Solutions of the epidemic of EIAV infection by HPM

NASA Astrophysics Data System (ADS)

Balamuralitharan, S.; Geethamalini, S.

2018-04-01

In this article, Homotopy Perturbation Method (HPM) is to process of estimate to the arrangements to a model for Equine Infectious Anemia Virus (EIAV) disease. This technique allows a direct scheme for solving the problem. MATLAB is operated to complete the computations. Graphical results are displayed and discussed quantitatively and simplicity of the method.

Experimental Rhodococcus equi and equine infectious anemia virus DNA vaccination in adult and neonatal horses: Effect of IL-12, dose, and route

PubMed Central

Mealey, R.H.; Stone, D.M.; Hines, M.T.; Alperin, D.C.; Littke, M.H.; Leib, S.R.; Leach, S.E.; Hines, S.A.

2012-01-01

Improving the ability of DNA-based vaccines to induce potent Type1/Th1 responses against intracellular pathogens in large outbred species is essential. Rhodoccocus equi and equine infectious anemia virus (EIAV) are two naturally occurring equine pathogens that also serve as important large animal models of neonatal immunity and lentiviral immune control. Neonates present a unique challenge for immunization due to their diminished immunologic capabilities and apparent Th2 bias. In an effort to augment R. equi- and EIAV-specific Th1 responses induced by DNA vaccination, we hypothesized that a dual promoter plasmid encoding recombinant equine IL-12 (rEqIL-12) would function as a molecular adjuvant. In adult horses, DNA vaccines induced R. equi- and EIAV-specific antibody and lymphoproliferative responses, and EIAV-specific CTL and tetramer-positive CD8+ T lymphocytes. These responses were not enhanced by the rEqIL-12 plasmid. In neonatal foals, DNA immunization induced EIAV-specific antibody and lymphoproliferative responses, but not CTL. The R. equi vapA vaccine was poorly immunogenic in foals even when co-administered with the IL-12 plasmid. It was concluded that DNA immunization was capable of inducing Th1 responses in horses; dose and route were significant variables, but rEqIL-12 was not an effective molecular adjuvant. Additional work is needed to optimize DNA vaccine-induced Th1 responses in horses, especially in neonates. PMID:17889970

Equine Myxovirus Resistance Protein 2 Restricts Lentiviral Replication by Blocking Nuclear Uptake of Capsid Protein.

PubMed

Ji, Shuang; Na, Lei; Ren, Huiling; Wang, Yujie; Wang, Xiaojun

2018-05-09

Human Myxovirus resistance 2 (huMxB) has been shown to be a determinant type I interferon-induced host factor involved in the inhibition of HIV-1 as well as many other primate lentiviruses. This blocking occurs after the reverse transcription of viral RNA and ahead of the integration into the host DNA, which is closely connected to the ability of the protein to bind the viral capsid. To date, Mx2s derived from non-primate animals have shown no capacity for HIV-1 suppression. In this study, we examined the restrictive effect of equine Mx2 (eqMx2) on both the equine infectious anemia virus (EIAV) and HIV-1 and investigated possible mechanisms for its specific function. We demonstrated that IFNα/β upregulates the expression of eqMx2 in equine monocyte-derived macrophages (eMDMs). Overexpression of eqMx2 significantly suppresses the replication of EIAV, HIV-1, and SIVs, but not that of MLV. Knockdown of eqMx2 transcription weakens the inhibition of EIAV replication by type I interferon. Interestingly, immunofluorescence assays suggest that the subcellular localization of eqMx2 changes following virus infection, from being dispersed in the cytoplasm to being accumulated at the nuclear envelope. Furthermore, eqMx2 blocks the nuclear uptake of the proviral genome by binding to the viral capsid. The N-truncated mutant of eqMx2 lost the ability to bind the viral capsid as well as the restriction effect for lentiviruses. These results improve our understanding of the Mx2 protein in non-primate animals. IMPORTANCE Previous research has shown that the antiviral ability of Mx2s is confined to primates, particularly humans. EIAV has been shown to be insensitive to the restriction by human MxB. Here, we described the function of equine Mx2. This protein plays an important role in the suppression of EIAV, HIV-1, and SIVs. The antiviral activity of eqMx2 depends on its subcellular location as well as its capsid binding capacity. Our results showed that following viral infection, eqMx2 changes its original cytoplasmic location and accumulates at the nuclear envelope where it binds to the viral capsid and blocks the nuclear entry of reverse transcribed proviral DNAs. In contrast, huMxB does not bind to the EIAV capsid and shows no EIAV restriction effect. These studies expand our understanding of the function of the equine Mx2 protein. Copyright © 2018 Ji et al.

The risk of introduction of equine infectious anemia virus into USA via cloned horse embryos imported from Canada.

PubMed

Asseged, B D; Habtemariam, T; Tameru, B; Nganwa, D

2012-01-15

Deriving horse oocytes in the USA is hampered by the lack of abattoirs processing horse carcasses which could provide abundant quantities of ovaries from slaughtered mares. Therefore, several cloning industries in the USA are attempting to import cloned horse embryos from Canada. Like any agricultural commodity, cloned embryos pose a risk of introduction of exotic animal diseases into the importing country. Under such circumstances, risk assessment could provide an objective, transparent, and internationally accepted means for evaluating the risk. This quantitative risk assessment (QRA) was initiated to determine the risk of introduction of Equine infectious anemia virus (EIAV) into the USA via cloned horse embryos imported from Canada. In assessing the risk, a structured knowledge base regarding cloning in relation to Equine infectious anemia (EIA) was first developed. Based on the knowledge base, a scenario tree was developed to determine conditions (with mathematical probabilities) that could lead to the introduction and maintenance of EIAV along the cloning pathway. Parameters for the occurrence of the event at each node were estimated using published literature. Using @Risk software and setting Monte Carlo simulation at 50,000 iterations, the probability of importing an EIAV-infected cloned horse embryo was 1.8 × 10(-9) (R = 1.5 × 10(-12) to 2.9 × 10(-8)). Taking into account the current protocol for equine cloning and assuming the yield of 5 to 30 clones per year, the possible number of EIAV-infected cloned horse embryos ranged from 2.0 × 10(-10) to 9.1 × 10(-5) (Mean = 1.4×10(-6)) per year. Consequently, it would take up to 1.5 × 10(7) (R = 1.6 × 10(4) to 5.1 × 10(10)) years for EIAV to be introduced into the USA. Based on the knowledge base and our critical pathway analysis, the biological plausibility of introducing EIAV into USA via cloned horse embryos imported from Canada is extremely low. Copyright © 2012 Elsevier Inc. All rights reserved.

Development, evaluation, and laboratory validation of immunoassays for the diagnosis of equine infectious anemia (EIA) using recombinant protein produced from a synthetic p26 gene of EIA virus.

PubMed

Singha, Harisankar; Goyal, Sachin K; Malik, Praveen; Khurana, Sandip K; Singh, Raj K

2013-12-01

Equine infectious anemia (EIA)-a retroviral disease caused by equine infectious anemia virus (EIAV)-is a chronic, debilitating disease of horses, mules, and donkeys. EIAV infection has been reported worldwide and is recognized as pathogen of significant economic importance to the horse industry. This disease falls under regulatory control program in many countries including India. Control of EIA is based on identification of inapparent carriers by detection of antibodies to EIAV in serologic tests and "Stamping Out" policy. The current internationally accepted test for diagnosis of EIA is the agar gel immune-diffusion test (AGID), which detects antibodies to the major gag gene (p26) product. The objective of this study was to develop recombinant p26 based in-house immunoassays [enzyme linked immunosorbent assays (ELISA), and AGID] for EIA diagnosis. The synthetic p26 gene of EIAV was expressed in Escherichia coli and diagnostic potential of recombinant p26 protein were evaluated in ELISA and AGID on 7,150 and 1,200 equine serum samples, respectively, and compared with commercial standard AGID kit. The relative sensitivity and specificity of the newly developed ELISA were 100 and 98.6 %, respectively. Whereas, relative sensitivity and specificity of the newly developed AGID were in complete agreement in respect to commercial AGID kit. Here, we have reported the validation of an ELISA and AGID on large number of equine serum samples using recombinant p26 protein produced from synthetic gene which does not require handling of pathogenic EIAV. Since the indigenously developed reagents would be economical than commercial diagnostic kit, the rp26 based-immunoassays could be adopted for the sero-diagnosis and control of EIA in India.

Comparison of HIV- and EIAV-based vectors on their efficiency in transducing murine and human hematopoietic repopulating cells.

PubMed

Siapati, Elena K; Bigger, Brian W; Miskin, James; Chipchase, Daniel; Parsley, Kathryn L; Mitrophanous, Kyriacos; Themis, Mike; Thrasher, Adrian J; Bonnet, Dominique

2005-09-01

The use of lentiviral vectors for gene transfer into hematopoietic stem cells has raised considerable interest as these vectors can permanently integrate their genome into quiescent cells. Vectors based on alternative lentiviruses would theoretically be safer than HIV-1-based vectors and could also be used in HIV-positive patients, minimizing the risk of generating replication-competent virus. Here we report the use of third-generation equine infectious anemia virus (EIAV)- and HIV-1-based vectors with minimal viral sequences and absence of accessory proteins. We have compared their efficiency in transducing mouse and human hematopoietic stem cells both in vitro and in vivo to that of a previously documented second-generation HIV-1 vector. The third-generation EIAV- and HIV-based vectors gave comparable levels of transduction and transgene expression in both mouse and human NOD/SCID repopulating cells but were less efficient than the second-generation HIV-1 vector in human HSCs. For the EIAV vector this is possibly a reflection of the lower protein expression levels achieved in human cells, as vector copy number analysis revealed that this vector exhibited a trend to integrate equally efficiently compared to the third-generation HIV-1 vector in both mouse and human HSCs. Interestingly, the presence or absence of Tat in viral preparations did not influence the transduction efficiency of HIV-1 vectors in human HSCs.

Viral load and clinical disease enhancement associated with a lentivirus cytotoxic T lymphocyte vaccine regimen

PubMed Central

Mealey, Robert H.; Leib, Steven R.; Littke, Matt H.; Wagner, Bettina; Horohov, David W.; McGuire, Travis C.

2009-01-01

Effective DNA-based vaccines against lentiviruses will likely induce CTL against conserved viral proteins. Equine infectious anemia virus (EIAV) infects horses worldwide, and serves as a useful model for lentiviral immune control. Although attenuated live EIAV vaccines have induced protective immune responses, DNA-based vaccines have not. In particular, DNA-based vaccines have had limited success in inducing CTL responses against intracellular pathogens in the horse. We hypothesized that priming with a codon-optimized plasmid encoding EIAV Gag p15/p26 with co-administration of a plasmid encoding an equine IL-2/IgG fusion protein as a molecular adjuvant, followed by boosting with a vaccinia vector expressing Gag p15/p26, would induce protective Gag-specific CTL responses. Although the regimen induced Gag-specific CTL in four of seven vaccinated horses, CTL were not detected until after the vaccinia boost, and protective effects were not observed in EIAV challenged vaccinates. Unexpectedly, vaccinates had significantly higher viral loads and more severe clinical disease, associated with the presence of vaccine-induced CTL. It was concluded that 1.) further optimization of the timing and route of DNA immunization was needed for efficient CTL priming in vivo, 2.) co-administration of the IL-2/IgG plasmid did not enhance CTL priming by the Gag p15/p26 plasmid, 3.) vaccinia vectors are useful for lentivirus-specific CTL induction in the horse, 4.) Gag-specific CTL alone are either insufficient or a more robust Gag-specific CTL response is needed to limit EIAV viremia and clinical disease, and 5.) CTL-inducing vaccines lacking envelope immunogens can result in lentiviral disease enhancement. Although the mechanisms for enhancement associated with this vaccine regimen remain to be elucidated, these results have important implications for development of lentivirus T cell vaccines. PMID:19368787

Studies of Genetic Variation in the AIDS Virus: Relevance to Disease Pathogenesis Anti-Viral Therapy, and Vaccine Development

DTIC Science & Technology

1990-06-30

lentiviral systems including equine infectious anemia virus (EIAV), visna virus, and simian immunodeficiency virus (SIV) (119,120,154). For EIAV, it is clear...a pig-tailed macaque that possesses altered biologic and antigenic properties leading to a broader host-range and a rapid, fatal immunodeficiency ...envelope/LTR region of a replication-defective variant of feline leukemia virus (FeLV), when introduced into a replication competent construct of FeLV, was

Response of ELA-A1 horses immunized with lipopeptide containing an equine infectious anemia virus ELA-A1-restricted CTL epitope to virus challenge.

PubMed

Ridgely, Sherritta L; Zhang, Baoshan; McGuire, Travis C

2003-01-17

Lipopeptide containing an ELA-A1-restricted cytotoxic T lymphocyte (CTL) epitope from the envelope surface unit (SU) protein of the EIAV(WSU5) strain was used to immunize three horses having the ELA-A1 haplotype. Peptide-specific ELA-A1-restricted CTL were induced in all three horses, although these were present transiently in PBMC. These horses were further immunized with lipopeptide containing the corresponding CTL epitope from the EIAV(PV) strain. Then, the three immunized horses and three non-immunized horses were challenged by intravenous inoculation with 300 TCID(50) EIAV(PV). All horses developed cell free viremia, fever and thrombocytopenia. However, there was a statistically lower fever and thrombocytopenia severity score in the immunized group. Shorter duration of plasma viral load in two of the three immunized horses likely explains the less severe clinical disease in this group. Results indicate that lipopeptide immunization had a protective effect against development of clinical disease following virus challenge.

Oxidant-antioxidant imbalance in horses infected with equine infectious anaemia virus.

PubMed

Bolfă, Pompei Florin; Leroux, Caroline; Pintea, Adela; Andrei, Sanda; Cătoi, Cornel; Taulescu, Marian; Tăbăran, Flaviu; Spînu, Marina

2012-06-01

This study assesses the impact of equine infectious anaemia virus (EIAV) infection on the oxidant/antioxidant equilibrium of horses. Blood samples from 96 Romanian horses aged 1-25 years, were divided into different groups according to their EIAV-infection status, age, and time post-seroconversion. The effect of infection on oxidative stress was estimated by measuring enzymatic antioxidants (superoxide dismutase [SOD], glutathione peroxidase [GPx] and catalase), non-enzymatic antioxidants (uric acid and carotenoids), and lipid peroxidation (malondialdehyde [MDA]). Infection modified the oxidant/antioxidant equilibrium in the horses, influencing GPx and uric acid levels (P<0.05). Time post-seroconversion also contributed to oxidative stress imbalance, exhibiting a significant influence on both SOD and MDA concentrations in the blood (P<0.05). Animal age did not have a significant influence on oxidative stress. Recently infected horses (<1 year following seroconversion), and horses >5 years old, represented the most vulnerable category in terms of oxidative stress, followed by recently infected animals <5 years old. The results of this study are novel in implicating EIAV infection in the development of oxidative stress in horses. Copyright © 2011 Elsevier Ltd. All rights reserved.

Serosurveillance of infectious agents in equines of the Central Valley of Costa Rica.

PubMed

Jiménez, D; Romero-Zuñiga, J J; Dolz, G

2014-01-01

Blood samples from 181 equines from the Central Valley of Costa Rica were collected in the year 2012 to determine the presence of antibodies against selected infectious agents in horses and to determine the risk factors associated with these agents. The presence of antibodies against Equine Infectious Anemia Virus (EIAV), Equine Herpes Virus 1 and 4 (EHV-1 and EHV-4), West Nile Virus (WNV), Influenza A Virus (IAV), Equine Viral Arteritis Virus (EVAV), Babesia caballi, Theileria equi, Neospora caninum and Chlamydia abortus was determined using commercial assays, and risk factors associated with seropositivity to the different infectious agents was established. The most seroprevalent agent detected was EHV-4 (96.7%), followed by WNV (44.2%), and IAV (41.8%). Horses >3 years, used for work or sports, and with access to pastures, had significantly increased probability to be seropositive to WNV, whereas horses used for breeding and recreational purposes, being stabled, and without access to pastures, had significantly greater probability to be seropositive to IAV. Seroprevalence to B. caballi (19.9%) was lower than to T. equi (38.1%). For B. caballi, access to pastures was determined as a risk factor, whereas being older than 3 years was established as a risk factor for T. equi. Low seroprevalences were determined for EHV-1 (5.0%), EVAV (5.0%), C. abortus (4.8%), and N. caninum (4.4%). Mares having history of abortion were more likely to be seropositive to EHV-1, whereas horses >3 years, used for work and sports, and mares having multiple parturitions, were more likely to be seropositive to N. caninum. None of the horses were seropositive to EIAV. Earlier, only diseases caused by EIAV, WNV and piroplasmosis were reported in Costa Rica. The present study however, determined the presence of carriers for EHV-1, EHV-4, and EIAV.

Serosurveillance of infectious agents in equines of the Central Valley of Costa Rica

PubMed Central

Jiménez, D.; Romero-Zuñiga, J.J.; Dolz, G.

2014-01-01

Blood samples from 181 equines from the Central Valley of Costa Rica were collected in the year 2012 to determine the presence of antibodies against selected infectious agents in horses and to determine the risk factors associated with these agents. The presence of antibodies against Equine Infectious Anemia Virus (EIAV), Equine Herpes Virus 1 and 4 (EHV-1 and EHV-4), West Nile Virus (WNV), Influenza A Virus (IAV), Equine Viral Arteritis Virus (EVAV), Babesia caballi, Theileria equi, Neospora caninum and Chlamydia abortus was determined using commercial assays, and risk factors associated with seropositivity to the different infectious agents was established. The most seroprevalent agent detected was EHV-4 (96.7%), followed by WNV (44.2%), and IAV (41.8%). Horses >3 years, used for work or sports, and with access to pastures, had significantly increased probability to be seropositive to WNV, whereas horses used for breeding and recreational purposes, being stabled, and without access to pastures, had significantly greater probability to be seropositive to IAV. Seroprevalence to B. caballi (19.9%) was lower than to T. equi (38.1%). For B. caballi, access to pastures was determined as a risk factor, whereas being older than 3 years was established as a risk factor for T. equi. Low seroprevalences were determined for EHV-1 (5.0%), EVAV (5.0%), C. abortus (4.8%), and N. caninum (4.4%). Mares having history of abortion were more likely to be seropositive to EHV-1, whereas horses >3 years, used for work and sports, and mares having multiple parturitions, were more likely to be seropositive to N. caninum. None of the horses were seropositive to EIAV. Earlier, only diseases caused by EIAV, WNV and piroplasmosis were reported in Costa Rica. The present study however, determined the presence of carriers for EHV-1, EHV-4, and EIAV. PMID:26623349

PAQ: Partition Analysis of Quasispecies.

PubMed

Baccam, P; Thompson, R J; Fedrigo, O; Carpenter, S; Cornette, J L

2001-01-01

The complexities of genetic data may not be accurately described by any single analytical tool. Phylogenetic analysis is often used to study the genetic relationship among different sequences. Evolutionary models and assumptions are invoked to reconstruct trees that describe the phylogenetic relationship among sequences. Genetic databases are rapidly accumulating large amounts of sequences. Newly acquired sequences, which have not yet been characterized, may require preliminary genetic exploration in order to build models describing the evolutionary relationship among sequences. There are clustering techniques that rely less on models of evolution, and thus may provide nice exploratory tools for identifying genetic similarities. Some of the more commonly used clustering methods perform better when data can be grouped into mutually exclusive groups. Genetic data from viral quasispecies, which consist of closely related variants that differ by small changes, however, may best be partitioned by overlapping groups. We have developed an intuitive exploratory program, Partition Analysis of Quasispecies (PAQ), which utilizes a non-hierarchical technique to partition sequences that are genetically similar. PAQ was used to analyze a data set of human immunodeficiency virus type 1 (HIV-1) envelope sequences isolated from different regions of the brain and another data set consisting of the equine infectious anemia virus (EIAV) regulatory gene rev. Analysis of the HIV-1 data set by PAQ was consistent with phylogenetic analysis of the same data, and the EIAV rev variants were partitioned into two overlapping groups. PAQ provides an additional tool which can be used to glean information from genetic data and can be used in conjunction with other tools to study genetic similarities and genetic evolution of viral quasispecies.

Equine infectious anemia prevalence in feral donkeys from Northeast Brazil.

PubMed

Oliveira, Fernanda G; Cook, R Frank; Naves, João H F; Oliveira, Cairo H S; Diniz, Rejane S; Freitas, Francisco J C; Lima, Joseney M; Sakamoto, Sidnei M; Leite, Rômulo C; Issel, Charles J; Reis, Jenner K P

2017-05-01

Equine infectious anemia virus (EIAV) is an important cause of morbidity and mortality throughout the world. Although the virus infects all members of the Equidae the vast majority of studies have been conducted in horses (Equus caballus) with comparatively little information available for other equid species. Brazil has one of the most abundant donkey (E. asinus) populations of any nation although the economic importance of these animals is declining as transportation becomes increasingly mechanized. As a result, considerable numbers of donkeys especially in the Northeast of the country have been released and allowed pursue an almost feral existence. Consequently, this large and growing population constitutes a significant risk as a reservoir for the maintenance and transmission of important equine infectious diseases such as glanders and equine arteritis virus in addition to EIAV. This study examines the prevalence of EIA in a semi-wild donkey population from Mossoró city, in Northeast Brazil, using AGID followed by cELISA, rgp90 ELISA and immunoblot (IB). Serum samples were collected from 367 donkeys without obvious EIA clinical signs. Subsequent testing revealed seropositive rates of 1.6% (6/367) in officially approved AGID tests, 3.3% (12/367) in cELISA and 14.4% (53/367) in the rgp90 ELISA. However, 88.7% (47/53) of the rgp90 ELISA positive samples were almost certainly false reactions because they failed to react with two or more antigens in IB. Consequently, the rpg90 ELISA has a similar sensitivity to AGID with donkey serum samples. Such high false positive rates have not been observed previously with serum samples from horses. Another highly significant finding is that 56.9% (33/58) of the donkey serum samples tested in IB had reactivity to EIAV p26 only. Although this could result from recent infection with the virus, it has been found that in some equids p26 only reactivity persists for extensive periods of time suggesting exposure to antigens possessing cross-reactive determinants or EIAV strains with envelope glycoproteins that are different from any that have been previously characterized and so undetectable by current IB techniques. Copyright © 2017 Elsevier B.V. All rights reserved.

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases ▿ †

PubMed Central

Zielonka, Jörg; Bravo, Ignacio G.; Marino, Daniela; Conrad, Elea; Perković, Mario; Battenberg, Marion; Cichutek, Klaus; Münk, Carsten

2009-01-01

The mammalian APOBEC3 (A3) proteins comprise a multigene family of cytidine deaminases that act as potent inhibitors of retroviruses and retrotransposons. The A3 locus on the chromosome 28 of the horse genome contains multiple A3 genes: two copies of A3Z1, five copies of A3Z2, and a single copy of A3Z3, indicating a complex evolution of multiple gene duplications. We have cloned and analyzed for expression the different equine A3 genes and examined as well the subcellular distribution of the corresponding proteins. Additionally, we have tested the functional antiretroviral activity of the equine and of several of the human and nonprimate A3 proteins against the Equine infectious anemia virus (EIAV), the Simian immunodeficiency virus (SIV), and the Adeno-associated virus type 2 (AAV-2). Hematopoietic cells of horses express at least five different A3s: A3Z1b, A3Z2a-Z2b, A3Z2c-Z2d, A3Z2e, and A3Z3, whereas circulating macrophages, the natural target of EIAV, express only part of the A3 repertoire. The five A3Z2 tandem copies arose after three consecutive, recent duplication events in the horse lineage, after the split between Equidae and Carnivora. The duplicated genes show different antiviral activities against different viruses: equine A3Z3 and A3Z2c-Z2d are potent inhibitors of EIAV while equine A3Z1b, A3Z2a-Z2b, A3Z2e showed only weak anti-EIAV activity. Equine A3Z1b and A3Z3 restricted AAV and all equine A3s, except A3Z1b, inhibited SIV. We hypothesize that the horse A3 genes are undergoing a process of subfunctionalization in their respective viral specificities, which might provide the evolutionary advantage for keeping five copies of the original gene. PMID:19458006

Photosensitization is required for antiretroviral activity of hypericin

NASA Astrophysics Data System (ADS)

Carpenter, Susan; Tossberg, John; Kraus, George A.

1991-06-01

In a seminal series of papers, Meruelo and co-workers have described the potent antiretroviral effect of hypericin. Interestingly, hypericin was found to inhibit not only the production of infectious virus from chronically infected cells, but was also shown to directly inhibit reverse transcriptase activity of mature virions. The effect of hypericin on cells chronically infected with equine infectious anemia virus (EIAV), a retrovirus genetically related to HIV, is demonstrated. At concentrations of 10 (mu) g/ml, hypericin reduced production of infectious EIAV by 99.99 without causing obvious cytopathic effects. Interestingly, the results indicated that the antiretroviral activity of hypericin was wholly dependent on the presence of light. No decrease in viral infectivity was observed when hypericin and virus were incubated in the dark. Moreover, it appeared that light was an absolute requirement for the antiviral activity, as even high concentrations of hypericin (10 (mu) g/ml) were unable to reduce infectivity of as few as 100 infectious virions.

Structural And Functional Studies of ALIX Interactions With YPXnL Late Domains of HIV-1 And EIAV

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

Zhai, Q.; Fisher, R.D.; Chung, H.-Y.

2009-05-28

Retrovirus budding requires short peptide motifs (late domains) located within the viral Gag protein that function by recruiting cellular factors. The YPX{sub n}L late domains of HIV and other lentiviruses recruit the protein ALIX (also known as AIP1), which also functions in vesicle formation at the multivesicular body and in the abscission stage of cytokinesis. Here, we report the crystal structures of ALIX in complex with the YPX{sub n}L late domains from HIV-1 and EIAV. The two distinct late domains bind at the same site on the ALIX V domain but adopt different conformations that allow them to make equivalentmore » contacts. Binding studies and functional assays verified the importance of key interface residues and revealed that binding affinities are tuned by context-dependent effects. These results reveal how YPX{sub n}L late domains recruit ALIX to facilitate virus budding and how ALIX can bind YPX{sub n}L sequences with both n = 1 and n = 3.« less

PREVALENCE OF ANTIBODIES AGAINST INFLUENZA VIRUS IN NON-VACCINATED EQUINES FROM THE BRAZILIAN PANTANAL

PubMed Central

Silva, Lucas Gaíva E; Borges, Alice Mamede Costa Marques; Villalobos, Eliana Monteforte Cassaro; Lara, Maria do Carmo Custodio Souza Hunold; Cunha, Elenice Maria Siquetin; de Oliveira, Anderson Castro Soares; Braga, Ísis Assis; Aguiar, Daniel Moura

2014-01-01

The prevalence of antibodies against Equine Influenza Virus (EIV) was determined in 529 equines living on ranches in the municipality of Poconé, Pantanal area of Brazil, by means of the hemagglutination inhibition test, using subtype H3N8 as antigen. The distribution and possible association among positive animal and ranches were evaluated by the chi-square test, spatial autoregressive and multiple linear regression models. The prevalence of antibodies against EIV was estimated at 45.2% (95% CI 30.2 - 61.1%) with titers ranging from 20 to 1,280 HAU. Seropositive equines were found on 92.0% of the surveyed ranches. Equine from non-flooded ranches (66.5%) and negativity in equine infectious anemia virus (EIAV) (61.7%) were associated with antibodies against EIV. No spatial correlation was found among the ranches, but the ones located in non-flooded areas were associated with antibodies against EIV. A negative correlation was found between the prevalence of antibodies against EIV and the presence of EIAV positive animals on the ranches. The high prevalence of antibodies against EIV detected in this study suggests that the virus is circulating among the animals, and this statistical analysis indicates that the movement and aggregation of animals are factors associated to the transmission of the virus in the region. PMID:25351542

Effects of human SAMHD1 polymorphisms on HIV-1 susceptibility

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

White, Tommy E.; Brandariz-Nuñez, Alberto; Valle-Casuso, Jose Carlos

SAMHD1 is a human restriction factor that prevents efficient infection of macrophages, dendritic cells and resting CD4+ T cells by HIV-1. Here we explored the antiviral activity and biochemical properties of human SAMHD1 polymorphisms. Our studies focused on human SAMHD1 polymorphisms that were previously identified as evolving under positive selection for rapid amino acid replacement during primate speciation. The different human SAMHD1 polymorphisms were tested for their ability to block HIV-1, HIV-2 and equine infectious anemia virus (EIAV). All studied SAMHD1 variants block HIV-1, HIV-2 and EIAV infection when compared to wild type. We found that these variants did notmore » lose their ability to oligomerize or to bind RNA. Furthermore, all tested variants were susceptible to degradation by Vpx, and localized to the nuclear compartment. We tested the ability of human SAMHD1 polymorphisms to decrease the dNTP cellular levels. In agreement, none of the different SAMHD1 variants lost their ability to reduce cellular levels of dNTPs. Finally, we found that none of the tested human SAMHD1 polymorphisms affected the ability of the protein to block LINE-1 retrotransposition. - Highlights: • Human SAMHD1 single-nucleotide polymorphisms block HIV-1 and HIV-2 infection. • SAMHD1 polymorphisms do not affect its ability to block LINE-1 retrotransposition. • SAMHD1 polymorphisms decrease the cellular levels of dNTPs.« less

Transduction of Photoreceptors With Equine Infectious Anemia Virus Lentiviral Vectors: Safety and Biodistribution of StarGen for Stargardt Disease

PubMed Central

Binley, Katie; Widdowson, Peter; Loader, Julie; Kelleher, Michelle; Iqball, Sharifah; Ferrige, Georgina; de Belin, Jackie; Carlucci, Marie; Angell-Manning, Diana; Hurst, Felicity; Ellis, Scott; Miskin, James; Fernandes, Alcides; Wong, Paul; Allikmets, Rando; Bergstrom, Christopher; Aaberg, Thomas; Yan, Jiong; Kong, Jian; Gouras, Peter; Prefontaine, Annick; Vezina, Mark; Bussieres, Martin; Naylor, Stuart; Mitrophanous, Kyriacos A.

2013-01-01

Purpose. StarGen is an equine infectious anemia virus (EIAV)-based lentiviral vector that expresses the photoreceptor-specific adenosine triphosphate (ATP)-binding cassette transporter (ABCA4) protein that is mutated in Stargardt disease (STGD1), a juvenile macular dystrophy. EIAV vectors are able to efficiently transduce rod and cone photoreceptors in addition to retinal pigment epithelium in the adult macaque and rabbit retina following subretinal delivery. The safety and biodistribution of StarGen following subretinal delivery in macaques and rabbits was assessed. Methods. Regular ophthalmic examinations, IOP measurements, ERG responses, and histopathology were carried out in both species to compare control and vector-treated eyes. Tissue and fluid samples were obtained to evaluate the persistence, biodistribution, and shedding of the vector following subretinal delivery. Results. Ophthalmic examinations revealed a slightly higher level of inflammation in StarGen compared with control treated eyes in both species. However, inflammation was transient and no overt toxicity was observed in StarGen treated eyes and there were no abnormal clinical findings. There was no StarGen-associated rise in IOP or abnormal ERG response in either rabbits or macaques. Histopathologic examination of the eyes did not reveal any detrimental changes resulting from subretinal administration of StarGen. Although antibodies to StarGen vector components were detected in rabbit but not macaque serum, this immunologic response did not result in any long-term toxicity. Biodistribution analysis demonstrated that the StarGen vector was restricted to the ocular compartment. Conclusions. In summary, these studies demonstrate StarGen to be well tolerated and localized following subretinal administration. PMID:23620430

Protective effects of broadly neutralizing immunoglobulin against homologous and heterologous equine infectious anemia virus infection in horses with severe combined immunodeficiency.

PubMed

Taylor, Sandra D; Leib, Steven R; Wu, Wuwei; Nelson, Robert; Carpenter, Susan; Mealey, Robert H

2011-07-01

Using the equine infectious anemia virus (EIAV) lentivirus model system, we previously demonstrated protective effects of broadly neutralizing immune plasma in young horses (foals) with severe combined immunodeficiency (SCID). However, in vivo selection of a neutralization-resistant envelope variant occurred. Here, we determined the protective effects of purified immunoglobulin with more potent broadly neutralizing activity. Overall, protection correlated with the breadth and potency of neutralizing activity in vitro. Four of five SCID foals were completely protected against homologous challenge, while partial protection occurred following heterologous challenge. These results support the inclusion of broadly neutralizing antibodies in lentivirus control strategies.

Temperature inducible β-sheet structure in the transactivation domains of retroviral regulatory proteins of the Rev family

NASA Astrophysics Data System (ADS)

Thumb, Werner; Graf, Christine; Parslow, Tristram; Schneider, Rainer; Auer, Manfred

1999-11-01

The interaction of the human immunodeficiency virus type 1 (HIV-1) regulatory protein Rev with cellular cofactors is crucial for the viral life cycle. The HIV-1 Rev transactivation domain is functionally interchangeable with analog regions of Rev proteins of other retroviruses suggesting common folding patterns. In order to obtain experimental evidence for similar structural features mediating protein-protein contacts we investigated activation domain peptides from HIV-1, HIV-2, VISNA virus, feline immunodeficiency virus (FIV) and equine infectious anemia virus (EIAV) by CD spectroscopy, secondary structure prediction and sequence analysis. Although different in polarity and hydrophobicity, all peptides showed a similar behavior with respect to solution conformation, concentration dependence and variations in ionic strength and pH. Temperature studies revealed an unusual induction of β-structure with rising temperatures in all activation domain peptides. The high stability of β-structure in this region was demonstrated in three different peptides of the activation domain of HIV-1 Rev in solutions containing 40% hexafluoropropanol, a reagent usually known to induce α-helix into amino acid sequences. Sequence alignments revealed similarities between the polar effector domains from FIV and EIAV and the leucine rich (hydrophobic) effector domains found in HIV-1, HIV-2 and VISNA. Studies on activation domain peptides of two dominant negative HIV-1 Rev mutants, M10 and M32, pointed towards different reasons for the biological behavior. Whereas the peptide containing the M10 mutation (L 78E 79→D 78L 79) showed wild-type structure, the M32 mutant peptide (L 78L 81L 83→A 78A 81A 83) revealed a different protein fold to be the reason for the disturbed binding to cellular cofactors. From our data, we conclude, that the activation domain of Rev proteins from different viral origins adopt a similar fold and that a β-structural element is involved in binding to a cellular cofactor.

Detection of West Nile Virus and other common equine viruses in three locations from the Leeward Islands, West Indies.

PubMed

Bolfa, Pompei; Jeon, Isaac; Loftis, Amanda; Leslie, Teresa; Marchi, Silvia; Sithole, Fortune; Beck, Cecile; Lecollinet, Sylvie; Zientara, Stephan; Hans, Aymeric; Issel, Charles J

2017-10-01

Equines in the West Indies are used for recreational purposes, tourism industry, racing and agriculture or can be found in feral populations. Little is known in the Caribbean basin about the prevalence of some major equine infectious diseases, some with zoonotic potential, listed as reportable by the OIE. Our objective was to study the prevalence of antibodies for West Nile Virus (WNV), Equine Herpes Virus-1 and 4 (EHV-1 and EHV-4), Equine Influenza (EI), Equine Viral Arteritis (EVA) and Equine Infectious Anemia Virus (EIAV) using a retrospective serological convenience study. We used 180 equine serum samples, 140 from horses and 40 from donkeys in St. Kitts, Nevis, and Sint Eustatius, collected between 2006 and 2015 that were tested with ELISA kits and virus neutralization (for WNV and EVA). Combining ELISA with virus neutralization testing, 25 (13.8%) equine sera were WNV positive (a mixture of indigenous and imported equines) and 3 sera (1.6%) showed doubtful results. For EHV-1, 41 equines (23.7%), mean age 6.7 years, were seropositive. For EHV-4, 138 equines were found seropositive (82.8%), mean age 6.3 years. For EI, 49 equines (27.2%), mean age 7.5 years, were seropositive on ELISA, some previously vaccinated horses. No antibodies against EAV were found on virus neutralization testing, although one animal (0.6%), was EAV positive on ELISA. All samples were EIAV negative. The seroprevalence for EHV-1 and EHV-4 is similar to other parts of the world. For the first time in the study location serologic evidence of antibodies against WNV and EI is reported. This was found in both indigenous and imported animals, highlighting the need for developing proper surveillance plans based on complementary methods of virus detection. Further studies will be needed to define the prevalence, rates of transmission, characterize local virus strains, and study their impact on these populations. Copyright © 2017 Elsevier B.V. All rights reserved.

Biophysical characterization and crystal structure of the Feline Immunodeficiency Virus p15 matrix protein.

PubMed

Serrière, Jennifer; Robert, Xavier; Perez, Magali; Gouet, Patrice; Guillon, Christophe

2013-06-24

Feline Immunodeficiency Virus (FIV) is a viral pathogen that infects domestic cats and wild felids. During the viral replication cycle, the FIV p15 matrix protein oligomerizes to form a closed matrix that underlies the lipidic envelope of the virion. Because of its crucial role in the early and late stages of viral morphogenesis, especially in viral assembly, FIV p15 is an interesting target in the development of potential new therapeutic strategies. Our biochemical study of FIV p15 revealed that it forms a stable dimer in solution under acidic conditions and at high concentration, unlike other retroviral matrix proteins. We determined the crystal structure of full-length FIV p15 to 2 Å resolution and observed a helical organization of the protein, typical for retroviral matrix proteins. A hydrophobic pocket that could accommodate a myristoyl group was identified, and the C-terminal end of FIV p15, which is mainly unstructured, was visible in electron density maps. As FIV p15 crystallizes in acidic conditions but with one monomer in the asymmetric unit, we searched for the presence of a biological dimer in the crystal. No biological assembly was detected by the PISA server, but the three most buried crystallographic interfaces have interesting features: the first one displays a highly conserved tryptophan acting as a binding platform, the second one is located along a 2-fold symmetry axis and the third one resembles the dimeric interface of EIAV p15. Because the C-terminal end of p15 is involved in two of these three interfaces, we investigated the structure and assembly of a C-terminal-truncated form of p15 lacking 14 residues. The truncated FIV p15 dimerizes in solution at a lower concentration and crystallizes with two molecules in the asymmetric unit. The EIAV-like dimeric interface is the only one to be retained in the new crystal form. The dimeric form of FIV p15 in solution and its extended C-terminal end are characteristic among lentiviral matrix proteins. Crystallographic interfaces revealed several interactions that might be involved in FIV replication. Further studies are needed to better understand their biological relevance in the function of FIV Gag during viral replication.

Gradient isolator for flow field of fuel cell assembly

DOEpatents

Ernst, W.D.

1999-06-15

Isolator(s) include isolating material and optionally gasketing material strategically positioned within a fuel cell assembly. The isolating material is disposed between a solid electrolyte and a metal flow field plate. Reactant fluid carried by flow field plate channel(s) forms a generally transverse electrochemical gradient. The isolator(s) serve to isolate electrochemically a portion of the flow field plate, for example, transversely outward from the channel(s), from the electrochemical gradient. Further, the isolator(s) serve to protect a portion of the solid electrolyte from metallic ions. 4 figs.

Gradient isolator for flow field of fuel cell assembly

DOEpatents

Ernst, William D.

1999-01-01

Isolator(s) include isolating material and optionally gasketing material strategically positioned within a fuel cell assembly. The isolating material is disposed between a solid electrolyte and a metal flow field plate. Reactant fluid carried by flow field plate channel(s) forms a generally transverse electrochemical gradient. The isolator(s) serve to isolate electrochemically a portion of the flow field plate, for example, transversely outward from the channel(s), from the electrochemical gradient. Further, the isolator(s) serve to protect a portion of the solid electrolyte from metallic ions.

Laboratory bioassays and field-cage trials of Metarhizium spp. isolates with field-collected Mormon crickets (Anabrus simplex)

USDA-ARS?s Scientific Manuscript database

The Mormon cricket, Anabrus simplex, is an important pest in the western United States. This study evaluates the virulence of 32 isolates of Metarhizium towards field-collected Mormon crickets. Additionally, several isolates were tested in outdoor field-cage studies. All 32 Metarhizium isolates were...

In Vitro Susceptibilities of Mycoplasma hyopneumoniae Field Isolates

PubMed Central

Vicca, J.; Stakenborg, T.; Maes, D.; Butaye, P.; Peeters, J.; de Kruif, A.; Haesebrouck, F.

2004-01-01

The in vitro susceptibilities of 21 Mycoplasma hyopneumoniae field isolates were determined using a broth microdilution technique. One isolate showed acquired resistance to lincomycin, tilmicosin, and tylosin, while five isolates were resistant to flumequine and enrofloxacin. Acquired resistance against these antimicrobials in M. hyopneumoniae field isolates was not reported previously. PMID:15504886

Competition Between Fusarium pseudograminearum and Cochliobolus sativus Observed in Field and Greenhouse Studies.

