isolation and processing for epicardial therapy during coronary artery bypass surgery.

Mechanical modeling for magnetorheological elastomer isolators based on constitutive equations and electromagnetic analysis

NASA Astrophysics Data System (ADS)

Wang, Qi; Dong, Xufeng; Li, Luyu; Ou, Jinping

2018-06-01

As constitutive models are too complicated and existing mechanical models lack universality, these models are beyond satisfaction for magnetorheological elastomer (MRE) devices. In this article, a novel universal method is proposed to build concise mechanical models. Constitutive model and electromagnetic analysis were applied in this method to ensure universality, while a series of derivations and simplifications were carried out to obtain a concise formulation. To illustrate the proposed modeling method, a conical MRE isolator was introduced. Its basic mechanical equations were built based on equilibrium, deformation compatibility, constitutive equations and electromagnetic analysis. An iteration model and a highly efficient differential equation editor based model were then derived to solve the basic mechanical equations. The final simplified mechanical equations were obtained by re-fitting the simulations with a novel optimal algorithm. In the end, verification test of the isolator has proved the accuracy of the derived mechanical model and the modeling method.

Immunomagnetic separation for MEMS-based biosensor of waterborne pathogens detection

NASA Astrophysics Data System (ADS)

Guo, Jianjiang; Zhang, Rongbiao

2017-07-01

Rapid isolation and detection of special pathogens present in environmental drinking water is critical for water quality monitoring. Numerical analysis and experimental investigations on immunomagnetic capture and isolation of waterborne pathogens with magnetic nanoparticles (MNPs) in microfluidic channel are performed. A finite-element COMSOL-based model is established to demonstrate the novel method of on-chip capturing pathogens using MNPs together with periodic pulse magnetic field. Simulation results determine the optimum magnetic pole current and switching frequency for magnetic separation. With the magnetic isolation experiment platform built up, as a pathogen example of Escherichia coli O157:H7, the performance of the method is experimentally verified. Both numerical and experimental results are found to agree reasonably well. Results of these investigations show that the capture efficiency of the immunomagnetic separation method is more than 92%, which could be encouraging for the design and optimization of MEMS-based biosensor of waterborne pathogen detection.

Isolation of Brucella inopinata-Like Bacteria from White's and Denny's Tree Frogs.

PubMed

Kimura, Masanobu; Une, Yumi; Suzuki, Michio; Park, Eun-Sil; Imaoka, Koichi; Morikawa, Shigeru

2017-05-01

Brucella inopinata strain BO1 and B. sp. strain BO2 isolated from human patients, respectively, are genetically different from classical Brucella species. We isolated bacteria of the genus Brucella from two species of wild-caught tropical frogs kept in the facilities in Japan: White's tree frog, which inhabits Oceania, and Denny's tree frog, which inhabits Southeast Asia. Phylogenetic analyses based on 16S rRNA and recA gene sequences and multilocus sequence analysis showed that two isolates of Brucella spp. showed significant similarity to BO1, BO2, and the isolates from other wild-caught frogs. These results suggest that a variety of frog species are susceptible to a novel clade of Brucella bacteria, including B. inopinata.

Characterization of Pseudomonas pathovars isolated from rosaceous fruit trees in East Algeria.

PubMed

Harzallah, D; Sadallah, S; Larous, L

2004-01-01

A survey of bacterial diseases due to Pseudomonas on rosaceous fruit trees was conducted. In forty two orchards located in the Constantine region ( East Algeria). Pseudomonas isolates were identified on the bases of their cultural and biochemical characteristics . A total of fifty nine phytopathogenic bacteria were isolated from diseased pome and stone fruit trees. Thirty one strains comparable to Pseudomonas syringae pv. syringae were isolated from cherry (Prunus avium L.), plum (P. domestica L.), apricot (P. armeniaca L.), almond (P. dulcis L.) and pear trees (Pirus communis L.); sixteen strains comparable to Pseudomonas syringae pv. morsprunorum were obtained from samples of cherry and plum. Twelve strains of Pseudomonas viridiflava were isolated from cherry, apricot and peach (Prunus persica L.).

78 FR 8195 - Biweekly Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-05

... of the bases for the contention and a concise statement of the alleged facts or expert opinion which..., ``Allowable Value for Primary Containment and Drywell Isolation Instrumentation,'' Function 3.c, ``Reactor Core Isolation Cooling (RCIC) Steam Supply Line Pressure--Low.'' This TS allowable value will be...

A microfluidic chip integrated with a high-density PDMS-based microfiltration membrane for rapid isolation and detection of circulating tumor cells.

PubMed

Fan, Xiaoyun; Jia, Chunping; Yang, Jun; Li, Gang; Mao, Hongju; Jin, Qinghui; Zhao, Jianlong

2015-09-15

Isolation of circulating tumor cells (CTCs) by size exclusion is a widely researched technique that offers the advantage of capturing tumor cells without reliance on cell surface expression markers. In this work, we report the development of a novel polydimethylsiloxane (PDMS) membrane filter-based microdevice for rapid and highly efficient isolation of CTCs from peripheral blood. A precise and highly porous PDMS microfilter was fabricated and integrated into the microfiltration chip by combining a sacrificial transferring film with a sandwich molding method. We achieved >90% recovery when isolating lung cancer cells from spiked blood samples, with a relatively high processing throughput of 10 mL/h. In contrast to existing CTC filtration systems, which rely on low-porosity track-etch filters or expensive lithography-based filters, our microfiltration chip does not require complex e-beam lithography or the reactive ion etching process, therefore it offers a low-cost alternative tool for highly efficient CTC enrichment and in situ analysis. Thus, this new microdevice has the potential for use in routine monitoring of cancer development and cancer therapy in a clinical setting. Copyright © 2015 Elsevier B.V. All rights reserved.