PubMed

Troth, Erin E Gunnink; Johnston, Jeffrey A; Dyer, Alan T

2018-02-01

Among root pathogens, one of the most documented antagonisms is the suppression of Cochliobolus sativus by Fusarium (roseum) species. Unfortunately, previous studies involved single isolates of each pathogen and thus, provided no indication of the spectrum of responses that occur across the respective species. To investigate the variability in interactions between Cochliobolus sativus and Fusarium pseudograminearum, field and greenhouse trials were conducted that included monitoring of spring wheat plant health and monitoring of pathogen populations via quantitative real-time polymerase chain reaction. The interactions between two isolates of C. sativus and four isolates of F. pseudograminearum were explored in three geographically distinct wheat fields. To complement field trials and to limit potentially confounding environmental variables that are often associated with field studies, greenhouse trials were performed that investigated the interactions among and between three isolates of C. sativus and four isolates of F. pseudograminearum. Across field locations, C. sativus isolate Cs2344 consistently and significantly reduced Fusarium populations by an average of 20.1%. Similarly, F. pseudograminearum isolate Fp2228 consistently and significantly reduced C. sativus field populations by an average of 30.9%. No interaction was detected in the field between pathogen species with regards to disease or crop losses. Greenhouse results confirmed a powerful (>99%), broadly effective suppression of Fusarium populations by isolate Cs2344. Among greenhouse trials, additional isolate-isolate interactions were observed affecting Fusarium populations. Due to lower C. sativus population sizes in greenhouse trials, significant Fusarium suppression of C. sativus was only detected in one isolate-isolate interaction. This study is the first to demonstrate suppression of Fusarium spp. by C. sativus in field and greenhouse settings. These findings also reveal a complex competitive interaction between these two pathogen species that was previously unknown.

Characterization of field isolates of Magnaporthe oryzae with mating type, DNA fingerprinting, and pathogenicity assays

USDA-ARS?s Scientific Manuscript database

Due to the harmful nature of the rice blast fungus, Magnaporthe oryzae, it is beneficial to characterize field isolates to help aid in the deployment of resistance (R) genes in rice. In the present study, 190 field isolates of M. oryzae, collected from rice fields of Yunnan province in China, were a...

Genetic structure and variability of virus populations in cross-protected grapevines superinfected by Grapevine fanleaf virus.

PubMed

Vigne, Emmanuelle; Marmonier, Aurélie; Komar, Véronique; Lemaire, Olivier; Fuchs, Marc

2009-09-01

Recombination was assessed in a vineyard site in which grapevines cross-protected with mild strains GHu of Grapevine fanleaf virus (GFLV) or Ta of Arabis mosaic virus (ArMV) were superinfected with GFLV field isolates following transmission by the nematode vector Xiphinema index. The genetic structure and variability within RNA2 of isolates from grapevines co-infected with GFLV field isolates and either GFLV-GHu or ArMV-Ta were characterized to identify intra- and interspecies recombinants. Sequence analysis and phylogenetic relationships inferred intraspecies recombination among GFLV field isolates but not between field isolates and GFLV-GHu. SISCAN analysis confirmed a mosaic structure for two GFLV field isolates for which recombination sites were located in the movement protein and coat protein genes. One of the recombinants was found in eight grapevines that were in close spatial proximity within the vineyard site, suggesting its transmission by X. index. No interspecies recombination was detected between GFLV field isolates and ArMV-Ta. Altogether, our findings suggest that mild protective strains GFLV-GHu and ArMV-Ta did not assist the emergence of viable recombinants to detectable level during a 12-year cross-protection trial. To our knowledge, this is the first extensive characterization of the genetic structure and variability of virus isolates in cross-protected plants.

Structural and Biochemical Studies of ALIX/AlP1 and Its Role in Retrovirus Budding

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

Fisher,R.; Chung, H.; Zhai, Q.

2007-01-01

ALIX/AIP1 functions in enveloped virus budding, endosomal protein sorting, and many other cellular processes. Retroviruses, including HIV-1, SIV, and EIAV, bind and recruit ALIX through YPXnL late-domain motifs (X = any residue; n = 1-3). Crystal structures reveal that human ALIX is composed of an N-terminal Bro1 domain and a central domain that is composed of two extended three-helix bundles that form elongated arms that fold back into a 'V.'. The structures also reveal conformational flexibility in the arms that suggests that the V domain may act as a flexible hinge in response to ligand binding. YPXnL late domains bindmore » in a conserved hydrophobic pocket on the second arm near the apex of the V, whereas CHMP4/ESCRT-III proteins bind a conserved hydrophobic patch on the Bro1 domain, and both interactions are required for virus budding. ALIX therefore serves as a flexible, extended scaffold that connects retroviral Gag proteins to ESCRT-III and other cellular-budding machinery.« less

Diversity and abundance of Beauveria bassiana in soils, stink bugs and plant tissues of common bean from organic and conventional fields.

PubMed

Ramos, Yordanys; Portal, Orelvis; Lysøe, Erik; Meyling, Nicolai V; Klingen, Ingeborg

2017-11-01

The aim of this study was to evaluate the natural occurrence of Beauveria spp. in soil, from infections in the stink bug Piezodorus guildinii, an important pest of common bean (Phaseolus vulgaris) and as endophytes in bean plant tissue. Twelve conventional and 12 organic common bean fields in the Villa Clara province, Cuba were sampled from September 2014 to April 2015. One hundred and fifty Beauveria isolates were obtained from soil samples, bean plant parts and stink bugs. The overall frequency of occurrence of Beauveria isolates in conventional fields (8.4%) was significantly lower than that in organic fields (23.6%). Beauveria were also obtained significantly more frequently from bean roots in organic fields (15.0%) compared to bean roots in conventional fields (3.3%). DNA sequencing of the intergenic Bloc region was performed for Beauveria species identification. All isolates where characterized as Beauveria bassiana (Balsamo-Crivelli) Vuillemin, and clustered with isolates of neotropical origin previously described as AFNEO_1. The Cuban B. bassiana isolates formed five clusters in the phylogeny. Isolates of two clusters originated from all four locations, organic and conventional fields, as well as soil, plants and stink bugs. Organic fields contained isolates of all five clusters while conventional fields only harbored isolates of the two most frequent ones. Mating type PCR assays revealed that mating type distribution was skewed, with MAT1/MAT2 proportion of 146/4, indicating limited potential for recombination. The present study is the first to report of B. bassiana as a naturally occurring endophyte in common bean. Further, it shows that B. bassiana occurs naturally in diverse environments of common bean fields, and constitutes a potential reservoir of natural enemies against pest insects particularly in organic fields. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae

PubMed Central

Li, Zhigang; Hu, Songnian; Yao, Nan; Dean, Ralph A.; Zhao, Wensheng; Shen, Mi; Zhang, Haiwang; Li, Chao; Liu, Liyuan; Cao, Lei; Xu, Xiaowen; Xing, Yunfei; Hsiang, Tom; Zhang, Ziding; Xu, Jin-Rong; Peng, You-Liang

2012-01-01

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus. PMID:22876203

Functional Interplay Between Murine Leukemia Virus Glycogag, Serinc5, and Surface Glycoprotein Governs Virus Entry, with Opposite Effects on Gammaretroviral and Ebolavirus Glycoproteins.

PubMed

Ahi, Yadvinder S; Zhang, Shu; Thappeta, Yashna; Denman, Audrey; Feizpour, Amin; Gummuluru, Suryaram; Reinhard, Bjoern; Muriaux, Delphine; Fivash, Matthew J; Rein, Alan

2016-11-22

Gammaretroviruses, such as murine leukemia viruses (MLVs), encode, in addition to the canonical Gag, Pol, and Env proteins that will form progeny virus particles, a protein called "glycogag" (glycosylated Gag). MLV glycogag contains the entire Gag sequence plus an 88-residue N-terminal extension. It has recently been reported that glycogag, like the Nef protein of HIV-1, counteracts the antiviral effects of the cellular protein Serinc5. We have found, in agreement with prior work, that glycogag strongly enhances the infectivity of MLVs with some Env proteins but not those with others. In contrast, however, glycogag was detrimental to MLVs carrying Ebolavirus glycoprotein. Glycogag could be replaced, with respect to viral infectivity, by the unrelated S2 protein of equine infectious anemia virus. We devised an assay for viral entry in which virus particles deliver the Cre recombinase into cells, leading to the expression of a reporter. Data from this assay showed that both the positive and the negative effects of glycogag and S2 upon MLV infectivity are exerted at the level of virus entry. Moreover, transfection of the virus-producing cells with a Serinc5 expression plasmid reduced the infectivity and entry capability of MLV carrying xenotropic MLV Env, particularly in the absence of glycogag. Conversely, Serinc5 expression abrogated the negative effects of glycogag upon the infectivity and entry capability of MLV carrying Ebolavirus glycoprotein. As Serinc5 may influence cellular phospholipid metabolism, it seems possible that all of these effects on virus entry derive from changes in the lipid composition of viral membranes. Many murine leukemia viruses (MLVs) encode a protein called "glycogag." The function of glycogag is not fully understood, but it can assist HIV-1 replication in the absence of the HIV-1 protein Nef under some circumstances. In turn, Nef counteracts the cellular protein Serinc5. Glycogag enhances the infectivity of MLVs with some but not all MLV Env proteins (which mediate viral entry into the host cell upon binding to cell surface receptors). We now report that glycogag acts by enhancing viral entry and that, like Nef, glycogag antagonizes Serinc5. Surprisingly, the effects of glycogag and Serinc5 upon the entry and infectivity of MLV particles carrying an Ebolavirus glycoprotein are the opposite of those observed with the MLV Env proteins. The unrelated S2 protein of equine infectious anemia virus (EIAV) is functionally analogous to glycogag in our experiments. Thus, three retroviruses (HIV-1, MLV, and EIAV) have independently evolved accessory proteins that counteract Serinc5. Copyright © 2016 Ahi et al.

Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles

PubMed Central

2012-01-01

Background Haemophilus parasuis is the causative agent of Glässer’s disease and is a pathogen of swine in high-health status herds. Reports on serotyping of field strains from outbreaks describe that approximately 30% of them are nontypeable and therefore cannot be traced. Molecular typing methods have been used as alternatives to serotyping. This study was done to compare random amplified polymorphic DNA (RAPD) profiles and whole cell protein (WCP) lysate profiles as methods for distinguishing H. parasuis reference strains and field isolates. Results The DNA and WCP lysate profiles of 15 reference strains and 31 field isolates of H. parasuis were analyzed using the Dice and neighbor joining algorithms. The results revealed unique and reproducible DNA and protein profiles among the reference strains and field isolates studied. Simpson’s index of diversity showed significant discrimination between isolates when three 10mer primers were combined for the RAPD method and also when both the RAPD and WCP lysate typing methods were combined. Conclusions The RAPD profiles seen among the reference strains and field isolates did not appear to change over time which may reflect a lack of DNA mutations in the genes of the samples. The recent field isolates had different WCP lysate profiles than the reference strains, possibly because the number of passages of the type strains may affect their protein expression. PMID:22703293

Dielectrophoretic Isolation and Detection of cfc-DNA Nanoparticulate Biomarkers and Virus from Blood

PubMed Central

Sonnenberg, Avery; Marciniak, Jennifer Y.; McCanna, James; Krishnan, Rajaram; Rassenti, Laura; Kipps, Thomas J.; Heller, Michael J.

2015-01-01

Dielectrophoretic (DEP) microarray devices allow important cellular nanoparticulate biomarkers and virus to be rapidly isolated, concentrated and detected directly from clinical and biological samples. A variety of sub-micron nanoparticulate entities including cell free circulating (cfc) DNA, mitochondria and virus can be isolated into DEP high-field areas on microelectrodes, while blood cells and other micron-size entities become isolated into DEP low-field areas between the microelectrodes. The nanoparticulate entities are held in the DEP high-field areas while cells are washed away along with proteins and other small molecules which are not affected by the DEP electric fields. DEP carried out on 20 µL of whole blood obtained from Chronic Lymphocytic Leukemia (CLL) patients showed a considerable amount of SYBR Green stained DNA fluorescent material concentrated in the DEP high-field regions. Whole blood obtained from healthy individuals showed little or no fluorescent DNA materials in the DEP high-field regions. Fluorescent T7 bacteriophage virus could be isolated directly from blood samples, and fluorescently stained mitochondria could be isolated from biological buffer samples. Using newer DEP microarray devices, high molecular weight (hmw) DNA could be isolated from serum and detected at levels as low as 8–16 ng/mL. PMID:23436471

Monoclonal antibodies of African swine fever virus: antigenic differences among field virus isolates and viruses passaged in cell culture.

PubMed Central

García-Barreno, B; Sanz, A; Nogal, M L; Viñuela, E; Enjuanes, L

1986-01-01

An analysis of the binding properties of a collection of monoclonal antibodies to African swine fever virus particles showed that virus field isolates passaged in porcine macrophages changed antigenically more than a strain of a cell-adapted virus passaged in Vero cells. From seven clones isolated from the spleen of a field-infected pig, we found four clones that had the same antigenic properties, one clone that had large changes in proteins p150 and p27 and small changes in proteins p37 and p14, and two clones that had minor changes in proteins p150 and p27, respectively. An analysis of the binding properties of the monoclonal antibodies to 23 field isolates from Africa, Europe, and America showed that the African isolates differed among themselves more than the European and the American isolates; in this study we found changes in 8 of the 10 virus proteins tested. The most variable proteins in the African isolates were p150, p27, p14, and p12. In contrast to the African isolates, protein p12 from the non-African viruses did not change. The clustering of the field virus isolates in six antigenic homology groups indicated the existence of a complex variety of African swine fever virus serotypes. PMID:2422393

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.

(GTG)5-PCR fingerprinting for the classification and identification of coagulase-negative Staphylococcus species from bovine milk and teat apices: a comparison of type strains and field isolates.

PubMed

Braem, G; De Vliegher, S; Supré, K; Haesebrouck, F; Leroy, F; De Vuyst, L

2011-01-10

Due to significant financial losses in the dairy cattle farming industry caused by mastitis and the possible influence of coagulase-negative staphylococci (CNS) in the development of this disease, accurate identification methods are needed that untangle the different species of the diverse CNS group. In this study, 39 Staphylococcus type strains and 253 field isolates were subjected to (GTG)(5)-PCR fingerprinting to construct a reference framework for the classification and identification of different CNS from (sub)clinical milk samples and teat apices swabs. Validation of the reference framework was performed by dividing the field isolates in two separate groups and testing whether one group of field isolates, in combination with type strains, could be used for a correct classification and identification of a second group of field isolates. (GTG)(5)-PCR fingerprinting achieved a typeability of 94.7% and an accuracy of 94.3% compared to identifications based on gene sequencing. The study shows the usefulness of the method to determine the identity of bovine Staphylococcus species, provided an identification framework updated with field isolates is available. Copyright © 2010 Elsevier B.V. All rights reserved.

Highly Diverse Endophytic and Soil Fusarium oxysporum Populations Associated with Field-Grown Tomato Plants

PubMed Central

Demers, Jill E.; Gugino, Beth K.

2014-01-01

The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates. PMID:25304514

Dynamic blocked transfer stiffness method of characterizing the magnetic field and frequency dependent dynamic viscoelastic properties of MRE

NASA Astrophysics Data System (ADS)

Poojary, Umanath R.; Hegde, Sriharsha; Gangadharan, K. V.

2016-11-01

Magneto rheological elastomer (MRE) is a potential resilient element for the semi active vibration isolator. MRE based isolators adapt to different frequency of vibrations arising from the source to isolate the structure over wider frequency range. The performance of MRE isolator depends on the magnetic field and frequency dependent characteristics of MRE. Present study is focused on experimentally evaluating the dynamic stiffness and loss factor of MRE through dynamic blocked transfer stiffness method. The dynamic stiffness variations of MRE exhibit strong magnetic field and mild frequency dependency. Enhancements in dynamic stiffness saturate with the increase in magnetic field and the frequency. The inconsistent variations of loss factor with the magnetic field substantiate the inability of MRE to have independent control over its damping characteristics.

Inheritance of Carboxin Resistance in a European Field Isolate of Ustilago nuda.

PubMed

Newcombe, G; Thomas, P L

2000-02-01

ABSTRACT Two carboxin-resistant field isolates of Ustilago nuda from Europe were crossed with a carboxin-sensitive field isolate from North America. Meiotic tetrads isolated from germinating F(1) teliospores of one of the hybrids were tested for carboxin resistance and mating type. Carboxin resistance was shown to be controlled by a single gene (CBX1R), because a 1:1 segregation of carboxin resistance was observed in all 27 tetrads. Tetrad analysis indicated that the loci for carboxin resistance (Cbx1) and mating type (MAT1) segregate independently but may be located on the same chromosome. Tetrad analysis was not possible with the F(1) hybrid of he other field isolate, and its resistance cannot yet be attributed to CBX1R. Carboxin resistance was qualitatively dominant to sensitivity in vitro, as demonstrated by triad analysis of germinating F(1) teliospores. Quantitative in planta infection percents supported the conclusion that CBX1R is dominant, although incompletely, in the F(1) hybrid of one of the field isolates. Also, fewer than expected carboxin-sensitive F(2) individuals were observed in planta. However, inoculations of host plants with U. nuda have resulted in similar, unexpected variation in the past.

CPm gene diversity in field isolates of Citrus tristeza virus from Colombia.

PubMed

Oliveros-Garay, Oscar Arturo; Martinez-Salazar, Natalhie; Torres-Ruiz, Yanneth; Acosta, Orlando

2009-01-01

The nucleotide sequence diversity of the CPm gene from 28 field isolates of Citrus tristeza virus (CTV) was assessed by SSCP and sequence analyses. These isolates showed two major shared haplotypes, which differed in distribution: A1 was the major haplotype in 23 isolates from different geographic regions, whereas R1 was found in isolates from a discrete region. Phylogenetic reconstruction clustered A1 within an independent group, while R1 was grouped with mild isolates T30 from Florida and T385 from Spain. Some isolates contained several minor haplotypes, which were very similar to, and associated with, the major haplotype.

Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.

PubMed

Shome, Rajeswari; Krithiga, Natesan; Shankaranarayana, Padmashree B; Jegadesan, Sankarasubramanian; Udayakumar S, Vishnu; Shome, Bibek Ranjan; Saikia, Girin Kumar; Sharma, Narendra Kumar; Chauhan, Harshad; Chandel, Bharat Singh; Jeyaprakash, Rajendhran; Rahman, Habibur

2016-03-31

Brucellosis is one of the most important zoonotic diseases that affects multiple livestock species and causes great economic losses. The highly conserved genomes of Brucella, with > 90% homology among species, makes it important to study the genetic diversity circulating in the country. A total of 26 Brucella spp. (4 reference strains and 22 field isolates) and 1 B. melitensis draft genome sequence from India (B. melitensis Bm IND1) were included for sequence typing. The field isolates were identified by biochemical tests and confirmed by both conventional and quantitative polymerase chain reaction (qPCR) targeting bcsp 31Brucella genus-specific marker. Brucella speciation and biotyping was done by Bruce ladder, probe qPCR, and AMOS PCRs, respectively, and genotyping was done by multilocus sequence typing (MLST). The MLST typing of 27 Brucella spp. revealed five distinct sequence types (STs); the B. abortus S99 reference strain and 21 B. abortus field isolates belonged to ST1. On the other hand, the vaccine strain B. abortus S19 was genotyped as ST5. Similarly, B. melitensis 16M reference strain and one B. melitensis field isolate were grouped into ST7. Another B. melitensis field isolate belonged to ST8 (draft genome sequence from India), and only B. suis 1330 reference strain was found to be ST14. The sequences revealed genetic similarity of the Indian strains to the global reference and field strains. The study highlights the usefulness of MLST for typing of field isolates and validation of reference strains used for diagnosis and vaccination against brucellosis.

Phylloplane bacteria increase seedling emergence, growth and yield of field-grown groundnut (Arachis hypogaea L.).

PubMed

Kishore, G K; Pande, S; Podile, A R

2005-01-01

To isolate and characterize groundnut-associated bacterial isolates for growth promotion of groundnut in field. Three hundred and ninety-three groundnut-associated bacteria, representing the geocarposphere, phylloplane and rhizosphere, and endophytes were applied as seed treatment in greenhouse. Maximum increase in plant biomass (up to 26%) was observed following treatment with a rhizosphere isolate identified as Bacillus firmis GRS 123, and two phylloplane isolates Bacillus megaterium GPS 55 and Pseudomonas aeruginosa GPS 21. There was no correlation between the production of L-tryptophan-derived auxins and growth promotion by the test isolates. Actively growing cells and peat formulations of GRS 123 and GPS 55, and actively growing cells of GPS 21, significantly increased the plant growth and pod yield (up to 19%) in field. Rifampicin-resistant mutants of GRS 123 and GPS 21 colonized the ecto- and endorhizospheres of groundnut, respectively, up to 100 days after sowing (DAS), whereas GPS 55 was recovered from both the habitats at 100 DAS. Seed bacterization with phylloplane isolates promoted groundnut growth indicating the possibility of isolating rhizosphere beneficial bacteria from different habitats. Identification of phylloplane bacteria as effective plant growth-promoting rhizobacteria (PGPR) broadens the spectrum of PGPR available for field application.

Noise cancellation in magnetoencephalography and electroencephalography with isolated reference sensors

DOEpatents

Kraus, Jr., Robert H.; Espy, Michelle A.; Matlachov, Andrei; Volegov, Petr

2010-06-01

An apparatus measures electromagnetic signals from a weak signal source. A plurality of primary sensors is placed in functional proximity to the weak signal source with an electromagnetic field isolation surface arranged adjacent the primary sensors and between the weak signal source and sources of ambient noise. A plurality of reference sensors is placed adjacent the electromagnetic field isolation surface and arranged between the electromagnetic isolation surface and sources of ambient noise.

Genetic diversity demonstrated by pulsed field gel electrophoresis of Salmonella enterica isolates obtained from diverse sources in Mexico

USDA-ARS?s Scientific Manuscript database

This study was conducted to determine the genetic diversity of Salmonella isolates recovered from a variety of sources using pulsed-field gel electrophoresis (PFGE) to assess their possible relatedness. Salmonella was isolated from ca. 52% of samples from a pepper var. Bell production system. A to...

Ecology of hymexazol-insensitive Pythium species in field soils.

PubMed

Ali-Shtayeh, Mohammed; Salah, Ayman M A; Jamous, Rana M

2003-01-01

Soils from 100 irrigated fields (95 under vegetables, 5 under citrus) in different geographical locations in the West Bank (Palestinian Autonomous Territory) were surveyed for hymexazol-insensitive (HIS) Pythium species using the surface soil dilution plate (SSDP) method with the VP3 medium amended with 50 mg/L hymexazol (HMI) (VP3H50), over a period of 12 months. HIS Pythium species were isolated from 37% of the soils surveyed, with mean population levels ranging from 4.3-1422 CFU g(-1) dry weight. Eight HIS Pythium taxa were recovered on the VP3H50 medium, the most abundant of which was P. vexans (found in 29% of field soils surveyed). Seasonal variations in population levels of HIS Pythium species were studied in four fields over a period of 12 months. Significant seasonal variations in HIS population levels were detected in the four fields, with the highest population levels of HIS Pythium spp. encountered in spring and the lowest population levels in winter in three of the fields surveyed. Effects of HMI on linear growth and colony morphology of 149 Pythium ssp. isolates were examined on CMA amended with HMI at five concentrations. Pythium vexans isolates responded differently from those of the other Pythium species. Isolates of this important pathogen were more insensitive to HMI at high concentrations than the other main species tested. A large proportion of the P. ultimum isolates was either insensitive or weakly sensitive to HMI. Furthermore, a few isolates of other Pythium species were insensitive to the fungicide at various concentrations. The colony morphology of P. vexans isolates was not affected by HMI, whereas colonies of the other species showed sparse growth on the HMI amended medium relative to the control. The pathogenicity of P. vexans and P. ultimum isolates to cucumber seedlings was examined in growth chambers. Insensitive isolates of both species were found to be more virulent damping-off pathogens than the sensitive isolates. The present study demonstrates that HMI can not be used effectively in controlling Pythium spp. in soil inhabited with high densities of HIS Pythium spp. pathogens.

Isolation and identification of gold nanoparticles synthesizing fungi from Indian Kolar Gold Field mine soil.

PubMed

Lakshmi, V Jhansi; Kannan, K P

2016-07-01

An indigenous fungal strain was isolated from Indian Kolar Gold Field mine soil. The isolate was heterothallic, branched septate, deeply floccose, fast-growing, dull green with white background conidial columnar mycelium from Aspergillus section Fumigati. Diverse metabolic patterns of the isolate exhibit high metal, thermal resistance which grews well from 28 ± 1 degrees C to 37 degrees C and pH concentration was significant on the growth of isolate. Phylogenetic analysis of 16srRNA β-Tubulin gene sequence established relationship among isolate and other taxa. Molecular identification and morphological features of fungal isolate were consistent with those of Neosartorya udagawae. Heterothallic N. udagawae FJ830683 strain was closely related to homothallic N. aureola EF661890. Fungal isolate extract synthesized narrow sized stable Gold nanoparticles (AuNPs).

Studies of Isolated and Non-isolated Photospheric Bright Points in an Active Region Observed by the New Vacuum Solar Telescope

NASA Astrophysics Data System (ADS)

Liu, Yanxiao; Xiang, Yongyuan; Erdélyi, Robertus; Liu, Zhong; Li, Dong; Ning, Zongjun; Bi, Yi; Wu, Ning; Lin, Jun

2018-03-01

Properties of photospheric bright points (BPs) near an active region have been studied in TiO λ 7058 Å images observed by the New Vacuum Solar Telescope of the Yunnan Observatories. We developed a novel recognition method that was used to identify and track 2010 BPs. The observed evolving BPs are classified into isolated (individual) and non-isolated (where multiple BPs are observed to display splitting and merging behaviors) sets. About 35.1% of BPs are non-isolated. For both isolated and non-isolated BPs, the brightness varies from 0.8 to 1.3 times the average background intensity and follows a Gaussian distribution. The lifetimes of BPs follow a log-normal distribution, with characteristic lifetimes of (267 ± 140) s and (421 ± 255) s, respectively. Their size also follows log-normal distribution, with an average size of about (2.15 ± 0.74) × 104 km2 and (3.00 ± 1.31) × 104 km2 for area, and (163 ± 27) km and (191 ± 40) km for diameter, respectively. Our results indicate that regions with strong background magnetic field have higher BP number density and higher BP area coverage than regions with weak background field. Apparently, the brightness/size of BPs does not depend on the background field. Lifetimes in regions with strong background magnetic field are shorter than those in regions with weak background field, on average.

Sensitivity of infectious bovine rhinotracheitis virus to ether.

PubMed

Crandell, R A; Melloh, A J; Sorlie, P

1975-12-01

The sensitivity of 12 field isolates of infectious boviine rhinotracheitis (IBR) virus and four commercial modified-live infectious bovine rhinotracheitis virus vaccine strains was determined after exposure to 20% ethyl ether (anesthetic) for 16 h at 4 c. The infectivity of five field strains was reduced by varying degrees, whereas seven were found to be resistant. Three vaccine strains were moderately sensitive, and one strain was resistant. Four of the sensitive field strains were isolated from the conjunctiva and the other was isolated from the surface of the epiglottis of natural infective cattle. Strains of virus isolated from fetal tissue and nasal cavity were resistant. All viruses were readily inactivated by chloroform treatment.

Molecular detection of establishment and geographical distribution of Brazilian isolates of Neozygites tanajoae, a fungus pathogenic to cassava green mite, in Benin (West Africa)

PubMed Central

Hanna, Rachid; von Tiedemann, Andreas

2010-01-01

Diagnostic PCR with two specific primer pairs (NEOSSU and 8DDC) were used to monitor the establishment and geographical distribution of Brazilian isolates of Neozygites tanajoae Delalibera, Hajek and Humber (Entomophthorales: Neozygitaceae) released in Benin for the biological control of the cassava green mite, Mononychellus tanajoa (Bondar) (Acari: Tetranychidae). A total of 141 cassava fields were visited and samples of M. tanajoa suspected to be infected by N. tanajoae were collected in 60 fields distributed between the coastal Southern Forest Mosaic (SFM) and the Northern Guinea Savanna (NGS) zones of Benin, West Africa. Analysis of DNA samples of dead mites using the species specific NEOSSU primers revealed the presence of N. tanajoae in 46 fields. The second country specific pair of primers 8DDC revealed the presence of Brazilian isolates of N. tanajoae in 36 fields, representing 78.3% of fields positive for N. tanajoae. Brazilian isolates occurred from SFM to NGS zones in Benin, however, they were concentrated in fields located within former release zones (e.g. Department of Ouémé in the South and Borgou in the North). In contrast, the indigenous African isolates of N. tanajoae were evenly distributed in the sub-humid and humid savannah zones of the country. The mean infection rate of M. tanajoa with indigenous isolates of N. tanajoae was relatively low (5.3%) compared to Brazilian isolates (28%), indicating a higher biocontrol potential of the latter. This first post-release monitoring using PCR techniques showed that the Brazilian strains of N. tanajoae is well established in Benin and spread effectively in this area. PMID:20838883

Pock forming ability of fowl pox virus isolated from layer chicken and its adaptation in chicken embryo fibroblast cell culture

PubMed Central

Gilhare, Varsha Rani; Hirpurkar, S. D.; Kumar, Ashish; Naik, Surendra Kumar; Sahu, Tarini

2015-01-01

Aim: The objective of the present study was to examine pock forming ability of field strain and vaccine strain of fowl pox virus (FPV) in chorioallantoic membrane (CAM) of embryonated chicken eggs and its adaptation in chicken embryo fibroblast (CEF) cell culture. Materials and Methods: Dry scabs were collected from 25 affected birds in glycerin-saline and preserved at 4°C until processed. Virus was isolated in 10-day-old embryonated chicken eggs by dropped CAM method. The identity of the virus is confirmed by clinical findings of affected birds, pock morphology and histopathology of infected CAM. In addition one field isolate and vaccine strain of FPV was adapted to CEF cell culture. CEF cell culture was prepared from 9-day-old embryonated chicken eggs. Result: Clinical symptoms observed in affected birds include pox lesion on comb, wattle, eyelids and legs, no internal lesions were observed. All field isolates produced similar findings in CAM. Pocks produced by field isolates ranged from 3 mm to 5 mm at the third passage while initial passages edematous thickening and necrosis of CAM was observed. Pocks formed by lyophilized strain were ranges from 0.5 mm to 2.5 mm in diameter scattered all over the membrane at the first passage. Intra-cytoplasmic inclusion bodies are found on histopathology of CAM. At third passage level, the CEF inoculated with FPV showed characteristic cytopathic effect (CPE) included aggregation of cells, syncytia and plaque formation. Conclusion: FPV field isolates and vaccine strain produced distinct pock lesions on CAMs. Infected CAM showed intracytoplasmic inclusion bodies. The CEF inoculated with FPV field isolate as well as a vaccine strain showed characteristic CPE at third passage level. PMID:27047081

Pock forming ability of fowl pox virus isolated from layer chicken and its adaptation in chicken embryo fibroblast cell culture.

PubMed

Gilhare, Varsha Rani; Hirpurkar, S D; Kumar, Ashish; Naik, Surendra Kumar; Sahu, Tarini

2015-03-01

The objective of the present study was to examine pock forming ability of field strain and vaccine strain of fowl pox virus (FPV) in chorioallantoic membrane (CAM) of embryonated chicken eggs and its adaptation in chicken embryo fibroblast (CEF) cell culture. Dry scabs were collected from 25 affected birds in glycerin-saline and preserved at 4°C until processed. Virus was isolated in 10-day-old embryonated chicken eggs by dropped CAM method. The identity of the virus is confirmed by clinical findings of affected birds, pock morphology and histopathology of infected CAM. In addition one field isolate and vaccine strain of FPV was adapted to CEF cell culture. CEF cell culture was prepared from 9-day-old embryonated chicken eggs. Clinical symptoms observed in affected birds include pox lesion on comb, wattle, eyelids and legs, no internal lesions were observed. All field isolates produced similar findings in CAM. Pocks produced by field isolates ranged from 3 mm to 5 mm at the third passage while initial passages edematous thickening and necrosis of CAM was observed. Pocks formed by lyophilized strain were ranges from 0.5 mm to 2.5 mm in diameter scattered all over the membrane at the first passage. Intra-cytoplasmic inclusion bodies are found on histopathology of CAM. At third passage level, the CEF inoculated with FPV showed characteristic cytopathic effect (CPE) included aggregation of cells, syncytia and plaque formation. FPV field isolates and vaccine strain produced distinct pock lesions on CAMs. Infected CAM showed intracytoplasmic inclusion bodies. The CEF inoculated with FPV field isolate as well as a vaccine strain showed characteristic CPE at third passage level.

Comparison of genetic diversity and population structure between two Schistosoma japonicum isolates--the field and the laboratory.

PubMed

Bian, Chao-Rong; Gao, Yu-Meng; Lamberton, Poppy H L; Lu, Da-Bing

2015-06-01

Schistosomiasis japonicum is one of the most important human parasitic diseases, and a number of studies have recently elucidated the difference in biological characteristics of S. japonicum among different parasite isolates, for example, between the field and the laboratory isolates. Therefore, the understanding of underlying genetic mechanism is of both theoretical and practical importance. In this study, we used six microsatellite markers to assess genetic diversity, population structure, and the bottleneck effect (a sharp reduction in population size) of two parasite populations, one field and one laboratory. A total of 136 S. japonicum cercariae from the field and 86 from the laboratory, which were genetically unique within single snails, were analyzed. The results showed bigger numbers of alleles and higher allelic richness in the field parasite population than in the laboratory indicating lower genetic diversity in the laboratory parasites. A bottleneck effect was detected in the laboratory population. When the field and laboratory isolates were combined, there was a clear distinction between two parasite populations using the software Structure. These genetic differences may partially explain the previously observed contrasted biological traits.

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.

Isolation and purification of Gallid herpesvirus 2 strains currently distributed in Japan.

PubMed

Machida, Yuka; Murata, Shiro; Matsuyama-Kato, Ayumi; Isezaki, Masayoshi; Taneno, Akira; Sakai, Eishi; Konnai, Satoru; Ohashi, Kazuhiko

2017-01-20

Gallid herpesvirus 2 (GaHV-2) causes malignant lymphomas in chickens (Marek's disease, MD). Although MD is controlled through vaccination efforts, field isolates of GaHV-2 have increased in virulence worldwide and even cause MD in vaccinated chickens. GaHV-2 strains are classified into four categories (mild, virulent, very virulent and very virulent +) based on the virulence exhibited in experimental infection in unvaccinated or MD-vaccinated susceptible chickens. Although MD cases are sporadically reported in Japan, the recent field strains of GaHV-2 in Japan have not been characterized. During isolation of recent field strains by using primary chicken kidney cell cultures, a method classically used for GaHV-2 isolation, vaccine strains were simultaneously isolated. Therefore, it is necessary to separate vaccine strains to characterize the virulence and pathogenicity of the GaHV-2 strains currently distributed in Japan. In this study, we prepared cell suspensions from the spleens of MD-symptomatic chickens, inoculated day-old-chicks and isolated GaHV-2 strains by primary chicken kidney cell cultures at 2-3 weeks post inoculation. The isolated strains were passaged several times on chicken embryo fibroblast cells, and PCR analysis revealed that the isolated strains were not contaminated with vaccine strains. Moreover, the contaminant vaccine strains were completely removed by the purification of plaques observed in chicken kidney cells. These procedures are necessary to isolate GaHV-2 field strains from vaccine strains in order to carry out future studies to characterize these strains and glean insights into GaHV-2 virulence and pathogenicity.

Induction of avirulence by AVR-Pita1 in virulent U.S. field isolates of Magnaporthe oryzae

USDA-ARS?s Scientific Manuscript database

The AVR-Pita1 gene, from the Chinese isolate O-137 of Magnaporthe oryzae, is an effector that determines the efficacy of the Pi-ta rice blast resistance gene. In the present study, the avirulence function of AVR-Pita1 was induced by transformation of field isolates (TM2, ZN19, B2 and B8) that origin...

Evaluation of atoxigenic isolates of Aspergillus flavus as potential biocontrol agents for aflatoxin in maize.

PubMed

Atehnkeng, J; Ojiambo, P S; Ikotun, T; Sikora, R A; Cotty, P J; Bandyopadhyay, R

2008-10-01

Aflatoxin contamination resulting from maize infection by Aspergillus flavus is both an economic and a public health concern. Therefore, strategies for controlling aflatoxin contamination in maize are being investigated. The abilities of eleven naturally occurring atoxigenic isolates in Nigeria to reduce aflatoxin contamination in maize were evaluated in grain competition experiments and in field studies during the 2005 and 2006 growing seasons. Treatments consisted of inoculation of either grains in vials or ears at mid-silking stage in field plots, with the toxigenic isolate (La3228) or atoxigenic isolate alone and co-inoculation of each atoxigenic isolate and La3328. Aflatoxin B(1) + B(2) concentrations were significantly (p < 0.05) lower in the co-inoculation treatments compared with the treatment in which the aflatoxin-producing isolate La3228 was inoculated alone. Relative levels of aflatoxin B(1) + B(2) reduction ranged from 70.1% to 99.9%. Among the atoxigenics, two isolates from Lafia, La3279 and La3303, were most effective at reducing aflatoxin B(1) + B(2) concentrations in both laboratory and field trials. These two isolates have potential value as agents for the biocontrol of aflatoxin contamination in maize. Because these isolates are endemic to West Africa, they are both more likely than introduced isolates to be well adapted to West African environments and to meet regulatory concerns over their use throughout that region.

Chlorhexidine digluconate effects on planktonic growth and biofilm formation in some field isolates of animal bacterial pathogens.

PubMed

Ebrahimi, Azizollah; Hemati, Majid; Habibian Dehkordi, Saeed; Bahadoran, Shahab; Khoshnood, Sheida; Khubani, Shahin; Dokht Faraj, Mahdi; Hakimi Alni, Reza

2014-05-01

To study chlorhexidine digluconate disinfectant effects on planktonic growth and biofilm formation in some bacterial field isolates from animals. The current study investigated chlorhexidine digluconate effects on planktonic growth and biofilm formation in some field isolates of veterinary bacterial pathogens. Forty clinical isolates of Escherichia coli, Salmonella serotypes, Staphylococcus. aureus and Streptococcus agalactiae (10 isolates for each) were examined for chlorhexidine digluconate effects on biofilm formation and planktonic growth using microtiter plates. In all of the examined strains in the presence of chlorhexidine digluconate, biofilm development and planktonic growth were affected at the same concentrations of the disinfectant. Chlorhexidine digluconate inhibited the planktonic growth of different bacterial species at sub-MICs. But they were able to induce biofilm development of the E. coli, Salmonella spp., S. aureus and Str. agalactiae strains. Bacterial resistance against chlorhexidine is increasing. Sub-MIC doses of chlorhexidine digluconate can stimulate the formation of biofilm strains.

An outbreak of chickenpox in a military field hospital--the implications for biological warfare.

PubMed Central

Hepburn, N C; Brooks, T J

1991-01-01

An outbreak of chickenpox with spread to patients and staff on the isolation ward of a British field hospital during the Gulf war is described. The implications for the design and operation of field hospital isolation units should transmissible biological warfare agents be encountered in any future conflict are discussed. PMID:1774746

Diversity of Cultivable Methane-Oxidizing Bacteria in Microsites of a Rice Paddy Field: Investigation by Cultivation Method and Fluorescence in situ Hybridization (FISH)

PubMed Central

Dianou, Dayéri; Ueno, Chihoko; Ogiso, Takuya; Kimura, Makoto; Asakawa, Susumu

2012-01-01

The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH4 emission from this ecosystem. PMID:22446309

SYMBIODINIUM ISOLATES FROM STONY CORAL: ISOLATION, GROWTH CHARACTERISTICS AND EFFECTS OF UV IRRADIATION

EPA Science Inventory

Symbiodinium spp. Isolates from Stony Coral: Isolation, Growth Characteristics and Effects of UV Irradiation (Abstract). J. Phycol. 37(3):42-43.

Symbiodinium species were isolated from Montipora capitata, Acropora palmata and two field samples of Porites porites. Cultures ...

Genetic and antigenic relationship of foot-and-mouth disease virus serotype O isolates with the vaccine strain O1/BFS.

PubMed

Xu, Wanhong; Zhang, Zhidong; Nfon, Charles; Yang, Ming

2018-05-15

Foot-and-mouth disease serotype O viruses (FMDV/O) are responsible for the most outbreaks in FMD endemic countries. O1/BFS is one of the recommended FMD/O vaccine strains by World Reference Laboratory for FMD. In the current study, FMDV/O1 BFS vaccine strain and serotype O field isolates (45) were analyzed phylogenetically and antigenically to gain more insight into the genetic and antigenic characteristics of the vaccine strain and field isolates. O1/BFS showed similarity with 89% of the field isolates using a virus neutralization test (VNT). The P1 region encoding the FMDV capsid was sequenced and analysed for 46 strains of FMDV/O. Phylogenetic analysis showed these viruses originated from five continents and covered eight of 11 reported topotypes. Five isolates that demonstrated low antigenic similarities with O1/BFS were analyzed for their antigenic variation at the known neutralizing antigenic sites. Three of the five isolates demonstrated unique amino acid substitutions at various antigenic sites. No unique amino acid substitutions were observed for the other two unmatched isolates. Positively selected residues were identified on the surface of the FMD virus capsid supporting that it is important to continuously monitor field isolates for their antigenic and phenotypic changes. In conclusion, the vaccine strain O1/BFS is likely to confer protection against 89% of the 45 FMDV/O isolates based on VNT. Thus O1/BFS vaccine strain is still suitable for use in global FMD serotype O outbreak control. Combining data from phylogenetic, molecular and antigenic analysis can provide improvements in the process of vaccine selection. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Environmental Monitoring and Surveillance of Rodents and Vectors for Francisella tularensis Following Outbreaks of Human Tularemia in Georgia.

PubMed

Elashvili, Eka; Kracalik, Ian; Burjanadze, Irma; Datukishvili, Sophio; Chanturia, Gvantsa; Tsertsvadze, Nikoloz; Beridze, Levan; Shavishvili, Merab; Dzneladze, Archil; Grdzelidze, Marina; Imnadze, Paata; Pearson, Andrew; Blackburn, Jason K

2015-10-01

Tularemia is a re-emerging bacterial zoonosis, broadly distributed across the northern hemisphere. In Georgia, there is a history of human tularemia outbreaks dating back to the 1940s. In response to outbreaks, health officials initiated long-term field surveillance and environmental monitoring. The objective of our study was to obtain information from 57 years of field surveys to identify species that play a role in the occurrence Francisella tularensis subsp. holarctica in the environment in Georgia. We collected historical data on human outbreaks, field collections, population dynamics of the common vole (Microtus arvalis), and conducted surveys on small mammals and vectors from five regions in Georgia during 1956-2012. Bacterial isolation was conducted using standard culturing techniques, and isolation rates for species were obtained for a subset of years. We used a Spearman rank correlation to test for associations between the density of the common vole and isolation rates. From 1956 through 2012, there were four recorded outbreaks of human tularemia (362 cases). A total of 465 bacterial isolates of F. tularensis subsp. holarctica were obtained from 27 species and environmental samples. The number of isolations was highest in the common vole (M. arvalis; 149 isolates; 32%) and Dermacentor marginatus ticks (132 isolates; 28%); isolation rates ranged between 0-0.91% and 0-0.47%, respectively. Population dynamics of the common vole were not correlated with the isolation rate. Given the history of tularemia re-emergence in Georgia, continued field surveys and environmental monitoring may provide an early indication of outbreak risk in humans. In conclusion, our findings provide evidence of long-standing foci of F. tularensis subsp. holarctica that are likely maintained by the common vole-tick cycle.

Electricity Generation in Microbial Fuel Cell (MFC) by Bacterium Isolated from Rice Paddy Field Soil

NASA Astrophysics Data System (ADS)

Fakhirruddin, Fakhriah; Amid, Azura; Salim, Wan Wardatul Amani Wan; Suhaida Azmi, Azlin

2018-03-01

Microbial fuel cell (MFC) is an alternative approach in generating renewable energy by utilising bacteria that will oxidize organic or inorganic substrates, producing electrons yielded as electrical energy. Different species of exoelectrogenic bacteria capable of generating significant amount of electricity in MFC has been identified, using various organic compounds for fuel. Soil sample taken from rice paddy field is proven to contain exoelectrogenic bacteria, thus electricity generation using mixed culture originally found in the soil, and pure culture isolated from the soil is studied. This research will isolate the exoelectrogenic bacterial species in the rice paddy field soil responsible for energy generation. Growth of bacteria isolated from the MFC is observed by measuring the optical density (OD), cell density weight (CDW) and viable cell count. Mixed bacterial species found in paddy field soil generates maximum power of 77.62 μW and 0.70 mA of current. In addition, the research also shows that the pure bacterium in rice paddy field soil can produce maximum power and current at 51.32 μW and 0.28 mA respectively.

Genetic Characterization of Atypical Enteropathogenic Escherichia coli Isolates from Ewes' Milk, Sheep Farm Environments, and Humans by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis

PubMed Central

Otero, Verónica; Rodríguez-Calleja, José-María; Otero, Andrés; García-López, María-Luisa

2013-01-01

A collection of 81 isolates of enteropathogenic Escherichia coli (EPEC) was obtained from samples of bulk tank sheep milk (62 isolates), ovine feces (4 isolates), sheep farm environment (water, 4 isolates; air, 1 isolate), and human stool samples (9 isolates). The strains were considered atypical EPEC organisms, carrying the eae gene without harboring the pEAF plasmid. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 19 sequence types (ST) were detected, with none of them having been previously reported for atypical EPEC. The most frequent ST included 41 strains isolated from milk and human stool samples. Genetic typing by pulsed-field gel electrophoresis (PFGE) resulted in 57 patterns which grouped in 24 clusters. Comparison of strains isolated from the different samples showed phylogenetic relationships between milk and human isolates and also between milk and water isolates. The results obtained show a possible risk for humans due to the presence of atypical EPEC in ewes' milk and suggest a transmission route for this emerging pathogen through contaminated water. PMID:23872571

Adaptation of the Sensititre broth microdilution technique to antimicrobial susceptibility testing of Mycoplasma hyopneumoniae.

PubMed

Tanner, A C; Erickson, B Z; Ross, R F

1993-09-01

A broth microdilution technique is described for determining the antimicrobial susceptibility of Mycoplasma hyopneumoniae, using commercially prepared Sensititre plates. Twenty-five field isolates and two reference strains (J & 232), were tested against seven antimicrobials. Field isolates were tested in duplicate and reference strains, four times to estimate reproducibility. Ninety-seven percent of the duplicate MIC results for the field isolates were in agreement, or within one log2 dilution. Similar results were obtained with the reference strains. The isolates were susceptible to lincomycin-spectinomycin, tylosin and oxytetracycline or resistant to amoxycillin, apramycin and erythromycin. Susceptibility to furaltadone varied. This method retains the accuracy and reproducibility of broth MIC determinations, while avoiding the lengthy preparation of antimicrobial dilutions normally associated with more traditional methods.

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.

ALG-2 activates the MVB sorting function of ALIX through relieving its intramolecular interaction

PubMed Central

Sun, Sheng; Zhou, Xi; Corvera, Joe; Gallick, Gary E; Lin, Sue-Hwa; Kuang, Jian

2015-01-01

The modular adaptor protein ALIX is critically involved in endosomal sorting complexes required for transport (ESCRT)-mediated multivesicular body (MVB) sorting of activated epidermal growth factor receptor (EGFR); however, ALIX contains a default intramolecular interaction that renders ALIX unable to perform this ESCRT function. The ALIX partner protein ALG-2 is a calcium-binding protein that belongs to the calmodulin superfamily. Prompted by a defined biological function of calmodulin, we determined the role of ALG-2 in regulating ALIX involvement in MVB sorting of activated EGFR. Our results show that calcium-dependent ALG-2 interaction with ALIX completely relieves the intramolecular interaction of ALIX and promotes CHMP4-dependent ALIX association with the membrane. EGFR activation induces increased ALG-2 interaction with ALIX, and this increased interaction is responsible for increased ALIX association with the membrane. Functionally, inhibition of ALIX activation by ALG-2 inhibits MVB sorting of activated EGFR as effectively as inhibition of ALIX interaction with CHMP4 does; however, inhibition of ALIX activation by ALG-2 does not affect cytokinetic abscission or equine infectious anemia virus (EIAV) budding. These findings indicate that calcium-dependent ALG-2 interaction with ALIX is specifically responsible for generating functional ALIX that supports MVB sorting of ubiquitinated membrane receptors. PMID:27462417

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...

Molecular characterization of acquired enrofloxacin resistance in Mycoplasma synoviae field isolates.

PubMed

Lysnyansky, I; Gerchman, I; Mikula, I; Gobbo, F; Catania, S; Levisohn, S

2013-07-01

The in vitro activity of enrofloxacin against 73 Mycoplasma synoviae field strains isolated in Israel and Europe was determined by broth microdilution. Decreased susceptibility to enrofloxacin was identified in 59% of strains, with the MICs ranging from 1 to >16 μg/ml. The estimated MIC50 and MIC90 values for enrofloxacin were 2 and 8 μg/ml, respectively. Moreover, this study showed that 92% of recent Israeli field isolates (2009 to 2011) of M. synoviae have MICs of ≥ 2 μg/ml to enrofloxacin. Comparison of the quinolone resistance-determining regions (QRDRs) in M. synoviae isolates revealed a clear correlation between the presence of one of the amino acid substitutions Asp79-Asn, Thr80-Ala/Ile, Ser81-Pro, and Asp84-Asn/Tyr/His of the ParC QRDR and decreased susceptibility to enrofloxacin (MIC, ≥ 1 μg/ml). Amino acid substitutions at positions GyrA 87, GyrB 401/402, and ParE 420/454 were also identified, but there was no clear-cut correlation with susceptibility to enrofloxacin. Comparison of vlhA molecular profiles revealed the presence of 9 different genotypes in the Israeli M. synoviae field isolates and 10 genotypes in the European isolates; only one vlhA genotype (type 4) was identified in both cohorts. Based on results of vlhA molecular typing, several mechanisms for emergence and dissemination of Israeli enrofloxacin-resistant M. synoviae isolates are suggested.

Molecular Characterization of Acquired Enrofloxacin Resistance in Mycoplasma synoviae Field Isolates

PubMed Central

Gerchman, I.; Mikula, I.; Gobbo, F.; Catania, S.; Levisohn, S.

2013-01-01

The in vitro activity of enrofloxacin against 73 Mycoplasma synoviae field strains isolated in Israel and Europe was determined by broth microdilution. Decreased susceptibility to enrofloxacin was identified in 59% of strains, with the MICs ranging from 1 to >16 μg/ml. The estimated MIC50 and MIC90 values for enrofloxacin were 2 and 8 μg/ml, respectively. Moreover, this study showed that 92% of recent Israeli field isolates (2009 to 2011) of M. synoviae have MICs of ≥2 μg/ml to enrofloxacin. Comparison of the quinolone resistance-determining regions (QRDRs) in M. synoviae isolates revealed a clear correlation between the presence of one of the amino acid substitutions Asp79-Asn, Thr80-Ala/Ile, Ser81-Pro, and Asp84-Asn/Tyr/His of the ParC QRDR and decreased susceptibility to enrofloxacin (MIC, ≥1 μg/ml). Amino acid substitutions at positions GyrA 87, GyrB 401/402, and ParE 420/454 were also identified, but there was no clear-cut correlation with susceptibility to enrofloxacin. Comparison of vlhA molecular profiles revealed the presence of 9 different genotypes in the Israeli M. synoviae field isolates and 10 genotypes in the European isolates; only one vlhA genotype (type 4) was identified in both cohorts. Based on results of vlhA molecular typing, several mechanisms for emergence and dissemination of Israeli enrofloxacin-resistant M. synoviae isolates are suggested. PMID:23612192

Variable-Number Tandem Repeats That Are Useful in Genotyping Isolates of Salmonella enterica subsp. enterica Serovars Typhimurium and Newport▿

PubMed Central

Witonski, D. ; Stefanova, R.; Ranganathan, A.; Schutze, G. E.; Eisenach, K. D.; Cave, M. D.

2006-01-01

The genome of Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 was analyzed for direct repeats, and 54 sequences containing variable-number tandem repeat loci were identified. Ten primer pairs that anneal upstream and downstream of each selected locus were designed and used to amplify PCR targets in isolates of S. enterica serovars Typhimurium and Newport. Four of the 10 loci did not show polymorphism in the length of products. Six loci were selected for analysis. Isolates of S. enterica serovars Typhimurium and Newport that were related to specific outbreaks and showed identical pulsed-field gel electrophoresis patterns were indistinguishable by the length of the six variable-number tandem repeats. Isolates that differed in their pulsed-field gel electrophoresis patterns showed polymorphism in variable-number tandem repeat profiles. Length of the products was confirmed by DNA sequence analysis. Only 2 of the 10 loci contained exact integers of the direct repeat. Eight loci contained partial copies. The partial copies were maintained at the ends of the variable-number tandem repeat loci in all isolates. In spite of having partial copies that were maintained in all isolates, the number of direct repeats at a locus was polymorphic. Six variable-number tandem repeat loci were useful in distinguishing isolates of S. enterica serovars Typhimurium and Newport that had different pulsed-field gel electrophoresis patterns and in identifying outbreak-associated cases that shared a common pulsed-field gel pattern. PMID:16943354

Novel components of leaf bacterial communities of field-grown tomato plants and their potential for plant growth promotion and biocontrol of tomato diseases.

PubMed

Romero, Fernando M; Marina, María; Pieckenstain, Fernando L

2016-04-01

This work aimed to characterize potentially endophytic culturable bacteria from leaves of cultivated tomato and analyze their potential for growth promotion and biocontrol of diseases caused by Botrytis cinerea and Pseudomonas syringae. Bacteria were obtained from inner tissues of surface-disinfected tomato leaves of field-grown plants. Analysis of 16S rRNA gene sequences identified bacterial isolates related to Exiguobacterium aurantiacum (isolates BT3 and MT8), Exiguobacterium spp. (isolate GT4), Staphylococcus xylosus (isolate BT5), Pantoea eucalypti (isolate NT6), Bacillus methylotrophicus (isolate MT3), Pseudomonas veronii (isolates BT4 and NT2), Pseudomonas rhodesiae (isolate BT2) and Pseudomonas cichorii (isolate NT3). After seed inoculation, BT2, BT4, MT3, MT8, NT2 and NT6 were re-isolated from leaf extracts. NT2, BT2, MT3 and NT6 inhibited growth of Botrytis cinerea and Pseudomonas syringae pv. tomato in vitro, produced antimicrobial compounds and reduced leaf damage caused by B. cinerea. Some of these isolates also promoted growth of tomato plants, produced siderophores, the auxin indole-3-acetic and solubilized inorganic phosphate. Thus, bacterial communities of leaves from field-grown tomato plants were found to harbor potentially endophytic culturable beneficial bacteria capable of antagonizing pathogenic microorganisms and promoting plant growth, which could be used as biological control agents and biofertilizers/biostimulators for promotion of tomato plant growth. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

The soil sulphate effect and maize plant (Zea mays L.) growth of sulphate reducing bacteria (SRB) inoculation in acid sulfate soils with the different soil water condition

NASA Astrophysics Data System (ADS)

Asmarlaili, S.; Rauf, A.; Hanafiah, D. S.; Sudarno, Y.; Abdi, P.

2018-02-01

The objective of the study was to determine the potential application of sulphate reducing bacteria on acid sulfate soil with different water content in the green house. The research was carried out in the Laboratory and Green House, Faculty of Agriculture, Universitas Sumatera Utara. This research used Randomized Block Design with two treatments factors, ie sulphate reducing bacteria (SRB) isolate (control, LK4, LK6, TSM4, TSM3, AP4, AP3, LK4 + TSM3, LK4 + AP4, LK4 + AP3, LK6 + TSM3, LK6 + AP4, LK6 + AP3, TSM4 + TSM3, TSM4 + AP4, TSM4 + AP3) and water condition (100% field capacity and 110% field capacity). The results showed that application of isolate LK4 + AP4 with water condition 110% field capacity decreased the soil sulphate content (27.38 ppm) significantly after 6 weeks. Application of isolate LK4 + AP3 with water condition 110% field capacity increased soil pH (5.58) after-week efficacy 6. Application of isolate LK4 with water condition 110% field capacity increased plant growth (140 cm; 25.74 g) significantly after week 6. The best treatment was application isolate LK4 with water condition 110% field Capacity (SRB population 2.5x108; soil sulphate content 29.10ppm; soil acidity 4.78; plant height 140cm; plant weight 25.74g).

Heterogeneity in pepper isolates of cucumber mosaic virus

USGS Publications Warehouse

Rodriguez-Alvarado, G.; Kurath, G.; Dodds, J.A.

1995-01-01

Twenty-four cucumber mosaic cucumovirus (CMV) field isolates from pepper crops in Cali-fornia were characterized and compared by nucleic acid hybridization subgrouping, virion electrophoresis, and biological effects in several hosts. Isolates, belonging to subgroup I or subgroup II, were found that induced severe symptoms in mechanically inoculated bell pep-pers. Only two isolates, both from subgroup II, were mild. A group of 19 isolates collected from a single field were all in subgroup II and appeared identical by virion electrophoresis, but they exhibited varying degrees of symptom severity in peppers. As a more detailed indicator of heterogeneity, these 19 isolates were examined by RNase protection assays to delect sequence variation in the coat protein gene region of their genomes. The patterns of bands observed were complex and a high degree of genomic heterogeneity was detected between isolates, with no apparent correlation to symptomatology in bell pepper.

Salmonella enterica Pulsed-Field Gel Electrophoresis Clusters, Minnesota, USA, 2001–2007

PubMed Central

Hedberg, Craig W.; Meyer, Stephanie; Boxrud, David J.; Smith, Kirk E.

2010-01-01

We determined characteristics of Salmonella enterica pulsed-field gel electrophoresis clusters that predict their being solved (i.e., that result in identification of a confirmed outbreak). Clusters were investigated by the Minnesota Department of Health by using a dynamic iterative model. During 2001–2007, a total of 43 (12.5%) of 344 clusters were solved. Clusters of >4 isolates were more likely to be solved than clusters of 2 isolates. Clusters in which the first 3 case isolates were received at the Minnesota Department of Health within 7 days were more likely to be solved than were clusters in which the first 3 case isolates were received over a period >14 days. If resources do not permit investigation of all S. enterica pulsed-field gel electrophoresis clusters, investigation of clusters of >4 cases and clusters in which the first 3 case isolates were received at a public health laboratory within 7 days may improve outbreak investigations. PMID:21029524

Chlorhexidine Digluconate Effects on Planktonic Growth and Biofilm Formation in Some Field Isolates of Animal Bacterial Pathogens

PubMed Central

Ebrahimi, Azizollah; Hemati, Majid; Habibian Dehkordi, Saeed; Bahadoran, Shahab; Khoshnood, Sheida; Khubani, Shahin; Dokht Faraj, Mahdi; Hakimi Alni, Reza

2014-01-01

Background: To study chlorhexidine digluconate disinfectant effects on planktonic growth and biofilm formation in some bacterial field isolates from animals. Objectives: The current study investigated chlorhexidine digluconate effects on planktonic growth and biofilm formation in some field isolates of veterinary bacterial pathogens. Materials and Methods: Forty clinical isolates of Escherichia coli, Salmonella serotypes, Staphylococcus. aureus and Streptococcus agalactiae (10 isolates for each) were examined for chlorhexidine digluconate effects on biofilm formation and planktonic growth using microtiter plates. In all of the examined strains in the presence of chlorhexidine digluconate, biofilm development and planktonic growth were affected at the same concentrations of the disinfectant. Results: Chlorhexidine digluconate inhibited the planktonic growth of different bacterial species at sub-MICs. But they were able to induce biofilm development of the E. coli, Salmonella spp., S. aureus and Str. agalactiae strains. Conclusions: Bacterial resistance against chlorhexidine is increasing. Sub-MIC doses of chlorhexidine digluconate can stimulate the formation of biofilm strains. PMID:24872940

Genome Sequence of Canine Parvovirus Strain SC02/2011, Isolated from a Puppy with Severe Diarrhea in South China

PubMed Central

Cheng, Yi; Ji, Yikuan; Wang, Yu; Sun, Leilei; Huang, Jiaxin

2012-01-01

A widespread hemorrhagic gastroenteritis in young dogs occurred in South China. A virulent field canine parvovirus (CPV) strain, SC02/2011, was isolated from a puppy showing enteric signs in Guangdong, China. The genome of CPV strain SC02/2011 was sequenced and analyzed, which will promote a better understanding of the molecular epidemiology and genetic diversity of CPV field isolates in South China. PMID:23166228

The swimming polarity of multicellular magnetotactic prokaryotes can change during an isolation process employing magnets: evidence of a relation between swimming polarity and magnetic moment intensity.

PubMed

de Melo, Roger Duarte; Acosta-Avalos, Daniel

2017-09-01

Magnetotactic microorganisms are characterized by swimming in the direction of an applied magnetic field. In nature, two types of swimming polarity have been observed: north-seeking microorganisms that swim in the same direction as the magnetic field, and south-seeking microorganisms that swim in the opposite direction. The present work studies the reversal in the swimming polarity of the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis following an isolation process using high magnetic fields from magnets. The proportion of north- and south-seeking organisms was counted as a function of the magnetic field intensity used during the isolation of the organisms from sediment. It was observed that the proportion of north-seeking organisms increased when the magnetic field was increased. The magnetic moment for north- and south-seeking populations was estimated using the U-turn method. The average magnetic moment was higher for north- than south-seeking organisms. The results suggest that the reversal of swimming polarity must occur during the isolation process in the presence of high magnetic fields and magnetic field gradients. It is shown for the first time that the swimming polarity reversal depends on the magnetic moment intensity of multicellular magnetotactic prokaryotes, and new studies must be undertaken to understand the role of magnetic moment polarity and oxygen gradients in determination of swimming polarity.

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.

An Adjustable Gas-Mixing Device to Increase Feasibility of In Vitro Culture of Plasmodium falciparum Parasites in the Field

PubMed Central

Volkman, Sarah K.; Ahouidi, Ambroise D.; Ndiaye, Daouda; Mboup, Souleymane; Wirth, Dyann F.

2014-01-01

A challenge to conducting high-impact and reproducible studies of the mechanisms of P. falciparum drug resistance, invasion, virulence, and immunity is the lack of robust and sustainable in vitro culture in the field. While the technology exists and is routinely utilized in developed countries, various factors–from cost, to supply, to quality–make it hard to implement in malaria endemic countries. Here, we design and rigorously evaluate an adjustable gas-mixing device for the in vitro culture of P. falciparum parasites in the field to circumvent this challenge. The device accurately replicates the gas concentrations needed to culture laboratory isolates, short-term adapted field isolates, cryopreserved previously non-adapted isolates, as well as to adapt ex vivo isolates to in vitro culture in the field. We also show an advantage over existing alternatives both in cost and in supply. Furthermore, the adjustable nature of the device makes it an ideal tool for many applications in which varied gas concentrations could be critical to culture success. This adjustable gas-mixing device will dramatically improve the feasibility of in vitro culture of Plasmodium falciparum parasites in malaria endemic countries given its numerous advantages. PMID:24603696

Can the tardigrade Hypsibius dujardini survive in the absence of the geomagnetic field?

PubMed Central

Erdmann, Weronika; Idzikowski, Bogdan; Kowalski, Wojciech; Szymański, Bogdan; Kosicki, Jakub Z.; Kaczmarek, Łukasz

2017-01-01

Earth's geomagnetic field has undergone critical changes in the past. Studies on the influence of the magnetic field on Earth’s organisms are crucial for the understanding of evolution of life on Earth and astrobiological considerations. Numerous studies conducted both on plants and animals confirmed the significant influence of the geomagnetic field on the metabolism of living organisms. Water bears (Tardigrada), which are a mong the most resistant animals due to their cryptobiotic abilities, show significant resistance to a number of environmental stressors, but the influence of the geomagnetic field on their fitness has not been addressed before. In our studies, we used eutardigrade Hypsibius dujardini to analyse whether isolation from the geomagnetic field had an effect on mortality. We found that Hypsibius dujardini specimens demonstrated relatively high mortality during anhydrobiosis, also in control groups exposed to the normal geomagnetic field. Moreover, similar mortality was observed in anhydrobiotic specimens isolated from the geomagnetic field. However, a significant difference was noted between tardigrade survival and the moment of their isolation from the geomagnetic field. In particular, tardigrade mortality substantially increased in absence of a magnetic field during the process of entering anhydrobiosis and returning to active life. Our results suggest that these processes rely on complex metabolic processes that are critically influenced by the geomagnetic field. PMID:28886031

Can the tardigrade Hypsibius dujardini survive in the absence of the geomagnetic field?

PubMed

Erdmann, Weronika; Idzikowski, Bogdan; Kowalski, Wojciech; Szymański, Bogdan; Kosicki, Jakub Z; Kaczmarek, Łukasz

2017-01-01

Earth's geomagnetic field has undergone critical changes in the past. Studies on the influence of the magnetic field on Earth's organisms are crucial for the understanding of evolution of life on Earth and astrobiological considerations. Numerous studies conducted both on plants and animals confirmed the significant influence of the geomagnetic field on the metabolism of living organisms. Water bears (Tardigrada), which are a mong the most resistant animals due to their cryptobiotic abilities, show significant resistance to a number of environmental stressors, but the influence of the geomagnetic field on their fitness has not been addressed before. In our studies, we used eutardigrade Hypsibius dujardini to analyse whether isolation from the geomagnetic field had an effect on mortality. We found that Hypsibius dujardini specimens demonstrated relatively high mortality during anhydrobiosis, also in control groups exposed to the normal geomagnetic field. Moreover, similar mortality was observed in anhydrobiotic specimens isolated from the geomagnetic field. However, a significant difference was noted between tardigrade survival and the moment of their isolation from the geomagnetic field. In particular, tardigrade mortality substantially increased in absence of a magnetic field during the process of entering anhydrobiosis and returning to active life. Our results suggest that these processes rely on complex metabolic processes that are critically influenced by the geomagnetic field.

Physical and Electronic Isolation of Carbon Nanotube Conductors

NASA Technical Reports Server (NTRS)

OKeeffe, James; Biegel, Bryan (Technical Monitor)

2001-01-01

Multi-walled nanotubes are proposed as a method to electrically and physically isolate nanoscale conductors from their surroundings. We use tight binding (TB) and density functional theory (DFT) to simulate the effects of an external electric field on multi-wall nanotubes. Two categories of multi-wall nanotube are investigated, those with metallic and semiconducting outer shells. In the metallic case, simulations show that the outer wall effectively screens the inner core from an applied electric field. This offers the ability to reduce crosstalk between nanotube conductors. A semiconducting outer shell is found not to perturb an electric field incident on the inner core, thereby providing physical isolation while allowing the tube to remain electrically coupled to its surroundings.

Further RIOTS4 Characterization of Field OB Stars in the SMC

NASA Astrophysics Data System (ADS)

Oey, M. S.; Barnes, Jesse R.; Paggeot, Kevin J.; Dorigo Jones, John; Castro, Norberto; Simon-Diaz, Sergio; Kratter, Kaitlin M.; Moe, Maxwell; Szymanski, Michal

2018-06-01

We present recent results from the Runaways and O-Type Star Spectroscopic Survey of the SMC (RIOTS4), a survey quantifying properties of the field OB stars in the Small Magellanic Cloud (SMC). Based on PSF-fitting photometry and astrometry of OGLE-III I-band images, we quantify the degree of isolation for the target OB stars, classifying them as "tip-of-the-iceberg" stars accompanied by small, sparse, clusters; or as true, isolated field stars. Many of these field stars must be runaways, which we evaluate using GAIA DR2 proper motions. We measure v sin i using the IACOB code Fourier analysis, finding that the bimodal distribution of projected rotation velocities is less pronounced for O stars than early B stars. We examine rotation in relation to relative isolation and runaway status.

Subtyping Listeria monocytogenes isolates genetically related to the Swiss epidemic clone.

PubMed Central

Boerlin, P; Bannerman, E; Jemmi, T; Bille, J

1996-01-01

Macrorestriction analysis by pulsed-field gel electrophoresis was used to assess the diversity of strains within the epidemic-associated electrophoretic type 1 (ET1) clone of Listeria monocytogenes. For this purpose, a total of 144 isolates from Switzerland shown by multilocus enzyme electrophoresis to belong to the ET1 were examined. These isolates were subtyped by macrorestriction analysis using the enzymes ApaI and SmaI and field inversion gel electrophoresis. Among these 144 isolates, 45 were isolated in human listeriosis cases of the postepidemic period of 1988 to 1993 and 44 were isolated in animal listeriosis cases of the same period. Forty-seven isolates were from the epidemic period of 1983 to 1987, and eight additional isolates were from cattle from two different farms. Twenty-nine different subtypes could be identified among the 144 isolates tested. Five major subtypes were found more frequently than the others during the postepidemic period, both in humans and in animals. Two of these subtypes had been previously implicated in outbreaks of listeriosis, thus suggesting that particular pulsed-field gel electrophoresis subtypes may be frequently associated with disease in humans and animals. Two of these frequent subtypes were also suspected to be related to small clusters of listeriosis cases during the postepidemic period. The results obtained by typing epidemiologically related isolates from different animals within the same farms and from different body sites of a given patient confirmed the potential of macrorestriction analysis for epidemiological studies restricted to short periods of time and to small number of isolates. The analysis of 47 isolates related to the Swiss listeriosis epidemic period of 1983 to 1987 and the use of Southern blotting and hybridization experiments show that the interpretation of relatedness between isolates presenting slightly different macrorestriction patterns may be more complex than commonly accepted. In such cases, careful interpretation of the potential molecular mechanisms leading to the differences observed between patterns is necessary. PMID:8862575

Development and validation of a lateral MREs isolator

NASA Astrophysics Data System (ADS)

Xing, Zhi-Wei; Yu, Miao; Fu, Jie; Zhao, Lu-Jie

2015-02-01

A novel lateral vibration isolator utilizing magnetorheological elastomers (MREs) with the field-dependent damping and stiffness was proposed in order to improve the adaptive performance. First, soft silicone rubber MREs with a highly adjustable shear storage modulus was fabricated. Then, the lateral MREs isolator was developed with a unique laminated structure of MRE layers and steel plates, which enables to withstand large vertical loads and adapts to the situation of large lateral displacement. Also, the electromagnetic analysis and design employed electromagnetic finite element method (FEM) to optimize magnetic circuit inside the proposed device. To evaluate the effectiveness of the lateral MREs isolator, a series of experimental tests were carried out under various applied magnetic fields. Experimental results show that the proposed MREs isolator can triumphantly change the lateral stiffness and equivalent damping up to 140% and 125%, respectively. This work demonstrates the performance of the designed lateral MREs isolator and its capacity in vibration mitigation for the complex situation.

Dynamic changes in the rice blast population in the USA over six decades

USDA-ARS?s Scientific Manuscript database

Rice blast disease caused by Magnaporthe oryzae is one of the most destructive diseases of rice. Field isolates of M. oryzae rapidly adapt to the hosts and climate. Tracking the genetic and pathogenic variability of the field isolates is essential to understand how M. oryzae interacts with hosts an...

Virus excretion and antibody dynamics in goats inoculated with a field isolate of peste des petits ruminants virus.

PubMed

Liu, W; Wu, X; Wang, Z; Bao, J; Li, L; Zhao, Y; Li, J

2013-11-01

A field isolate of peste des petits ruminants virus (PPRV) from an outbreak in Tibet, China, was inoculated into goats to investigate the dynamics of virus excretion and antibody production. Further, animals received PPRV vaccine strain Nigeria 75/1. Ocular, nasal and oral samples were tested for the presence of virus antigen by one-step real-time qualitative RT-PCR (qRT-PCR); competitive ELISA (c-ELISA) was used for the measurement of specific antibodies against PPRV. Virus particles could be detected as early as day 3 post-inoculation (pi) and virus excretion lasted for up to day 26 pi. All four goats inoculated with the PPRV field isolate were seropositive as early as day 10 pi. In animals inoculated with the vaccine strain, antibody was detected at day 14 pi, and levels of neutralizing antibodies remained above the protection threshold level (1 : 8) for 8 months. Both virus particles and neutralizing antibodies were detected earlier in goats challenged with the field isolate than in those receiving the vaccine strain. © 2013 Blackwell Verlag GmbH.

Overexpression of ShCYP51B and ShatrD in Sclerotinia homoeocarpa Isolates Exhibiting Practical Field Resistance to a Demethylation Inhibitor Fungicide

PubMed Central

Hulvey, Jon; Popko, James T.; Sang, Hyunkyu; Berg, Andrew

2012-01-01

We investigated genetic factors that govern the reduced propiconazole sensitivity of Sclerotinia homoeocarpa field isolates collected during a 2-year field efficacy study on dollar spot disease of turf in five New England sites. These isolates displayed a >50-fold range of in vitro sensitivity to a sterol demethylation inhibitor (DMI) fungicide, propiconazole, making them ideal for investigations of genetic mechanisms of reduced DMI sensitivity. The CYP51 gene homolog in S. homoeocarpa (ShCYP51B), encoding the enzyme target of DMIs, is likely a minor genetic factor for reduced propiconazole sensitivity, since there were no differences in constitutive relative expression (RE) values and only 2-fold-higher induced RE values for insensitive than for sensitive isolate groups. Next, we mined RNA-Seq transcriptome data for additional genetic factors and found evidence for the overexpression of a homolog of Botrytis cinerea atrD (BcatrD), ShatrD, a known efflux transporter of DMI fungicides. The ShatrD gene showed much higher constitutive and induced RE values for insensitive isolates. Several polymorphisms were found upstream of ShatrD but were not definitively linked to overexpression. The screening of constitutive RE values of ShCYP51B and ShatrD in isolates from two golf courses that exhibited practical field resistance to propiconazole uncovered evidence for significant population-specific overexpression of both genes. However, linear regression demonstrated that the RE of ShatrD displays a more significant relationship with propiconazole sensitivity than that of ShCYP51B. In summary, our results suggest that efflux is a major determinant of the reduced DMI sensitivity of S. homoeocarpa genotypes in New England, which may have implications for the emergence of practical field resistance in this important turfgrass pathogen. PMID:22798361

Aeromonas isolates from human diarrheic stool and groundwater compared by pulsed-field gel electrophoresis.

PubMed

Borchardt, Mark A; Stemper, Mary E; Standridge, Jon H

2003-02-01

Gastrointestinal infections of Aeromonas species are generally considered waterborne; for this reason, Aeromonas hydrophila has been placed on the United States Environmental Protection Agency Contaminant Candidate List of emerging pathogens in drinking water. In this study, we compared pulsed-field gel electrophoresis patterns of Aeromonas isolates from stool specimens of patients with diarrhea with Aeromonas isolates from patients' drinking water. Among 2,565 diarrheic stool specimens submitted to a Wisconsin clinical reference laboratory, 17 (0.66%) tested positive for Aeromonas. Groundwater isolates of Aeromonas were obtained from private wells throughout Wisconsin and the drinking water of Aeromonas-positive patients. The analysis showed that the stool and drinking water isolates were genetically unrelated, suggesting that in this population Aeromonas gastrointestinal infections were not linked with groundwater exposures.

Aeromonas Isolates from Human Diarrheic Stool and Groundwater Compared by Pulsed-Field Gel Electrophoresis

PubMed Central

Stemper, Mary E.; Standridge, Jon H.

2003-01-01

Gastrointestinal infections of Aeromonas species are generally considered waterborne; for this reason, Aeromonas hydrophila has been placed on the United States Environmental Protection Agency Contaminant Candidate List of emerging pathogens in drinking water. In this study, we compared pulsed-field gel electrophoresis patterns of Aeromonas isolates from stool specimens of patients with diarrhea with Aeromonas isolates from patients’ drinking water. Among 2,565 diarrheic stool specimens submitted to a Wisconsin clinical reference laboratory, 17 (0.66%) tested positive for Aeromonas. Groundwater isolates of Aeromonas were obtained from private wells throughout Wisconsin and the drinking water of Aeromonas-positive patients. The analysis showed that the stool and drinking water isolates were genetically unrelated, suggesting that in this population Aeromonas gastrointestinal infections were not linked with groundwater exposures. PMID:12603994

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.

Methylene blue induced morphological deformations in Plasmodium falciparum gametocytes: implications for transmission-blocking.

PubMed

Wadi, Ishan; Pillai, C Radhakrishna; Anvikar, Anupkumar R; Sinha, Abhinav; Nath, Mahendra; Valecha, Neena

2018-01-08

Malaria remains a global health problem despite availability of effective tools. For malaria elimination, drugs targeting sexual stages of Plasmodium falciparum need to be incorporated in treatment regimen along with schizonticidal drugs to interrupt transmission. Primaquine is recommended as a transmission blocking drug for its effect on mature gametocytes but is not extensively utilized because of associated safety concerns among glucose-6-phosphate dehydrogenase (G6PD) deficient patients. In present work, methylene blue, which is proposed as an alternative to primaquine is investigated for its gametocytocidal activity amongst Indian field isolates. An effort has been made to establish Indian field isolates of P. falciparum as in vitro model for gametocytocidal drugs screening. Plasmodium falciparum isolates were adapted to in vitro culture and induced to gametocyte production by hypoxanthine and culture was enriched for gametocyte stages using N-acetyl-glucosamine. Gametocytes were incubated with methylene blue for 48 h and stage specific gametocytocidal activity was evaluated by microscopic examination. Plasmodium falciparum field isolates RKL-9 and JDP-8 were able to reproducibly produce gametocytes in high yield and were used to screen gametocytocidal drugs. Methylene blue was found to target gametocytes in a concentration dependent manner by either completely eliminating gametocytes or rendering them morphologically deformed with mean IC 50 (early stages) as 424.1 nM and mean IC 50 (late stages) as 106.4 nM. These morphologically altered gametocytes appeared highly degenerated having shrinkage, distortions and membrane deformations. Field isolates that produce gametocytes in high yield in vitro can be identified and used to screen gametocytocidal drugs. These isolates should be used for validation of gametocytocidal hits obtained previously by using lab adapted reference strains. Methylene blue was found to target gametocytes produced from Indian field isolates and is proposed to be used as a gametocytocidal adjunct with artemisinin-based combination therapy. Further exploration of methylene blue in clinical studies amongst Indian population, including G6PD deficient patients, is recommended.

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.

Host specificity and ecology of infectious hematopoietic necrosis virus (IHNV) in Pacific salmonids

USGS Publications Warehouse

Kurath, G.; Garver, A.; Purcell, M.K.; Penaranda, Ma.; Rudakova,; Cipriano, R.C.; Bruckner, A.W.; Shchelkunov, I.S.

2011-01-01

Some circumstances IHNV infection can cause acute disease with mortality ranging from 5-90% in host populations. Genetic typing of IHNV field isolates has shown that three major genetic groups of the virus occur in North America. These groups are designated the U, M, and L virus genogroups because they occur in the upper, middle, and lower portions of the geographic range of IHNV in western North America. Among field isolates there is some indication of host specificity: most IHNV isolated from sockeye salmon (Oncorhynchus nerka) is in the U genogroup, and most IHNV isolated from rainbow and steelhead trout (Oncorhynchus mykiss) is in the M genogroup. Experimental challenges confirm that U isolates are highly virulent for sockeye salmon, but not rainbow trout. In contrast, M isolates are virulent in rainbow trout but not in sockeye salmon. Studies comparing U and M virus infections show that virulence is associated with more rapid virus replication in the first few days after infection. In addition, high virulence isolates persist at higher viral loads in the host, while low virulence isolates do not persist. These host-specific aspects of the different IHNV genogroups are important for understanding the ecology of IHNV emergence events in the field. The recent emergence of U IHNV in Russian sockeye salmon of the Kamchatka Peninsula, and the emergence of M IHNV in steelhead trout on the Olympic Peninsula in the U.S.A, serve as examples of the relevance of IHNV host specificity.

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.

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...

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.

Microbial enhanced heavy crude oil recovery through biodegradation using bacterial isolates from an Omani oil field.

PubMed

Al-Sayegh, Abdullah; Al-Wahaibi, Yahya; Al-Bahry, Saif; Elshafie, Abdulkadir; Al-Bemani, Ali; Joshi, Sanket

2015-09-16

Biodegradation is a cheap and environmentally friendly process that could breakdown and utilizes heavy crude oil (HCO) resources. Numerous bacteria are able to grow using hydrocarbons as a carbon source; however, bacteria that are able to grow using HCO hydrocarbons are limited. In this study, HCO degrading bacteria were isolated from an Omani heavy crude oil field. They were then identified and assessed for their biodegradation and biotransformation abilities under aerobic and anaerobic conditions. Bacteria were grown in five different minimum salts media. The isolates were identified by MALDI biotyper and 16S rRNA sequencing. The nucleotide sequences were submitted to GenBank (NCBI) database. The bacteria were identified as Bacillus subtilis and B. licheniformis. To assess microbial growth and biodegradation of HCO by well-assay on agar plates, samples were collected at different intervals. The HCO biodegradation and biotransformation were determined using GC-FID, which showed direct correlation of microbial growth with an increased biotransformation of light hydrocarbons (C12 and C14). Among the isolates, B. licheniformis AS5 was the most efficient isolate in biodegradation and biotransformation of the HCO. Therefore, isolate AS5 was used for heavy crude oil recovery experiments, in core flooding experiments using Berea core plugs, where an additional 16 % of oil initially in place was recovered. This is the first report from Oman for bacteria isolated from an oil field that were able to degrade and transform HCO to lighter components, illustrating the potential use in HCO recovery. The data suggested that biodegradation and biotransformation processes may lead to additional oil recovery from heavy oil fields, if bacteria are grown in suitable medium under optimum growth conditions.

Karyotype analysis of anuran trypanosomes by pulsed-field gradient gel electrophoresis.

PubMed

Lun, Z R; Desser, S S

1995-12-01

The chromosomes of 12 species and isolates of anuran trypanosomes were investigated by pulsed-field gradient gel electrophoresis. Twelve to 16 chromosomes ranging from 0.45 to 2.2 megabase pairs were found in each of these trypanosomes. Minichromosomes were not observed in any of the examined isolates. Results indicate that different species of anuran trypanosomes display distinct karyotype patterns, and that isolates from the same region are similar. Our findings also reveal that most chromosome profiles of these trypanosomes are in accordance with isoenzyme and random amplified polymorphic DNA analysis data.

Molecular characterization of bovine leukemia virus from Moldovan dairy cattle.

PubMed

Pluta, Aneta; Rola-Łuszczak, Marzena; Kubiś, Piotr; Balov, Svetlana; Moskalik, Roman; Choudhury, Bhudipa; Kuźmak, Jacek

2017-06-01

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL), a disease that has worldwide distribution. Whilst it has been eradicated in most of Western Europe and Scandinavia, it remains a problem in other regions, particularly Eastern Europe and South America. For this study, in 2013, 24 cattle from three farms in three regions of Moldova were screened by ELISA and nested PCR. Of these cattle, 14 which were PCR positive, and these were molecularly characterized based on the nucleotide sequence of the env gene and the deduced amino acid sequence of the encoded gp51 protein. Our results demonstrated a low level of genetic variability (0-2.9%) among BLV field strains from Moldova, in contrast to that observed for other retroviruses, including human immunodeficiency virus (HIV) (20-38%) Mason IL (Trudy vologod moloch Inst 146-164, 1970) and equine infectious anemia virus (EIAV) (~40%) Willems L et al (AIDS Res Hum Retroviruses 16(16):1787-1795, 2000), where the envelope gene exhibits high levels of variation Polat M et al (Retrovirology 13(1):4, 2016). Sequence comparisons and phylogenetic analysis revealed that BLV genotype 7 (G7) is predominant in Moldova and that the BLV population in Moldovan cattle is a mixture of at least three new sub-genotypes: G7D, G7E and G4C. Neutrality tests revealed that negative selection was the major force operating upon the 51-kDa BLV envelope surface glycoprotein subunit gp51, although one positively selected site within conformational epitope G was detected in the N-terminal part of gp51. Furthermore, two functional domains, linear epitope B and the zinc-binding domain, were found to have an elevated ratio of nonsynonymous to synonymous codon differences. Together, these data suggest that the evolutionary constraints on epitopes G and B and the zinc-binding domains of gp51 differ from those on the other domains, with a tendency towards formation of homogenous genetic groups, which is a common concept of global BLV diversification during virus transmission that may be associated with genetic drift.