Aircraft control surface failure detection and isolation using the OSGLR test. [orthogonal series generalized likelihood ratio

NASA Technical Reports Server (NTRS)

Bonnice, W. F.; Motyka, P.; Wagner, E.; Hall, S. R.

1986-01-01

The performance of the orthogonal series generalized likelihood ratio (OSGLR) test in detecting and isolating commercial aircraft control surface and actuator failures is evaluated. A modification to incorporate age-weighting which significantly reduces the sensitivity of the algorithm to modeling errors is presented. The steady-state implementation of the algorithm based on a single linear model valid for a cruise flight condition is tested using a nonlinear aircraft simulation. A number of off-nominal no-failure flight conditions including maneuvers, nonzero flap deflections, different turbulence levels and steady winds were tested. Based on the no-failure decision functions produced by off-nominal flight conditions, the failure detection and isolation performance at the nominal flight condition was determined. The extension of the algorithm to a wider flight envelope by scheduling on dynamic pressure and flap deflection is examined. Based on this testing, the OSGLR algorithm should be capable of detecting control surface failures that would affect the safe operation of a commercial aircraft. Isolation may be difficult if there are several surfaces which produce similar effects on the aircraft. Extending the algorithm over the entire operating envelope of a commercial aircraft appears feasible.

Isolation and Evaluation of Oil-Producing Microalgae from Subtropical Coastal and Brackish Waters

PubMed Central

Lim, David K. Y.; Garg, Sourabh; Timmins, Matthew; Zhang, Eugene S. B.; Thomas-Hall, Skye R.; Schuhmann, Holger; Li, Yan; Schenk, Peer M.

2012-01-01

Microalgae have been widely reported as a promising source of biofuels, mainly based on their high areal productivity of biomass and lipids as triacylglycerides and the possibility for cultivation on non-arable land. The isolation and selection of suitable strains that are robust and display high growth and lipid accumulation rates is an important prerequisite for their successful cultivation as a bioenergy source, a process that can be compared to the initial selection and domestication of agricultural crops. We developed standard protocols for the isolation and cultivation for a range of marine and brackish microalgae. By comparing growth rates and lipid productivity, we assessed the potential of subtropical coastal and brackish microalgae for the production of biodiesel and other oil-based bioproducts. This study identified Nannochloropsis sp., Dunaniella salina and new isolates of Chlorella sp. and Tetraselmis sp. as suitable candidates for a multiple-product algae crop. We conclude that subtropical coastal microalgae display a variety of fatty acid profiles that offer a wide scope for several oil-based bioproducts, including biodiesel and omega-3 fatty acids. A biorefinery approach for microalgae would make economical production more feasible but challenges remain for efficient harvesting and extraction processes for some species. PMID:22792403

Seismic isolation of buildings using composite foundations based on metamaterials

NASA Astrophysics Data System (ADS)

Casablanca, O.; Ventura, G.; Garescı, F.; Azzerboni, B.; Chiaia, B.; Chiappini, M.; Finocchio, G.

2018-05-01

Metamaterials can be engineered to interact with waves in entirely new ways, finding application on the nanoscale in various fields such as optics and acoustics. In addition, acoustic metamaterials can be used in large-scale experiments for filtering and manipulating seismic waves (seismic metamaterials). Here, we propose seismic isolation based on a device that combines some properties of seismic metamaterials (e.g., periodic mass-in-mass systems) with that of a standard foundation positioned right below the building for isolation purposes. The concepts on which this solution is based are the local resonance and a dual-stiffness structure that preserves large (small) rigidity for compression (shear) effects. In other words, this paper introduces a different approach to seismic isolation by using certain principles of seismic metamaterials. The experimental demonstrator tested on the laboratory scale exhibits a spectral bandgap that begins at 4.5 Hz. Within the bandgap, it filters more than 50% of the seismic energy via an internal dissipation process. Our results open a path toward the seismic resilience of buildings and a critical infrastructure to shear seismic waves, achieving higher efficiency compared to traditional seismic insulators and passive energy-dissipation systems.

H-alpha LEGUS: Insights into the Field OB Star Population in Nearby Galaxies

NASA Astrophysics Data System (ADS)

Lee, Janice; Thilker, David; Kayitesi, Bridget; Chandar, Rupali; Halpha LEGUS Team

2018-01-01

The question of whether O-stars can form in isolation, without attendant clusters or associations of lower mass stars, is a topic of interest because the answer to the question can distinguish between models of star formation. To begin to investigate whether such isolated O-stars can be identified in nearby galaxies beyond the Local Group, we identify candidate field OB-stars in NGC 1313, NGC 4395 and NGC 7793, the three nearest spiral galaxies in the HST Legacy ExtraGalactic Ultraviolet Survey (LEGUS). Candidates are selected using a technique based on: (1) a reddening-free Q parameter, adapted for photometry in HST filters covering the NUV, U, & B bands; (2) isolation based on projected distance from the nearest young cluster and candidate OB star, and (3) the presence of an HII region, identified based on HST H-alpha narrowband imaging. Our catalogs enable a range of follow-up studies on massive stars, and in particular provide targets for future spectroscopic observation and analysis. We describe the candidate OB star sample, the spatial distribution of the stars, and their HII region properties, with special focus on the most isolated objects in the sample.