Isolation of azole-resistant Aspergillus fumigatus from the environment in the south-eastern USA.

PubMed

Hurst, Steven F; Berkow, Elizabeth L; Stevenson, Katherine L; Litvintseva, Anastasia P; Lockhart, Shawn R

2017-09-01

Azole resistance in isolates of the fungus Aspergillus fumigatus has been associated with agricultural use of azole fungicides. Environmental isolation of resistant isolates has been reported in Asia, Africa, Europe and South America. To determine whether A. fumigatus isolates containing TR34/L98H or TR46/Y121F/T289A can be found in fields in the USA treated with agricultural azoles. Crop debris was collected and screened for A. fumigatus. All A. fumigatus isolates were screened for azole resistance. The CYP51A gene of azole-resistant isolates was sequenced. The population structure of a subset of isolates was determined using microsatellite typing. This article identifies azole-resistant A. fumigatus isolates containing the TR34/L98H mutation in an experimental peanut field that had been treated with azole fungicides. These findings suggest the development of resistance to azole antifungals in A. fumigatus may be present where agricultural azoles are used in the USA. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy 2017. This work is written by US Government employees and is in the public domain in the US.

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.

High-Isolation Low Cross-Polarization Phased-Array Antenna for MPAR Application

NASA Astrophysics Data System (ADS)

Saeidi-Manesh, Hadi; Karimkashi, Shaya; Zhang, Guifu; Doviak, Richard J.

2017-12-01

The design and analysis of 12 × 12-element planar array of a dual-polarized aperture-coupled microstrip patch antenna operating in the frequency band of 2.7 GHz to 3.0 GHz for multifunction applications are presented. High-isolation between horizontal and vertical polarization ports and low cross-polarization are achieved through an aperture-coupled feed. The reflection coefficient and the isolation of horizontal and vertical ports at different scan angles are examined. The array antenna is fabricated and its radiation patterns are measured in the far-field and near-field chambers. The embedded element pattern of designed element is measured in the near-field chamber and is used for calculating the array scanning radiation pattern.

Characterization of two Austrian porcine reproductive and respiratory syndrome virus (PRRSV) field isolates reveals relationship to East Asian strains.

PubMed

Sinn, Leonie J; Zieglowski, Leonie; Koinig, Hanna; Lamp, Benjamin; Jansko, Bettina; Mößlacher, Georg; Riedel, Christiane; Hennig-Pauka, Isabel; Rümenapf, Till

2016-01-11

Porcine reproductive and respiratory syndrome virus (PRRSV) causes major problems for the swine industry worldwide. Due to Austria's central location in Europe, a large number of animals are transported through the country. However, little is known about current PRRSV strains and epidemiology. We determined full-length genome sequences of two Austrian field isolates (AUT13-883 and AUT14-440) from recent PRRSV outbreaks and of a related German isolate (GER09-613). Phylogenetic analysis revealed that the strains belong to European genotype 1 subtype 1 and form a cluster together with a South Korean strain. Remarkably, AUT14-440 infected the simian cell line MARC-145 without prior adaptation. In addition, this isolate showed exceptional deletions in nonstructural protein 2, in the overlapping region of glycoprotein 3 and 4 and in the 3' untranslated region. Both Austrian isolates caused similar lung lesions but only pigs infected with AUT14-440 developed clear clinical signs of infection. Taken together, the genetic and biological characterization of two novel Austrian PRRSV field isolates revealed similarities to East Asian strains. This stresses the necessity for a more detailed analysis of current PRRSV strains in Europe beyond the determination of short ORF5 and ORF7 sequences.

Study on osmoprotectant rhizobacteria to improve mung bean growth under drought stress

NASA Astrophysics Data System (ADS)

Maryani, Y.; Sudadi; Dewi, W. S.; Yunus, A.

2018-03-01

Climate change leads to irregular rainwater availability for crops and thus enhances drought stress. Furthermore, nowadays we face climate disadvantages such as long dry season, short rainy season and high air temperature caused by climate change. This research aimed at studying the ability of osmoprotectant rhizobacteria isolates to support mung bean growth under drought stress. The rhizobacteria were isolated from mung bean’s rhizosphere. The results showed that isolates of strain Al24-k and Ver5-k produced glycine betaine 9.6306 mg g‑1 cell, 1.7667 x 107 CFU g‑1 soil and 11.4870 mg g”1 cell, 1.9667 x 107 CFU g‑1 soil. The isolated rhizobacteria from mung bean’s rhizosphere under field capacity of soil moisture produced glycine betaine 6.8000 mg g‑1 cell, 1.2556 x 107 CFU g‑1 soil. Under 75% field capacity of soil moisture, isolates produced glycine betaine of 6.4059 mg g‑1 cell, 1.3111 x 107 CFU g‑1 soil, while under 50% from field capacity, the isolates produced glycine betaine of 7.4108 mg g‑1 cell, 1.6667 x 107 CFU g‑1 soil. The osmoprotectant rhizobacteria improved the resilience of mung bean to drought stress.

Increased frequency of self-fertile isolates in Phytophthora infestans may attribute to their higher fitness relative to the A1 isolates

PubMed Central

Zhu, Wen; Shen, Lin-Lin; Fang, Zhi-Guo; Yang, Li-Na; Zhang, Jia-Feng; Sun, Dan-Li; Zhan, Jiasui

2016-01-01

Knowledge of population dynamics of mating types is important for better understanding pathogen’s evolutionary potential and sustainable management of natural and chemical resources such as host resistances and fungicides. In this study, 2250 Phytophthora infestans isolates sampled from 61 fields across China were assayed for spatiotemporal dynamics of mating type frequency. Self-fertile isolates dominated in ~50% of populations and all but one cropping region with an average frequency of 0.64 while no A2 isolates were detected. Analyses of 140 genotypes consisting of 82 self-fertile and 58 A1 isolates indicated that on average self-fertile isolates grew faster, demonstrated higher aggressiveness and were more tolerant to fungicides than A1 isolates; Furthermore, pattern of association between virulence complexity (defined as the number of differential cultivars on which an isolate can induce disease) and frequency was different in the two mating types. In A1 isolates, virulence complexity was negatively correlated (r = −0.515, p = 0.043) with frequency but this correlation was positive (r = 0.532, p = 0.037) in self-fertile isolates. Our results indicate a quick increase of self-fertile isolates possibly attributable to their higher fitness relative to A1 mating type counterpart in the field populations of P. infestans in China. PMID:27384813

Field study on the epidemiology and pathogenicity of different isolates of bovine Ostertagia spp.

PubMed

Al Saqur, I; Armour, J; Bairden, K; Dunn, A M; Jennings, F W; Murray, M

1982-11-01

The epidemiological features of three different isolates of bovine Ostertagia spp under similar initial levels of larval challenge were compared in the field. Two of the isolates, consisting mainly of Ostertagia ostertagi, and a low proportion of Skrjabinagia lyrata conformed in epidemiological behaviour with those investigated by previous workers, though the worm burdens which established did not give rise to the expected clinical signs. The third isolate behaved in a different way, yielding very high faecal egg counts which were followed by high pasture larval counts, heavy worm burdens and severe clinical disease. This isolate, while consisting mainly of O ostertagi and a few S lyrata, also contained a proportion of O leptospicularis, and it is suggested that this species may influence the dynamics of the host-parasite relationship in bovine ostertagiasis.

Measuring the absolute carrier-envelope phase of many-cycle laser fields

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

Tzallas, P.; Skantzakis, E.; Charalambidis, D.

2010-12-15

The carrier-envelope phase (CEP) of high-peak-power, many-cycle laser fields becomes a crucial parameter when such fields are used, in conjunction with polarization gating techniques, in isolated attosecond (asec) pulse generation. However, its measurement has not been achieved so far. We demonstrate a physical process sensitive to the CEP value of such fields and describe a method for its online shot-to-shot monitoring. This work paves the way for the exploitation of energetic isolated asec pulses in studies of nonlinear extreme ultraviolet (XUV) processes and XUV-pump-XUV-probe experiments with asec resolutions.

Whole Genome Shotgun Analysis: the Resolving Power to Distinguish 2009 and 2010 Clinical Isolates of Salmonella Typhimurium Possessing the Same PFGE Type

USDA-ARS?s Scientific Manuscript database

Between 2009 and 2011, Salmonella enterica subsp. enterica serovar Typhimurium with the JPXX01.0014 pulse field gel electrophoresis (PFGE) type was isolated across the United States. The 2009 isolates were associated with an outbreak from an unidentified food source, while later isolates were linked...

DNA fingerprinting of isolates of Streptococcus mutans by pulsed-field gel electrophoresis.

PubMed

Mineyama, R; Yoshino, S; Maeda, N

2007-01-01

Forty isolates and five standard laboratory strains, representing serotypes c, e and f of Streptococcus mutans were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of the genomic DNA with BssH II. The digestion patterns of standard laboratory strains were characteristic of serotypes c, e and f. Serotypes c and f generated diagnostic DNA fragments of approximately 145 kbp and of approximately 130-175 kbp in length, respectively. Serotype e generated a ladder of at least 14 fragments of 15-155 kbp in length. The digestion patterns of isolates were essentially similar to those of the standard laboratory strains. The patterns of almost all isolates obtained from a single individual were identical, but patterns of a few different types were also observed among isolates obtained from two individuals. Digestion with BssH II revealed differences among isolates obtained from different individuals. We used differences in banding patterns among isolates to construct a dendrogram. The dendrogram included two major clusters, one that consisted of isolates of serotypes c and f, and an other that consisted of isolates of serotype e. Our results indicate that BssH II is a useful enzyme for distinguishing among isolates of S. mutans and that digestion patterns obtained by PFGE can be used for chromosomal DNA fingerprinting.

Phylogenetic analysis of Hungarian goose parvovirus isolates and vaccine strains.

PubMed

Tatár-Kis, Tímea; Mató, Tamás; Markos, Béla; Palya, Vilmos

2004-08-01

Polymerase chain reaction and sequencing were used to analyse goose parvovirus field isolates and vaccine strains. Two fragments of the genome were amplified. Fragment "A" represents a region of VP3 gene, while fragment "B" represents a region upstream of the VP3 gene, encompassing part of the VP1 gene. In the region of fragment "A" the deduced amino acid sequence of the strains was identical, therefore differentiation among strains could be done only at the nucleotide level, which resulted in the formation of three groups: Hungarian, West-European and Asian strains. In the region of fragment "B", separation of groups could be done by both nucleotide and deduced amino acid sequence level. The nucleotide sequences resulted in the same groups as for fragment "A" but with a different clustering pattern among the Hungarian strains. Within the "Hungarian" group most of the recent field isolates fell into one cluster, very closely related or identical to each other, indicating a very slow evolutionary change. The attenuated strains and field isolates from 1979/80 formed a separate cluster. When vaccine strains and field isolates were compared, two specific amino acid differences were found that can be considered as possible markers for vaccinal strains. Sequence analysis of fragment "B" seems to be a suitable method for differentiation of attenuated vaccine strains from virulent strains. Copyright 2004 Houghton Trust Ltd

Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

PubMed

Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

2010-06-01

Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

A Field Experiment to Assess the Rate of Infestation in Honey Bee Populations of Two Metarhizium anisopliae Isolates on Varroa destructor (Acari: Mesostigmata).

PubMed

Pirali-Kheirabadi, Khodadad; Teixeira-da-Silva, Jaime A; Razzaghi-Abyaneh, Mehdi; Nazemnia, Mehdi

2013-01-01

The protective effect of two isolates of an entomopathogenic fungus, Metarhizium anisopliae (DEMI 002 and Iran 437C) on the adult stage of Varroa destructor was evaluated in comparison with fluvalinate strips in the field. A total of 12 honey bee colonies were provided from an apiculture farm. The selected hives were divided into 4 groups (3 hives per group). The first group was the control, treated with distilled water. The other two groups were exposed to different fungi (M. anisopliae isolates DEMI 002 and Iran 437C) and the last group was treated with one strip of fluvalinate per colony. The number of fallen mites was counted using sticky traps during a 6-day period, six days before and after treatments. A fungal suspension at a concentration of 5× 10(6) conidia/mL was sprayed onto the frames and the number of fallen mites was counted. Metarhizium anisopliae DEMI 002 and Iran 437C isolates were as effective (i.e., caused as much mite fall) as the fluvalinate strip in controlling bee colonies than no treatment. Both M. anisopliae isolates are promising candidates as agents in the control of Varroa mites under field conditions. Isolate DEMI 002 can be considered as a possible non-chemical biocontrol agent for controlling bee infestation with V. destructor in the field. In order to substantiate this hypothesis, tests are currently being performed using larger colonies and larger doses than tested in the present study in our beekeeping.

A Field Experiment to Assess the Rate of Infestation in Honey Bee Populations of Two Metarhizium anisopliae Isolates on Varroa destructor (Acari: Mesostigmata)

PubMed Central

Pirali-kheirabadi, Khodadad; Teixeira-da-Silva, Jaime A; Razzaghi-Abyaneh, Mehdi; Nazemnia, Mehdi

2013-01-01

Background: The protective effect of two isolates of an entomopathogenic fungus, Metarhizium anisopliae (DEMI 002 and Iran 437C) on the adult stage of Varroa destructor was evaluated in comparison with fluvalinate strips in the field. Methods: A total of 12 honey bee colonies were provided from an apiculture farm. The selected hives were divided into 4 groups (3 hives per group). The first group was the control, treated with distilled water. The other two groups were exposed to different fungi (M. anisopliae isolates DEMI 002 and Iran 437C) and the last group was treated with one strip of fluvalinate per colony. The number of fallen mites was counted using sticky traps during a 6-day period, six days before and after treatments. A fungal suspension at a concentration of 5× 106 conidia/mL was sprayed onto the frames and the number of fallen mites was counted. Results: Metarhizium anisopliae DEMI 002 and Iran 437C isolates were as effective (i.e., caused as much mite fall) as the fluvalinate strip in controlling bee colonies than no treatment. Conclusion: Both M. anisopliae isolates are promising candidates as agents in the control of Varroa mites under field conditions. Isolate DEMI 002 can be considered as a possible non-chemical biocontrol agent for controlling bee infestation with V. destructor in the field. In order to substantiate this hypothesis, tests are currently being performed using larger colonies and larger doses than tested in the present study in our beekeeping. PMID:23785691

Spatial and Temporal Factors Associated with an Increased Prevalence of Listeria monocytogenes in Spinach Fields in New York State

PubMed Central

Weller, Daniel; Wiedmann, Martin

2015-01-01

While rain and irrigation events have been associated with an increased prevalence of foodborne pathogens in produce production environments, quantitative data are needed to determine the effects of various spatial and temporal factors on the risk of produce contamination following these events. This study was performed to quantify these effects and to determine the impact of rain and irrigation events on the detection frequency and diversity of Listeria species (including L. monocytogenes) and L. monocytogenes in produce fields. Two spinach fields, with high and low predicted risks of L. monocytogenes isolation, were sampled 24, 48, 72, and 144 to 192 h following irrigation and rain events. Predicted risk was a function of the field's proximity to water and roads. Factors were evaluated for their association with Listeria species and L. monocytogenes isolation by using generalized linear mixed models (GLMMs). In total, 1,492 (1,092 soil, 334 leaf, 14 fecal, and 52 water) samples were collected. According to the GLMM, the likelihood of Listeria species and L. monocytogenes isolation from soil samples was highest during the 24 h immediately following an event (odds ratios [ORs] of 7.7 and 25, respectively). Additionally, Listeria species and L. monocytogenes isolates associated with irrigation events showed significantly lower sigB allele type diversity than did isolates associated with precipitation events (P = <0.001), suggesting that irrigation water may be a point source of L. monocytogenes contamination. Small changes in management practices (e.g., not irrigating fields before harvest) may therefore reduce the risk of L. monocytogenes contamination of fresh produce. PMID:26116668

The effects of two Ureaplasma diversum strains on early pregnancy in heifers.

PubMed Central

Gale, S P

1987-01-01

Two field isolates of Ureaplasma diversum spp. were used to infect heifers at the time of insemination in a preliminary study to observe the effect of infection on early pregnancy. M84-14c-1 was a field isolate from a bull's prepuce typed by immunofluorescence to be similar to U. diversum strain T-44 (Group C). M84-477c-4 was a field isolate from bovine semen typed by immunofluorescence to be similar to U. diversum strain T-288 (Group A). All three heifers infected with M84-477c-4 had a mild granular vulvitis at some time during the trial. None was pregnant when slaughtered 27 days after infection. The result of infection with M84-14c-1, a preputial isolate, was not consistent. One heifer had no infection and a normal pregnancy, one heifer was infected with an abnormal pregnancy, and one heifer was open but ureaplasmas were not detected until day 17 of the trial. PMID:3453276

Distribution and identification of proteolytic Bacillus spp. in paddy field soil under rice cultivation.

PubMed

Watanabe, K; Hayano, K

1993-07-01

Proteolytic bacteria in paddy field soils under rice cultivation were characterized and enumerated using azocoll agar plates. Bacillus spp. were the proteolytic bacteria that were most frequently present, comprising 59% of the isolates. They were always the numerically dominant proteolytic bacteria isolated from three kinds of fertilizer treatments (yearly application of rice-straw compost and chemical fertilizer, yearly application of chemical fertilizer, and no fertilizer application) and at three different stages of rice development (vegetative growth stage, maximal tillering stage, and harvest stage). Of the 411 proteolytic bacteria isolated, 124 isolates had stronger proteolytic activity than others on the basis of gelatin liquefaction tests and most of them were Bacillus spp. (100% in 1989 and 92.4% in 1991). Bacillus subtilis and Bacillus cereus were the main bacteria of this group and Bacillus mycoides, Bacillus licheniformis, and Bacillus megaterium were also present. We conclude that these Bacillus spp. are the primary source of soil protease in these paddy fields.

Terahertz isolator based on nonreciprocal magneto-metasurface.

PubMed

Chen, Sai; Fan, Fei; Wang, Xianghui; Wu, Pengfei; Zhang, Hui; Chang, Shengjiang

2015-01-26

A magneto-metasurface with nonreciprocal terahertz (THz) transmission has been proposed to form a THz isolator. Importantly, we have discussed the two necessary conditions for THz nonreciprocal transmission in the metasurface: (1) There should be magneto-optical responses for THz waves in the metasurface; (2) The transmission system of the metasurface needs to be asymmetric for forward and backward waves. These two conditions lead to the time reversal symmetry breaking of system, and the magnetoplasmon mode splitting and nonreciprocal resonance enhancement can be observed in the asymmetry magneto-metasurface. Moreover, the isolation dependences and tunability on the external magnetic field and temperature have also been investigated, which shows that the best operating state with a high isolation can be designed. The numerical simulations show a maximum isolation of 43 dB and a 10 dB operating bandwidth of 20 GHz under an external magnetic field of 0.3 T, and the insertion loss is smaller than 1.79 dB. This low-loss, high isolation, easy coupling THz isolator has broadly potentials for THz application systems.

Higher isolation of NDM-1 producing Acinetobacter baumannii from the sewage of the hospitals in Beijing.

PubMed

Zhang, Chuanfu; Qiu, Shaofu; Wang, Yong; Qi, Lihua; Hao, Rongzhang; Liu, Xuelin; Shi, Yun; Hu, Xiaofeng; An, Daizhi; Li, Zhenjun; Li, Peng; Wang, Ligui; Cui, Jiajun; Wang, Pan; Huang, Liuyu; Klena, John D; Song, Hongbin

2014-01-01

Multidrug resistant microbes present in the environment are a potential public health risk. In this study, we investigate the presence of New Delhi metallo-β-lactamase 1 (NDM-1) producing bacteria in the 99 water samples in Beijing City, including river water, treated drinking water, raw water samples from the pools and sewage from 4 comprehensive hospitals. For the bla NDM-1 positive isolate, antimicrobial susceptibility testing was further analyzed, and Pulsed Field Gel Electrophoresis (PFGE) was performed to determine the genetic relationship among the NDM-1 producing isolates from sewage and human, as well as the clinical strains without NDM-1. The results indicate that there was a higher isolation of NDM-1 producing Acinetobacter baumannii from the sewage of the hospitals, while no NDM-1 producing isolates were recovered from samples obtained from the river, drinking, or fishpond water. Surprisingly, these isolates were markedly different from the clinical isolates in drug resistance and pulsed field gel electrophoresis profiles, suggesting different evolutionary relationships. Our results showed that the hospital sewage may be one of the diffusion reservoirs of NDM-1 producing bacteria.

Interactive Effects of Large- and Small-Scale Sources of Feral Honey-Bees for Sunflower in the Argentine Pampas

PubMed Central

Sáez, Agustín; Sabatino, Malena; Aizen, Marcelo A.

2012-01-01

Pollinators for animal pollinated crops can be provided by natural and semi-natural habitats, ranging from large vegetation remnants to small areas of non-crop land in an otherwise highly modified landscape. It is unknown, however, how different small- and large-scale habitat patches interact as pollinator sources. In the intensively managed Argentine Pampas, we studied the additive and interactive effects of large expanses (up to 2200 ha) of natural habitat, represented by untilled isolated “sierras”, and narrow (3–7 m wide) strips of semi-natural habitat, represented by field margins, as pollinator sources for sunflower (Helianthus annus). We estimated visitation rates by feral honey-bees, Apis mellifera, and native flower visitors (as a group) at 1, 5, 25, 50 and 100 m from a field margin in 17 sunflower fields 0–10 km distant from the nearest sierra. Honey-bees dominated the pollinator assemblage accounting for >90% of all visits to sunflower inflorescences. Honey-bee visitation was strongly affected by proximity to the sierras decreasing by about 70% in the most isolated fields. There was also a decline in honey-bee visitation with distance from the field margin, which was apparent with increasing field isolation, but undetected in fields nearby large expanses of natural habitat. The probability of observing a native visitor decreased with isolation from the sierras, but in other respects visitation by flower visitors other than honey-bees was mostly unaffected by the habitat factors assessed in this study. Overall, we found strong hierarchical and interactive effects between the study large and small-scale pollinator sources. These results emphasize the importance of preserving natural habitats and managing actively field verges in the absence of large remnants of natural habitat for improving pollinator services. PMID:22303477

Interactive effects of large- and small-scale sources of feral honey-bees for sunflower in the Argentine Pampas.

PubMed

Sáez, Agustín; Sabatino, Malena; Aizen, Marcelo A

2012-01-01

Pollinators for animal pollinated crops can be provided by natural and semi-natural habitats, ranging from large vegetation remnants to small areas of non-crop land in an otherwise highly modified landscape. It is unknown, however, how different small- and large-scale habitat patches interact as pollinator sources. In the intensively managed Argentine Pampas, we studied the additive and interactive effects of large expanses (up to 2200 ha) of natural habitat, represented by untilled isolated "sierras", and narrow (3-7 m wide) strips of semi-natural habitat, represented by field margins, as pollinator sources for sunflower (Helianthus annus). We estimated visitation rates by feral honey-bees, Apis mellifera, and native flower visitors (as a group) at 1, 5, 25, 50 and 100 m from a field margin in 17 sunflower fields 0-10 km distant from the nearest sierra. Honey-bees dominated the pollinator assemblage accounting for >90% of all visits to sunflower inflorescences. Honey-bee visitation was strongly affected by proximity to the sierras decreasing by about 70% in the most isolated fields. There was also a decline in honey-bee visitation with distance from the field margin, which was apparent with increasing field isolation, but undetected in fields nearby large expanses of natural habitat. The probability of observing a native visitor decreased with isolation from the sierras, but in other respects visitation by flower visitors other than honey-bees was mostly unaffected by the habitat factors assessed in this study. Overall, we found strong hierarchical and interactive effects between the study large and small-scale pollinator sources. These results emphasize the importance of preserving natural habitats and managing actively field verges in the absence of large remnants of natural habitat for improving pollinator services.

From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

NASA Technical Reports Server (NTRS)

Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

Visible optical isolator using ZnSe

NASA Technical Reports Server (NTRS)

Wunderlich, J. A.; Deshazer, L. G.

1977-01-01

A compact Faraday effect optical isolator was constructed for visible wavelengths and tested at 5145 A. The nonreciprocal element of the isolator was polycrystalline zinc selenide placed in the magnetic field of a permanent magnet. For 5145 A the isolator had a 2.06-dB insertion loss and a 25.5-dB isolation. Indices of refraction and Verdet constants were measured for zinc selenide in the wavelength region from 4700 to 6300 A.

Laser-Induced Thermal Acoustic Measurements in a Highly Back-Pressured Scramjet Isolator Model: A Research Plan

NASA Technical Reports Server (NTRS)

Middleton, Troy F.; Balla, Robert J.; Baurle, Robert A.; Wilson, Lloyd G.

2008-01-01

Under the Propulsion Discipline of NASA s Fundamental Aeronautics Program s Hypersonics Project, a test apparatus, for testing a scramjet isolator model, is being constructed at NASA's Langley Research Center. The test apparatus will incorporate a 1-inch by 2-inch by 15-inch-long scramjet isolator model supplied with 2.1 lbm/sec of unheated dry air through a Mach 2.5 converging-diverging nozzle. The planned research will incorporate progressively more challenging measurement techniques to characterize the flow field within the isolator, concluding with the application of the Laser-Induced Thermal Acoustic (LITA) measurement technique. The primary goal of this research is to use the data acquired to validate Computational Fluid Dynamics (CFD) models employed to characterize the complex flow field of a scramjet isolator. This paper describes the test apparatus being constructed, pre-test CFD simulations, and the LITA measurement technique.

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.

Optical Isolators With Transverse Magnets

NASA Technical Reports Server (NTRS)

Fan, Yuan X.; Byer, Robert L.

1991-01-01

New design for isolator includes zigzag, forward-and-backward-pass beam path and use of transverse rather than longitudinal magnetic field. Design choices produce isolator with as large an aperture as desired using low-Verdet-constant glass rather than more expensive crystals. Uses commercially available permanent magnets in Faraday rotator. More compact and less expensive. Designed to transmit rectangular beam. Square cross section of beam extended to rectangular shape by increasing one dimension of glass without having to increase magnetic field. Potentially useful in laser systems involving slab lasers and amplifiers. Has applications to study of very-high-power lasers for fusion research.

Field emission from isolated individual vertically aligned carbon nanocones

NASA Astrophysics Data System (ADS)

Baylor, L. R.; Merkulov, V. I.; Ellis, E. D.; Guillorn, M. A.; Lowndes, D. H.; Melechko, A. V.; Simpson, M. L.; Whealton, J. H.

2002-04-01

Field emission from isolated individual vertically aligned carbon nanocones (VACNCs) has been measured using a small-diameter moveable probe. The probe was scanned parallel to the sample plane to locate the VACNCs, and perpendicular to the sample plane to measure the emission turn-on electric field of each VACNC. Individual VACNCs can be good field emitters. The emission threshold field depends on the geometric aspect ratio (height/tip radius) of the VACNC and is lowest when a sharp tip is present. VACNCs exposed to a reactive ion etch process demonstrate a lowered emission threshold field while maintaining a similar aspect ratio. Individual VACNCs can have low emission thresholds, carry high current densities, and have long emission lifetime. This makes them very promising for various field emission applications for which deterministic placement of the emitter with submicron accuracy is needed.

Detection of a Bacteriophage Gene Encoding a Mu-like Portal Protein in Haemophilus parasuis Reference Strains and Field Isolates by Nested Polymerase Chain Reaction

USDA-ARS?s Scientific Manuscript database

A nested PCR assay was developed to determine the presence of a gene encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field isolates of Haemophilus parasuis. Specific primers, based on the gene’s sequence, were utilized. A majority of the virulent reference strai...

Confirming and identifying new loci for rice blast disease resistance using magnaporthe oryzae field isolates in the US

USDA-ARS?s Scientific Manuscript database

Quantitative trait loci (QTL) in rice play important roles in controlling rice blast disease. In the present study, 10 field isolates of the races IA1, IB1, IB17, and IC1 of U.S. rice blast fungus Magnaporthe oryzae collected in 1996 and 2009 were used to identify blast resistance QTL with a recombi...

Complete genome sequence of Cupriavidus basilensis 4G11, isolated from the Oak Ridge Field Research Center site

DOE PAGES

Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; ...

2015-05-14

Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%.

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.

Molecular Epidemiology of Brucella abortus Isolates from Cattle, Elk, and Bison in the United States, 1998 to 2011

PubMed Central

Stuber, Tod; Quance, Christine; Edwards, William H.; Tiller, Rebekah V.; Linfield, Tom; Rhyan, Jack; Berte, Angela; Harris, Beth

2012-01-01

A variable-number tandem repeat (VNTR) protocol targeting 10 loci in the Brucella abortus genome was used to assess genetic diversity among 366 field isolates recovered from cattle, bison, and elk in the Greater Yellowstone Area (GYA) and Texas during 1998 to 2011. Minimum spanning tree (MST) and unweighted-pair group method with arithmetic mean (UPGMA) analyses of VNTR data identified 237 different VNTR types, among which 14 prominent clusters of isolates could be identified. Cattle isolates from Texas segregated into three clusters: one comprised of field isolates from 1998 to 2005, one comprised of vaccination-associated infections, and one associated with an outbreak in Starr County in January 2011. An isolate obtained from a feral sow trapped on property adjacent to the Starr County herd in May 2011 clustered with the cattle isolates, suggesting a role for feral swine as B. abortus reservoirs in Starr County. Isolates from a 2005 cattle outbreak in Wyoming displayed VNTR-10 profiles matching those of strains recovered from Wyoming and Idaho elk. Additionally, isolates associated with cattle outbreaks in Idaho in 2002, Montana in 2008 and 2011, and Wyoming in 2010 primarily clustered with isolates recovered from GYA elk. This study indicates that elk play a predominant role in the transmission of B. abortus to cattle located in the GYA. PMID:22427502

Sensitivity to azoxystrobin in Didymella bryoniae isolates collected before and after field use of strobilurin fungicides.

PubMed

Keinath, Anthony P

2009-10-01

Isolates of Didymella bryoniae (Auersw.) Rehm, causal agent of gummy stem blight on cucurbits, developed insensitivity to azoxystrobin in the eastern United States 2 years after first commercial use in 1998. Baseline sensitivity of this fungus to azoxystrobin has never been reported. The objectives were to compare baseline sensitivities of D. bryoniae from South Carolina and other locations to sensitivities of isolates exposed to azoxystrobin for one or more seasons, and to compare sensitivity in vitro and in vivo. Sixty-one isolates of D. bryoniae collected before 1998 were sensitive. Median EC50 was 0.055 mg L(-1) azoxystrobin (range 0.005 to 0.81). Forty isolates collected after exposure during 1998 also were sensitive. Fifty-three of 64 isolates collected in South and North Carolina between 2000 and 2006 were insensitive to 10 mg L(-1) azoxystrobin. Sensitive and insensitive isolates were distinguished by disease severity on Cucumis melo L. seedlings treated with azoxystrobin (20 or 200 mg L(-1)). An azoxystrobin baseline sensitivity distribution was established in vitro for isolates of D. bryoniae never exposed to strobilurins. Baseline values were comparable with those of other ascomycetes. Insensitive isolates were found in fields with a history of strobilurin applications. An in vivo method distinguished sensitive and insensitive isolates. Copyright 2009 Society of Chemical Industry.

Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors

PubMed Central

2013-01-01

Background Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations. Results To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70–15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization. Conclusions We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization. PMID:24341723

Ab Initio Simulations of a Supernova-driven Galactic Dynamo in an Isolated Disk Galaxy

DOE PAGES

Butsky, Iryna; Zrake, Jonathan; Kim, Ji-hoon; ...

2017-07-10

Here, we study the magnetic field evolution of an isolated spiral galaxy, using isolated Milky Way–mass galaxy formation simulations and a novel prescription for magnetohydrodynamic (MHD) supernova feedback. Our main result is that a galactic dynamo can be seeded and driven by supernova explosions, resulting in magnetic fields whose strength and morphology are consistent with observations. In our model, supernovae supply thermal energy and a low-level magnetic field along with their ejecta. The thermal expansion drives turbulence, which serves a dual role by efficiently mixing the magnetic field into the interstellar medium and amplifying it by means of a turbulentmore » dynamo. The computational prescription for MHD supernova feedback has been implemented within the publicly available ENZO code and is fully described in this paper. This improves upon ENZO's existing modules for hydrodynamic feedback from stars and active galaxies. We find that the field attains microgauss levels over gigayear timescales throughout the disk. The field also develops a large-scale structure, which appears to be correlated with the disk's spiral arm density structure. We find that seeding of the galactic dynamo by supernova ejecta predicts a persistent correlation between gas metallicity and magnetic field strength. We also generate all-sky maps of the Faraday rotation measure from the simulation-predicted magnetic field, and we present a direct comparison with observations.« less

Ab Initio Simulations of a Supernova-driven Galactic Dynamo in an Isolated Disk Galaxy

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

Butsky, Iryna; Zrake, Jonathan; Kim, Ji-hoon

We study the magnetic field evolution of an isolated spiral galaxy, using isolated Milky Way–mass galaxy formation simulations and a novel prescription for magnetohydrodynamic (MHD) supernova feedback. Our main result is that a galactic dynamo can be seeded and driven by supernova explosions, resulting in magnetic fields whose strength and morphology are consistent with observations. In our model, supernovae supply thermal energy and a low-level magnetic field along with their ejecta. The thermal expansion drives turbulence, which serves a dual role by efficiently mixing the magnetic field into the interstellar medium and amplifying it by means of a turbulent dynamo.more » The computational prescription for MHD supernova feedback has been implemented within the publicly available ENZO code and is fully described in this paper. This improves upon ENZO 's existing modules for hydrodynamic feedback from stars and active galaxies. We find that the field attains microgauss levels over gigayear timescales throughout the disk. The field also develops a large-scale structure, which appears to be correlated with the disk’s spiral arm density structure. We find that seeding of the galactic dynamo by supernova ejecta predicts a persistent correlation between gas metallicity and magnetic field strength. We also generate all-sky maps of the Faraday rotation measure from the simulation-predicted magnetic field, and we present a direct comparison with observations.« less

Ab Initio Simulations of a Supernova-driven Galactic Dynamo in an Isolated Disk Galaxy

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

Butsky, Iryna; Zrake, Jonathan; Kim, Ji-hoon

Here, we study the magnetic field evolution of an isolated spiral galaxy, using isolated Milky Way–mass galaxy formation simulations and a novel prescription for magnetohydrodynamic (MHD) supernova feedback. Our main result is that a galactic dynamo can be seeded and driven by supernova explosions, resulting in magnetic fields whose strength and morphology are consistent with observations. In our model, supernovae supply thermal energy and a low-level magnetic field along with their ejecta. The thermal expansion drives turbulence, which serves a dual role by efficiently mixing the magnetic field into the interstellar medium and amplifying it by means of a turbulentmore » dynamo. The computational prescription for MHD supernova feedback has been implemented within the publicly available ENZO code and is fully described in this paper. This improves upon ENZO's existing modules for hydrodynamic feedback from stars and active galaxies. We find that the field attains microgauss levels over gigayear timescales throughout the disk. The field also develops a large-scale structure, which appears to be correlated with the disk's spiral arm density structure. We find that seeding of the galactic dynamo by supernova ejecta predicts a persistent correlation between gas metallicity and magnetic field strength. We also generate all-sky maps of the Faraday rotation measure from the simulation-predicted magnetic field, and we present a direct comparison with observations.« less

Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Isolates Determined by Pulsed-Field Gel Electrophoresis: Comparison of Isolates from Avian Wildlife, Domestic Animals, and the Environment in Norway

PubMed Central

Refsum, Thorbjørn; Heir, Even; Kapperud, Georg; Vardund, Traute; Holstad, Gudmund

2002-01-01

The molecular epidemiology of 142 isolates of Salmonella enterica serovar Typhimurium from avian wildlife, domestic animals, and the environment in Norway was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis of the data. The bacterial isolates comprised 79 isolates from wild-living birds, including 46 small passerines and 26 gulls, and 63 isolates of nonavian origin, including 50 domestic animals and 13 environmental samples. Thirteen main clusters were discernible at the 90% similarity level. Most of the isolates (83%) were grouped into three main clusters. These were further divided into 20 subclusters at the 95% similarity level. Isolates from passerines, gulls, and pigeons dominated within five subclusters, whereas isolates from domestic animals and the environment belonged to many different subclusters with no predominance. The results support earlier results that passerines constitute an important source of infection to humans in Norway, whereas it is suggested that gulls and pigeons, based on PFGE analysis, represent only a minor source of human serovar Typhimurium infections. Passerines, gulls, and pigeons may also constitute a source of infection of domestic animals and feed plants or vice versa. Three isolates from cattle and a grain source, of which two were multiresistant, were confirmed as serovar Typhimurium phage type DT 104. These represent the first reported phage type DT 104 isolates from other sources than humans in Norway. PMID:12406755

Is the Fungus Magnaporthe Losing DNA Methylation?

PubMed Central

Ikeda, Ken-ichi; Van Vu, Ba; Kadotani, Naoki; Tanaka, Masaki; Murata, Toshiki; Shiina, Kohta; Chuma, Izumi; Tosa, Yukio; Nakayashiki, Hitoshi

2013-01-01

The long terminal repeat retrotransposon, Magnaporthe gypsy-like element (MAGGY), has been shown to be targeted for cytosine methylation in a subset of Magnaporthe oryzae field isolates. Analysis of the F1 progeny from a genetic cross between methylation-proficient (Br48) and methylation-deficient (GFSI1-7-2) isolates revealed that methylation of the MAGGY element was governed by a single dominant gene. Positional cloning followed by gene disruption and complementation experiments revealed that the responsible gene was the DNA methyltransferase, MoDMT1, an ortholog of Neurospora crassa Dim-2. A survey of MAGGY methylation in 60 Magnaporthe field isolates revealed that 42 isolates from rice, common millet, wheat, finger millet, and buffelgrass were methylation proficient while 18 isolates from foxtail millet, green bristlegrass, Japanese panicgrass, torpedo grass, Guinea grass, and crabgrass were methylation deficient. Phenotypic analyses showed that MoDMT1 plays no major role in development and pathogenicity of the fungus. Quantitative polymerase chain reaction analysis showed that the average copy number of genomic MAGGY elements was not significantly different between methylation-deficient and -proficient field isolates even though the levels of MAGGY transcript were generally higher in the former group. MoDMT1 gene sequences in the methylation-deficient isolates suggested that at least three independent mutations were responsible for the loss of MoDMT1 function. Overall, our data suggest that MoDMT1 is not essential for the natural life cycle of the fungus and raise the possibility that the genus Magnaporthe may be losing the mechanism of DNA methylation on the evolutionary time scale. PMID:23979580

Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center

PubMed Central

Wu, Xiaoqin; Deutschbauer, Adam M.; Kazakov, Alexey E.; Wetmore, Kelly M.; Cwick, Bryson A.; Walker, Robert M.; Novichkov, Pavel S.; Arkin, Adam P.

2017-01-01

ABSTRACT We present here the draft genome sequences of two Janthinobacterium lividum strains, GW456P and GW458P, isolated from groundwater samples collected from a background site at the Oak Ridge Field Research Center. Production of a purple pigment by these two strains was observed when grown on diluted (1/10) LB agar plates. PMID:28663297

Complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from lettuce (Lactuca sativa) originating from a conventional field in Norway.

PubMed

Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

2016-12-01

Here, we present the 3,795,952 bp complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from conventionally grown lettuce ( Lactuca sativa ) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017580.

Distinct Transcriptional Profiles and Phenotypes Exhibited by Escherichia coli O157:H7 Isolates Related to the 2006 Spinach-Associated Outbreak

PubMed Central

Kyle, Jennifer L.; Huynh, Steven; Carter, Michelle Q.; Brandl, Maria T.; Mandrell, Robert E.

2012-01-01

In 2006, a large outbreak of Escherichia coli O157:H7 was linked to the consumption of ready-to-eat bagged baby spinach in the United States. The likely sources of preharvest spinach contamination were soil and water that became contaminated via cattle or feral pigs in the proximity of the spinach fields. In this study, we compared the transcriptional profiles of 12 E. coli O157:H7 isolates that possess the same two-enzyme pulsed-field gel electrophoresis (PFGE) profile and are related temporally or geographically to the above outbreak. These E. coli O157:H7 isolates included three clinical isolates, five isolates from separate bags of spinach, and single isolates from pasture soil, river water, cow feces, and a feral pig. The three clinical isolates and two spinach bag isolates grown in cultures to stationary phase showed decreased expression of many σS-regulated genes, including gadA, osmE, osmY, and katE, compared with the soil, water, cow, feral pig, and the other three spinach bag isolates. The decreased expression of these σS-regulated genes was correlated with the decreased resistance of the isolates to acid stress, osmotic stress, and oxidative stress but increases in scavenging ability. We also observed that intraisolate variability was much more pronounced among the clinical and spinach isolates than among the environmental isolates. Together, the transcriptional and phenotypic differences of the spinach outbreak isolates of E. coli O157:H7 support the hypothesis that some variants within the spinach bag retained characteristics of the preharvest isolates, whereas other variants with altered gene expression and phenotypes infected the human host. PMID:22081562

Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

PubMed Central

Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

1999-01-01

Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships. PMID:10405383

In Vitro Morphological Characteristics of Pyrenophora tritici-repentis Isolates from Several Algerian Agro-Ecological Zones

PubMed Central

Benslimane, Hamida; Aouali, Souhila; Khalfi, Assia; Ali, Shaukat; Bouznad, Zouaoui

2017-01-01

Tan spot caused by the fungus Pyrenophora triticirepentis is a serious disease of wheat, which is on increase in recent years in Mediterranean region. In the field this fungus produces a diamond-shaped necrotic lesions with a yellow halo on wheat foliage. The objective of this study was to characterize and compare several monospore isolates of P. tritici-repentis collected from different infected wheat fields in various locations of Algeria, and find the morphological differences between them, if any. The results revealed wide morphologically variation among the isolates based on colony colors and texture, mycelial radial growth and conidial size. PMID:28381957

Improved determination of vector lithospheric magnetic anomalies from MAGSAT data

NASA Technical Reports Server (NTRS)

Ravat, Dhananjay

1993-01-01

Scientific contributions made in developing new methods to isolate and map vector magnetic anomalies from measurements made by Magsat are described. In addition to the objective of the proposal, the isolation and mapping of equatorial vector lithospheric Magsat anomalies, isolation of polar ionospheric fields during the period were also studied. Significant progress was also made in isolation of polar delta(Z) component and scalar anomalies as well as integration and synthesis of various techniques of removing equatorial and polar ionospheric effects. The significant contributions of this research are: (1) development of empirical/analytical techniques in modeling ionospheric fields in Magsat data and their removal from uncorrected anomalies to obtain better estimates of lithospheric anomalies (this task was accomplished for equatorial delta(X), delta(Z), and delta(B) component and polar delta(Z) and delta(B) component measurements; (2) integration of important processing techniques developed during the last decade with the newly developed technologies of ionospheric field modeling into an optimum processing scheme; and (3) implementation of the above processing scheme to map the most robust magnetic anomalies of the lithosphere (components as well as scalar).

Designing Security-Hardened Microkernels For Field Devices

NASA Astrophysics Data System (ADS)

Hieb, Jeffrey; Graham, James

Distributed control systems (DCSs) play an essential role in the operation of critical infrastructures. Perimeter field devices are important DCS components that measure physical process parameters and perform control actions. Modern field devices are vulnerable to cyber attacks due to their increased adoption of commodity technologies and that fact that control networks are no longer isolated. This paper describes an approach for creating security-hardened field devices using operating system microkernels that isolate vital field device operations from untrusted network-accessible applications. The approach, which is influenced by the MILS and Nizza architectures, is implemented in a prototype field device. Whereas, previous microkernel-based implementations have been plagued by poor inter-process communication (IPC) performance, the prototype exhibits an average IPC overhead for protected device calls of 64.59 μs. The overall performance of field devices is influenced by several factors; nevertheless, the observed IPC overhead is low enough to encourage the continued development of the prototype.

Streptococcus pneumoniae Isolates with Reduced Susceptibility to Ciprofloxacin in Spain: Clonal Diversity and Appearance of Ciprofloxacin-Resistant Epidemic Clones

PubMed Central

Alou, Luis; Ramirez, Mario; García-Rey, César; Prieto, José; de Lencastre, Hermínia

2001-01-01

Analysis of the pulsed-field gel electrophoretic profiles of 82 pneumococcal isolates with reduced susceptibility to ciprofloxacin (RSC) and of 90 co-occurring susceptible isolates indicates a considerable genetic diversity among isolates with RCS and points to a close relation between the two groups. This finding suggests that pneumococci with RCS emerge through independent mutational events. PMID:11557501

In vivo conformation of mitochondrial DNA revealed by pulsed-field gel electrophoresis in the true slime mold, Physarum polycephalum.

PubMed

Sakurai, R; Sasaki, N; Takano, H; Abe, T; Kawano, S

2000-04-28

Pulsed-field gel electrophoresis (PFGE) was used to examine the in vivo and in vitro conformations of Physarum polycephalum mitochondrial DNA (mtDNA). We used plugs containing isolated mitochondria, isolated mitochondrial nucleoids (mt-nuclei), and isolated mtDNA, in addition to whole cells. The mtDNA contained in the myxamoebae, plasmodia, isolated mitochondria, and isolated mt-nuclei was circular, but most of the isolated mtDNA had been site-specifically fragmented and linearized during DNA preparation and storage under low ionic strength conditions. Restriction mapping of Physarum mtDNA by the direct digestion of the isolated mt-nuclei from two different strains, DP89 x AI16 and KM88 x AI16, resulted in the circular form. A linear mitochondrial plasmid, mF, is known to promote mitochondrial fusion and integration of itself into the mtDNA in Physarum. Linearization of mtDNA by the integration of the mF plasmid was demonstrated when we used PFGE to analyze isolated mitochondria from the plasmodial strain DP89 x NG7 carrying the mF plasmid (mF+). The PFGE system can be used not only to determine whether the form of mtDNA is linear or circular but also to analyze the dynamic conformational changes of mtDNA.

Antigenic and genetic comparison of foot-and-mouth disease virus serotype O Indian vaccine strain, O/IND/R2/75 against currently circulating viruses

PubMed Central

Mahapatra, Mana; Yuvaraj, S.; Madhanmohan, M.; Subramaniam, S.; Pattnaik, B.; Paton, D.J.; Srinivasan, V.A.; Parida, Satya

2015-01-01

Foot-and-mouth disease (FMD) virus serotype O is the most common cause of FMD outbreaks in India and three of the six lineages that have been described are most frequently detected, namely Ind2001, PanAsia and PanAsia 2. We report the full capsid sequence of 21 serotype O viruses isolated from India between 2002 and 2012. All these viruses belong to the Middle East–South Asia (ME–SA) topotype. The serological cross-reactivity of a bovine post-vaccination serum pool raised against the current Indian vaccine strain, O/IND/R2/75,was tested by virus neutralisation test with the 23 Indian field isolates, revealing a good match between the vaccine and the field isolates. The cross reactivity of the O/IND/R2/75 vaccine with 19 field isolates from other countries (mainly from Asia and Africa) revealed a good match to 79% of the viruses indicating that the vaccine strain is broadly cross-reactive and could be used to control FMD in other countries. Comparison of the capsid sequences of the serologically non-matching isolates with the vaccine strain sequence identified substitutions in neutralising antigenic sites 1 and 2, which could explain the observed serological differences. PMID:25500306

Laser-Induced Thermal Acoustics Theory and Expected Experimental Errors when Applied to a Scramjet Isolator Model

NASA Technical Reports Server (NTRS)

Middleton, Troy F.; Balla, Robert Jeffrey; Baurle, Robert A.; Wilson, Lloyd G.

2011-01-01

A scramjet isolator model test apparatus is being assembled in the Isolator Dynamics Research Lab (IDRL) at the NASA Langley Research Center in Hampton, Virginia. The test apparatus is designed to support multiple measurement techniques for investigating the flow field in a scramjet isolator model. The test section is 1-inch high by 2-inch wide by 24-inch long and simulates a scramjet isolator with an aspect ratio of two. Unheated, dry air at a constant stagnation pressure and temperature is delivered to the isolator test section through a Mach 2.5 planar nozzle. The isolator test section is mechanically back-pressured to contain the resulting shock train within the 24-inch isolator length and supports temperature, static pressure, and high frequency pressure measurements at the wall. Additionally, nonintrusive methods including laser-induced thermal acoustics (LITA), spontaneous Raman scattering, particle image velocimetry, and schlieren imaging are being incorporated to measure off-wall fluid dynamic, thermodynamic, and transport properties of the flow field. Interchangeable glass and metallic sidewalls and optical access appendages permit making multiple measurements simultaneously. The measurements will be used to calibrate computational fluid dynamics turbulence models and characterize the back-pressured flow of a scramjet isolator. This paper describes the test apparatus, including the optical access appendages; the physics of the LITA method; and estimates of LITA measurement uncertainty for measurements of the speed of sound and temperature.

Laboratory investigation of a multistate food-borne outbreak of Escherichia coli O157:H7 by using pulsed-field gel electrophoresis and phage typing.

PubMed Central

Barrett, T J; Lior, H; Green, J H; Khakhria, R; Wells, J G; Bell, B P; Greene, K D; Lewis, J; Griffin, P M

1994-01-01

Two hundred thirty-three isolates of Escherichia coli O157:H7 were analyzed by both pulsed-field gel electrophoresis (PFGE) and bacteriophage typing. All 26 isolates from persons whose illness was associated with a recent multistate outbreak of E. coli O157:H7 infections linked to the consumption of undercooked hamburgers and all 27 isolates from incriminated lots of hamburger meat had the same phage type and the same PFGE pattern. Twenty-five of 74 E. coli O157:H7 isolates from Washington State and 10 of 27 isolates from other states obtained during the 6 months before the outbreak had the same phage type as the outbreak strain, but only 1 isolate had the same PFGE pattern. PFGE thus appeared to be a more sensitive method than bacteriophage typing for distinguishing outbreak and non-outbreak-related strains. The PFGE patterns of seven preoutbreak sporadic isolates and five sporadic isolates from the outbreak period differed from that of the outbreak strain by a single band, making it difficult to identify these isolates as outbreak or non-outbreak related. Phage typing and PFGE with additional enzymes were helpful in resolving this problem. While not as sensitive as PFGE, phage typing was helpful in interpreting PFGE data and could have been used as a simple, rapid screen to eliminate the need for performing PFGE on unrelated isolates. Images PMID:7883892

Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.

PubMed

Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate; Leão, Sylvia Cardoso

2014-08-01

Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Phenotypic and Genotypic Changes over Time and across Facilities of Serial Colonizing and Infecting Escherichia coli Isolates Recovered from Injured Service Members

PubMed Central

Beckius, Miriam L.; Zera, Wendy C.; Yu, Xin; Cheatle, Kristelle A.; Aggarwal, Deepak; Li, Ping; Lloyd, Bradley A.; Tribble, David R.; Weintrob, Amy C.; Murray, Clinton K.

2014-01-01

Escherichia coli is the most common colonizing and infecting organism isolated from U.S. service members injured during deployment. Our objective was to evaluate the phenotypic and genotypic changes of infecting and colonizing E. coli organisms over time and across facilities to better understand their transmission patterns. E. coli isolates were collected via surveillance cultures and infection workups from U.S. military personnel injured during deployment (June 2009 to May 2011). The isolates underwent antimicrobial susceptibility testing, pulsed-field gel electrophoresis, and multiplex PCR for phylotyping to determine their resistance profiles and clonality. A total of 343 colonizing and 136 infecting E. coli isolates were analyzed, of which 197 (57%) and 109 (80%) isolates, respectively, produced extended-spectrum β-lactamases (ESBL). Phylogroup A was predominant among both colonizing (38%) and infecting isolates (43%). Although 188 unique pulsed-field types (PFTs) were identified from the colonizing isolates, and 54 PFTs were identified from the infecting isolates, there was a lack of PFT overlap between study years, combat zones, and military treatment facilities. On a per-subject basis, 26% and 32% of the patients with serial colonizing isolates and 10% and 21% with serial infecting isolates acquired changes in their phylogroup and PFT profiles, respectively, over time. The production of ESBL remained high over time and across facilities, with no substantial changes in antimicrobial susceptibilities. Overall, our results demonstrated an array of genotypic and phenotypic differences for the isolates without large clonal clusters; however, the same PFTs were occasionally observed in the colonizing and infecting isolates, suggesting that the source of infections may be endogenous host organisms. PMID:25143566

Identification and differentiation of species and strains of Arthrobacter and Microbacterium barkeri isolated from smear cheeses with Amplified Ribosmal DNA Restriction Analysis (ARDRA) and pulsed field gel electrophoresis (PFGE).

PubMed

Hoppe-Seyler, T S; Jaeger, B; Bockelmann, W; Noordman, W H; Geis, A; Heller, K J

2003-09-01

ARDRA (Amplified Ribosomal-DNA Restriction Analysis) was used to differentiate among species and genera of Arthrobacter and Microbacteria. Species-specific restriction patterns of PCR-products were obtained with NciI for Arthrobacter citreus (DSM 20133T), A. sulfureus (DSM 20167T), A. globiformis (DSM 20124T) and A. nicotianae strains (DSM 20123T, MGE 10D, CA13, CA14, isolate 95293, 95294, and 95299), A. rhombi CCUG 38813T, and CCUG 38812, and Microbacterium barkeri strains (DSM 30123T, MGE 10D, CA12 and CA15, isolate 95292, and isolate 95207). All yellow pigmented coryneforme bacteria isolated from the smear of surface ripened cheeses were identified as either A. nicotianae or M. barkeri strains. Using pulsed field gel electrophoresis (PFGE) strain specific restriction pattern for all Arthrobacter species and Microbacteria tested were obtained with restriction enzymes AscI and SpeI.

Differentiation of canine distemper virus isolates in fur animals from various vaccine strains by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism according to phylogenetic relations in china

PubMed Central

2011-01-01

In order to effectively identify the vaccine and field strains of Canine distemper virus (CDV), a new differential diagnostic test has been developed based on reverse transcription-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). We selected an 829 bp fragment of the nucleoprotein (N) gene of CDV. By RFLP analysis using BamHI, field isolates were distinguishable from the vaccine strains. Two fragments were obtained from the vaccine strains by RT-PCR-RFLP analysis while three were observed in the field strains. An 829 nucleotide region of the CDV N gene was analyzed in 19 CDV field strains isolated from minks, raccoon dogs and foxes in China between 2005 and 2007. The results suggest this method is precise, accurate and efficient. It was also determined that three different genotypes exist in CDV field strains in fur animal herds of the north of China, most of which belong to Asian type. Mutated field strains, JSY06-R1, JSY06-R2 and JDH07-F1 also exist in Northern China, but are most closely related to the standard virulent strain A75/17, designated in Arctic and America-2 genetype in the present study, respectively. PMID:21352564

Enzyme Mini-Test for Field Identification of Leishmania Isolates from U.S. Military Personnel.

DTIC Science & Technology

1985-08-15

8217.*". .. , 00 ENZYME MINI-TEST FOR FIELD IDENTIFICATION OF ’ r LEISHMANIA ISOLATES FROM U.S. MILITARY la ...No 0704-0188% __REPORTDOCUMENTATION__PAGEExp Date Jun30, 1986 la REPORT SECURITY CLASSIFICATION lb RESTRICTIVE MARKINGS Unclassified 2a SECURITY...Soc. Trop. Med. ’* Mcreevy, P. B., P. D. Kreutzer, E. D. Frank-, H. A. Stim- son , C. N. Oster and L. D. H-ndricks. 1983. Taxonomy, clinical pathology

Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.

PubMed

Wu, Xiaoqin; Deutschbauer, Adam M; Kazakov, Alexey E; Wetmore, Kelly M; Cwick, Bryson A; Walker, Robert M; Novichkov, Pavel S; Arkin, Adam P; Chakraborty, Romy

2017-06-29

We present here the draft genome sequences of two Janthinobacterium lividum strains, GW456P and GW458P, isolated from groundwater samples collected from a background site at the Oak Ridge Field Research Center. Production of a purple pigment by these two strains was observed when grown on diluted (1/10) LB agar plates. Copyright © 2017 Wu et al.

Genomic characterization of Indian isolates of egg drop syndrome 1976 virus.

PubMed

Raj, G D; Sivakumar, S; Sudharsan, S; Mohan, A C; Nachimuthu, K

2001-02-01

Five Indian isolates of egg drop syndrome (EDS) 1976 virus and the reference strain 127 were compared by restriction enzyme analysis of viral DNA, and the hexon gene amplified by polymerase chain reaction. Using these techniques, no differences were seen among these viruses. However, partial sequencing of the hexon gene revealed major differences (4.6%) in one of the isolates sequenced, EDS Kerala. Phylogenetic analysis also placed this isolate in a different lineage compared with the other isolates. The need for constant monitoring of the genetic nature of the field isolates of EDS viruses is emphasized.

Diversity of cultivable β-glycosidase-producing micro-organisms isolated from the soil of a ginseng field and their ginsenosides-hydrolysing activity.

PubMed

Fu, Y; Yin, Z; Wu, L; Yin, C

2014-02-01

This research aimed to explore the diversity of cultivable β-glycosidase-producing micro-organisms in ginseng field soil. Fifty-three strains showing β-glucosidase activity were isolated from a ginseng field, using a newly designed Esculin-R2A agar. All the isolated strains belonged to the genus Agrobacterium, Arthrobacter, Burkholderia, Dyella, Edaphobacter, Luteibacter, Mucilaginibacter, Paenibacillus, Phenylobacterium, Pseudomonas, Sphingomonas and Streptomyces. The main β-glucosidase-producing micro-organisms in the ginseng field soil were Sphingomonas, Burkholderia, Luteibacter and Streptomyces, while concentrations of Agrobacterium, Arthrobacter, Paenibacillus and Pseudomonas were relatively low. Of these micro-organisms, the strain GS 09 could hydrolyse major ginsenosides Rb1, Rb2 and Rc to the active metabolite compound K. The strain GS 09 belonged to the genus Sphingomonas, and its 16S rRNA gene sequence showed 100% similarities with that of Sphingomonas asaccharolytica. This is the first study to provide information of cultivable β-glycosidase-producing micro-organisms in ginseng field soil. The strain GS 09 has potential to be applied on the preparation for minor ginsenoside C-K in pharmaceutical industry. © 2013 The Society for Applied Microbiology.

Exploration of the susceptibility of AChE from the poultry red mite Dermanyssus gallinae (Acari: Mesostigmata) to organophosphates in field isolates from France.

PubMed

Roy, Lise; Chauve, Claude; Delaporte, Jean; Inizan, Gilbert; Buronfosse, Thierry

2009-06-01

The red fowl mite Dermanyssus gallinae (De Geer, 1778) is a hematophagous mite species, which is very commonly found in layer facilities in Europe. The economic and animal health impact of this parasite is quite important. In laying hen houses, organophosphates are almost the only legally usable chemicals. Detecting a target resistance can be useful in order to limit the emergence of resistant populations. The acetylcholinesterase (AChE) activity and the enzyme sensitivity to paraoxon was investigated in 39 field samples and compared to a susceptible reference strain (SSK). Insensitivity factor values (expressed as IC50 ratio) obtained from field isolates compared to SSK revealed some polymorphism but not exceeding a 6-fold difference. The kinetic characteristics of AChE from some field samples showed some difference in KM values for acetylthiocholine and inhibition kinetics performed with diethyl paraoxon exhibited a 5.5-fold difference in the bimolecular rate constant in one field isolate. Taken together, these data suggested that differences in AChE susceptibility to organophosphates may exist in D. gallinae but no resistant population was found.

Intensity distributions and isolated attosecond pulse generation from molecular high-order harmonic generation in H2+ driven by nonhomogeneous field

NASA Astrophysics Data System (ADS)

Feng, Liqiang; Chu, Tianshu

2017-10-01

Intensity distributions and isolated attosecond pulse generation from the molecular high-order harmonic generation (MHHG) in H2+ and T2+ driven by the nonhomogeneous field have been theoretically investigated. (i) Generally speaking, the intensities of the harmonics driven by the homogeneous field can be enhanced as the initial vibrational state increases and much more intense harmonics can be obtained from the light nuclei. However, with the introduction of the nonhomogeneous effect, the enhanced ratios of the harmonic yields are decreased as the initial vibrational state increases. Moreover, the intensities of the harmonics from H2+ and T2+ are very sensitive to the nonhomogeneous effect of the laser field. (ii) The contributions of the MHHG from the two-H nuclei present the periodic variation as a function of the laser phase for the case of the symmetric nonhomogeneous field. However, for the case of the positive and the negative asymmetric nonhomogeneous fields, the left-H and the right-H play the dominating role in the MHHG, respectively. Moreover, as the angle between the laser polarization direction and the molecular axis increases, the intensity differences of the harmonics from the two-H nuclei are increased. (iii) By properly adding a half-cycle pulse into the positive asymmetric nonhomogeneous field, a supercontinuum with the bandwidth of 279 eV and an isolated 25 as pulse can be obtained.

Characterization and Field Studies of a Cucumber Mosaic Virus Isolate from Spinach in the Winter Garden Area of Texas

Treesearch

A. Dan Wilson; R.S. Halliwell

1985-01-01

An isolate of cucumber mosaic virus (CMV) was identified from spinach in the Winter Garden area of Texas. The isolate was very closely related serologically to strain S of CMVand is designated the Texas spinach isolate of CMV-S. The virus infected 39 species of crop plants and wild hosts in 12 of 13 families tested. The green peach aphid efficiently transmitted the...

Genotypic Characterization of Streptococcus infantarius subsp. coli Isolates from Sea Otters with Infective Endocarditis and/or Septicemia and from Environmental Mussel Samples

PubMed Central

Counihan-Edgar, Katrina L.; Gill, Verena A.; Doroff, Angela M.; Burek, Kathleen A.; Miller, Woutrina A.; Shewmaker, Patricia L.; Jang, Spencer; Goertz, Caroline E. C.; Tuomi, Pamela A.; Miller, Melissa A.; Jessup, David A.

2012-01-01

Pulsed-field gel electrophoresis (PFGE) was used to type 128 Streptococcus infantarius subsp. coli isolates from sea otters and mussels. Six SmaI PFGE groups were detected, with one predominant group representing 57% of the isolates collected over a wide geographic region. Several sea otter and mussel isolates were highly related, suggesting that an environmental infection source is possible. PMID:23052307

Evaluation of a multiplex PCR to identify and serotype Actinobacillus pleuropneumoniae serovars 1, 5, 7, 12 and 15.

PubMed

Turni, C; Singh, R; Schembri, M A; Blackall, P J

2014-10-01

The aim of this study was to validate a multiplex PCR for the species identification and serotyping of Actinobacillus pleuropneumoniae serovars 1, 5, 7, 12 and 15. All 15 reference strains and 411 field isolates (394 from Australia, 11 from Indonesia, five from Mexico and one from New Zealand) of A. pleuropneumoniae were tested with the multiplex PCR. The specificity of this multiplex PCR was validated on 26 non-A. pleuropneumoniae species. The multiplex PCR gave the expected results with all 15 serovar reference strains and agreed with conventional serotyping for all field isolates from serovars 1 (n = 46), 5 (n = 81), 7 (n = 80), 12 (n = 16) and serovar 15 (n = 117). In addition, a species-specific product was amplified in the multiplex PCR with all 411 A. pleuropneumoniae field isolates. Of 25 nontypeable field isolates only two did not yield a serovar-specific band in the multiplex PCR. This multiplex PCR for serovars 1, 5, 7, 12 and 15 is species specific and capable of serotyping isolates from diverse locations. Significance and impact of the study: A multiplex PCR that can recognize serovars 1, 5, 7, 12 and 15 of A. pleuropneumoniae was developed and validated. This novel diagnostic tool will enable frontline laboratories to provide key information (the serovar) to guide targeted prevention and control programmes for porcine pleuropneumonia, a serious economic disease of pigs. The previous technology, traditional serotyping, is typically provided by specialized reference laboratories, limiting the capacity to respond to this key disease. © 2014 The Society for Applied Microbiology.

Interactions between Head Blight Pathogens: Consequences for Disease Development and Toxin Production in Wheat Spikes

PubMed Central

Siou, Dorothée; Gélisse, Sandrine; Laval, Valérie; Elbelt, Sonia; Repinçay, Cédric; Bourdat-Deschamps, Marjolaine; Lannou, Christian

2014-01-01

Head blight (HB) is one of the most damaging diseases on wheat, inducing significant yield losses and toxin accumulation in grains. Fungal pathogens responsible for HB include the genus Microdochium, with two species, and the toxin producer genus Fusarium, with several species. Field studies and surveys show that two or more species can coexist within a same field and coinfect the same plant or the same spike. In the current study, we investigated how the concomitant presence of F. graminearum and another of the HB complex species influences the spike colonization and the toxin production by the fungi. To study these interactions, 17 well-characterized isolates representing five species were inoculated alone or in pairs on wheat spikes in greenhouse and field experiments. The fungal DNA in the grains was estimated by quantitative PCR and toxin contents (deoxynivalenol and nivalenol) by ultraperformance liquid chromatography-UV detection-tandem mass spectrometry. The responses of the different isolates to the presence of a competitor were variable and isolate specific more than species specific. The development of the most aggressive isolates was either unchanged or a slightly increased, while the development of the less aggressive isolates was reduced. The main outcome of the study was that no trend of increased toxin production was observed in coinoculations compared to single inoculations. On the contrary, the amount of toxin produced was often lower than expected in coinoculations. We thus conclude against the hypothesis that the co-occurrence of several HB-causing species in the same field might aggravate the risk linked to fusarium toxins in wheat production. PMID:25416772

Measuring microbial fitness in a field reciprocal transplant experiment.

PubMed

Boynton, Primrose J; Stelkens, Rike; Kowallik, Vienna; Greig, Duncan

2017-05-01

Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Comparison of apoptosis in human primary pulmonary endothelial cells and a brain microvascular endothelial cell line co-cultured with Plasmodium falciparum field isolates.

PubMed

Essone, Jean Claude Biteghe Bi; N'Dilimabaka, Nadine; Ondzaga, Julien; Lekana-Douki, Jean Bernard; Mba, Dieudonné Nkoghe; Deloron, Philippe; Mazier, Dominique; Gay, Frédrérick; Touré Ndouo, Fousseyni S

2017-06-27

Plasmodium falciparum infection can progress unpredictably to severe forms including respiratory distress and cerebral malaria. The mechanisms underlying the variable natural course of malaria remain elusive. The cerebral microvascular endothelial cells-D3 and lung endothelial cells both from human were cultured separately and challenged with P. falciparum field isolates taken directly from malaria patients or 3D7 strain (in vitro maintained culture). The capacity of these P. falciparum isolates to induce endothelial cell apoptosis via cytoadherence or not was then assessed. Overall, 27 P. falciparum isolates were collected from patients with uncomplicated malaria (n = 25) or severe malaria (n = 2). About half the isolates (n = 17) were able to bind brain endothelial cells (12 isolates, 44%) or lung endothelial cells (17 isolates, 63%) or both (12 isolates, 44%). Sixteen (59%) of the 27 isolates were apoptogenic for brain and/or lung endothelial cells. The apoptosis stimulus could be cytoadherence, direct cell-cell contact without cytoadherence, or diffusible soluble factors. While some of the apoptogenic isolates used two stimuli (direct contact with or without cytoadherence, plus soluble factors) to induce apoptosis, others used only one. Among the 16 apoptogenic isolates, eight specifically targeted brain endothelial cells, one lung endothelial cells, and seven both. These results indicate that the brain microvascular cell line was more susceptible to apoptosis triggered by P. falciparum than the primary pulmonary endothelial cells and may have relevance to host-parasite interaction.

Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh using small RNA deep sequencing

USDA-ARS?s Scientific Manuscript database

The complete genome sequence of a Southern tomato virus (STV) isolate on tomato plants in a seed production field in Bangladesh was obtained for the first time using next generation sequencing. The identified isolate STV_BD-13 shares high degree of sequence identity (99%) with several known STV isol...

Characterisation of nasal Staphylococcus delphini and Staphylococcus pseudintermedius isolates from healthy donkeys in Tunisia.

PubMed

Gharsa, H; Slama, K Ben; Gómez-Sanz, E; Gómez, P; Klibi, N; Zarazaga, M; Boudabous, A; Torres, C

2015-07-01

Staphylococcus intermedius group (SIG) bacteria can colonise the nares of some animals but are also emerging pathogens in humans and animals. To analyse SIG nasal carriage in healthy donkeys destined for food consumption in Tunisia and to characterise recovered isolates. Nasal swabs from 100 healthy donkeys were tested for SIG recovery, and isolates were identified by biochemical and molecular methods. Antimicrobial susceptibility of isolates was tested and detection of antimicrobial resistance and virulence genes was performed. Isolates were typed at the clonal level by multilocus sequence typing and SmaI pulsed-field gel electrophoresis. Staphylococcus delphini and Staphylococcus pseudintermedius (included in SIG) were obtained in 19% and 2% of the tested samples, respectively, and one isolate per sample was characterised. All isolates were meticillin susceptible and mecA negative. Most S. delphini and S. pseudintermedius isolates showed susceptibility to all antimicrobials tested, with the exception of 2 isolates resistant to tetracycline (tet(M) gene) or fusidic acid. The following toxin genes were identified (percentage of isolates): lukS-I (100%), lukF-I (9.5%), siet (100%), se-int (90%), seccanine (19%) and expA (9.5%). Thirteen different pulsed-field gel electrophoresis profiles were identified among the 21 SIG isolates. Additionally, the following 9 different sequence types (STs) were detected by multilocus sequence typing, 6 of them new: ST219 (6 isolates), ST12 (5 isolates), ST220 (3 isolates), ST13, ST50, ST193, ST196, ST218 and ST221 (one isolate each). Staphylococcus delphini and S. pseudintermedius are common nasal colonisers of donkeys, generally susceptible to the antimicrobials tested; nevertheless, these SIG isolates contain virulence genes, including the recently described exfoliative gene (expA) and several enterotoxin genes, with potential implications for public health. This is the first description of S. delphini in Tunisia. The Summary is available in Chinese - see Supporting information. © 2014 EVJ Ltd.

Microbial degradation of total petroleum hydrocarbons in crude oil: a field-scale study at the low-land rainforest of Ecuador.

PubMed

Maddela, Naga Raju; Scalvenzi, Laura; Venkateswarlu, Kadiyala

2017-10-01

A field-level feasibility study was conducted to determine total petroleum hydrocarbon (TPH)-degrading potential of two bacterial strains, Bacillus thuringiensis B3 and B. cereus B6, and two fungi, Geomyces pannorum HR and Geomyces sp. strain HV, all soil isolates obtained from an oil field located in north-east region of Ecuador. Crude oil-treated soil samples contained in wooden boxes received a mixture of all the four microorganisms and were incubated for 90 days in an open low-land area of Amazon rainforest. The percent removal of TPHs in soil samples that received the mixed microbial inoculum was 87.45, indicating the great potential of the soil isolates in field-scale removal of crude oil. The TPHs-degrading efficiency was verified by determining the toxicity of residues, remained in soil after biodegradation, toward viability of Artemia salina or seed germination and plant growth of cowpea. Our results clearly suggest that the selected soil isolates of bacteria and fungi could be effectively used for large-scale bioremediation of sites contaminated with crude oil.

A New Approach to Isolating External Magnetic Field Components in Spacecraft Measurements of the Earth's Magnetic Field Using Global Positioning System observables

NASA Technical Reports Server (NTRS)

Raymond, C.; Hajj, G.

1994-01-01

We review the problem of separating components of the magnetic field arising from sources in the Earth's core and lithosphere, from those contributions arising external to the Earth, namely ionospheric and magnetospheric fields, in spacecraft measurements of the Earth's magnetic field.

Hy-wire and fast electric field change measurements near an isolated thunderstorm, appendix C

NASA Technical Reports Server (NTRS)

Holzworth, R. H.; Levine, D. M.

1983-01-01

Electric field measurements near an isolated thunderstorm at 6.4 km distance are presented from both a tethered balloon experiment called Hy-wire and also from ground based fast and slow electric field change systems. Simultaneous measurements were made of the electric fields during several lightning flashes at the beginning of the storm which the data clearly indicate were cloud-to-ground flashes. In addition to providing a comparison between the Hy-wire technique for measuring electric fields and more traditional methods, these data are interesting because the lightning flashes occurred prior to changes in the dc electric field, although Hy-wire measured changes in the dc field of up to 750 V/m in the direction opposite to the fair weather field a short time later. Also, the dc electric field was observed to decay back to its preflash value after each flash. The data suggest that Hy-wire was at the field reversal distance from this storm and suggest the charge realignment was taking place in the cloud with a time constant on the order of 20 seconds.

Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes.

PubMed

Chan, Ernest R; Barnwell, John W; Zimmerman, Peter A; Serre, David

2015-03-01

Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology.

Comparative Analysis of Field-Isolate and Monkey-Adapted Plasmodium vivax Genomes

PubMed Central

Chan, Ernest R.; Barnwell, John W.; Zimmerman, Peter A.; Serre, David

2015-01-01

Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology. PMID:25768941

Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate.

PubMed

Bhagwat, Basdeo; Dickison, Virginia; Ding, Xinlun; Walker, Melanie; Bernardy, Michael; Bouthillier, Michel; Creelman, Alexa; DeYoung, Robyn; Li, Yinzi; Nie, Xianzhou; Wang, Aiming; Xiang, Yu; Sanfaçon, Hélène

2016-06-01

In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

[Tracing to the source of staphylococcus aureus isolates from ice cream].

PubMed

Zhang, Yan-Jun; Xu, Dan-Ge; Fang, Ye-Zhen; Gong, Pu; Zhu, Min; Bao, Fang-Zhen

2008-07-01

To investigate the contamination of Staphylococcus aureus isolates in ice cream by phenotypic typing and molecular typing. The Staphylococcus aureus isolates were separated from ice cream, filler, cutter, salves and material. The separated isolates were characterized by drug-resistance, staphylococcal enterotoxin (SEA-E), SE (A-E, G-J) genes and pulsed-field gel electrophoresis (PFGE) types. Two Staphylococcus aureus isolates were separated, one from ice cream, another from cutter. Their characteristics of drug-resistance, staphylococcal enterotoxin (SEA-E), SE (A-E,G-J) genes and PFGE type were the same. The two Staphylococcus aureus isolates were the same clone. The contaminated Staphylococcus aureus isolates could be traced to the contaminated cutters.

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.

Molecular Investigation of Tularemia Outbreaks, Spain, 1997–2008

PubMed Central

Ariza-Miguel, Jaime; Johansson, Anders; Fernández-Natal, María Isabel; Martínez-Nistal, Carmen; Orduña, Antonio; Rodríguez-Ferri, Elías F.; Hernández, Marta

2014-01-01

Tularemia outbreaks occurred in northwestern Spain in 1997–1998 and 2007–2008 and affected >1,000 persons. We assessed isolates involved in these outbreaks by using pulsed-field gel electrophoresis with 2 restriction enzymes and multilocus variable number tandem repeat analysis of 16 genomic loci of Francisella tularensis, the cause of this disease. Isolates were divided into 3 pulsotypes by pulsed-field gel electrophoresis and 8 allelic profiles by multilocus variable number tandem repeat analysis. Isolates obtained from the second tularemia outbreak had the same genotypes as isolates obtained from the first outbreak. Both outbreaks were caused by genotypes of genetic subclade B.Br:FTNF002–00, which is widely distributed in countries in central and western Europe. Thus, reemergence of tularemia in Spain was not caused by the reintroduction of exotic strains, but probably by persistence of local reservoirs of infection. PMID:24750848

Evaluation, grafting success and field establishment of cashew rootstock as influenced by VAM fungi.

PubMed

Lakshmipathy, R; Balakrishna, A N; Bagyaraj, D J; Sumana, D A; Kumar, D P

2004-11-01

Seven isolates of vesicular arbuscular mycorrhizal (VAM) fungi were isolated from cashew rhizosphere soil of different cashew growing regions of South India. These seven isolates along with two more VAM fungi namely Acaulospora laevis and Glomus mosseae, which were found to be better symbionts for cashew during our earlier study were used to study their effectiveness on the growth and nutrition of cashew rootstock Ullal-1. Four promising VAM fungi were selected based on this study. Rootstocks inoculated with these four fungi were evaluated for their vigour through grafting success, using Ullal-3 cashew variety as scion. Grafting success was more in rootstocks inoculated with A. laevis and one of local isolates Glomus etunicatum. Grafts with rootstock treated with G. etunicatum and A. laevis survived and performed better when planted in the field compared to the uninoculated and other VAM fungal treatments.

Migratory Bee Hive Transportation Contributes Insignificantly to Transgenic Pollen Movement Between Spatially Isolated Alfalfa Seed Fields.

PubMed

Boyle, Natalie K; Kesoju, Sandya R; Greene, Stephanie L; Martin, Ruth C; Walsh, Douglas B

2017-02-01

Contracted commercial beekeeping operations provide an essential pollination service to many agricultural systems worldwide. Increased use of genetically engineered crops in agriculture has raised concerns over pollinator-mediated gene flow between transgenic and conventional agricultural varieties. This study evaluated whether contracted migratory beekeeping practices influence transgenic pollen flow among spatially isolated alfalfa fields. Twelve honey bee (Apis mellifera L.) colonies were permitted to forage on transgenic alfalfa blossoms for 1 wk in Touchet, WA. The hives were then transported 112 km to caged conventional alfalfa plots following one and two nights of isolation (8 and 32 h, respectively) from the transgenic source. Alfalfa seed harvested from the conventional plots was assessed for the presence of the transgene using a new seedling germination assay. We found that 8 h of isolation from a transgenic alfalfa source virtually eliminated the incidence of cross-pollination between the two varieties.

Genomic Comparisons and Shiga Toxin Production among Escherichia coli O157:H7 Isolates from a Day Care Center Outbreak and Sporadic Cases in Southeastern Wisconsin

PubMed Central

Gouveia, S.; Proctor, M. E.; Lee, M.-S.; Luchansky, J. B.; Kaspar, C. W.

1998-01-01

Contour-clamped homogeneous electric field pulsed-field gel electrophoresis (CHEF-PFGE) was used to compare Wisconsin isolates of Escherichia coli O157:H7, including 39 isolates from a 1994 day care center outbreak, 28 isolates from 18 individuals from the surrounding geographic area with sporadic cases occurring during the 3 months before the outbreak, and 3 isolates, collected in 1995, from patients with hemolytic-uremic syndrome (HUS) who were from eastern Wisconsin counties other than those inhabited by the day care center and sporadic-case individuals. The technique of CHEF-PFGE using XbaI identified seven highly related restriction endonuclease digestion profiles (REDPs) (93 to 98% similarity) among the 39 day care center isolates and nine XbaI REDPs (63 to 93% similarity) among the 28 isolates from sporadic-case individuals, including REDP 33, which was exhibited by both day care and sporadic-case isolates. PFGE analyses of sequential E. coli O157:H7 isolates from symptomatic day care center attendees revealed that the REDPs of 25 isolates from eight patients were indistinguishable whereas the REDPs of 2 of 6 isolates from two patients differed slightly (93 to 95% similarity). The REDPs of the three isolates from 1995 HUS patients were 78 to 83% similar, with REDP 26 being exhibited by one HUS-associated isolate and an isolate from one day care attendee who did not develop HUS. The genes for both Shiga toxins I and II (stx1 and stx2, respectively) were detected in all but one isolate (sporadic case), and Shiga toxin production by the day care center isolates was not significantly different from that of the other isolates, including the three HUS-associated isolates. Analyses of E. coli O157:H7 isolates from both the day care center outbreak and sporadic cases by CHEF-PFGE permitted us to define the REDP variability of an outbreak and geographic region and demonstrated that the day care center outbreak and a HUS case in 1995 were caused by E. coli O157:H7 strains endemic to eastern Wisconsin. PMID:9508303

Phenotypic and molecular fingerprinting of fast growing rhizobia of field-grown pigeonpea from the eastern edge of the Brazilian Pantanal.

PubMed

Costa, F M; Schiavo, J A; Brasil, M S; Leite, J; Xavier, G R; Fernandes, P I

2014-01-21

The aim of this study was to evaluate the diversity of rhizobial isolates obtained from root nodules of pigeonpea plants grown at the eastern edge of the Brazilian Pantanal. The bacterial isolates were isolated from root nodules from field-growing pigeonpea grown in two rural settlements of the Aquidauana municipality. The bacterial isolates were characterized phenotypically by means of cultural characterization, intrinsic antibiotic resistance (IAR), salt and high incubation temperature tolerance, and amylolytic and cellulolytic activities. The molecular characterization of the bacterial isolates was carried out using amplified ribosomal DNA restriction analysis (ARDRA) and Box-polymerase chain reaction (PCR) techniques. In addition, the symbiotic performance of selected rhizobial isolates was evaluated in a greenhouse experiment using sterile substrate. The phenotypic characterization revealed that the bacterial strains obtained from pigeonpea root nodules presented characteristics that are uncommon among rhizobial isolates, indicating the presence of new species nodulating the pigeonpea plants in the Brazilian Pantanal. The molecular fingerprinting of these bacterial isolates also showed a highly diverse collection, with both techniques revealing less than 25% similarity among bacterial isolates. The evaluation of symbiotic performance also indicated the presence of microorganisms with high potential to increase the growth and nitrogen content at the shoots of pigeonpea plants. The results obtained in this study indicate the presence of a highly diversified rhizobial community nodulating the pigeonpea at the eastern edge of the Brazilian Pantanal.

Antigenic and genetic comparison of foot-and-mouth disease virus serotype O Indian vaccine strain, O/IND/R2/75 against currently circulating viruses.

PubMed

Mahapatra, Mana; Yuvaraj, S; Madhanmohan, M; Subramaniam, S; Pattnaik, B; Paton, D J; Srinivasan, V A; Parida, Satya

2015-01-29

Foot-and-mouth disease (FMD) virus serotype O is the most common cause of FMD outbreaks in India and three of the six lineages that have been described are most frequently detected, namely Ind2001, PanAsia and PanAsia 2. We report the full capsid sequence of 21 serotype O viruses isolated from India between 2002 and 2012. All these viruses belong to the Middle East-South Asia (ME-SA) topotype. The serological cross-reactivity of a bovine post-vaccination serum pool raised against the current Indian vaccine strain, O/IND/R2/75,was tested by virus neutralisation test with the 23 Indian field isolates, revealing a good match between the vaccine and the field isolates. The cross reactivity of the O/IND/R2/75 vaccine with 19 field isolates from other countries (mainly from Asia and Africa) revealed a good match to 79% of the viruses indicating that the vaccine strain is broadly cross-reactive and could be used to control FMD in other countries. Comparison of the capsid sequences of the serologically non-matching isolates with the vaccine strain sequence identified substitutions in neutralising antigenic sites 1 and 2, which could explain the observed serological differences. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Burkholderia pseudomallei traced to water treatment plant in Australia.