Cluster Analysis of Campylobacter jejuni Genotypes Isolated from Small and Medium-Sized Mammalian Wildlife and Bovine Livestock from Ontario Farms.

PubMed

Viswanathan, M; Pearl, D L; Taboada, E N; Parmley, E J; Mutschall, S K; Jardine, C M

2017-05-01

Using data collected from a cross-sectional study of 25 farms (eight beef, eight swine and nine dairy) in 2010, we assessed clustering of molecular subtypes of C. jejuni based on a Campylobacter-specific 40 gene comparative genomic fingerprinting assay (CGF40) subtypes, using unweighted pair-group method with arithmetic mean (UPGMA) analysis, and multiple correspondence analysis. Exact logistic regression was used to determine which genes differentiate wildlife and livestock subtypes in our study population. A total of 33 bovine livestock (17 beef and 16 dairy), 26 wildlife (20 raccoon (Procyon lotor), five skunk (Mephitis mephitis) and one mouse (Peromyscus spp.) C. jejuni isolates were subtyped using CGF40. Dendrogram analysis, based on UPGMA, showed distinct branches separating bovine livestock and mammalian wildlife isolates. Furthermore, two-dimensional multiple correspondence analysis was highly concordant with dendrogram analysis showing clear differentiation between livestock and wildlife CGF40 subtypes. Based on multilevel logistic regression models with a random intercept for farm of origin, we found that isolates in general, and raccoons more specifically, were significantly more likely to be part of the wildlife branch. Exact logistic regression conducted gene by gene revealed 15 genes that were predictive of whether an isolate was of wildlife or bovine livestock isolate origin. Both multiple correspondence analysis and exact logistic regression revealed that in most cases, the presence of a particular gene (13 of 15) was associated with an isolate being of livestock rather than wildlife origin. In conclusion, the evidence gained from dendrogram analysis, multiple correspondence analysis and exact logistic regression indicates that mammalian wildlife carry CGF40 subtypes of C. jejuni distinct from those carried by bovine livestock. Future studies focused on source attribution of C. jejuni in human infections will help determine whether wildlife transmit Campylobacter jejuni directly to humans. © 2016 Blackwell Verlag GmbH.

Characterization and virulence of Beauveria spp. recovered from emerald ash borer in southwestern Ontario, Canada.

PubMed

Johny, Shajahan; Kyei-Poku, George; Gauthier, Debbie; Frankenhuyzen, Kees van; Krell, Peter J

2012-09-15

The emerald ash borer (EAB), Agrilus planipennis (Coleoptera: Buprestidae), is an invasive wood boring beetle that is decimating North America's ash trees (Fraxinus spp.). To find effective and safe indigenous biocontrol agents to manage EAB, we conducted a survey in 2008-2009 of entomopathogenic fungi (EPF) infecting EAB in five outbreak sites in southwestern Ontario, Canada. A total of 78 Beauveria spp. isolates were retrieved from dead and mycosed EAB cadavers residing in the phloem tissues of dead ash barks, larval frass extracted from feeding galleries under the bark of dead trees. Molecular characterization using sequences of the ITS, 5' end of EF1-α and intergenic Bloc region fragments revealed that Beauveria bassiana and Beauveria pseudobassiana were commonly associated with EAB in the sampled sites. Based on phylogenetic analysis inferred from ITS sequences, 17 of these isolates clustered with B. bassiana, which further grouped into three different sub-clades. However, the combined EF1-α and Bloc sequences detected five genotypes among the three sub-clades. The remaining 61 isolates clustered with B. pseudobassiana, which had identical ITS sequences but were further subdivided into two genotypes by variation in the EF1-α and Bloc regions. Initial virulence screening against EAB adults of 23 isolates representing the different clades yielded 8 that produced more than 90% mortality in a single concentration assay. These isolates differed in virulence based on LC(50) values estimated from multiple concentration bioassay and based on mean survival times at a conidia concentration of 2×10(6) conidia/ml. B. bassiana isolate L49-1AA was significantly more virulent and produced more conidia on EAB cadavers compared to the other indigenous isolates and the commercial strain B. bassiana GHA suggesting that L49-1AA may have potential as a microbiological control agent against EAB. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

If you build it will they come? Addressing social isolation within a technology-based HIV intervention for young black men who have sex with men.

PubMed

LeGrand, Sara; Muessig, Kathryn E; Pike, Emily C; Baltierra, Nina; Hightow-Weidman, Lisa B

2014-01-01

The rate of HIV infections among young black men who have sex with men (YBMSM) continues to rise at an alarming pace. YBMSM are particularly vulnerable to social isolation and a lack of social support due to experiences with racism and homophobia, which may have implications for sexual risk behaviors. The purpose of this study was to explore perceptions of social isolation and sense of community among YBMSM, the need for and receptivity to social networking features designed to reduce social isolation and build community within an Internet- and mobile phone-based primary and secondary HIV prevention intervention for YBMSM and to identify strategies to develop these features. Focus groups were conducted with 22 YBMSM aged 20-30 years at three sites in North Carolina. Data from the focus groups were thematically analyzed using NVivo. Feelings of social isolation and lack of a sense of community were strongly endorsed by participants with homophobia, lack of opportunities for social engagement, and a focus on sex rather than friendship in interpersonal relationships with other YBMSM cited as contributing factors. Participants were receptive to a social networking intervention designed to reduce social isolation and build community. Recommendations offered by participants to increase acceptability and usability of such features included: availability of information about healthy relationships, the ability to connect with other YBMSM and health care providers, and ensuring the site had ongoing facilitation by the study team as well as monitoring for inappropriate content. The development of a social networking feature of an HIV prevention intervention may present an opportunity to reduce social isolation, build community, and reduce risky sexual behaviors among YBMSM. The findings from this study are being used to inform the development of a social networking feature for an existing Internet- and mobile phone-based primary and secondary HIV prevention intervention for YBMSM.

Evaluation of DNA extraction methods for PCR-based detection of Listeria monocytogenes from vegetables.

PubMed

Vojkovska, H; Kubikova, I; Kralik, P

2015-03-01

Epidemiological data indicate that raw vegetables are associated with outbreaks of Listeria monocytogenes. Therefore, there is a demand for the availability of rapid and sensitive methods, such as PCR assays, for the detection and accurate discrimination of L. monocytogenes. However, the efficiency of PCR methods can be negatively affected by inhibitory compounds commonly found in vegetable matrices that may cause false-negative results. Therefore, the sample processing and DNA isolation steps must be carefully evaluated prior to the introduction of such methods into routine practice. In this study, we compared the ability of three column-based and four magnetic bead-based commercial DNA isolation kits to extract DNA of the model micro-organism L. monocytogenes from raw vegetables. The DNA isolation efficiency of all isolation kits was determined using a triplex real-time qPCR assay designed to specifically detect L. monocytogenes. The kit with best performance, the PowerSoil(™) Microbial DNA Isolation Kit, is suitable for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. Coupled with the triplex real-time qPCR assay, this DNA isolation kit is applicable to the samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. Several recent outbreaks of Listeria monocytogenes have been associated with the consumption of fruits and vegetables. Real-time PCR assays allow fast detection and accurate quantification of microbes. However, the success of real-time PCR is dependent on the success with which template DNA can be extracted. The results of this study suggest that the PowerSoil(™) Microbial DNA Isolation Kit can be used for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. This method is applicable to samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. © 2014 The Society for Applied Microbiology.

If you build it will they come? Addressing social isolation within a technology-based HIV intervention for young black men who have sex with men

PubMed Central

LeGrand, Sara; Muessig, Kathryn E.; Pike, Emily C.; Baltierra, Nina; Hightow-Weidman, Lisa B.

2014-01-01

The rate of HIV infections among young black men who have sex with men (YBMSM) continues to rise at an alarming pace. YBMSM are particularly vulnerable to social isolation and a lack of social support due to experiences with racism and homophobia, which may have implications for sexual risk behaviors. The purpose of this study was to explore perceptions of social isolation and sense of community among YBMSM, the need for and receptivity to social networking features designed to reduce social isolation and build community within an internet and mobile phone-based primary and secondary HIV prevention intervention for YBMSM and to identify strategies to develop these features. Focus groups were conducted with 22 YBMSM ages 20–30 at three sites in North Carolina. Data from the focus groups were thematically analyzed using NVivo. Feelings of social isolation and lack of a sense of community were strongly endorsed by participants with homophobia, lack of opportunities for social engagement, and a focus on sex rather than friendship in interpersonal relationships with other YBMSM cited as contributing factors. Participants were receptive to a social networking intervention designed to reduce social isolation and build community. Recommendations offered by participants to increase acceptability and usability of such features included: availability of information about healthy relationships, the ability to connect with other YBMSM and health care providers, and ensuring the site had ongoing facilitation by the study team as well as monitoring for inappropriate content. The development of a social networking feature of an HIV prevention intervention may present an opportunity to reduce social isolation, build community and reduce risky sexual behaviors among YBMSM. The findings from this study are being used to inform the development of a social networking feature for an existing internet and mobile phone-based primary and secondary HIV prevention intervention for YBMSM. PMID:24617609

Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco

PubMed Central

Bouklata, Nada; Supply, Philip; Jaouhari, Sanae; Charof, Reda; Seghrouchni, Fouad; Sadki, Khalid; El Achhab, Youness; Nejjari, Chakib; Filali-Maltouf, Abdelkarim

2015-01-01

Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context. PMID:26285026

The predominance of Ethiopian specific Mycobacterium tuberculosis families and minimal contribution of Mycobacterium bovis in tuberculous lymphadenitis patients in Southwest Ethiopia.

PubMed

Tadesse, Mulualem; Abebe, Gemeda; Bekele, Alemayehu; Bezabih, Mesele; de Rijk, Pim; Meehan, Conor J; de Jong, Bouke C; Rigouts, Leen

2017-11-01

Ethiopia has an extremely high rate of extrapulmonary tuberculosis, dominated by tuberculous lymphadenitis (TBLN). However, little is known about Mycobacterium tuberculosis complex (MTBc) lineages responsible for TBLN in Southwest Ethiopia. A total of 304 MTBc isolates from TBLN patients in Southwest Ethiopia were genotyped primarily by spoligotyping. Isolates of selected spoligotypes were further analyzed by 15-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) (n=167) and qPCR-based single nucleotide polymorphism (n=38). Isolates were classified into main phylogenetic lineages and families by using the reference strain collections and identification tools available at MIRU-VNTRplus data base. Resistance to rifampicin was determined by Xpert MTB/RIF. The majority of isolates (248; 81.6%) belonged to the Euro-American lineage (Lineage 4), with the ill-defined T and Haarlem as largest families comprising 116 (38.2%) and 43 (14.1%) isolates respectively. Of the T family, 108 isolates were classified as being part of the newly described Ethiopian families, namely Ethiopia_2 (n=44), Ethiopia_3 (n=34) and Ethiopia_H 37 Rv-like (n=30). Other sub-lineages included URAL (n=18), S (n=17), Uganda I (n=16), LAM (n=13), X (n=5), TUR (n=5), Uganda II (n=4) and unknown (n=19). Lineage 3 (Delhi/CAS) was the second most common lineage comprising 44 (14.5%) isolates. Interestingly, six isolates (2%) were belonged to Lineage 7, unique to Ethiopia. Lineage 1 (East-African Indian) and Lineage 2 (Beijing) were represented by 3 and 1 isolates respectively. M. bovis was identified in only two (0.7%) TBLN cases. The cluster rate was highest for Ethiopia_3 isolates showing clonal similarity with isolates from North Ethiopia. Lineage 3 was significantly associated with rifampicin resistance. In TBLN in Southwest Ethiopia, the recently described Ethiopia specific Lineage 4 families were predominant, followed by Lineage 3 and Lineage 4-Haarlem. The contribution of M. bovis in TBLN infection is minimal. Copyright © 2017. Published by Elsevier B.V.