PubMed

Inglis, T J; Garrow, S C; Henderson, M; Clair, A; Sampson, J; O'Reilly, L; Cameron, B

2000-01-01

Burkholderia pseudomallei was isolated from environmental specimens 1 year after an outbreak of acute melioidosis in a remote coastal community in northwestern Australia. B. pseudomallei was isolated from a water storage tank and from spray formed in a pH-raising aerator unit. Pulsed-field gel electrophoresis confirmed the aerator and storage tank isolates were identical to the outbreak strain, WKo97.

Identification of Brucella ovis exclusive genes in field isolates from Argentina.

PubMed

Alvarez, Lucía Paula; García-Effrón, Guillermo; Robles, Carlos Alejandro

2016-03-01

Brucellosis caused by Brucella ovis is one of the most important infectious diseases of sheep. The aim of this study was to determine the presence of genes both inside and outside the specific B. ovis pathogenicity island 1 (BOPI-1) in a large collection of field isolates of B. ovis and other Brucella spp. from Argentina. The BOV_A0500 gene from B. ovis BOPI-1 was identified in all 104 B. ovis isolates studied. The BOPI-1 complete sequence was found to be conserved in 10 B. ovis strains from the collection, for which whole genome sequencing was performed. The BOV_0198 gene, which is outside BOPI-1 and considered exclusive to B. ovis, showed 90-100% identity with genomic regions of B. ovis, B. melitensis, B. abortus, B. canis, B. suis, B. microti, B. ceti and B. pinnipedialis. The results demonstrate that BOPI-1 is the only exclusive genetic region of B. ovis and marine Brucella spp. and that it is highly conserved in B. ovis field isolates from Argentina. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of field isolates of Trichoderma antagonistic against Rhizoctonia solani.

PubMed

Anees, Muhammad; Tronsmo, Arne; Edel-Hermann, Véronique; Hjeljord, Linda Gordon; Héraud, Cécile; Steinberg, Christian

2010-09-01

The aim of the present study was to characterize sixteen isolates of Trichoderma originating from a field of sugar beet where disease patches caused by Rhizoctonia solani were observed. Use of both molecular and morphological characteristics gave consistent identification of the isolates. Production of water-soluble and volatile inhibitors, mycoparasitism and induced systemic resistance in plant host were investigated using in vitro and in vivo tests in both sterilized and natural soils. This functional approach revealed the intra-specific diversity as well as biocontrol potential of the different isolates. Different antagonistic mechanisms were evident for different strains. The most antagonistic strain, T30 was identified as Trichoderma gamsii. This is the first report of an efficient antagonistic strain of T. gamsii being able to reduce the disease in different conditions. The ability to produce water-soluble inhibitors or coil around the hyphae of the pathogen in vitro was not related to the disease reduction in vivo. Additionally, the strains collected from the high disease areas in the field were better antagonists. The antagonistic activity was not characteristic of a species but that of a population. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Mito-magneto: A Tool for Nanoparticle Mediated Mitochondria Isolation†

PubMed Central

Banik, Bhabatosh; Askins, Brett W.; Dhar, Shanta

2016-01-01

The field of intracellular organelle targeting using nanoparticles (NPs) is mushrooming rapidly. Thus, the area of nanotechnology-enabled targeting of mitochondrion, the cellular powerhouse, for diseases characterized by mitochondrial dysfunctions such as cancer, diseases of the central nervous system, cardiovascular diseases is also growing at a rapid pace. Optimization of NP’s ability to target the mitochondria requires quantification of the particles in this subcellular organelle and isolation of mitochondria from cells. Conventional gradient centrifugation used in currently available methods may not be appropriate for NP containing mitochondria isolation as these particles undergo Brownian motion under centrifugal forces yielding irreproducible results. There is only one method for centrifugation free mitochondria isolation, however this method requires immune-precipitation. Thus, a reliable centrifugation and immune-precipitation free method is urgently needed to support this growing field of nanotechnology-based mitochondria targeting. Here, we report a mitochondria-targeted magnetic NP, Mito-magneto, to avoid centrifugation and immune precipitation methods for isolation of functional, respiration active pure mitochondria which can be used to analyze and quantify mitochondria targeting properties of various NPs to provide an important tool for the growing field of “mitochondrial nanomedicine”. PMID:27735003

Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011-2014.

PubMed

Lu, Huaguang; Tang, Yi; Dunn, Patricia A; Wallner-Pendleton, Eva A; Lin, Lin; Knoll, Eric A

2015-10-15

Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates.

Prevalence, distribution, and diversity of Escherichia coli in plants manufacturing goat milk powder in Shaanxi, China.

PubMed

Xi, Meili; Feng, Yuqing; Li, Qiong; Yang, Qinnan; Zhang, Baigang; Li, Guanghui; Shi, Chao; Xia, Xiaodong

2015-04-01

The aim of the study was to investigate the prevalence, distribution, and diversity of Escherichia coli in goat-milk-powder plants in Shaanxi, China. Three plants manufacturing goat milk powder in Shaanxi province were visited once for sampling during 2012 and 2013. Samples were taken for isolation of E. coli. Isolates were characterized by antimicrobial susceptibility testing and detection of virulence genes. All isolates were further examined by pulsed-field gel electrophoresis analysis. In total, 53 E. coli strains were isolated from 32 positive samples out of 534 samples. Among E. coli isolates, resistance was most frequently observed to trimethoprim-sulfamethoxazole (75.5%), whereas all isolates were sensitive to gatifloxacin, kanamycin, amikacin, and amoxicillin-clavulanate. The 6 virulence genes of pathogenic E. coli were not detected. Pulsed-field gel electrophoresis results showed that E. coli strains in plants were genetically diverse and milk storage tank could be an important contamination source. This study could provide useful information for plants manufacturing goat milk powder to establish proper management practices that help minimize the chance of microbial contamination. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Multiple-locus variable-number tandem-repeats analysis of Listeria monocytogenes using multicolour capillary electrophoresis and comparison with pulsed-field gel electrophoresis typing.

PubMed

Lindstedt, Bjørn-Arne; Tham, Wilhelm; Danielsson-Tham, Marie-Louise; Vardund, Traute; Helmersson, Seved; Kapperud, Georg

2008-02-01

The multiple-locus variable-number tandem-repeats analysis (MLVA) method for genotyping has proven to be a fast and reliable typing tool in several bacterial species. MLVA is in our laboratory the routine typing method for Salmonella enterica subsp. enterica serovar Typhimurium and Escherichia coli O157. The gram-positive bacteria Listeria monocytogenes, while not isolated as frequent as S. Typhimurium and E. coli, causes severe illness with an overall mortality rate of 30%. Thus, it is important that any outbreak of this pathogen is detected early and a fast trace to the source can be performed. In view of this, we have used the information provided by two fully sequenced L. monocytogenes strains to develop a MLVA assay coupled with high-resolution capillary electrophoresis and compared it to pulsed-field gel electrophoresis (PFGE) in two sets of isolates, one Norwegian (79 isolates) and one Swedish (61 isolates) set. The MLVA assay could resolve all of the L. monocytogenes serotypes tested, and was slightly more discriminatory than PFGE for the Norwegian isolates (28 MLVA profiles and 24 PFGE profiles) and opposite for the Swedish isolates (42 MLVA profiles and 43 PFGE profiles).

Genetic diversity of human isolates of Salmonella enterica serovar Enteritidis in Malaysia.

PubMed

Bakeri, S A; Yasin, R M; Koh, Y T; Puthucheary, S D; Thong, K L

2003-01-01

The study was undertaken to determine clonal relationship and genetic diversity of the human strains of Salmonella enterica serovar Enteritidis isolated from 1995 to 2002 from different parts of Malaysia. Antimicrobial susceptibility test, plasmid profiling and pulsed-field gel electrophoresis were applied to analyse 65 human isolates of S. Enteritidis obtained over an eight year period from different parts of Malaysia. Four nonhuman isolates were included for comparison. A total of 14 distinct XbaI-pulsed-field profiles (PFPs) were observed, although a single PFP X1 was predominant and this particular clone was found to be endemic in Malaysia. The incidence of drug resistant S. Enteritidis remained relatively low with only 37% of the strains analysed being resistant to one or more antimicrobial agents. All except one resistant strain carried at least one plasmid ranging in size from 3.7 to 62 MDa giving nine plasmid profiles. The three isolates from raw milk and one from well-water had similar PFPs to that of the human isolates. Salmonella Enteritidis strains were more diverse than was previously thought. Fourteen subtypes were noted although one predominant clone persisted in Malaysia. The combination of pulsed-field gel electrophoresis, plasmid profiling and antibiograms provided additional discrimination to the highly clonal strains of S. Enteritidis. This is the first report to assess the genotypes of the predominant clinical S. Enteritidis in different parts of the country. As S. Enteritidis is highly endemic in Malaysia, the data generated would be useful for tracing the source during outbreaks of gastroenteritis in the study area.

TU-H-BRA-02: The Physics of Magnetic Field Isolation in a Novel Compact Linear Accelerator Based MRI-Guided Radiation Therapy System

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

Low, D; Mutic, S; Shvartsman, S

Purpose: To develop a method for isolating the MRI magnetic field from field-sensitive linear accelerator components at distances close to isocenter. Methods: A MRI-guided radiation therapy system has been designed that integrates a linear accelerator with simultaneous MR imaging. In order to accomplish this, the magnetron, port circulator, radiofrequency waveguide, gun driver, and linear accelerator needed to be placed in locations with low magnetic fields. The system was also required to be compact, so moving these components far from the main magnetic field and isocenter was not an option. The magnetic field sensitive components (exclusive of the waveguide) were placedmore » in coaxial steel sleeves that were electrically and mechanically isolated and whose thickness and placement were optimized using E&M modeling software. Six sets of sleeves were placed 60° apart, 85 cm from isocenter. The Faraday effect occurs when the direction of propagation is parallel to the magnetic RF field component, rotating the RF polarization, subsequently diminishing RF power. The Faraday effect was avoided by orienting the waveguides such that the magnetic field RF component was parallel to the magnetic field. Results: The magnetic field within the shields was measured to be less than 40 Gauss, significantly below the amount needed for the magnetron and port circulator. Additional mu-metal was employed to reduce the magnetic field at the linear accelerator to less than 1 Gauss. The orientation of the RF waveguides allowed the RT transport with minimal loss and reflection. Conclusion: One of the major challenges in designing a compact linear accelerator based MRI-guided radiation therapy system, that of creating low magnetic field environments for the magnetic-field sensitive components, has been solved. The measured magnetic fields are sufficiently small to enable system integration. This work supported by ViewRay, Inc.« less

Genetic relatedness and virulence factors of bovine Staphylococcus aureus isolated from teat skin and milk.

PubMed

da Costa, L B; Rajala-Schultz, P J; Hoet, A; Seo, K S; Fogt, K; Moon, B S

2014-11-01

The objective of this study was to assess the role of teat skin colonization in Staphylococcus aureus intramammary infections (IMI) by evaluating genetic relatedness of Staph. aureus isolates from milk and teat skin of dairy cows using pulsed-field gel electrophoresis and characterizing the isolates based on the carriage of virulence genes. Cows in 4 known Staph. aureus-positive herds were sampled and Staph. aureus was detected in 43 quarters of 20 cows, with 10 quarters positive in both milk and skin (20 isolates), 18 positive only in milk, and 15 only on teat skin. Quarters with teat skin colonized with Staph. aureus were 4.5 times more likely to be diagnosed with Staph. aureus IMI than quarters not colonized on teat skin. Three main clusters were identified by pulsed-field gel electrophoresis using a cutoff of 80% similarity. All 3 clusters included both milk and skin isolates. The majority of isolates (72%) belonged to one predominant cluster (B), with 60% of isolates in the cluster originating from milk and 40% from teat skin. Genotypic variability was observed within 10 pairs (formed by isolates originating from milk and teat skin of the same quarter), where isolates in 5 out of the 10 pairs belonged to the same cluster. Forty-two virulence factors were screened using PCR. Some virulence factors were carried more frequently by teat skin isolates than by milk isolates or isolates from quarters with high somatic cell counts. Isolates in the predominant cluster B carried virulence factors clfA and clfB significantly more often than isolates in the minor clusters, which may have assisted them in becoming predominant in the herds. The present findings suggest that teat skin colonization with Staph. aureus can be an important factor involved in Staph. aureus IMI. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Methicillin-resistant Staphylococcus aureus producing Panton-Valentine leukocidin in a retrospective case series from 12 French hospital laboratories, 2000-2003.

PubMed

Robert, J; Etienne, J; Bertrand, X

2005-07-01

A retrospective analysis of hospital laboratory databases for 2000-2003 found that 0.4-1.0% of methicillin-resistant Staphylococcus aureus isolates had an antibiotic susceptibility pattern associated previously with the production of Panton-Valentine leukocidin (PVL). Of 81 isolates of this type, 35 were available for molecular testing. Each of the 35 available isolates carried the PVL genes, and 33 of these 35 isolates had an identical SmaI pulsed-field gel electrophoresis pattern.

Pasteurella multocida urinary tract infection with molecular evidence of zoonotic transmission.

PubMed

Liu, Wendy; Chemaly, Roy F; Tuohy, Marion J; LaSalvia, Margaret M; Procop, Gary W

2003-02-15

We describe a patient with a urinary tract infection (UTI) caused by Pasteurella multocida. Pulsed-field gel electrophoresis revealed that the clinical isolate recovered from the patient was identical (100% band match) to P. multocida isolates recovered from the patient's cat, but the isolate differed from an isolate recovered from a visiting cat and from a laboratory control strain. The patient also had abnormal urologic anatomy secondary to surgery; this has also been associated with P. multocida UTI.

Comparative analysis of Micrococcus luteus isolates from blood cultures of patients with pulmonary hypertension receiving epoprostenol continuous infusion.

PubMed

Hirata, Yoshinori; Sata, Makoto; Makiuchi, Yuko; Morikane, Keita; Wada, Akihito; Okabe, Nobuhiko; Tomoike, Hitonobu

2009-12-01

During the period 2002-2008, at the National Cardiovascular Center, Osaka, 28 Micrococcus luteus isolates and one Kocuria spp. isolate were obtained from blood cultures of pulmonary hypertension (PH) patients who were receiving continuous infusion therapy with epoprostenol. Pulsed-field gel electrophoresis patterns of the isolates were unrelated, suggesting that the infections had multiple origins. The preparation of epoprostenol solution by patients themselves was thought to be a risk factor.

AFLP analysis of a worldwide collection of Didymella bryoniae.

PubMed

Kothera, Ronald T; Keinath, Anthony P; Dean, Ralph A; Farnham, Mark W

2003-03-01

Didymella bryoniae (anamorph Phoma cucurbitacearum) is an ascomycete that causes gummy stem blight, a foliar disease that occurs on cucurbits in greenhouses and fields throughout the world. In a previous study using RAPD analysis, little genetic diversity was found among isolates of D. bryoniae from New York and South Carolina, USA. Here we report the use of amplified fragment length polymorphism (AFLP) analysis to assess the genetic variation within a worldwide collection of D. bryoniae, 102 field and greenhouse isolates from ten states in the USA (California, Delaware, Florida, Georgia, Indiana, Maryland, Michigan, Oklahoma, South Carolina, and Texas) and seven other countries (Australia, Canada, China, Greece, Israel, Sweden, and The Netherlands) were examined. Seven different AFLP primer-pair combinations generated 450 bands, of which 134 were polymorphic (30%). Using cluster analysis, two groups and a total of seven subgroups were delineated. Representative isolates varied in their virulence on muskmelon and watermelon seedlings, but the degree of virulence was not strongly associated with AFLP groupings. However, isolates from the northern USA grouped separately from isolates originating from the southern USA.

AquaPathogen X--A template database for tracking field isolates of aquatic pathogens

USGS Publications Warehouse

Emmenegger, Evi; Kurath, Gael

2012-01-01

AquaPathogen X is a template database for recording information on individual isolates of aquatic pathogens and is available for download from the U.S. Geological Survey (USGS) Western Fisheries Research Center (WFRC) website (http://wfrc.usgs.gov). This template database can accommodate the nucleotide sequence data generated in molecular epidemiological studies along with the myriad of abiotic and biotic traits associated with isolates of various pathogens (for example, viruses, parasites, or bacteria) from multiple aquatic animal host species (for example, fish, shellfish, or shrimp). The simultaneous cataloging of isolates from different aquatic pathogens is a unique feature to the AquaPathogen X database, which can be used in surveillance of emerging aquatic animal diseases and clarification of main risk factors associated with pathogen incursions into new water systems. As a template database, the data fields are empty upon download and can be modified to user specifications. For example, an application of the template database that stores the epidemiological profiles of fish virus isolates, called Fish ViroTrak (fig. 1), was also developed (Emmenegger and others, 2011).

Phylogenetic analysis of porcine reproductive and respiratory syndrome virus isolates from Northern Ireland.

PubMed

Smith, Natalie; Power, Ultan F; McKillen, John

2018-05-29

To investigate the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) in Northern Ireland, the ORF5 gene from nine field isolates was sequenced and phylogenetically analysed. The results revealed relatively high diversity amongst isolates, with 87.6-92.2% identity between farms at the nucleotide level and 84.1-93.5% identity at the protein level. Phylogenetic analysis confirmed that all nine isolates belonged to the European (type 1) genotype and formed a cluster within the subtype 1 subgroup. This study provides the first report on PRRSV isolate diversity in Northern Ireland.

Burkholderia pseudomallei traced to water treatment plant in Australia.

PubMed Central

Inglis, T. J.; Garrow, S. C.; Henderson, M.; Clair, A.; Sampson, J.; O'Reilly, L.; Cameron, B.

2000-01-01

Burkholderia pseudomallei was isolated from environmental specimens 1 year after an outbreak of acute melioidosis in a remote coastal community in northwestern Australia. B. pseudomallei was isolated from a water storage tank and from spray formed in a pH-raising aerator unit. Pulsed-field gel electrophoresis confirmed the aerator and storage tank isolates were identical to the outbreak strain, WKo97. PMID:10653571

Isolation and identification of group A rotaviruses among neonatal diarrheic calves, Morocco.

PubMed

Ennima, Imane; Sebbar, Ghizlane; Harif, Bachir; Amzazi, Saaid; Loutfi, Chafiqa; Touil, Nadia

2016-05-05

Group A rotaviruses (RVA) are the main cause of neonatal calve diarrhea (NCD) in Morocco. In this study, we isolated RVA strains from NCD clinical samples in order to support RVA disease control in Morocco. This isolation process constitutes a first step toward vaccine development. Thirteen fecal samples were obtained from calves with a single episode of neonate calf diarrhea at three different dairies and two samples were collected from field during a severe NCD outbreak. Diagnosis of RVA infection was based on fecal immune-chromatographic rapid test and further evaluated for their hemagglutination (HA) activity. RVA isolation was carried out on MA104 cells after inoculates were treated with different concentrations of trypsin TPCK. All RVA isolates were confirmed by LSI VetMAX™ Triplex Ruminant Rotavirus & Coronavirus Real-Time PCR kit. G and P typing were determined by direct sequencing of the VP4 and VP7 amplicons. RVA isolation was achieved for nine clinical samples following one or two passages (60 %) and was properly depended on HA activity and trypsin treatment of inoculates. The first sign of CPE detected consisted of increased cell granularity, obscure cell boundaries, cell rounding, and eventual degeneration and detachment of cells. At lower TPCK concentration (3-10 μg/inoculum), no changes at the cellular level were observed, while cells activated with 25-30 μg of trypsin/inoculums, they degenerated and trypsin cytotoxicity was enhanced. Appreciable changes in cell's morphology were detected with optimal trypsin concentration of 15-20 μg trypsin/inoculums. Data from qRT-PCR confirmed that unsuccessful cultivations have No-Ct, and all nine isolates have Ct values ranged between 12.17 and 24.69. Analysis sequencing revealed that field isolates were of G6 P[5] serotype and isolates from the dairy NCD samples were of G10 P[14] serotype. To our knowledge, this is the first study in Morocco which reports the circulation of G10P[14] in NCD on dairy farms and G6P[5] in the field. Our study constitutes a crucial and a necessary step allowing preventive and veterinary medicine to support RVA disease controls in the country.

Genotypic analysis of strains of mutans streptococci by pulsed-field gel electrophoresis.

PubMed

Mineyama, R; Yoshino, S; Fukushima, K

2004-01-01

The species and serotypes of various strains of S. mutans and S. sobrinus were characterized by pulsed-field gel electrophoresis after the genomic DNA from the various strains had been digested with five restriction enzymes (EcoR I, Xba I, Hind III, Sfi I and BssH II) separately. Among these restriction enzymes, BssH II was very useful for the characterization of species and serotypes and, in particular, digestion discriminated between serotypes d and g. The restriction patterns obtained from the genomic DNA of isolates isolated from children's saliva were essentially identical to those from the genomic DNA of the standard laboratory strains. Patterns of BssH II digests of the genomic DNA of 10 isolates identified as S. sobrinus were characteristic of serotype g of the standard laboratory strains. Our results indicate that digestion with BssH II and subsequence analysis by pulsed-field gel electrophoresis should be useful for the characterization of species and serotypes and for epidemiological studies of mutans streptococci.

High Levels of Antimicrobial Resistance among Escherichia coli Isolates from Livestock Farms and Synanthropic Rats and Shrews in the Mekong Delta of Vietnam

PubMed Central

Nhung, N. T.; Cuong, N. V.; Campbell, J.; Hoa, N. T.; Bryant, J. E.; Truc, V. N. T.; Kiet, B. T.; Jombart, T.; Trung, N. V.; Hien, V. B.; Thwaites, G.; Baker, S.

2014-01-01

In Mekong Delta farms (Vietnam), antimicrobials are extensively used, but limited data are available on levels of antimicrobial resistance (AMR) among Escherichia coli isolates. We performed a structured survey of AMR in E. coli isolates (n = 434) from 90 pig, chicken, and duck farms. The results were compared with AMR among E. coli isolates (n = 234) from 66 small wild animals (rats and shrews) trapped on farms and in forests and rice fields. The isolates were susceptibility tested against eight antimicrobials. E. coli isolates from farmed animals were resistant to a median of 4 (interquartile range [IQR], 3 to 6) antimicrobials versus 1 (IQR, 1 to 2) among wild mammal isolates (P < 0.001). The prevalences of AMR among farmed species isolates (versus wild animals) were as follows: tetracycline, 84.7% (versus 25.6%); ampicillin, 78.9% (versus 85.9%); trimethoprim-sulfamethoxazole, 52.1% (versus 18.8%); chloramphenicol, 39.9% (versus 22.5%); amoxicillin-clavulanic acid, 36.6% (versus 34.5%); and ciprofloxacin, 24.9% (versus 7.3%). The prevalence of multidrug resistance (MDR) (resistance against three or more antimicrobial classes) among pig isolates was 86.7% compared to 66.9 to 72.7% among poultry isolates. After adjusting for host species, MDR was ∼8 times greater among isolates from wild mammals trapped on farms than among those trapped in forests/rice fields (P < 0.001). Isolates were assigned to unique profiles representing their combinations of susceptibility results. Multivariable analysis of variance indicated that AMR profiles from wild mammals trapped on farms and those from domestic animals were more alike (R2 range, 0.14 to 0.30) than E. coli isolates from domestic animals and mammals trapped in the wild (R2 range, 0.25 to 0.45). The results strongly suggest that AMR on farms is a key driver of environmental AMR in the Mekong Delta. PMID:25398864

Molecular Epidemiology of Mycobacterium tuberculosis Isolates in 100 Patients With Tuberculosis Using Pulsed Field Gel Electrophoresis

PubMed Central

Pooideh, Mohammad; Jabbarzadeh, Ismail; Ranjbar, Reza; Saifi, Mahnaz

2015-01-01

Background: Tuberculosis (TB) is a widespread infectious disease. Today, TB has created a public health crisis in the world. Genotyping of Mycobacterium tuberculosis isolates is useful for surveying the dynamics of TB infection, identifying new outbreaks, and preventing the disease. Different molecular methods for clustering of M. tuberculosis isolates have been used. Objectives: During a one year study of genotyping, 100 M. tuberculosis isolates from patients referred to Pasteur Institute of Iran were collected and their genotyping was accomplished using pulsed field gel electrophoresis (PFGE) method. Materials and Methods: Identification of all M. tuberculosis isolates was accomplished using standard biochemical and species-specific polymerase chain reaction (PCR) methods. Antibiotic susceptibility tests were performed using proportional method. After preparing PFGE plaques for each isolate of M. tuberculosis, XbaI restriction enzyme was applied for genome digestion. Finally, the digested DNA fragments were separated on 1% agarose gel and analyzed with GelCompar II software. Results: Genotyping of the studied isolates in comparison with the molecular weight marker revealed two common types; pulsotype A with 71 isolates and one multidrug resistant mycobacterium (MDR) case, and pulsotype B including 29 isolates and three MDR cases. No correlation between the antibiotypes and pulsotypes was observed. Conclusions: Molecular epidemiology studies of infectious diseases have been useful when bacterial isolates have been clustered in a period of time and in different geographical regions with variable antibiotic resistance patterns. In spite of high geographical differences and different antibiotic resistant patterns, low genetic diversity among the studied TB isolates may refer to the low rate of mutations in XbaI restriction sites in the mycobacterial genome. We also identified three MDR isolates in low-incidence pulsotype B, which could be disseminated and is highly important to consider in TB surveillance programs to prevent the spread of MDR-TB isolates in the population. PMID:26396714

Molecular epidemiology of Klebsiella pneumoniae K1 and K2 isolates in Japan.

PubMed

Harada, Sohei; Ishii, Yoshikazu; Saga, Tomoo; Aoki, Kotaro; Tateda, Kazuhiro

2018-03-20

Although severe infections caused by hypervirulent Klebsiella pneumoniae isolates, such as K1 isolates belonging to sequence type (ST) 23, have been a significant problem in Asian countries, epidemiology of these isolates in Japan remains unclear. We performed a nationwide molecular epidemiological study of K. pneumoniae K1 and K2 isolates in Japan. Of the 259K. pneumoniae isolates collected, 14 and 16 isolates were identified as capsular genotypes K1 and K2, respectively. All K1 isolates were ST23 or its closely related clones and showed high genetic similarity by pulsed-field gel electrophoresis (PFGE) and the DiversiLab system (DL). K2 isolates, belonging to ST14, ST25, ST65, ST86, and ST110, were more genetically diverse than K1 isolates. Isolates belonging to a specific ST showed identical virulence gene profiles with a few exceptions. PFGE and DL results using K1 and K2 isolates were generally in agreement. Copyright © 2018. Published by Elsevier Inc.

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.

Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts

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

Stenger, Drake C., E-mail: drake.stenger@ars.usda.

Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of themore » corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection. -- Highlights: •Sampling protocol minimized differential selection/history among isolates. •Polymorphism among consensus sequences dominated by negative/purifying selection. •Within-isolate N:S ratio corrected for RT-PCR error by bootstrapping. •Within-isolate mutant spectrum dominated by new mutations yet to undergo selection.« less

Comparison of seven protocols to identify fecal contamination sources using Escherichia coli

USGS Publications Warehouse

Stoeckel, D.M.; Mathes, M.V.; Hyer, K.E.; Hagedorn, C.; Kator, H.; Lukasik, J.; O'Brien, T. L.; Fenger, T.W.; Samadpour, M.; Strickler, K.M.; Wiggins, B.A.

2004-01-01

Microbial source tracking (MST) uses various approaches to classify fecal-indicator microorganisms to source hosts. Reproducibility, accuracy, and robustness of seven phenotypic and genotypic MST protocols were evaluated by use of Escherichia coli from an eight-host library of known-source isolates and a separate, blinded challenge library. In reproducibility tests, measuring each protocol's ability to reclassify blinded replicates, only one (pulsed-field gel electrophoresis; PFGE) correctly classified all test replicates to host species; three protocols classified 48-62% correctly, and the remaining three classified fewer than 25% correctly. In accuracy tests, measuring each protocol's ability to correctly classify new isolates, ribotyping with EcoRI and PvuII approached 100% correct classification but only 6% of isolates were classified; four of the other six protocols (antibiotic resistance analysis, PFGE, and two repetitive-element PCR protocols) achieved better than random accuracy rates when 30-100% of challenge isolates were classified. In robustness tests, measuring each protocol's ability to recognize isolates from nonlibrary hosts, three protocols correctly classified 33-100% of isolates as "unknown origin," whereas four protocols classified all isolates to a source category. A relevance test, summarizing interpretations for a hypothetical water sample containing 30 challenge isolates, indicated that false-positive classifications would hinder interpretations for most protocols. Study results indicate that more representation in known-source libraries and better classification accuracy would be needed before field application. Thorough reliability assessment of classification results is crucial before and during application of MST protocols.

Scarlet fever is caused by a limited number of Streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC.

PubMed

Silva-Costa, Catarina; Carriço, Joao A; Ramirez, Mario; Melo-Cristino, Jose

2014-03-01

Several outbreaks of scarlet fever caused by Streptococcus pyogenes were recently reported. Scarlet fever is historically considered a toxin-mediated disease, dependent on the production of the exotoxins SpeA and SpeC, but a strict association between scarlet fever and these exotoxins is not always detected. The aims of this study were to characterize the scarlet fever bacterial isolates recovered from patients in a Lisbon hospital and to identify any distinctive characteristics of such isolates. We characterized a collection of 303 pharyngeal S. pyogenes collected between 2002 and 2008. One-hundred and one were isolated from scarlet fever patients and 202 were associated to a diagnosis of tonsillo-pharyngitis. Isolates were characterized by T and emm typing, pulsed field gel electrophoresis profiling and superantigen gene profiling. The diversity of the scarlet fever isolates was lower than that of the pharyngitis isolates. Specific lineages of emm87, emm4 and emm3 were overrepresented in scarlet fever isolates but only 1 pulsed field gel electrophoresis major lineage was significantly associated with scarlet fever. Multivariate analysis indicated associations of ssa, speA and speC with scarlet fever. In nonoutbreak conditions, scarlet fever is caused by a number of distinct genetic lineages. The lower diversity of these isolates and the association with specific exotoxin genes indicates that some lineages are more prone to cause this presentation than others even in nonoutbreak conditions.

Characterization and Antimicrobial Resistance of Salmonella Typhimurium Isolates from Clinically Diseased Pigs in Korea.

PubMed

Oh, Sang-Ik; Kim, Jong Wan; Chae, Myeongju; Jung, Ji-A; So, Byungjae; Kim, Bumseok; Kim, Ha-Young

2016-11-01

This study investigated the prevalence of Salmonella enterica serovar and antimicrobial resistance in Salmonella Typhimurium isolates from clinically diseased pigs collected from 2008 to 2014 in Korea. Isolates were also characterized according to the presence of antimicrobial resistance genes and pulsed-field gel electrophoresis patterns. Among 94 Salmonella isolates, 81 (86.2%) were identified as being of the Salmonella Typhimurium serotype, followed by Salmonella Derby (6 of 94, 6.4%), Salmonella 4,[5],12:i:- (4 of 94, 4.3%), Salmonella Enteritidis (2 of 94, 2.1%), and Salmonella Brandenburg (1 of 94, 1.1%). The majority of Salmonella Typhimurium isolates were resistant to tetracycline (92.6%), followed by streptomycin (88.9%) and ampicillin (80.2%). Overall, 96.3% of Salmonella Typhimurium isolates showed multidrug-resistant phenotypes and commonly harbored the resistance genes bla TEM (64.9%), flo (32.8%), aadA (55.3%), strA (58.5%), strB (58.5%), sulII (53.2%), and tetA (61.7%). The pulsed-field gel electrophoresis analysis of 45 Salmonella Typhimurium isolates from individual farms revealed 27 distinct patterns that formed one major and two minor clusters in the dendrogram analysis, suggesting that most of the isolates (91.1%) from diseased pigs were genetically related. These findings can assist veterinarians in the selection of appropriate antimicrobial agents to combat Salmonella Typhimurium infections in pigs. Furthermore, they highlight the importance of continuous surveillance of antimicrobial resistance and genetic status in Salmonella Typhimurium for the detection of emerging resistance trends.

Molecular subtyping of Clostridium perfringens by pulsed-field gel electrophoresis to facilitate food-borne-disease outbreak investigations.

PubMed

Maslanka, S E; Kerr, J G; Williams, G; Barbaree, J M; Carson, L A; Miller, J M; Swaminathan, B

1999-07-01

Clostridium perfringens is a common cause of food-borne illness. The illness is characterized by profuse diarrhea and acute abdominal pain. Since the illness is usually self-limiting, many cases are undiagnosed and/or not reported. Investigations are often pursued after an outbreak involving large numbers of people in institutions, at restaurants, or at catered meals. Serotyping has been used in the past to assist epidemiologic investigations of C. perfringens outbreaks. However, serotyping reagents are not widely available, and many isolates are often untypeable with existing reagents. We developed a pulsed-field gel electrophoresis (PFGE) method for molecular subtyping of C. perfringens isolates to aid in epidemiologic investigations of food-borne outbreaks. Six restriction endonucleases (SmaI, ApaI, FspI, MluI, KspI, and XbaI) were evaluated with a select panel of C. perfringens strains. SmaI was chosen for further studies because it produced 11 to 13 well-distributed bands of 40 to approximately 1,100 kb which provided good discrimination between isolates. Seventeen distinct patterns were obtained with 62 isolates from seven outbreak investigations or control strains. In general, multiple isolates from a single individual had indistinguishable PFGE patterns. Epidemiologically unrelated isolates (outbreak or control strains) had unique patterns; isolates from different individuals within an outbreak had similar, if not identical, patterns. PFGE identifies clonal relationships of isolates which will assist epidemiologic investigations of food-borne-disease outbreaks caused by C. perfringens.

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.

Characterization of Isolates of Salmonella enterica Serovar Stanley, a Serovar Endemic to Asia and Associated with Travel

PubMed Central

Le Hello, Simon; Bortolaia, Valeria; Pulsrikarn, Chaiwat; Nielsen, Eva Møller; Pornruangmong, Srirat; Chaichana, Phattharaporn; Svendsen, Christina Aaby; Weill, François-Xavier; Aarestrup, Frank M.

2012-01-01

Salmonella enterica serovar Stanley (S. Stanley) is a common serovar in Southeast Asia and was the second most common serovar implicated in human salmonellosis in Thailand in the years 2002 to 2007. In contrast, this serovar is relatively uncommon in Europe. The objective of this study was to characterize a collection of S. Stanley strains isolated from Thai (n = 62), Danish (n = 39), and French (n = 24) patients to gain a broader understanding of the genetic diversity, population dynamics, and susceptibility to antimicrobials. All isolates were characterized by pulsed-field gel electrophoresis and antimicrobial susceptibility testing. The molecular mechanisms of resistance to extended-spectrum cephalosporins and plasmid-mediated resistance to quinolones were characterized by PCR and sequencing. Plasmid profiling, replicon typing, and microarray analysis were used to characterize the genetic mechanisms of antimicrobial resistance in 10 extended-spectrum cephalosporinase-producing isolates. Considerable genetic diversity was observed among the isolates characterized with 91 unique XbaI pulsed-field gel electrophoresis (PFGE) patterns, including 17 distinct clusters consisting of two to seven indistinguishable isolates. We found some of the S. Stanley isolates isolated from patients in Europe were acquired during travel to Southeast Asia, including Thailand. The presence of multiple plasmid lineages carrying the extended-spectrum cephalosporinase-encoding blaCMY-2 gene in S. Stanley isolates from the central part of Thailand was confirmed. Our results emphasize that Thai authorities, as well as authorities in other countries lacking prudent use of antimicrobials, should improve the ongoing efforts to regulate antimicrobial use in agriculture and in clinical settings to limit the spread of multidrug-resistant Salmonella isolates and plasmids among humans and pigs in Thailand and abroad. PMID:22205822

Characterization of isolates of Salmonella enterica serovar Stanley, a serovar endemic to Asia and associated with travel.

PubMed

Hendriksen, Rene S; Le Hello, Simon; Bortolaia, Valeria; Pulsrikarn, Chaiwat; Nielsen, Eva Møller; Pornruangmong, Srirat; Chaichana, Phattharaporn; Svendsen, Christina Aaby; Weill, François-Xavier; Aarestrup, Frank M

2012-03-01

Salmonella enterica serovar Stanley (S. Stanley) is a common serovar in Southeast Asia and was the second most common serovar implicated in human salmonellosis in Thailand in the years 2002 to 2007. In contrast, this serovar is relatively uncommon in Europe. The objective of this study was to characterize a collection of S. Stanley strains isolated from Thai (n = 62), Danish (n = 39), and French (n = 24) patients to gain a broader understanding of the genetic diversity, population dynamics, and susceptibility to antimicrobials. All isolates were characterized by pulsed-field gel electrophoresis and antimicrobial susceptibility testing. The molecular mechanisms of resistance to extended-spectrum cephalosporins and plasmid-mediated resistance to quinolones were characterized by PCR and sequencing. Plasmid profiling, replicon typing, and microarray analysis were used to characterize the genetic mechanisms of antimicrobial resistance in 10 extended-spectrum cephalosporinase-producing isolates. Considerable genetic diversity was observed among the isolates characterized with 91 unique XbaI pulsed-field gel electrophoresis (PFGE) patterns, including 17 distinct clusters consisting of two to seven indistinguishable isolates. We found some of the S. Stanley isolates isolated from patients in Europe were acquired during travel to Southeast Asia, including Thailand. The presence of multiple plasmid lineages carrying the extended-spectrum cephalosporinase-encoding bla(CMY-2) gene in S. Stanley isolates from the central part of Thailand was confirmed. Our results emphasize that Thai authorities, as well as authorities in other countries lacking prudent use of antimicrobials, should improve the ongoing efforts to regulate antimicrobial use in agriculture and in clinical settings to limit the spread of multidrug-resistant Salmonella isolates and plasmids among humans and pigs in Thailand and abroad.

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.

Effect of preceding crop on Fusarium species and mycotoxin contamination of wheat grains.

PubMed

Qiu, Jianbo; Dong, Fei; Yu, Mingzheng; Xu, Jianhong; Shi, Jianrong

2016-10-01

The Fusarium graminearum species complex infects several cereals and causes the reduction of grain yield and quality. Many factors influence the extent of Fusarium infection and mycotoxin levels. Such factors include crop rotation. In the present study, we explored the effect of rice or maize as former crops on mycotoxin accumulation in wheat grains. More than 97% of samples were contaminated with deoxynivalenol (DON). DON concentrations in wheat grains from rice and maize rotation fields were 884.37 and 235.78 µg kg(-1) . Zearalenone (ZEN) was detected in 45% of samples which were mainly collected from maize-wheat rotation systems. Fusarium strains were isolated and more F. graminearum sensu stricto (s. str.) isolates were cultured from wheat samples obtained from maize rotation fields. DON levels produced by Fusarium isolates from rice rotation fields were higher than those of samples from maize rotation fields. Rice-wheat rotation favours DON accumulation, while more ZEN contamination may occur in maize-wheat rotation models. Appropriate crop rotation may help to reduce toxin levels in wheat grains. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Coccidiosis in the Chukar Partridge ( Alectoris chukar ): A Survey of Coccidiosis Outbreaks and a Test of Anticoccidial Drugs Against Eimeria kofoidi.

PubMed

Gerhold, R W; Fuller, A L; McDougald, L R

2016-12-01

Field isolates of coccidia from 20 natural outbreaks in the chukar partridge ( Alectoris chukar ) were received from gamebird farms in 10 U.S. states. These were propagated in the laboratory and identified by microscopy and PCR. Of 20 samples, 18 were Eimeria kofoidi, two were Eimeria legionensis only, and one was a mixture of the two species. One isolate of E. kofoidi also contained an unidentified species detected only by PCR, nucleotide sequencing, and phylogenetic analysis. The efficacy of anticoccidial drugs against chukar coccidia was tested with experimental infections in battery cages. Isolates of E. kofoidi were used to infect 2-wk-old chukars. Anticoccidial products were given in the feed at levels approved for other poultry or for chukars. Tests were terminated at 6 days postinoculation with measurement of weight gains, fecal diarrhea scores, and necropsy to observe for lesion severity. Lasalocid (120 ppm) was moderately effective in one test. When tested against four field isolates, other ionophores (monensin, salinomycin, semduramicin) showed moderate effectiveness in reducing lesions and improving weight gains. Rofenaid (a potentiated sulfa mixture), robenidine (30 ppm), diclazuril (2 ppm), and decoquinate (80 ppm) were highly effective. In a test of nine products against a highly virulent field isolate, only diclazuril (2 ppm) and clopidol (125 ppm) reduced the severity of lesions and improved weight gain relative to infected controls, suggesting the extent to which previous drug usage had selected for drug resistance.

Study of the virulence and cross-neutralization capability of recent porcine parvovirus field isolates and vaccine viruses in experimentally infected pregnant gilts.