High genetic diversity among extraintestinal Escherichia coli isolates in pullets and layers revealed by a longitudinal study.

PubMed

Paudel, Surya; Stessl, Beatrix; Hess, Claudia; Zloch, Angelika; Hess, Michael

2016-10-07

Various information about the genetic diversity of Escherichia coli isolates from chickens are available but a detailed epidemiological investigation based upon isolates obtained from interrelated pullet and layer flocks is still missing. Therefore, in the course of a longitudinal epidemiological study on pullets and layers, 144 E. coli isolates from chickens with or without pathological lesions of the reproductive tract were serotyped and genotyped with pulsed-field gel electrophoresis (PFGE). These isolates were collected during rearing, peak and at the end of production. The actual study is the first of its kind so as to elucidate genetic relatedness among extraintestinal E. coli isolated from chickens with varying pathological conditions in interrelated layer farms/flocks at different stages of rearing. Serotyping revealed that 63.19 % of the isolates could not be assigned to any of the three serotypes tested whereas 30.55 % of the isolates belonged to serotype O1:K1, 4.86 % to O2:K1 and 1.38 % to O78:K80. After macrorestriction digest with XbaI, 91.66 % of the isolates were typeable resulting in 96 distinct PFGE profiles. Among them, five PFGE types included isolates collected from diseased chickens as well as from birds without pathological lesions. This finding shows that pathogenicity of E. coli in layers seems to be largely influenced by concurrent susceptibility factors. Furthermore, in six out of eight cases where two isolates were collected from each of eight birds, different PFGE types were found in the same or different organs of the same bird. The existence of predominant or persistent E. coli genotypes was only observed in two cases. It is concluded that extraintestinal E. coli genotypes and serotypes in pullets and layers are heterogenous and also do not maintain a single clonality within the same bird. The facts that E. coli strains did not show any definite clonal population structure based on geographical region, age of the host and pathological lesions should have relevance in further epidemiological studies and control strategies.

Pilot Study of Antimicrobial Resistance in Northern Bobwhites (Colinus virginianus).

PubMed

Zhang, Michael; Shen, Zhenyu; Rollins, Dale; Fales, William; Zhang, Shuping

2017-09-01

Antimicrobial resistance (AMR) is an important issue for both wildlife conservation and public health. The purpose of this study was to screen for AMR in fecal bacteria isolated from northern bobwhite (Colinus virginianus), a species that is an ecologically and economically important natural resource in the southern United States. The antimicrobial susceptibility profiles of 45 Escherichia coli isolates, 20 Enterococcus faecalis isolates, and 10 Enterococcus faecium isolates were determined using the Sensititer TM microbroth dilution minimum inhibitory concentration (MIC) plate, AVIAN1F. Overall, E. coli isolates had high MIC values for the following classes of antimicrobials: aminocoumarins, beta-lactams, lincosamides, macrolides, florfenicol, and sulfonamides. Enterococcus faecalis and E. faecium isolates had high MICs for aminocyclitols, aminoglycosides, beta-lactams, lincosamides, and sulfonamides. Enterococcus faecalis isolates also showed high MICs for aminocoumarins, while E. faecium isolates had high MICs for trimethoprim/sulfamethoxazole and tetracycline. Based on available veterinary interpretive criteria, 15% and 33% of E. coli isolates were resistant to sulphathiazole and sulphadimethoxine, respectively. Intermediate susceptibility to florfenicol was seen with 17.8% of E. coli isolates. Twenty percent of E. faecalis and 80% of E. faecium isolates were resistant to high-concentration streptomycin. One third of E. faecalis and 70% of E. faecium isolates were intermediately susceptible to erythromycin. Ten percent of E. faecium isolates were resistant to tetracycline and oxytetracycline. A comparison of available MIC suggests that AMR in wild bobwhite is less severe than in domestic poultry. Further investigation is needed to determine the source of AMR in wild bobwhite.

Phylogenetic analysis of Dengue virus 1 isolated from South Minas Gerais, Brazil

PubMed Central

Drumond, Betania Paiva; da Silva Fagundes, Luiz Gustavo; Rocha, Raissa Prado; Fumagalli, Marcilio Jorge; Araki, Carlos Shigueru; Colombo, Tatiana Elisa; Nogueira, Mauricio Lacerda; Castilho, Thiago Elias; da Silveira, Nelson José Freitas; Malaquias, Luiz Cosme Cotta; Coelho, Luiz Felipe Leomil

2016-01-01

Dengue is a major worldwide public health problem, especially in the tropical and subtropical regions of the world. Primary infection with a single Dengue virus serotype causes a mild, self-limiting febrile illness called dengue fever. However, a subset of patients who experience secondary infection with a different serotype can progress to a more severe form of the disease, called dengue hemorrhagic fever. The four Dengue virus serotypes (1–4) are antigenically and genetically distinct and each serotype is composed of multiple genotypes. In this study we isolated one Dengue virus 1 serotype, named BR/Alfenas/2012, from a patient with dengue hemorrhagic fever in Alfenas, South Minas Gerais, Brazil and molecular identification was performed based on the analysis of NS5 gene. Swiss mice were infected with this isolate to verify its potential to induce histopathological alterations characteristic of dengue. Liver histopathological analysis of infected animals showed the presence of inflammatory infiltrates, hepatic steatosis, as well as edema, hemorrhage and necrosis focal points. Phylogenetic and evolutionary analyses based on the envelope gene provided evidence that the isolate BR/Alfenas/2012 belongs to genotype V, lineage I and it is probably derived from isolates of Rio de Janeiro, Brazil. The isolate BR/Alfenas/2012 showed two unique amino acids substitutions (SER222THRE and PHE306SER) when compared to other Brazilian isolates from the same genotype/lineage. Molecular models were generated for the envelope protein indicating that the amino acid alteration PHE 306 SER could contribute to a different folding in this region located within the domain III. Further genetic and animal model studies using BR/Alfenas/2012 and other isolates belonging to the same lineage/genotype could help determine the relation of these genetic alterations and dengue hemorrhagic fever in a susceptible population. PMID:26887252

Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study.

PubMed

Jajou, Rana; de Neeling, Albert; van Hunen, Rianne; de Vries, Gerard; Schimmel, Henrieke; Mulder, Arnout; Anthony, Richard; van der Hoek, Wim; van Soolingen, Dick

2018-01-01

Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping. VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated. In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%). When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided.

Sky island bird populations isolated by ancient genetic barriers are characterized by different song traits than those isolated by recent deforestation.

PubMed

Purushotham, Chetana B; Robin, V V

2016-10-01

Various mechanisms of isolation can structure populations and result in cultural and genetic differentiation. Similar to genetic markers, for songbirds, culturally transmitted sexual signals such as breeding song can be used as a measure of differentiation as songs can also be impacted by geographic isolation resulting in population-level differences in song structure. Several studies have found differences in song structure either across ancient geographic barriers or across contemporary habitat barriers owing to deforestation. However, very few studies have examined the effect of both ancient barriers and recent deforestation in the same system. In this study, we examined the geographic variation in song structure across six populations of the White-bellied Shortwing, a threatened and endemic songbird species complex found on isolated mountaintops or "sky islands" of the Western Ghats. While some sky islands in the system are isolated by ancient valleys, others are separated by deforestation. We examined 14 frequency and temporal spectral traits and two syntax traits from 835 songs of 38 individuals across the six populations. We identified three major song clusters based on a discriminant model of spectral traits, degree of similarity of syntax features, as well as responses of birds to opportunistic playback. However, some traits like complex vocal mechanisms (CVM), relating to the use of syrinxes, clearly differentiated both ancient and recently fragmented populations. We suggest that CVMs may have a cultural basis and can be used to identify culturally isolated populations that cannot be differentiated using genetic markers or commonly used frequency-based song traits. Our results demonstrate the use of bird songs to reconstruct phylogenetic groups and impacts of habitat fragmentation even in complex scenarios of historic and contemporary isolation.

Isolation of quercetin from the methanolic extract of Lagerstroemia speciosa by HPLC technique, its cytotoxicity against MCF-7 cells and photocatalytic activity.

PubMed

Sai Saraswathi, V; Saravanan, D; Santhakumar, K

2017-06-01

The flavonoids present in the leaves of Lagerstroemia speciosa were extracted, characterized by spectral methods and studied for its cytotoxicity activity against MCF-cell lines and photocatalytic activity against azo dye. Direct and sequential soxhlet extraction was performed and its concentrated crude extract was subjected to high performance liquid chromatography. The yield obtained by the isolated compound (MEI-quercetin) from leaves of L. speciosa was found to be 1.8g from the methanolic extract. The phytochemical analysis and the Rf value of the isolated flavonoid was found to be 3.59. The isolated compound was characterized by Infrared Spectroscopy, NMR and Mass. Based on the characterization, the structure was elucidated as quercetin - a flavonoid. The isolated compound showed the significant in vitro cytotoxicity activity against MCF-7 cell lines at 500μg/ml when compared to the crude extract. Among the various concentrations (25, 50, 100, 250, and 500μg/ml), at higher concentration the cell viability was pronounced and also compared with that of the control. It was first time to report that the isolated flavonoid showed photocatalytic against azo dye-methyl orange. The dye degradation was monitored by UV-Vis spectrophotometry. The isolated compound showed dye degradation of 91.66% with the crude extract 82.47% at 160min. Hence in the present findings, the photocatalytic degradation of MO dye under UV irradiation was investigated over isolated compound of L. speciosa. Hence we expect that this can be used to treat the waste water in near future based on the photocatalytic technique. Copyright © 2017 Elsevier B.V. All rights reserved.

Prevalence of mcr-1 in E. coli from Livestock and Food in Germany, 2010-2015.