PubMed

Zeeuw, E J L; Leinecker, N; Herwig, V; Selbitz, H-J; Truyen, U

2007-02-01

The pathogenicity of two recent German field isolates of Porcine parvovirus (PPV-27a and PPV-143a) and two vaccine viruses [PPV-NADL-2 and PPV-IDT (MSV)], which are used for the production of inactivated vaccines, was investigated by inoculation of pregnant sows at day 40 of gestation. Post-infection sera of these sows as well as antisera prepared in rabbits by immunization with the four above-mentioned PPV isolates and with the virulent strain PPV-Challenge (Engl.) were tested for their homologous and heterologous neutralization activities. All antisera had high neutralization activity against the vaccine viruses, the PPV-Challenge (Engl.) virus and PPV-143a, but much lower activity against PPV-27a. These results suggest that PPV-27a represents a new antigenic variant or type of PPV and vaccines based on the established vaccine viruses may not be fully protective against this field isolate. PPV-27a has been characterized based on the amino acid sequences of the capsid protein as a member of a new and distinct PPV cluster (Zimmermann et al., 2006). Interestingly, the homologous neutralizing antibody titres of the sera of all three pigs and both rabbits inoculated or immunized with PPV-27a were 100- to 1000-fold lower than the heterologous titres against any of the other viruses. The low homologous neutralizing antibody titres suggest a possible, yet undefined, immune escape mechanism of this PPV isolate.

First Report of a New Isolate of Metarhizium rileyi from Maize Fields of Quivicán, Cuba.

PubMed

Álvarez, Sandra Pérez; Guerrero, Amaury Méndez; Duarte, Bernardo Nayar Débora; Tapia, Marco Antonio Magallanes; Medina, Jesús Alicia Chávez; Domínguez Rodríguez, Yoannis

2018-06-01

Metarhizium rileyi (Farlow) Samson is an important entomopathogenic fungus of more than 30 species of Lepidoptera larvae. The aim of this research was to characterize isolate of M. rileyi from Quivicán, Cuba on the basis of morphological and molecular approaches. The fungus was isolated from samples of S . frugiperda larvae collected from maize fields of Quivicán municipality, Mayabeque province, Cuba, and it was cultured on PDA + Ampicillin solid media for morphological characterization. The DNA was isolated using CTAB method and internal transcribed spacer (ITS1, ITS4) were used as the primers for the amplification. The amplified products of 1335 bp were purified and sequenced at CINVESTAV-IPN in both the directions using the above primers. A consensus sequence was obtained by alignment of the forward and reverse sequences for this region and deposited in GenBank (MG637450). The fungus produced slightly cottony colony of pale green color and dispersed conidia and septal mycelium were observed under the optical microscope. A BLAST search of the sequence in GenBank revealed a 99% of identity with several strains of N. rileyi (e.g., AF368501.1, AB268359.1 and EU553337.1) and M. rileyi (e.g., KY436756.1). This is the first report of M. rileyi isolate from maize fields of Quivicán in Cuba and this is important for biodiversity studies and is another possibility for Integrated Pest Management.

Real-time PCR to quantify composition of arbuscular mycorrhizal fungal communities--marker design, verification, calibration and field validation.

PubMed

Thonar, C; Erb, A; Jansa, J

2012-03-01

Quantitative real-time PCR (qPCR) is slowly becoming established as a tool to quantify abundance of different arbuscular mycorrhizal fungal (AMF) taxa in roots and in soil. Here, we describe the development and field validation of qPCR markers (i.e. primers with associated hydrolysis probes), targeting taxon-specific motifs in the nuclear large ribosomal subunit RNA genes. Design of such markers is complicated by the multinuclear and multigenomic cellular organization of these fungi and the high DNA sequence diversity within the smallest biologically relevant units (i.e. single-spore isolates). These limitations are further compounded by inefficient biomass production of these fungi, resulting in limited availability of pure genomic DNA (gDNA) of well-defined isolates for cross-specificity testing of the markers. Here we demonstrate, using a number of AMF isolates, the possibility to establish stringent qPCR running conditions allowing quantification of phylogenetically disjunctive AMF taxa. Further, we show that these markers can more generally be used to quantify abundance (i.e. number of target gene copies or amount of gDNA) of what is usually considered the level of AMF species, regardless of the isolate identities. We also illustrate the range of variation within qPCR signal strength across different AMF taxa with respect to the detected number of gene copies per unit amount of gDNA. This information is paramount for interpretation of the qPCR analyses of field samples. Finally, the field validation of these markers confirmed their potential to assess composition of field AMF communities and monitor the changes owing to agricultural practices such as soil tillage. © 2011 Blackwell Publishing Ltd.

Application of Pulsed-Field Gel Electrophoresis and Binary Typing as Tools in Veterinary Clinical Microbiology and Molecular Epidemiologic Analysis of Bovine and Human Staphylococcus aureus Isolates

PubMed Central

Zadoks, Ruth; van Leeuwen, Willem; Barkema, Herman; Sampimon, Otlis; Verbrugh, Henri; Schukken, Ynte Hein; van Belkum, Alex

2000-01-01

Thirty-eight bovine mammary Staphylococcus aureus isolates from diverse clinical, temporal, and geographical origins were genotyped by pulsed-field gel electrophoresis (PFGE) after SmaI digestion of prokaryotic DNA and by means of binary typing using 15 strain-specific DNA probes. Seven pulsed-field types and four subtypes were identified, as were 16 binary types. Concordant delineation of genetic relatedness was documented by both techniques, yet based on practical and epidemiological considerations, binary typing was the preferable method. Genotypes of bovine isolates were compared to 55 previously characterized human S. aureus isolates through cluster analysis of binary types. Genetic clusters containing strains of both human and bovine origin were found, but bacterial genotypes were predominantly associated with a single host species. Binary typing proved an excellent tool for comparison of S. aureus strains, including methicillin-resistant S. aureus, derived from different host species and from different databases. For 28 bovine S. aureus isolates, detailed clinical observations in vivo were compared to strain typing results in vitro. Associations were found between distinct genotypes and severity of disease, suggesting strain-specific bacterial virulence. Circumstantial evidence furthermore supports strain-specific routes of bacterial dissemination. We conclude that PFGE and binary typing can be successfully applied for genetic analysis of S. aureus isolates from bovine mammary secretions. Binary typing in particular is a robust and simple method and promises to become a powerful tool for strain characterization, for resolution of clonal relationships of bacteria within and between host species, and for identification of sources and transmission routes of bovine S. aureus. PMID:10790124

Tiamulin resistance in porcine Brachyspira pilosicoli isolates.

PubMed

Pringle, M; Landén, A; Franklin, A

2006-02-01

There are few studies on antimicrobial susceptibility of Brachyspira pilosicoli, therefore this study was performed to investigate the situation among isolates from pigs. The tiamulin and tylosin susceptibility was determined by broth dilution for 93 and 86 porcine B. pilosicoli isolates, respectively. The isolates came from clinical samples taken in Swedish pig herds during the years 2002 and 2003. The tylosin minimal inhibitory concentration (MIC) was >16 microg/ml for 50% (n=43) of the isolates tested. A tiamulin MIC >2 microg/ml was obtained for 14% (n=13) of the isolates and these were also tested against doxycycline, salinomycin, valnemulin, lincomycin and aivlosin. For these isolates the susceptibility to salinomycin and doxycycline was high but the MICs for aivlosin varied. The relationship between the 13 tiamulin resistant isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Among the 13 isolates 10 different PFGE patterns were identified.

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.

New Korean isolates of Pepper mild mottle virus (PMMoV) differ in symptom severity and subcellular localization of the 126 kDa protein

USDA-ARS?s Scientific Manuscript database

Two isolates of Pepper mild mottle virus (PMMoV) were selected from a nationwide survey of pepper fields in South Korea in 2014 and 2015, in which Cucumber mosaic virus was also detected; the two PMMoV isolates, Sangcheong 47 (S-47, KX399390) and Jeongsong 76 (J-76, KX399389), share ~99% nucleotide ...

Quantitative Field Testing Rotylenchulus reniformis DNA from Metagenomic Samples Isolated Directly from Soil

PubMed Central

Showmaker, Kurt; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

2011-01-01

A quantitative PCR procedure targeting the β-tubulin gene determined the number of Rotylenchulus reniformis Linford & Oliveira 1940 in metagenomic DNA samples isolated from soil. Of note, this outcome was in the presence of other soil-dwelling plant parasitic nematodes including its sister genus Helicotylenchus Steiner, 1945. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from soil. PMID:22194958

A N2-fixing endophytic Burkholderia sp. associated with maize plants cultivated in Mexico.

PubMed

Estrada, Paulina; Mavingui, Patrick; Cournoyer, Benoit; Fontaine, Fanette; Balandreau, Jacques; Caballero-Mellado, Jesus

2002-04-01

In the frame of a survey of potentially endophytic N2-fixing Burkholderia associated with maize in Mexico, its country of origin, the soil of an indigenous maize field near Oaxaca was studied. Under laboratory conditions, plant seedlings of two ancient maize varieties were used as a trap to select endophyte candidates from the soil sample. Among the N2 fixers isolated from inside plant tissues and able to grow on PCAT medium, the most abundant isolates belonged to genus Burkholderia (API 20NE, rrs sequences). Representative isolates obtained from roots and shoots of different plants appeared identical (rrs and nifH RFLP), showing that they were closely related. In addition, their 16S rDNA sequences differed from described Burkholderia species and, phylogenetically, they constituted a separate deep-branching new lineage in genus Burkholderia. This indicated that these isolates probably constituted a new species. An inoculation experiment confirmed that these N2-fixing Burkholderia isolates could densely colonize the plant tissues of maize. More isolates of this group were subsequently obtained from field-grown maize and teosinte plants. It was hypothesized that strains of this species had developed a sort of primitive symbiosis with one of their host plants, teosinte, which persisted during the domestication of teosinte into maize.

Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011–2014

PubMed Central

Lu, Huaguang; Tang, Yi; Dunn, Patricia A.; Wallner-Pendleton, Eva A.; Lin, Lin; Knoll, Eric A.

2015-01-01

Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates. PMID:26469681

Demonstration of Efficient Nonreciprocity in a Microwave Optomechanical Circuit*

NASA Astrophysics Data System (ADS)

Peterson, G. A.; Lecocq, F.; Cicak, K.; Simmonds, R. W.; Aumentado, J.; Teufel, J. D.

2017-07-01

The ability to engineer nonreciprocal interactions is an essential tool in modern communication technology as well as a powerful resource for building quantum networks. Aside from large reverse isolation, a nonreciprocal device suitable for applications must also have high efficiency (low insertion loss) and low output noise. Recent theoretical and experimental studies have shown that nonreciprocal behavior can be achieved in optomechanical systems, but performance in these last two attributes has been limited. Here, we demonstrate an efficient, frequency-converting microwave isolator based on the optomechanical interactions between electromagnetic fields and a mechanically compliant vacuum-gap capacitor. We achieve simultaneous reverse isolation of more than 20 dB and insertion loss less than 1.5 dB. We characterize the nonreciprocal noise performance of the device, observing that the residual thermal noise from the mechanical environments is routed solely to the input of the isolator. Our measurements show quantitative agreement with a general coupled-mode theory. Unlike conventional isolators and circulators, these compact nonreciprocal devices do not require a static magnetic field, and they allow for dynamic control of the direction of isolation. With these advantages, similar devices could enable programmable, high-efficiency connections between disparate nodes of quantum networks, even efficiently bridging the microwave and optical domains.

Biodegradation of isoproturon by Pseudoxanthomonas sp. isolated from herbicide-treated wheat fields of Tarai agro-ecosystem, Pantnagar.

PubMed

Giri, Krishna; Pandey, Shailseh; Kumar, Rajesh; Rai, J P N

2016-12-01

A gram-negative, rod-shaped, isoproturon (IPU) utilizing bacterium was isolated from herbicide-applied wheat fields of Tarai agro-ecosystem, Pantnagar. The phylogenetic sequence analysis based on 16S rRNA sequence revealed that the isolate could be a distinct species within the genus Pseudomonas. The isolate was a close relative of Pseudoxanthomonas japonensis (95 % similarity) and designated as K2. The bacterial isolate showed positive reaction for oxidase, catalase, and 20 carbohydrates using KB009 Part A and B HiCarbohydrate™ Kit. Degradation experiments were conducted using 200 mg l -1 initial IPU as a source of carbon at different pH and temperatures. Maximum IPU degradation by K2 was observed at pH 7.0 and 30 °C, while least degradation at 6.5 pH and 25 °C. Addition of dextrose along with IPU as an auxiliary carbon source increased IPU degradation by 4.72 %, as compared to the IPU degradation without dextrose under optimum conditions. 4-isopropylaniline was detected as a degradation by-product in the medium. The present study demonstrated the IPU metabolizing capacity of a novel bacterial isolate K2 that can be a better choice for the remediation of IPU-contaminated sites.

Long-term Behavioral Consequences of Brief, Repeated Neonatal Isolation

PubMed Central

Knuth, Emily D.; Etgen, Anne M.

2007-01-01

Rats subjected to stressful stimuli during the stress hyporesponsive period exhibit varied neuroendocrine and behavioral changes as neonates, adolescents and adults. The current work examined the effects of neonatal isolation stress, using a within-litter design, on adult anxiety-related behavior and endocrine stress reactivity. Neonatal rats were isolated daily for 1 hr from postnatal day (P) 4-9, a manipulation previously shown to induce hypothalamic-pituitary-adrenal (HPA) responses on P9 (Knuth and Etgen, 2005). Control animals were either handled briefly or left undisturbed (with-dam). Adult rats were tested for anxiety-related behavior using the elevated plus maze and open field, and for endocrine responses following restraint stress. Neonatal isolation decreased center exploration of the open field following 1 hr restraint, including decreased time in the center compared to with-dam or handled controls, and decreased center entries and distance traveled in the center compared to with-dam controls. It also decreased time in and entries into the open arms of the elevated plus maze compared to handled controls, suggesting enhanced anxiety-related behavior. Neonatal isolation had no effect on basal or restraint-induced levels of ACTH or corticosterone. These findings indicate that neonatal isolation may enhance anxiety-related behaviors, especially in response to stress, without altering HPA function. Section: Cognitive and Behavioral Neuroscience PMID:17125746

Social isolation and chronic handling alter endocannabinoid signaling and behavioral reactivity to context in adult rats

PubMed Central

Sciolino, Natale R.; Bortolato, Marco; Eisenstein, Sarah A.; Fu, Jin; Oveisi, Fariba; Hohmann, Andrea G.; Piomelli, Daniele

2010-01-01

Social deprivation in early life disrupts emotionality and attentional processes in humans. Rearing rats in isolation reproduces some of these abnormalities, which are attenuated by daily handling. However, the neurochemical mechanisms underlying these responses remain poorly understood. We hypothesized that post-weaning social isolation alters the endocannabinoid system, a neuromodulatory system that controls emotional responding. We characterized behavioral consequences of social isolation and evaluated whether handling would reverse social isolation-induced alterations in behavioral reactivity to context and the endocannabinoid system. At weaning, pups were single or group housed and concomitantly handled or not handled daily until adulthood. Rats were tested in emotionality- and attentional-sensitive behavioral assays (open field, elevated plus maze, startle and prepulse inhibition). Cannabinoid receptor densities and endocannabinoid levels were quantified in a separate group of rats. Social isolation negatively altered behavioral responding. Socially-isolated rats that were handled showed less deficits in the open field, elevated plus maze, and prepulse inhibition tests. Social isolation produced site-specific alterations (supraoptic nucleus, ventrolateral thalamus, rostral striatum) in cannabinoid receptor densities compared to group rearing. Handling altered the endocannabinoid system in neural circuitry controlling emotional expression. Handling altered endocannabinoid content (prefrontal and piriform cortices, nucleus accumbens) and cannabinoid receptor densities (lateral globus pallidus, cingulate and piriform cortices, hippocampus) in a region-specific manner. Some effects of social isolation on the endocannabinoid system were moderated by handling. Isolates were unresponsive to handling-induced increases in cannabinoid receptor densities (caudal striatum, anterior thalamus), but were sensitive to handling-induced increases in endocannabinoid content (piriform cortex), compared to group-reared rats. Our findings suggest alterations in the endocannabinoid system may contribute to the abnormal isolate phenotype. Handling modifies the endocannabinoid system and behavioral reactivity to context, but surmounts only some effects of social isolation. These data implicate a pivotal role for the endocannabinoid system in stress adaptation and emotionality-related disturbances. PMID:20394803

On the measurement of stationary electric fields in air

NASA Technical Reports Server (NTRS)

Kirkham, H.

2002-01-01

Applications and measurement methods for field measurements are reviewed. Recent developments using optical technology are examined. The various methods are compared. It is concluded that the best general purpose instrument is the isolated cylindrical field mill, but MEMS technology could furnish better instruments in the future.

Evolution of an experimental population of Phytophthora capsici in the field

USDA-ARS?s Scientific Manuscript database

Populations of the vegetable pathogen Phytophthora capsici are often highly diverse, with limited gene flow between fields. To investigate the structure of a newly established, experimental population, an uninfested research field was inoculated with two single zoospore isolates of P. capsici in Sep...

Complete genome sequence of a novel pararetrovirus isolated from soybean

USDA-ARS?s Scientific Manuscript database

We report the complete genome sequence of Soybean Putnam pararetrovirus (SPPRV), a new pararetrovirus isolated from a soybean field in Putnam County, Ohio, USA. Comparison of SPPRV with other plant-infecting pararetroviruses places it in the genus Caulimovirus of the family Caulimoviridae....

Occurrence and Partial Characterization of Lettuce big vein associated virus and Mirafiori lettuce big vein virus in Lettuce in Iran.

PubMed

Alemzadeh, E; Izadpanah, K

2012-12-01

Mirafiori lettuce big vein virus (MiLBVV) and lettuce big vein associated virus (LBVaV) were found in association with big vein disease of lettuce in Iran. Analysis of part of the coat protein (CP) gene of Iranian isolates of LBVaV showed 97.1-100 % nucleotide sequence identity with other LBVaV isolates. Iranian isolates of MiLBVV belonged to subgroup A and showed 88.6-98.8 % nucleotide sequence identity with other isolates of this virus when amplified by PCR primer pair MiLV VP. The occurrence of both viruses in lettuce crop was associated with the presence of resting spores and zoosporangia of the fungus Olpidium brassicae in lettuce roots under field and greenhouse conditions. Two months after sowing lettuce seed in soil collected from a lettuce field with big vein affected plants, all seedlings were positive for LBVaV and MiLBVV, indicating soil transmission of both viruses.

Isolation and Molecular Characterization of Leptospira interrogans and Leptospira borgpetersenii Isolates from the Urban Rat Populations of Kuala Lumpur, Malaysia

PubMed Central

Benacer, Douadi; Zain, Siti Nursheena Mohd; Amran, Fairuz; Galloway, Renee L.; Thong, Kwai Lin

2013-01-01

Rats are considered the principal maintenance hosts of Leptospira. The objectives of this study were isolation and identification of Leptospira serovars circulating among urban rat populations in Kuala Lumpur. Three hundred urban rats (73% Rattus rattus and 27% R. norvegicus) from three different sites were trapped. Twenty cultures were positive for Leptospira using dark-field microscopy. R. rattus was the dominant carrier (70%). Polymerase chain reaction (PCR) confirmed that all isolates were pathogenic Leptospira species. Two Leptospira serogroups, Javanica and Bataviae, were identified using microscopic agglutination test (MAT). Pulsed-field gel electrophoresis (PFGE) identified two serovars in the urban rat populations: L. borgpetersenii serovar Javanica (85%) and L. interrogans serovar Bataviae (15%). We conclude that these two serovars are the major serovars circulating among the urban rat populations in Kuala Lumpur. Despite the low infection rate reported, the high pathogenicity of these serovars raises concern of public health risks caused by rodent transmission of leptospirosis. PMID:23358635

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.

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.

Characterizing isolated attosecond pulses with angular streaking

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

Li, Siqi; Guo, Zhaoheng; Coffee, Ryan N.

Here, we present a reconstruction algorithm for isolated attosecond pulses, which exploits the phase dependent energy modulation of a photoelectron ionized in the presence of a strong laser field. The energy modulation due to a circularly polarized laser field is manifest strongly in the angle-resolved photoelectron momentum distribution, allowing for complete reconstruction of the temporal and spectral profile of an attosecond burst. We show that this type of reconstruction algorithm is robust against counting noise and suitable for single-shot experiments. This algorithm holds potential for a variety of applications for attosecond pulse sources.

Characterizing isolated attosecond pulses with angular streaking

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

Li, Sigi; Guo, Zhaoheng; Coffee, Ryan N.

We present a reconstruction algorithm for isolated attosecond pulses, which exploits the phase dependent energy modulation of a photoelectron ionized in the presence of a strong laser field. The energy modulation due to a circularly polarized laser field is manifest strongly in the angle-resolved photoelectron momentum distribution, allowing for complete reconstruction of the temporal and spectral profile of an attosecond burst. We show that this type of reconstruction algorithm is robust against counting noise and suitable for single-shot experiments. This algorithm holds potential for a variety of applications for attosecond pulse sources.

Probable nosocomial transmission of listeriosis in neonates.

PubMed

Lazarus, C; Leclercq, A; Lecuit, M; Vaillant, V; Coignard, B; Blanchard, H; Novakova, I; Astagneau, P

2013-10-01

Listeria monocytogenes was isolated in two neonates born consecutively in the same hospital in France. The isolates had indistinguishable pulsed-field electrophoresis profiles. Retrospective epidemiological investigations found no evidence of a food-borne or environmental source. Infection control protocols and decontamination processes were in accordance with standard recommendations. The timing of onset of these infections within the same maternity unit, and the similarity of pulsed-field gel electrophoresis profiles suggests cross-infection of L. monocytogenes between the two neonates. Copyright © 2013 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Characterizing isolated attosecond pulses with angular streaking

DOE PAGES

Li, Siqi; Guo, Zhaoheng; Coffee, Ryan N.; ...

2018-02-12

Here, we present a reconstruction algorithm for isolated attosecond pulses, which exploits the phase dependent energy modulation of a photoelectron ionized in the presence of a strong laser field. The energy modulation due to a circularly polarized laser field is manifest strongly in the angle-resolved photoelectron momentum distribution, allowing for complete reconstruction of the temporal and spectral profile of an attosecond burst. We show that this type of reconstruction algorithm is robust against counting noise and suitable for single-shot experiments. This algorithm holds potential for a variety of applications for attosecond pulse sources.

Characterizing isolated attosecond pulses with angular streaking

DOE PAGES

Li, Sigi; Guo, Zhaoheng; Coffee, Ryan N.; ...

2018-02-13

We present a reconstruction algorithm for isolated attosecond pulses, which exploits the phase dependent energy modulation of a photoelectron ionized in the presence of a strong laser field. The energy modulation due to a circularly polarized laser field is manifest strongly in the angle-resolved photoelectron momentum distribution, allowing for complete reconstruction of the temporal and spectral profile of an attosecond burst. We show that this type of reconstruction algorithm is robust against counting noise and suitable for single-shot experiments. This algorithm holds potential for a variety of applications for attosecond pulse sources.

Complete genome sequence of the biofilm-forming Microbacterium sp. strain BH-3-3-3, isolated from conventional field-grown lettuce (Lactuca sativa) in Norway.

PubMed

Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

2017-03-01

The genus Microbacterium contains bacteria that are ubiquitously distributed in various environments and includes plant-associated bacteria that are able to colonize tissue of agricultural crop plants. Here, we report the 3,508,491 bp complete genome sequence of Microbacterium sp. strain BH-3-3-3, isolated from conventionally grown lettuce ( Lactuca sativa ) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017674.

Electric field control of magnetic states in isolated and dipole-coupled FeGa nanomagnets delineated on a PMN-PT substrate.

PubMed

Ahmad, Hasnain; Atulasimha, Jayasimha; Bandyopadhyay, Supriyo

2015-10-09

We report observation of a 'non-volatile' converse magneto-electric effect in elliptical FeGa nanomagnets delineated on a piezoelectric PMN-PT substrate. The nanomagnets are first magnetized with a magnetic field directed along their nominal major axes. Subsequent application of a strong electric field across the piezoelectric substrate generates strain in the substrate, which is partially transferred to the nanomagnets and rotates the magnetizations of some of them away from their initial orientations. The rotated magnetizations remain in their new orientations after the field is removed, resulting in 'non-volatility'. In isolated nanomagnets, the magnetization rotates by <90° upon application of the electric field, but in a dipole-coupled pair consisting of one 'hard' and one 'soft' nanomagnet, which are both initially magnetized in the same direction by the magnetic field, the soft nanomagnet's magnetization rotates by [Formula: see text] upon application of the electric field because of the dipole influence of the hard nanomagnet. This effect can be utilized for a nanomagnetic NOT logic gate.

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.

Rapid, high efficiency isolation of pancreatic ß-cells.

PubMed

Clardy, Susan M; Mohan, James F; Vinegoni, Claudio; Keliher, Edmund J; Iwamoto, Yoshiko; Benoist, Christophe; Mathis, Diane; Weissleder, Ralph

2015-09-02

The ability to isolate pure pancreatic ß-cells would greatly aid multiple areas of diabetes research. We developed a fluorescent exendin-4-like neopeptide conjugate for the rapid purification and isolation of functional mouse pancreatic β-cells. By targeting the glucagon-like peptide-1 receptor with the fluorescent conjugate, β-cells could be quickly isolated by flow cytometry and were >99% insulin positive. These studies were confirmed by immunostaining, microscopy and gene expression profiling on isolated cells. Gene expression profiling studies of cytofluorometrically sorted β-cells from 4 and 12 week old NOD mice provided new insights into the genetic programs at play of different stages of type-1 diabetes development. The described isolation method should have broad applicability to the β-cell field.

A Survey of Aflatoxin-Producing Aspergillus sp. from Peanut Field Soils in Four Agroecological Zones of China

PubMed Central

Zhang, Chushu; Selvaraj, Jonathan Nimal; Yang, Qingli; Liu, Yang

2017-01-01

Peanut pods are easily infected by aflatoxin-producing Aspergillus sp.ecies from field soil. To assess the aflatoxin-producing Aspergillus sp. in different peanut field soils, 344 aflatoxin-producing Aspergillus strains were isolated from 600 soil samples of four agroecological zones in China (the Southeast coastal zone (SEC), the Yangtze River zone (YZR), the Yellow River zone (YR) and the Northeast zone (NE)). Nearly 94.2% (324/344) of strains were A. flavus and 5.8% (20/344) of strains were A. parasiticus. YZR had the highest population density of Aspergillus sp. and positive rate of aflatoxin production in isolated strains (1039.3 cfu·g−1, 80.7%), the second was SEC (191.5 cfu·g−1, 48.7%), the third was YR (26.5 cfu·g−1, 22.7%), and the last was NE (2.4 cfu·g−1, 6.6%). The highest risk of AFB1 contamination on peanut was in YZR which had the largest number of AFB1 producing isolates in 1g soil, followed by SEC and YR, and the lowest was NE. The potential risk of AFB1 contamination in peanuts can increase with increasing population density and a positive rate of aflatoxin-producing Aspergillus sp. in field soils, suggesting that reducing aflatoxigenic Aspergillus sp. in field soils could prevent AFB1 contamination in peanuts. PMID:28117685

A Survey of Aflatoxin-Producing Aspergillus sp. from Peanut Field Soils in Four Agroecological Zones of China.

PubMed

Zhang, Chushu; Selvaraj, Jonathan Nimal; Yang, Qingli; Liu, Yang

2017-01-20

Peanut pods are easily infected by aflatoxin-producing Aspergillus sp.ecies from field soil. To assess the aflatoxin-producing Aspergillus sp. in different peanut field soils, 344 aflatoxin-producing Aspergillus strains were isolated from 600 soil samples of four agroecological zones in China (the Southeast coastal zone (SEC), the Yangtze River zone (YZR), the Yellow River zone (YR) and the Northeast zone (NE)). Nearly 94.2% (324/344) of strains were A. flavus and 5.8% (20/344) of strains were A. parasiticus . YZR had the highest population density of Aspergillus sp. and positive rate of aflatoxin production in isolated strains (1039.3 cfu·g -1 , 80.7%), the second was SEC (191.5 cfu·g -1 , 48.7%), the third was YR (26.5 cfu·g -1 , 22.7%), and the last was NE (2.4 cfu·g -1 , 6.6%). The highest risk of AFB₁ contamination on peanut was in YZR which had the largest number of AFB₁ producing isolates in 1g soil, followed by SEC and YR, and the lowest was NE. The potential risk of AFB₁ contamination in peanuts can increase with increasing population density and a positive rate of aflatoxin-producing Aspergillus sp. in field soils, suggesting that reducing aflatoxigenic Aspergillus sp. in field soils could prevent AFB₁ contamination in peanuts.

FIELD-SCALE EVALUATION OF IN SITU COSOLVENT FLUSHING FOR ENCHANCED AQUIFER REMEDIATION

EPA Science Inventory

A comprehensive, field-scale evaluation of in situ cosolvent flushing for enhanced remediation of nonaqueous phase liquid (NAPL)-contaminated aquifers was performed in a hydraulically isolated test cell (about 4.3 m x 3.6 m) constructed at a field site at Hill Air Force Base, Uta...

First field trials with fungi against Anoplophora glabripennis

Treesearch

Thomas Dubois; Ann Hajek; Hu Jiafu; Zengzhi Li

2003-01-01

We have been evaluating the use of entomopathogenic fungi against A. glabripennis; so far, 20 strains have been isolated belonging to three species, 14 strains have been tested in the laboratory, five strains have been evaluated in caged field trials and two strains have been tested in the open field.

Field transmission of a microsporidian pathogen of gypsy moth, Lymantria dispar

Treesearch

Thomas Kolling; Andreas Linde

2007-01-01

The quantification of the transmission of entomopathogens is important for the evaluation of their establishment and potential as biological control agents, however, only few field or semi-field studies were performed. The microsporidium Vairimorpha sp. was isolated from a gypsy moth (Lymantria dispar) population in Bulgaria and is...

Differential aggressiveness of Bipolaris microstegii and B. drechsleri on Japanese Stiltgrass

USDA-ARS?s Scientific Manuscript database

Six populations of Japanese stiltgrass (JSG, Microstegium vimineum) were tested for susceptibility to both Bipolaris microstegii (5 isolates) and B. drechsleri (3 isolates), each capable of causing severe leaf blight disease in the field and each with potential for biological control of this species...

Causes of cotton Fusarium wilt outbreaks in Georgia

USDA-ARS?s Scientific Manuscript database

Severe outbreaks of Fusarium wilt of cotton in Georgia since 2011 raised concerns about the genotypes of the causal pathogen Fusarium oxysporum. We isolated 492 F. oxysporum isolates from 107 wilted plants collected from 7 fields in 5 counties and determined their population structure utilizing veg...

Shock Train/Boundary-Layer Interaction in Rectangular Scramjet Isolators

NASA Astrophysics Data System (ADS)

Geerts, Jonathan Simon

Numerous studies of the dual-mode scramjet isolator, a critical component in preventing inlet unstart and/or vehicle loss by containing a collection of flow disturbances called a shock train, have been performed since the dual-mode propulsion cycle was introduced in the 1960s. Low momentum corner flow and other three-dimensional effects inherent to rectangular isolators have, however, been largely ignored in experimental studies of the boundary layer separation driven isolator shock train dynamics. Furthermore, the use of two dimensional diagnostic techniques in past works, be it single-perspective line-of-sight schlieren/shadowgraphy or single axis wall pressure measurements, have been unable to resolve the three-dimensional flow features inside the rectangular isolator. These flow characteristics need to be thoroughly understood if robust dual-mode scramjet designs are to be fielded. The work presented in this thesis is focused on experimentally analyzing shock train/boundary layer interactions from multiple perspectives in aspect ratio 1.0, 3.0, and 6.0 rectangular isolators with inflow Mach numbers ranging from 2.4 to 2.7. Secondary steady-state Computational Fluid Dynamics studies are performed to compare to the experimental results and to provide additional perspectives of the flow field. Specific issues that remain unresolved after decades of isolator shock train studies that are addressed in this work include the three-dimensional formation of the isolator shock train front, the spatial and temporal low momentum corner flow separation scales, the transient behavior of shock train/boundary layer interaction at specific coordinates along the isolator's lateral axis, and effects of the rectangular geometry on semi-empirical relations for shock train length prediction. (Abstract shortened by ProQuest.).

Historical distribution and host-vector diversity of Francisella tularensis, the causative agent of tularemia, in Ukraine.

PubMed

Hightower, Jake; Kracalik, Ian T; Vydayko, Nataliya; Goodin, Douglas; Glass, Gregory; Blackburn, Jason K

2014-10-16

Francisella tularensis, the causative agent of tularemia, is a zoonotic agent that remains across much of the northern hemisphere, where it exists in enzootic cycles. In Ukraine, tularemia has a long history that suggests a need for sustained surveillance in natural foci. To better characterize the host-vector diversity and spatial distribution of tularemia, we analyzed historical data from field collections carried out from 1941 to 2008. We analyzed the spatial-temporal distribution of bacterial isolates collected from field samples. Isolates were characterized by source and dominant land cover type. To identify environmental persistence and spatial variation in the source of isolation, we used the space-time permutation and multinomial models in SaTScan. A total of 3,086 positive isolates were taken from 1,084 geographic locations. Isolation of F. tularensis was more frequent among arthropods [n = 2,045 (66.3%)] followed by mammals [n = 619 (20.1%)], water [n = 393 (12.7%)], and farm produce [n = 29 (0.94%)], respectively. Four areas of persistent bacterial isolation were identified. Water and farm produce as sources of bacterial isolation were clustered. Our findings confirm the presence of long-standing natural foci of F. tularensis in Ukraine. Given the history of tularemia as well as its environmental persistence there exists a possibility of (re)emergence in human populations. Heterogeneity in the distribution of tularemia isolate recovery related to land cover type supports the theory of natural nidality and clusters identify areas to target potential sources of the pathogen and improve surveillance.

Subtyping of Canadian isolates of Salmonella Enteritidis using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) alone and in combination with Pulsed-Field Gel Electrophoresis (PFGE) and phage typing.

PubMed

Ziebell, Kim; Chui, Linda; King, Robin; Johnson, Suzanne; Boerlin, Patrick; Johnson, Roger P

2017-08-01

Salmonella enterica subspecies enterica serovar Enteritidis (SE) is one of the most common causes of human salmonellosis and in Canada currently accounts for over 40% of human cases. Reliable subtyping of isolates is required for outbreak detection and source attribution. However, Pulsed-Field Gel Electrophoresis (PFGE), the current standard subtyping method for Salmonella spp., is compromised by the high genetic homogeneity of SE. Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) was introduced to supplement PFGE, although there is a lack of data on the ability of MLVA to subtype Canadian isolates of SE. Three subtyping methods, PFGE, MLVA and phage typing were compared for their discriminatory power when applied to three panels of Canadian SE isolates: Panel 1: 70 isolates representing the diversity of phage types (PTs) and PFGE subtypes within these PTs; Panel 2: 214 apparently unrelated SE isolates of the most common PTs; and Panel 3: 27 isolates from 10 groups of epidemiologically related strains. For Panel 2 isolates, four MLVA subtypes were shared among 74% of unrelated isolates and in Panel 3 isolates, one MLVA subtype accounted for 62% of the isolates. For all panels, combining results from PFGE, MLVA and PT gave the best discrimination, except in Panel 1, where the combination of PT and PFGE was equally as high, due to the selection criteria for this panel. However, none of these methods is sufficiently discriminatory alone for reliable outbreak detection or source attribution, and must be applied together to achieve sufficient discrimination for practical purposes. Even then, some large clusters were not differentiated adequately. More discriminatory methods are required for reliable subtyping of this genetically highly homogeneous serovar. This need will likely be met by whole genome sequence analysis given the recent promising reports and as more laboratories implement this tool for outbreak response and surveillance. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterizations of purple non-sulfur bacteria isolated from paddy fields, and identification of strains with potential for plant growth-promotion, greenhouse gas mitigation and heavy metal bioremediation.

PubMed

Sakpirom, Jakkapan; Kantachote, Duangporn; Nunkaew, Tomorn; Khan, Eakalak

2017-04-01

This study was aimed at selecting purple non-sulfur bacteria (PNSB) isolated from various paddy fields, including Cd- and Zn-contaminated paddy fields, based on their biofertilizer properties. Among 235 PNSB isolates, strain TN110 was most effective in plant growth-promoting substance (PGPS) production, releasing 3.2 mg/L of [Formula: see text] , 4.11 mg/L of 5-aminolevulinic acid (ALA) and 3.62 mg/L of indole-3-acetic acid (IAA), and reducing methane emission up to 80%. This strain had nifH, vnfG and anfG, which are the Mo, V and Fe nitrogenase genes encoded for key enzymes in nitrogen fixation under different conditions. This strain provided 84% and 55% removal of Cd and Zn, respectively. Another isolate, TN414, not only produced PGPS (1.30 mg/L of [Formula: see text] , 0.94 mg/L of ALA and 0.65 mg/L of IAA), but was also efficient in removing both Cd and Zn at 72% and 74%, respectively. Based on 16S rDNA sequencing, strain TN110 was identified as Rhodopseudomonas palustris, while strain TN414 was Rubrivivax gelatinosus. A combination of TN110 and TN414 could potentially provide a biofertilizer, which is a greener alternative to commercial/chemical fertilizers and an agent for bioremediation of heavy metals and greenhouse gas mitigation in paddy fields. Copyright © 2016 Institut Pasteur. All rights reserved.

Impact of untreated urban waste on the prevalence and antibiotic resistance profiles of human opportunistic pathogens in agricultural soils from Burkina Faso.

PubMed

Youenou, Benjamin; Hien, Edmond; Deredjian, Amélie; Brothier, Elisabeth; Favre-Bonté, Sabine; Nazaret, Sylvie

2016-12-01

This study examined the long-term effects of the landfill disposal of untreated urban waste for soil fertilization on the prevalence and antibiotic resistance profiles of various human opportunistic pathogens in soils from Burkina Faso. Samples were collected at three sites in the periphery of Ouagadougou during two campaigns in 2008 and 2011. At each site, amendment led to changes in physico-chemical characteristics as shown by the increase in pH, CEC, total C, total N, and metal contents. Similarly, the numbers of total heterotrophic bacteria were higher in the amended fields than in the control ones. No sanitation indicators, i.e., coliforms, Staphylococci, and Enterococci, were detected. Pseudomonas aeruginosa and Burkholderia cepacia complex (Bcc) were detected at a low level in one amended field. Stenotrophomonas maltophilia was detected from both campaigns at the three sites in the amended fields and only once in an unamended field. Diversity analysis showed some opportunistic pathogen isolates to be closely related to reference clinical strains responsible for nosocomial- or community-acquired infections in Northern countries. Antibiotic resistance tests showed that P. aeruginosa and Bcc isolates had a wild-type phenotype and that most S. maltophilia isolates had a multi-drug resistance profile with resistance to 7 to 15 antibiotics. Then we were able to show that amendment led to an increase of some human opportunistic pathogens including multi-drug resistant isolates. Although the application of untreated urban waste increases both soil organic matter content and therefore soil fertility, the consequences of this practice on human health should be considered.

Use of a rep-PCR system to predict species in the Aspergillus section Nigri.

PubMed

Palencia, Edwin R; Klich, Maren A; Glenn, Anthony E; Bacon, Charles W

2009-10-01

The Aspergillus niger aggregate within the A. section Nigri is a group of black-spored aspergilli of great agro-economic importance whose well defined taxonomy has been elusive. Rep-PCR has become a rapid and cost-effective method for genotyping fungi and bacteria. In the present study, we evaluated the discriminatory power of a semi-automated rep-PCR barcoding system to distinguish morphotypic species and compare the results with the data obtained from ITS and partial calmodulin regions. For this purpose, 20 morphotyped black-spored Aspergillus species were used to create the A. section Nigri library in this barcoding system that served to identify 34 field isolates. A pair-wise similarity matrix was calculated using the cone-based Pearson correlation method and the dendrogram was generated by the unweighted pair group method with arithmetic mean (UPGMA), illustrating four different clustered groups: the uniseriate cluster (I), the Aspergillus carbonarius cluster (II), and. the two A. niger aggregate clusters (named III.A and III.B). Rep-PCR showed higher resolution than the ITS and the partial calmodulin gene analytical procedures. The data of the 34 unknown field isolates, collected from different locations in the United States, indicated that only 12% of the field isolates were >95% similar to one of the genotypes included in the A. section Nigri library. However, 64% of the field isolates matched genotypes with the reference library (similarity values >90%). Based on these results, this barcoding procedure has the potential for use as a reproducible tool for identifying the black-spored aspergilli.

The establishment of Enterobacteriaceae and Salmonella London in a new dairy farm environment.

PubMed

Shipp, Ginger M; Dickson, James S

2011-03-01

Salmonella spp. are important zoonotic pathogens in humans and animals. A longitudinal study was conducted at the Iowa State University's campus (at the Dairy/Animal Science Education and Discovery Facility) to observe change in Enterobacteriaceae (specifically Salmonella) before and after the placement of dairy livestock. To our knowledge, this is the first study that evaluated environmental changes of Gram-negative organisms in a new dairy farm environment. Environmental samples were taken using drag swabs and immediately processed in the laboratory using phenotypic methods (replica plating, the BBL Crystal Identification System for enteric/nonfermenter organisms™, and plating on specialized media/broths). Genotypic methods were also used (BAX PCR™ and pulsed-field gel electrophoresis). Organisms identified as Salmonella were sent to the National Veterinary Services Laboratory (Ames, IA) for confirmatory serotyping. Resistance to antibiotics (ampicillin, nalidixic acid, and tetracycline) was determined by replica plating of Enterobacteriaceae and Salmonella isolates using the guidelines of the National Antimicrobial Resistance Monitoring System and Clinical and Laboratory Standards Institute. The microflora of Enterobacteriaceae changed as cattle were introduced and as time progressed. Additionally, multidrug-resistant isolates began to appear immediately after cattle were introduced (multidrug-resistant isolates were rare prior to introduction of livestock). Variables such as temperature and humidity did not affect the proliferation of bacterial organisms. Seventeen Salmonella isolates were identified as Salmonella London and three isolates as Salmonella Montevideo. Based on pulsed-field gel electrophoresis-generated dendrograms, it is likely that 17 Salmonella London isolates and 3 Salmonella Montevideo isolates are clonal.