PubMed

Irrgang, Alexandra; Roschanski, Nicole; Tenhagen, Bernd-Alois; Grobbel, Mirjam; Skladnikiewicz-Ziemer, Tanja; Thomas, Katharina; Roesler, Uwe; Käsbohrer, Annemarie

2016-01-01

Since the first description of a plasmid-mediated colistin resistance gene (mcr-1) in November 2015 multiple reports of mcr-1 positive isolates indicate a worldwide spread of this newly discovered resistance gene in Enterobacteriaceae. Although the occurrence of mcr-1 positive isolates of livestock, food, environment and human origin is well documented only few systematic studies on the prevalence of mcr-1 are available yet. Here, comprehensive data on the prevalence of mcr-1 in German livestock and food isolates are presented. Over 10.600 E. coli isolates from the national monitoring on zoonotic agents from the years 2010-2015 were screened for phenotypic colistin resistance (MIC value >2 mg/l). Of those, 505 resistant isolates were screened with a newly developed TaqMan-based real-time PCR for the presence of the mcr-1 gene. In total 402 isolates (79.8% of colistin resistant isolates) harboured the mcr-1 gene. The prevalence was depending on the food production chain. The highest prevalence was detected in the turkey food chain (10.7%), followed by broilers (5.6%). A low prevalence was determined in pigs, veal calves and laying hens. The mcr-1 was not detected in beef cattle, beef and dairy products in all years investigated. In conclusion, TaqMan based real-time PCR provides a fast and accurate tool for detection of mcr-1 gene. The overall detection rate of 3.8% for mcr-1 among all E. coli isolates tested is due to high prevalence of mcr-1 in poultry production chains. More epidemiological studies of other European countries are urgently needed to assess German prevalence data.

Variations in isoflavone levels in soy foods and soy protein isolates and issues related to isoflavone databases and food labeling.

PubMed

Setchell, Kenneth D R; Cole, Sidney J

2003-07-02

The reliability of databases on the isoflavone composition of foods designed to estimate dietary intakes is contingent on the assumption that soy foods are consistent in their isoflavone content. To validate this, total and individual isoflavone compositions were determined by HPLC for two different soy protein isolates used in the commercial manufacture of soy foods over a 3-year period (n = 30/isolate) and 85 samples of 40 different brands of soy milks. Total isoflavone concentrations differed markedly between the soy protein isolates, varying by 200-300% over 3 years, whereas the protein content varied by only 3%. Total isoflavone content varied by up to 5-fold among different commercial soy milks and was not consistent between repeat purchases. Whole soybean milks had significantly higher isoflavone levels than those made from soy protein isolates (mean +/- SD, 63.6 +/- 21.9 mg/L, n = 43, vs 30.2 +/- 5.8 mg/L, n = 38, respectively, p < 0.0001), although some isolated soy protein-based milks were similar in content to "whole bean" varieties. The ratio of genistein to daidzein isoflavone forms was higher in isolated soy protein-based versus "whole bean" soy milks (2.72 +/- 0.24 vs 1.62 +/- 0.47, respectively, p < 0.0001), and the greatest variability in isoflavone content was observed among brands of whole bean soy milks. These studies illustrate large variability in the isoflavone content of isolated soy proteins used in food manufacture and in commercial soy milks and reinforce the need to accurately determine the isoflavone content of foods used in dietary intervention studies while exposing the limitations of food databases for estimating daily isoflavone intakes.

Detection of Multidrug Resistance in Mycobacterium tuberculosis▿

PubMed Central

Sekiguchi, Jun-ichiro; Miyoshi-Akiyama, Tohru; Augustynowicz-Kopeć, Ewa; Zwolska, Zofia; Kirikae, Fumiko; Toyota, Emiko; Kobayashi, Intetsu; Morita, Koji; Kudo, Koichiro; Kato, Seiya; Kuratsuji, Tadatoshi; Mori, Toru; Kirikae, Teruo

2007-01-01

We developed a DNA sequencing-based method to detect mutations in the genome of drug-resistant Mycobacterium tuberculosis. Drug resistance in M. tuberculosis is caused by mutations in restricted regions of the genome. Eight genome regions associated with drug resistance, including rpoB for rifampin (RIF), katG and the mabA (fabG1)-inhA promoter for isoniazid (INH), embB for ethambutol (EMB), pncA for pyrazinamide (PZA), rpsL and rrs for streptomycin (STR), and gyrA for levofloxacin, were amplified simultaneously by PCR, and the DNA sequences were determined. It took 6.5 h to complete all procedures. Among the 138 clinical isolates tested, 55 were resistant to at least one drug. Thirty-four of 38 INH-resistant isolates (89.5%), 28 of 28 RIF-resistant isolates (100%), 15 of 18 EMB-resistant isolates (83.3%), 18 of 30 STR-resistant isolates (60%), and 17 of 17 PZA-resistant isolates (100%) had mutations related to specific drug resistance. Eighteen of these mutations had not been reported previously. These novel mutations include one in rpoB, eight in katG, one in the mabA-inhA regulatory region, two in embB, five in pncA, and one in rrs. Escherichia coli isolates expressing individually five of the eight katG mutations showed loss of catalase and INH oxidation activities, and isolates carrying any of the five pncA mutations showed no pyrazinamidase activity, indicating that these mutations are associated with INH and PZA resistance, respectively. Our sequencing-based method was also useful for testing sputa from tuberculosis patients and for screening of mutations in Mycobacterium bovis. In conclusion, our new method is useful for rapid detection of multiple-drug-resistant M. tuberculosis and for identifying novel mutations in drug-resistant M. tuberculosis. PMID:17108078

Epidemiologic and Genotypic Review of Carbapenemase-Producing Organisms in British Columbia, Canada, between 2008 and 2014

PubMed Central

Sekirov, Inna; Croxen, Matthew A.; Ng, Corrinne; Azana, Robert; Chang, Yin; Mataseje, Laura; Boyd, David; Mangat, Chand; Mack, Benjamin; Tadros, Manal; Brodkin, Elizabeth; Kibsey, Pamela; Stefanovic, Aleksandra; Champagne, Sylvie; Mulvey, Michael R.

2015-01-01

Carbapenemase-producing organisms (CPOs) are a serious emerging problem for health care facilities worldwide. Owing to their resistance to most antimicrobial therapies, CPOs are difficult to treat and pose a challenge for infection prevention and control. Since 2010, lab-based surveillance for CPOs and PCR-based testing were implemented in British Columbia (BC), Canada. A review of CPOs in BC from 2008 to March 2014 was done to characterize the resistance mechanisms and possible clonal strain transmission and to compare pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and plasmid restriction fragment length polymorphism (RFLP) as molecular typing tools. During this study period, a total of 177 CPO cases were identified. Patient demographics and travel history were reviewed, and a descriptive analysis was carried out. PFGE profiles, MLST, and plasmid RFLP analysis for a subset of Escherichia coli, Klebsiella pneumoniae, and Enterobacter species isolates were obtained and analyzed. Our findings demonstrate that CPOs have been increasing in number in BC over time, from 1 isolate/year retrospectively identified in 2008 and 2009 to 82 isolates in 2013 and 30 isolates in the first quarter of 2014. Overall, K. pneumoniae isolates lack clonality, although some seemingly related clusters have been found. Plasmid analysis showed evidence of the spread of plasmids carrying carbapenemase-encoding genes between the examined isolates. Analysis of Enterobacter cloacae isolates revealed a more clonal nature of these CPOs in BC. The presence of related clusters provides evidence of interpatient organism transmission both within and between institutions. Although in our study, NDM-harboring E. cloacae isolates appeared to spread clonally, the spread of carbapenem resistance in K. pneumoniae seems to be plasmid mediated. PMID:26607987

Seroprevalence, Isolation, Genotyping, and Pathogenicity of Toxoplasma gondii Strains from Sheep in China

PubMed Central

Yang, YuRong; Feng, YongJie; Yao, QiuXia; Wang, YingHua; Lu, YaoYao; Liang, HongDe; Zhu, XingQuan; Zhang, LongXian

2017-01-01

Toxoplasma gondii is an important cause of reproductive failure in small ruminants that also poses a risk to consumers who consume undercooked meat. However, little is known about sheep toxoplasmosis in China for the world. Therefore, this study was conducted to assess the prevalence of T. gondii infection in sheep from China, to isolate T. gondii via bioassay in mice and to evaluate the virulence of the isolated T. gondii based on vero cell invasion and mice. A total of 840 samples (304 unfrozen hearts and 536 sera) from sheep in China were collected from 2014 to 2016. Heart samples (n = 36) of T. gondii seropositive sheep (MAT, ≥25) were bioassayed in mice individually. DNA derived from cell cultured tachyzoites of the isolated T. gondii was characterized by PCR-RFLP of 10 loci (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). The virulence of the T. gondii was evaluated based on the mortality and encystation in mice, as well as their growth characteristics in cell culture. Antibodies to T. gondii were found in 174 of 840 (20.71%, 304 hearts juice and 536 sera) sheep by the modified agglutination test (cut-off 1:25). Viable T. gondii was isolated from the hearts of two of 36 seropositive sheep hearts. Both genotypes of the sheep heart isolates were ToxoDB#9. The virulence of the two ToxoDB#9 isolations varied significantly. To the best of our knowledge, this is the first report of isolation of ToxoDB#9 strain of T. gondii from sheep in China. PMID:28217119

Methicillin-Resistant Staphylococcus aureus from Brazilian Dairy Farms and Identification of Novel Sequence Types.

PubMed

Oliveira, C J B; Tiao, N; de Sousa, F G C; de Moura, J F P; Santos Filho, L; Gebreyes, W A

2016-03-01

The aim of this study was to investigate the phenotypic and genotypic diversity and anti-microbial resistance among staphylococci of dairy herds that originated from Paraiba State, north-eastern Brazil, a region where such studies are rare. Milk samples (n = 552) were collected from 15 dairy farms. Isolates were evaluated for anti-microbial susceptibility by Kirby-Bauer disc diffusion method. Confirmation of methicillin-resistant Staphylococcus aureus (MRSA) was performed using multiplex PCR targeting mecA and nuc genes in addition to phenotypic assay based on PBP-2a latex agglutination. Clonal relatedness of isolates was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) genotyping. Staphylococci were detected in 269 (49%) of the samples. Among these, 65 (24%) were S. aureus. The remaining 204 isolates were either coagulase-negative staphylococci (n = 188; 70%) or coagulase positive other than S. aureus (n = 16; 6%). Staphylococci were cultured in seven (35%) of the 20 hand swab samples, from which five isolates were S. aureus. The isolates were most commonly resistant against penicillin (43%), ampicillin (38%) and oxacillin (27%). The gene mecA was detected in 21 S. aureus from milk and in one isolate from a milker's hand. None of the isolates were resistant to vancomycin. PFGE findings showed high clonal diversity among the isolates. Based on MLST, we identified a total of 11 different sequence types (STs 1, 5, 6, 83, 97, 126, 1583, 1622, 1623, 1624 and 1625) with four novel STs (ST1622-ST1625). The findings show that MRSA is prevalent in milk from semi-extensive dairy cows in north-eastern Brazil, and further investigation on its extent in various types of milk production systems and the farm-to-table continuum is warranted. © 2015 Blackwell Verlag GmbH.