Outbreak of scarlet fever associated with emm12 type group A Streptococcus in 2011 in Shanghai, China.

PubMed

Chen, Mingliang; Yao, Weilei; Wang, Xiaohong; Li, Yuefang; Chen, Min; Wang, Gangyi; Zhang, Xi; Pan, Hao; Hu, Jiayu; Zeng, Mei

2012-09-01

An unprecedented, large outbreak of childhood scarlet fever occurred in Shanghai between April and July 2011. Investigation of the epidemiology could enhance our understanding of the factors related to the outbreak. We retrospectively analyzed the demographic and seasonal characteristics of children with scarlet fever and the outcome. During the peak month of the 2011 outbreak, 45 GAS isolates recovered from pediatric patients and 13 (43.3%) GAS isolates recovered from 30 asymptomatic student contacts were characterized by emm typing, superantigen profiles, pulsed-field gel electrophoresis genotypes, mutilocus sequence typing and antimicrobial susceptibility. The 2011 outbreak of scarlet fever started in April and peaked in May and June. Boys outnumbered girls (65.1% versus 34.9%). Preschool and primary school children accounted for 96% of cases. No severe outcome was found. emm1, emm12 and emm75 were identified among 58 GAS isolates, and 53 (91.4%) isolates belonged to emm12, st36. Ten pulsed-field gel electrophoresis genotypes were identified among emm12 GAS isolates, 43 (81.1%) shared SPYS16.001 genotype and the remaining 7 genotypes detected were related to SPYS16.001 closely or possibly. No streptococcal pyrogenic exotoxin A and streptococcal pyrogenic exotoxin M were detected in 58 isolates. All emm12 GAS isolates were resistant to azithromycin and clindamycin. emm12 GAS strain caused the large 2011 outbreak of scarlet fever in Shanghai. Antibiotic resistance to macrolides and clindamycin in GAS is prevalent in Shanghai.

Bordetella pertussis, Finland and France

PubMed Central

Elomaa, Annika; Brun, Delphine; Mertsola, Jussi; He, Qiushui; Guiso, Nicole

2006-01-01

We used pulsed-field gel electrophoresis analysis and genotyping to compare clinical isolates of Bordetella pertussis recovered since the early 1990s in Finland and France, 2 countries with similar histories of long-term mass vaccination with whole-cell pertussis vaccines. Isolates from both countries were similar genetically but varied temporally. PMID:16707058

Three pythium species isolated from severely stunted wheat during an outbreak in North Carolina

USDA-ARS?s Scientific Manuscript database

Large portions of eastern North Carolina experienced prolonged soil waterlogging in 2016. Severely stunted wheat plants from saturated fields were examined and Pythium consistently was associated with the symptoms observed. Three species of Pythium were identified among 15 isolates derived from wh...

Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases

USDA-ARS?s Scientific Manuscript database

The objectives of this study were; first, to describe gamithromycin susceptibility of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from cattle diagnosed with bovine respiratory disease (BRD) and previously treated with either gamithromycin for control of BRD (mass me...

The electric field changes and UHF radiations caused by the triggered lightning in Japan

NASA Technical Reports Server (NTRS)

Kawasaki, Zen-Ichiro; Kanao, Tadashi; Matsuura, Kenji; Nakano, Minoru; Horii, Kenji; Nakamura, Koichi

1991-01-01

In the rocket triggered lightning experiment of fiscal 1989, researchers observed electromagnetic field changes and UHF electromagnetic radiation accompanying rocket triggered lightning. It was found that no rapid changes corresponding to the return stroke of natural lightning were observed in the electric field changes accompanying rocket triggered lightning. However, continuous currents were present. In the case of rocket triggered lightning to the tower, electromagnetic field changes corresponding to the initiation of triggered lightning showed a bipolar pulse of a relatively large amplitude. In contrast, the rocket triggered lightning to the ground did not have such a bipolar pulse. The UHF radiation accompanying the rocket triggered lightning preceded the waveform portions corresponding to the first changes in electromagnetic fields. The number of isolated pulses in the UHF radiation showed a correlation with the time duration from rocket launching up to triggered lightning. The time interval between consecutive isolated pulses tended to get shorter with the passage of time, just like the stepped leaders of natural lightning.

Grain-grain interaction in stationary dusty plasma

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

Lampe, Martin; Joyce, Glenn

We present a particle-in-cell simulation study of the steady-state interaction between two stationary dust grains in uniform stationary plasma. Both the electrostatic force and the shadowing force on the grains are calculated explicitly. The electrostatic force is always repulsive. For two grains of the same size, the electrostatic force is very nearly equal to the shielded electric field due to a single isolated grain, acting on the charge of the other grain. For two grains of unequal size, the electrostatic force on the smaller grain is smaller than the isolated-grain field, and the force on the larger grain is largermore » than the isolated-grain field. In all cases, the attractive shadowing force exceeds the repulsive electrostatic force when the grain separation d is greater than an equilibrium separation d{sub 0}. d{sub 0} is found to be between 6λ{sub D} and 9λ{sub D} in all cases. The binding energy is estimated to be between 19 eV and 900 eV for various cases.« less

[Experimental transmission of Cryptosporidium baileyi (Apicomplexa: Cryptosporidiidae) isolated of broiler chicken to Japanese quail (Coturnix japonica)].

PubMed

Cardozo, Sergian V; Teixeira Filho, Walter L; Lopes, Carlos Wilson G

2005-01-01

In this work, oocysts of Cryptosporidium baileyi were isolated and identified in broiler chickens from three different Municipalities of the State of Rio de Janeiro, where they were isolated and identified by using the centrifuge- flotation technique associated to bright-field. Staining techniques, such as: modified Ziehl-Neelsen and safranin-methylene blue, were carried out to confirm natural infection. Oocysts of C. baileyi from broiler chickens were able to infect Coccidia-free Japanese quails, by observation of endogenous stages at histological sections, and the elimination of oocysts in the feces with prepatent period of seven days and patent period of 21 days after infection. Oocysts of C. baileyi from broiler chickens and Japanese quails were similar on bright-field microscopy. With respect to the staining techniques used in this research, all of them left to significant changes in length and width of oocysts, but shape indexes were maintained. Bright-field microscopy was the best technique for oocysts comparison shed by broiler chickens and Japanese quail because of no different among oocysts were observed.

Development and characterization of neutralizing monoclonal antibodies against canine distemper virus hemagglutinin protein.

PubMed

Bi, Zhenwei; Xia, Xingxia; Wang, Yongshan; Mei, Yongjie

2015-04-01

Canine distemper virus (CDV) causes a serious multisystemic disease in dogs and other carnivora. Hemagglutinin (H) protein-specific antibodies are mainly responsible for protective immunity against CDV infection. In the present study, six neutralizing MAbs to the H protein of CDV were newly obtained and characterized by immunizing BALB/c mice with a recent Chinese field isolate. Competitive binding inhibition assay revealed that they recognized four distinct antigenic regions of the H protein. Immunofluorescence assay and western blotting showed that all MAbs recognize the conformational rather than the linear epitopes of the H protein. Furthermore, in immunofluorescence and virus neutralization assays, two of the MAbs were found to react only with the recent Chinese field isolate and not with older CDV strains, including vaccine strain Onderstepoort, indicating there are neutralization-related antigenic variations between the recent Chinese field isolate and the older CDV strains examined in this study. The newly established MAbs are useful for differentiating the expanding CDV strains and could be used in immunotherapy and immunodiagnosis against infection with CDV. © 2015 The Societies and Wiley Publishing Asia Pty Ltd.

Similarities between Salmonella Enteritidis isolated from humans and captive wild animals in South Africa.

PubMed

Smith, Anthony M; Ismail, Husna; Henton, Maryke M; Keddy, Karen H

2014-12-15

Salmonella is well recognized as an aetiological agent of gastrointestinal and diarrhoeal disease. Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) is one of the commonest serotypes associated with foodborne illness. In South Africa, we compared Salmonella Enteritidis strains isolated from humans with gastroenteritis and strains isolated from captive wild animals, between June 2011 and July 2012. Bacteria were phenotypically characterized using standard microbiological techniques. Genotypic relatedness of isolates was investigated by pulsed-field gel electrophoresis (PFGE) analysis. a diversity of 27 PFGE patterns amongst 196 human non-invasive isolates was shown; two PFGE patterns predominated and accounted for 74% of all human isolates. Human isolates showed a 12% prevalence rate for nalidixic acid resistance. Animal isolates from 5 different sources were investigated. With the exception of an isolate from a ground hornbill, all animal isolates (jaguar, crocodile, lion and poultry) showed PFGE pattern matches to a human isolate. Animal isolates showed susceptibility to all antimicrobial agents tested, with the exception of nalidixic acid resistance in isolates from the lion and poultry source. Our data showed similarities between Salmonella Enteritidis strains isolated from humans and captive wild animals, suggesting a probable common source for strains from humans and animals.

Theoretical exploration of control factors for the high-order harmonic generation (HHG) spectrum in two-color field.

PubMed

Huang, Xinting; Yang, Dapeng; Yao, Li

2014-09-15

In this work, the laser-parameter effects on the high-order harmonic generation (HHG) spectrum and attosecond trains by mixing two-color laser field, a visible light field of 800 nm and a mid-infrared (mid-IR) laser pulses of 2400 nm, are theoretically demonstrated for the first time. Different schemes are applied to discuss the function of intensity, carrier-envelope phase (CEP) and pulse duration on the generation of an isolated attosecond pulse. As a consequence, an isolated 16as pulse is obtained by Fourier transforming an ultrabroad XUV continuum of 208 eV with the fundamental field of duration of 6 fs, 9×10(14)W/cm2 of intensity, the duration of 12 fs, the CEPs of the two driving pulses of -π and the relative strength ratio √R=0.2. Copyright © 2014 Elsevier B.V. All rights reserved.

Nucleic adaptability of heterokaryons to fungicides in a multinucleate fungus, Sclerotinia homoeocarpa.

PubMed

Kessler, Dylan; Sang, Hyunkyu; Bousquet, Amanda; Hulvey, Jonathan P; Garcia, Dawlyn; Rhee, Siyeon; Hoshino, Yoichiro; Yamada, Toshihiko; Jung, Geunhwa

2018-06-01

Sclerotinia homoeocarpa is the causal organism of dollar spot in turfgrasses and is a multinucleate fungus with a history of resistance to multiple fungicide classes. Heterokaryosis gives rise to the coexistence of genetically distinct nuclei within a cell, which contributes to genotypic and phenotypic plasticity in multinucleate fungi. We demonstrate that field isolates, resistant to either a demethylation inhibitor or methyl benzimidazole carbamate fungicide, can form heterokaryons with resistance to each fungicide and adaptability to serial combinations of different fungicide concentrations. Field isolates and putative heterokaryons were assayed on fungicide-amended media for in vitro sensitivity. Shifts in fungicide sensitivity and microsatellite genotypes indicated that heterokaryons could adapt to changes in fungicide pressure. Presence of both nuclei in heterokaryons was confirmed by detection of a single nucleotide polymorphism in the β-tubulin gene, the presence of microsatellite alleles of both field isolates, and the live-cell imaging of two different fluorescently tagged nuclei using laser scanning confocal microscopy. Nucleic adaptability of heterokaryons to fungicides was strongly supported by the visualization of changes in fluorescently labeled nuclei to fungicide pressure. Results from this study suggest that heterokaryosis is a mechanism by which the pathogen adapts to multiple fungicide pressures in the field. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular characterization of Coxiella burnetii isolates.

PubMed Central

Jäger, C.; Willems, H.; Thiele, D.; Baljer, G.

1998-01-01

Restriction fragment length polymorphism (RFLP) was used for the differentiation of 80 Coxiella burnetii isolates derived from animals and humans in Europe, USA, Africa and Asia. After NotI restriction of total C. burnetii DNA and pulsed field gel electrophoresis (PFGE) 20 different restriction patterns were distinguished. The index of discrimination for this typing system was 0.86. Comparison and phylogenetic analysis of the different RFLP patterns revealed evolutionary relationships among groups that corresponded to the geographical origin of the isolates. This finding was confirmed by genetic mapping. No correlation between restriction group and virulence of isolates was detected. PMID:9593485

Indistinguishable NDM-producing Escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017

PubMed Central

Mahon, Bláthnaid M; Brehony, Carina; McGrath, Elaine; Killeen, James; Cormican, Martin; Hickey, Paul; Keane, Shane; Hanahoe, Belinda; Dolan, Ann; Morris, Dearbháile

2017-01-01

In this study, New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae were identified in Irish recreational waters and sewage. Indistinguishable NDM-producing Escherichia coli by pulsed-field gel electrophoresis were isolated from sewage, a fresh water stream and a human source. NDM-producing Klebsiella pneumoniae isolated from sewage and seawater in the same area were closely related to each other and to a human isolate. This raises concerns regarding the potential for sewage discharges to contribute to the spread of carbapenemase-producing Enterobacteriaceae. PMID:28449738

Hollow-cylinder waveguide isolators for use at millimeter wavelengths

NASA Technical Reports Server (NTRS)

Kanda, M.; May, W. G.

1974-01-01

The device considered in this study is a semiconductor waveguide isolator consisting of a hollow column of a semiconductor mounted coaxially 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 (MMA) are presented. These theoretical predictions are compared with experimental results for an InSb isolator at 94 GHz and 75 K.

Application of pulsed-field gel electrophoresis to characterise and trace the prevalence of Enterobacter sakazakii in an infant formula processing facility.

PubMed

Mullane, N R; Whyte, P; Wall, P G; Quinn, T; Fanning, S

2007-05-01

Enterobacter sakazakii (E. sakazakii) contamination of powdered infant formula (PIF) and its processing environment was monitored between April 2005 and March 2006. The purpose of the monitoring programme was to locate points of contamination, investigate clonal persistence, and identify possible dissemination routes along the processing chain. A total of 80 E. sakazakii isolates were recovered from the manufacturing facility. The overall frequency of isolation of E. sakazakii in intermediate and final product was 2.5%, while specific locations in the processing environment were contaminated at frequencies up to 31%. All E. sakazakii isolates were characterised by pulsed-field gel electrophoresis (PFGE). XbaI macrorestriction digests yielded 19 unique pulse-types that could be grouped into 6 clusters of between 5 and 32 isolates. The formation of large clusters was consistent with the presence of a number of clones in the manufacturing environment. While the majority of isolates were of environmental origin (72.5%), no cluster was confined to one specific location and indistinguishable PFGE profiles were generated from isolates cultured from the manufacturing environment, sampling points along the processing chain and from intermediate and final product. These findings suggest that the manufacturing environment serves as a key route for sporadic contamination of PIF. These data will support the development of efficient intervention measures contributing to the reduction of E. sakazakii in the PIF processing chain.

Change in antimicrobial susceptibility of Mycoplasma gallisepticum field isolates.

PubMed

Gharaibeh, Saad; Al-Rashdan, Mohammad

2011-06-02

This study compares the antimicrobial susceptibility over time between two groups of Mycoplasma gallisepticum (MG) isolates from the same geographical area. Minimum inhibitory concentration of 13 antimicrobials was determined against two groups of MG isolates from chickens. Group 1 strains (n=22) were isolated in 2004-2005 while group 2 strains (n=7) were isolated in 2007-2008. Minimum inhibitory concentration 50 for group 1 versus group 2 was 4/4, 0.5/0.5, ≤ 0.031/≥ 64, ≤ 0.031/2, ≤ 0.031/0.125, 1/0.5, 1/1, ≤ 0.031/≤ 0.031, ≤ 0.031/2, ≤ 0.031/2, 1/4, ≤ 0.031/0.062, and 0.062/2 μg/ml against gentamicin, spectinomycin, erythromycin, tilmicosin, tylosin, florfenicol, thiamphenicol, tiamulin, ciprofloxacin, enrofloxacin, chlortetracycline, doxycycline, and oxytetracycline, respectively. There was a statistically significant increase in resistance of group 2 to erythromycin, tilmicosin, tylosin, ciprofloxacin, enrofloxacin, chlortetracycline, doxycycline, and oxytetracycline. This dramatic increase in resistance against 8 antimicrobials belonging to three different families of antimicrobials in a relatively short period of time appears to be rare and of concern. The cause of this increased resistance observed in group 2 of MG isolates was not determined and should be further investigated. Monitoring of MG field strain susceptibility is highly recommended to implement successful treatment and prophylaxis programs in endemic areas. Copyright © 2011 Elsevier B.V. All rights reserved.

Currents and fields of thin conductors in rf saddle coils.

PubMed

Carlson, J W

1986-10-01

The current distribution on thin conductors and rf field homogeneity for rf coils is described theoretically. After a pedagogical introduction to the techniques and an exact solution for the current or an isolated strip conductor, this article describes current distribution and field uniformity for a variety of conventional and quadrature rf coil designs.

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.

CHAMP Magnetic Anomalies of the Antarctic Crust

NASA Technical Reports Server (NTRS)

Kim, Hyung Rae; Gaya-Pique, Luis R.; vonFrese, Ralph R. B.; Taylor, Patrick T.; Kim, Jeong Woo

2003-01-01

Regional magnetic signals of the crust are strongly masked by the core field and its secular variations components and hence difficult to isolate in the satellite measurements. In particular, the un-modeled effects of the strong auroral external fields and the complicated- behavior of the core field near the geomagnetic poles conspire to greatly reduce the crustal magnetic signal-to-noise ratio in the polar regions relative to the rest of the Earth. We can, however, use spectral correlation theory to filter the static lithospheric and core field components from the dynamic external field effects. To help isolate regional lithospheric from core field components, the correlations between CHAMP magnetic anomalies and the pseudo magnetic effects inferred from gravity-derived crustal thickness variations can also be exploited.. Employing these procedures, we processed the CHAMP magnetic observations for an improved magnetic anomaly map of the Antarctic crust. Relative to the much higher altitude Orsted and noisier Magsat observations, the CHAMP magnetic anomalies at 400 km altitude reveal new details on the effects of intracrustal magnetic features and crustal thickness variations of the Antarctic.

Quincke random walkers

NASA Astrophysics Data System (ADS)

Pradillo, Gerardo; Heintz, Aneesh; Vlahovska, Petia

2017-11-01

The spontaneous rotation of a sphere in an applied uniform DC electric field (Quincke effect) has been utilized to engineer self-propelled particles: if the sphere is initially resting on a surface, it rolls. The Quincke rollers have been widely used as a model system to study collective behavior in ``active'' suspensions. If the applied field is DC, an isolated Quincke roller follows a straight line trajectory. In this talk, we discuss the design of a Quincke roller that executes a random-walk-like behavior. We utilize AC field - upon reversal of the field direction a fluctuation in the axis of rotation (which is degenerate in the plane perpendicular to the field and parallel to the surface) introduces randomness in the direction of motion. The MSD of an isolated Quincke walker depends on frequency, amplitude, and waveform of the electric field. Experiment and theory are compared. We also investigate the collective behavior of Quincke walkers,the transport of inert particles in a bath of Quincke walkers, and the spontaneous motion of a drop containing Quincke active particle. supported by NSF Grant CBET 1437545.

Quantitative and Isolated Measurement of Far-Field Light Scattering by a Single Nanostructure

NASA Astrophysics Data System (ADS)

Kim, Donghyeong; Jeong, Kwang-Yong; Kim, Jinhyung; Ee, Ho-Seok; Kang, Ju-Hyung; Park, Hong-Gyu; Seo, Min-Kyo

2017-11-01

Light scattering by nanostructures has facilitated research on various optical phenomena and applications by interfacing the near fields and free-propagating radiation. However, direct quantitative measurement of far-field scattering by a single nanostructure on the wavelength scale or less is highly challenging. Conventional back-focal-plane imaging covers only a limited solid angle determined by the numerical aperture of the objectives and suffers from optical aberration and distortion. Here, we present a quantitative measurement of the differential far-field scattering cross section of a single nanostructure over the full hemisphere. In goniometer-based far-field scanning with a high signal-to-noise ratio of approximately 27.4 dB, weak scattering signals are efficiently isolated and detected under total-internal-reflection illumination. Systematic measurements reveal that the total and differential scattering cross sections of a Au nanorod are determined by the plasmonic Fabry-Perot resonances and the phase-matching conditions to the free-propagating radiation, respectively. We believe that our angle-resolved far-field measurement scheme provides a way to investigate and evaluate the physical properties and performance of nano-optical materials and phenomena.

High pressure xenon ionization detector

DOEpatents

Markey, J.K.

1989-11-14

A method is provided for detecting ionization comprising allowing particles that cause ionization to contact high pressure xenon maintained at or near its critical point and measuring the amount of ionization. An apparatus is provided for detecting ionization, the apparatus comprising a vessel containing a ionizable medium, the vessel having an inlet to allow high pressure ionizable medium to enter the vessel, a means to permit particles that cause ionization of the medium to enter the vessel, an anode, a cathode, a grid and a plurality of annular field shaping rings, the field shaping rings being electrically isolated from one another, the anode, cathode, grid and field shaping rings being electrically isolated from one another in order to form an electric field between the cathode and the anode, the electric field originating at the anode and terminating at the cathode, the grid being disposed between the cathode and the anode, the field shaping rings being disposed between the cathode and the grid, the improvement comprising the medium being xenon and the vessel being maintained at a pressure of 50 to 70 atmospheres and a temperature of 0 to 30 C. 2 figs.

High pressure xenon ionization detector

DOEpatents

Markey, John K.

1989-01-01

A method is provided for detecting ionization comprising allowing particles that cause ionization to contact high pressure xenon maintained at or near its critical point and measuring the amount of ionization. An apparatus is provided for detecting ionization, the apparatus comprising a vessel containing a ionizable medium, the vessel having an inlet to allow high pressure ionizable medium to enter the vessel, a means to permit particles that cause ionization of the medium to enter the vessel, an anode, a cathode, a grid and a plurality of annular field shaping rings, the field shaping rings being electrically isolated from one another, the anode, cathode, grid and field shaping rings being electrically isolated from one another in order to form an electric field between the cathode and the anode, the electric field originating at the anode and terminating at the cathode, the grid being disposed between the cathode and the anode, the field shaping rings being disposed between the cathode and the grid, the improvement comprising the medium being xenon and the vessel being maintained at a pressure of 50 to 70 atmospheres and a temperature of 0.degree. to 30.degree. C.

Genetic Diversity of Plasmodium falciparum Field Isolates in Central Sudan Inferred by PCR Genotyping of Merozoite Surface Protein 1 and 2.

PubMed

Hamid, Muzamil M Abdel; Mohammed, Sara B; El Hassan, Ibrahim M

2013-02-01

Characterization of Plasmodium falciparum diversity is commonly achieved by amplification of the polymorphic regions of the merozoite surface proteins 1 (MSP1) and 2 (MSP2) genes. The present study aimed to determine the allelic variants distribution of MSP1 and MSP2 and multiplicity of infection in P. falciparum field isolates from Kosti, central Sudan, an area characterized by seasonal malaria transmission. Total 121 samples (N = 121) were collected during a cross-sectional survey between March and April 2003. DNA was extracted and MSP1 and MSP2 polymorphic loci were genotyped. The total number of alleles identified in MSP1 block 2 was 11, while 16 alleles were observed in MSP2 block 3. In MSP1, RO33 was found to be the predominant allelic type, carried alone or in combination with MAD20 and K1 types, whereas FC27 family was the most prevalent in MSP2. Sixty two percent of isolates had multiple genotypes and the overall mean multiplicity of infection was 1.93 (CI 95% 1.66-2.20). Age correlated with parasite density (P = 0.017). In addition, a positive correlation was observed between parasite densities and the number of alleles (P = 0.022). Genetic diversity in P. falciparum field isolates in central Sudan was high and consisted of multiple clones.

Field studies on two rock phosphate solubilizing actinomycete isolates as biofertilizer sources

NASA Astrophysics Data System (ADS)

Mba, Caroline C.

1994-03-01

Recently biotechnology is focusing attention on utilization of biological resources to solve a number of environmental problems such as soil fertility management. Results of microbial studies on earthworm compost in the University of Nigeria farm identified a number of rock phosphate solubilizing actinomycetes. Two of these, isclates 02 and 13, were found to be efficient rock phosphate (RP) solubilizers and fast-growing cellulolytic microbes producing extracellular hydrolase enzymes. In this preliminary field study the two microbial isolates were investigated with respect to their effects on the growth of soybean and egusi as well as their effect on the incidence of toxicity of poultry droppings. Application of these isolates in poultry manure-treated field plots, as microbial fertilizers, brought about yield increases of 43% and 17% with soybeans and 19% and 33% with egusi, respectively. Soil properties were also improved. With isolates 02 and 13, the soil available phosphorus increased at the five-leaf stage, while N-fixation in the soil increased by 45% or 11% relative to control. It was further observed that air-dried poultry manure after four days of incubation was still toxic to soybean. The toxic effect of the applied poultry manure was reduced or eliminated with microbial fertilizers 02 or 13, respectively. The beneficial effects of the microbial organic fertilizer are discussed. Justification for more intensive research on rock phosphate organic fertilizer is highlighted.

Genetic and antigenic relationships of vesicular stomatitis viruses from South America.

PubMed

Pauszek, Steven J; Barrera, Jose Del C; Goldberg, Tony; Allende, Rossana; Rodriguez, Luis L

2011-11-01

Vesicular stomatitis (VS) viruses have been classified into two serotypes: New Jersey (VSNJV) and Indiana (VSIV). Here, we have characterized field isolates causing vesicular stomatitis in Brazil and Argentina over a 35-year span. Cluster analysis based on either serological relatedness, as inferred from virus neutralization and complement fixation assays, or nucleotide sequences of two separate genes (phosphoprotein or glycoprotein) grouped the field isolates into two distinct monophyletic groups within the Indiana serogroup. One group included seven viruses from Brazil and Argentina that were serologically classified as Indiana-2 and Cocal virus (COCV). The other group contained three viruses from Brazil that were serologically classified as Indiana-3 and the prototype of this group, Alagoas virus (VSAV). Interestingly, two vesiculoviruses that were isolated from insects but do not cause disease in animals, one from Brazil (Maraba virus; MARAV) and the other from Colombia (CoAr 171638), grouped into two separate genetic lineages within the Indiana serotype. Our data provide support for the classification of viruses causing clinical VS in livestock in Brazil and Argentina into two distinct groups: Indiana-2 (VSIV-2) and Indiana-3 (VSIV-3). We suggest using nomenclature for these viruses that includes the serotype, year and place of occurrence, and affected host. This nomenclature is consistent with that currently utilized to describe field isolates of VSNJV or VSIV in scientific literature.

An integrated tunable isolator based on NiZn film fabricated by spin-spray plating

NASA Astrophysics Data System (ADS)

Guo, Rongdi; Lin, Hwaider; Shi, Wei; Gao, Yuan; Wang, Zhiguang; Sun, Nian Xiang; Yu, Zhong; Lan, Zhongwen

2018-05-01

An innovative type of tunable isolator with a planar comb-like microstrip transmission line, which generate circular polarization magnetic field, has been realized with polycrystalline NiZn ferrite thick films fabricated by spin-spray plating (SSP) process with thickness of 10μm. The phase compositions, microstructure, magnetic hysteresis loop, and ferromagnetic resonance (FMR) linewidth of NiZn ferrite thick films have been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), vibrating sample magnetometer (VSM) and electron spin resonance (ESR) spectrometer, respectively. The NiZn ferrite thick films possess 4800Gauss saturation magnetization and 190Oe FMR linewidth measured at X-band. With an in-plane dc magnetic bias perpendicular to the comb-like microstrip transmission line, the transmission direction of left-hand circular polarization (LHCP) and right-hand circular polarization (RHCP) were proved to be opposite. The non-reciprocal ferromagnetic resonance absorption leads to 11.6dB isolation and 5.78dB insertion loss at 17.57GHz with magnetic bias field of 3.5kOe. Furthermore, with external in-plane magnetic fields range from 0.5kOe to 3.5kOe, the central frequency was tuned from 5.63GHz to 17.57GHz. The state-of-the-art tunable isolator with a planar comb-like microstrip transmission line exhibit a great potential to be applied in different microwave components and radar system.

Isolation, identification and field tests of the sex pheromone of the carambola fruit borer, Eucosma notanthes.

PubMed

Hung, C C; Hwang, J S; Hung, M D; Yen, Y P; Hou, R F

2001-09-01

Two components, (Z)-8-dodecenyl acetate (Z8-12:Ac) and (Z)-8-dodecenol (Z8-12:OH), were isolated from sex pheromone glands of the carambola fruit borer, Eucosma notanthes, and were identified by GC, and GC-MS, chemical derivatization, and comparison of retention times. The ratio of the alcohol to acetate in the sex pheromone extracts was 2.7. However, synthetic mixtures (1 mg) in ratios ranging from 0.5 to 1.5 were more effective than other blends in trapping male moths in field tests.

Low power electromagnetic flowmeter providing accurate zero set

NASA Technical Reports Server (NTRS)

Fryer, T. B. (Inventor)

1971-01-01

A low power, small size electromagnetic flowmeter system is described which produces a zero output signal for zero flow. The system comprises an air core type electromagnetic flow transducer, a field current supply circuit for the transducer coils and a pre-amplifier and demodulation circuit connected to the output of the transducer. To prevent spurious signals at zero flow, separate, isolated power supplies are provided for the two circuits. The demodulator includes a pair of synchronous rectifiers which are controlled by signals from the field current supply circuit. Pulse transformer connected in front of the synchronous rectifiers provide isolation between the two circuits.

Genetic deletion of HRP2 and HRP3 in Indian Plasmodium falciparum population and false negative malaria rapid diagnostic test.

PubMed

Kumar, Navin; Pande, Veena; Bhatt, R M; Shah, Naman K; Mishra, Neelima; Srivastava, Bina; Valecha, Neena; Anvikar, Anupkumar R

2013-01-01

Genetic polymorphisms in diagnostic antigens are important factors responsible for variable performance of rapid diagnostic tests. Additionally, the failure of antigen expression due to gene deletion may also contribute to variable performance. We report Indian Plasmodium falciparum field isolates lacking both Pfhrp2 and Pfhrp3 genes leading to false negative results of rapid diagnostic tests. The study highlights need to determine the prevalence of P. falciparum isolates lacking these genes in larger field populations in India. Copyright © 2012 Elsevier B.V. All rights reserved.

Case report of Salmonella cross-contamination in a food laboratory.

PubMed

Rasschaert, Geertrui; De Reu, K; Heyndrickx, M; Herman, L

2016-03-10

This paper describes a case of Salmonella cross-contamination in a food laboratory. In 2012, chocolate bars shipped from Belgium to the USA were prevented from entering the USA because a Salmonella Rissen strain had been isolated from one of the chocolate bars in a Belgian food laboratory. However, a retrospective study of the Salmonella isolates sent from the laboratory to the Belgian National Reference Laboratory for Salmonella revealed that 7 weeks prior, a Salmonella Rissen strain has been isolated from fish meal in the same food laboratory. The chocolate bars were not expected to be contaminated with Salmonella because the ingredients all tested negative during the production process. Furthermore, because Salmonella Rissen is only rarely isolated from food, it was hypothesized that the two Salmonella Rissen isolates belonged to the same strain and that the second isolation event in this laboratory was caused by cross-contamination. To confirm this hypothesis, both Salmonella Rissen isolates were fingerprinted using different molecular techniques. To evaluate the discriminatory power of the techniques used, 11 other Salmonella Rissen isolates from different origins were included in the comparison. Pulsed-field gel electrophoresis, repetitive element palindromic PCR and three random amplified polymorphic DNA PCR assays were used. Repetitive element palindromic PCR and random amplified polymorphic DNA PCR assays were insufficiently discriminatory, whereas pulsed-field gel electrophoresis using the combination of two restriction enzymes showed sufficient discrimination to confirm the hypothesis. Although cross-contamination in food laboratories are rarely reported, cross-contamination can always occur. Laboratories should therefore always be aware of the possibility of cross-contamination, especially when enrichment is used in the microbiological analysis. Furthermore, it is advised that results showing isolates of the same serotype isolated in a short time frame from unrelated food products should be interpreted carefully and should be confirmed with additional strain typing.

Diversity of pulsed-field gel electrophoresis pulsotypes, serovars, and antibiotic resistance among Salmonella isolates from wild amphibians and reptiles in the California Central Coast.

PubMed

Gorski, Lisa; Jay-Russell, Michele T; Liang, Anita S; Walker, Samarpita; Bengson, Yingjia; Govoni, Jessica; Mandrell, Robert E

2013-06-01

A survey of cold-blooded vertebrates and associated surface waters in a produce-growing region on the Central California Coast was done between May and September 2011 to determine the diversity of Salmonella. Samples from 460 amphibians and reptiles and 119 water samples were collected and cultured for Salmonella. Animals sampled were frogs (n=331), lizards (n=59), newts (n=5), salamanders (n=6), snakes (n=39), and toads (n=20). Salmonella was isolated from 37 individual animals, including frogs, lizards, snakes, and toads. Snakes were the most likely to contain Salmonella, with 59% testing positive followed by 15.3% of lizards, 5% of toads, and 1.2% of frogs. Fifteen water samples (12.6%) were positive. Twenty-two different serovars were identified, and the majority of isolates were S. enterica subsp. IIIb, with subsp. I, II, and IIIa also found. The serovar isolated most frequently was S. enterica subsp. IIIb 16:z₁₀:e,n,x,z₁₅, from snakes and frogs in five different locations. S. enterica subsp. I serovar Typhimurium and the monophasic I 6,8:d:- were isolated from water, and subspecies I Duisburg and its variants were found in animals and water. Some samples contained more than one type of Salmonella. Analysis of pulsed-field gel electrophoresis pulsotypes indicated that some strains persisted in animals and water collected from the same location. Sixty-six isolates displayed antibiotic resistance, with 27 isolates resistant to more than one antibiotic, including a subspecies IIIb isolate from snake having resistance to five different antibiotics. Twenty-three isolates were resistant to more than one class of antibiotic, and six isolates were resistant to three classes. While these subspecies of IIIa and IIIb cause fewer instances of human illness, they may serve as reservoirs of antibiotic resistance, determinants in the environment, and be sources of contamination of leafy greens associated with product recalls.

DNA fingerprinting and analysis of population structure in the chestnut blight fungus, Cryphonectria parasitica.

PubMed

Milgroom, M G; Lipari, S E; Powell, W A

1992-06-01

We analyzed DNA fingerprints in the chestnut blight fungus, Cryphonectria parasitica, for stability, inheritance, linkage and variability in a natural population. DNA fingerprints resulting from hybridization with a dispersed moderately repetitive DNA sequence of C. parasitica in plasmid pMS5.1 hybridized to 6-17 restriction fragments per individual isolate. In a laboratory cross and from progeny from a single perithecium collected from a field population, the presence/absence of 11 fragments in the laboratory cross and 12 fragments in the field progeny set segregated in 1:1 ratios. Two fragments in each progeny set cosegregated; no other linkage was detected among the segregating fragments. Mutations, identified by missing bands, were detected for only one fragment in which 4 of 43 progeny lacked a band present in both parents; no novel fragments were detected in any progeny. All other fragments appeared to be stably inherited. Hybridization patterns did not change during vegetative growth or sporulation. However, fingerprint patterns of single conidial isolates of strains EP155 and EP67 were found to be heterogenous due to mutations that occurred during culturing in the laboratory since these strains were first isolated in 1976-1977. In a population sample of 39 C. parasitica isolates, we found 33 different fingerprint patterns with pMS5.1. Most isolates differed from all other isolates by the presence or absence of several fragments. Six fingerprint patterns each occurred twice. Isolates with identical fingerprints occurred in cankers on the same chestnut stems three times; isolates within the other three pairs were isolated from cankers more than 5 m apart. The null hypothesis of random mating in this population could not be rejected if the six putative clones were removed from the analysis. Thus, a rough estimate of the clonal fraction of this population is 6 in 39 isolates (15.4%).

Genetic diversity in the 3'-terminal region of papaya ringspot virus (PRSV-W) isolates from watermelon in Oklahoma.

PubMed

Abdalla, Osama A; Ali, Akhtar

2012-03-01

The 3'-terminal region (1191 nt) containing part of the NIb gene, complete coat protein (CP) and poly-A tail of 64 papaya ringspot virus (PRSV-W) isolates collected during 2008-2009 from watermelon in commercial fields of four different counties of Oklahoma were cloned and sequenced. Nucleotide and amino acid sequence identities ranged from 95.2-100% and 97.1-100%, respectively, among the Oklahoman PRSV-W isolates. Phylogenetic analysis showed that PRSW-W isolates clustered according to the locations where they were collected within Oklahoma, and each cluster contained two subgroups. All subgroups of Oklahoman PRSV-W isolates were on separate branches when compared to 35 known isolates originating from other parts of the world, including the one reported previously from the USA. This study helps in our understanding about the genetic diversity of PRSV-W isolates infecting cucurbits in Oklahoma.

Characterization of Salmonella enterica serovar Agona slaughter isolates from the animal arm of the National Antimicrobial Resistance Monitoring System-Enteric Bacteria (NARMS): 1997 through 2003.

PubMed

Douris, Aphrodite; Fedorka-Cray, Paula J; Jackson, Charlene R

2008-03-01

A total of 499 Salmonella enterica serovar Agona isolates from cattle, swine, chicken, and turkey samples were assayed for antimicrobial susceptibility and subtyped using pulsed-field gel electrophoresis (PFGE). Salmonella Agona isolates exhibited increased resistance to amoxicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur, cephalothin, and chloramphenicol, and a single isolate was resistant to ceftriaxone. Multiple drug resistance (MDR; resistance >or= 2 antimicrobials) was exhibited in 57% (n=282/499) of the Salmonella Agona isolates and 22% (n=111/499) of these Salmonella Agona isolates were resistant to five or more antimicrobials. PFGE patterns of 482 Salmonella Agona slaughter samples resulted in 165 unique patterns. Cluster analysis indicated that isolates indistinguishable by PFGE appeared to group according to antimicrobial resistance profiles. These data suggest that Salmonella Agona is increasing in prevalence in U.S. cattle presented for slaughter and should be further monitored.

Post-Newtonian celestial dynamics in cosmology: Field equations

NASA Astrophysics Data System (ADS)

Kopeikin, Sergei M.; Petrov, Alexander N.

2013-02-01

Post-Newtonian celestial dynamics is a relativistic theory of motion of massive bodies and test particles under the influence of relatively weak gravitational forces. The standard approach for development of this theory relies upon the key concept of the isolated astronomical system supplemented by the assumption that the background spacetime is flat. The standard post-Newtonian theory of motion was instrumental in the explanation of the existing experimental data on binary pulsars, satellite, and lunar laser ranging, and in building precise ephemerides of planets in the Solar System. Recent studies of the formation of large-scale structures in our Universe indicate that the standard post-Newtonian mechanics fails to describe more subtle dynamical effects in motion of the bodies comprising the astronomical systems of larger size—galaxies and clusters of galaxies—where the Riemann curvature of the expanding Friedmann-Lemaître-Robertson-Walker universe interacts with the local gravitational field of the astronomical system and, as such, cannot be ignored. The present paper outlines theoretical principles of the post-Newtonian mechanics in the expanding Universe. It is based upon the gauge-invariant theory of the Lagrangian perturbations of cosmological manifold caused by an isolated astronomical N-body system (the Solar System, a binary star, a galaxy, and a cluster of galaxies). We postulate that the geometric properties of the background manifold are described by a homogeneous and isotropic Friedmann-Lemaître-Robertson-Walker metric governed by two primary components—the dark matter and the dark energy. The dark matter is treated as an ideal fluid with the Lagrangian taken in the form of pressure along with the scalar Clebsch potential as a dynamic variable. The dark energy is associated with a single scalar field with a potential which is hold unspecified as long as the theory permits. Both the Lagrangians of the dark matter and the scalar field are formulated in terms of the field variables which play a role of generalized coordinates in the Lagrangian formalism. It allows us to implement the powerful methods of variational calculus to derive the gauge-invariant field equations of the post-Newtonian celestial mechanics of an isolated astronomical system in an expanding universe. These equations generalize the field equations of the post-Newtonian theory in asymptotically flat spacetime by taking into account the cosmological effects explicitly and in a self-consistent manner without assuming the principle of liner superposition of the fields or a vacuole model of the isolated system, etc. The field equations for matter dynamic variables and gravitational field perturbations are coupled in the most general case of an arbitrary equation of state of matter of the background universe. We introduce a new cosmological gauge which generalizes the de Donder (harmonic) gauge of the post-Newtonian theory in asymptotically flat spacetime. This gauge significantly simplifies the gravitational field equations and allows one to find out the approximations where the field equations can be fully decoupled and solved analytically. The residual gauge freedom is explored and the residual gauge transformations are formulated in the form of the wave equations for the gauge functions. We demonstrate how the cosmological effects interfere with the local system and affect the local distribution of matter of the isolated system and its orbital dynamics. Finally, we worked out the precise mathematical definition of the Newtonian limit for an isolated system residing on the cosmological manifold. The results of the present paper can be useful in the Solar System for calculating more precise ephemerides of the Solar System bodies on extremely long time intervals, in galactic astronomy to study the dynamics of clusters of galaxies, and in gravitational wave astronomy for discussing the impact of cosmology on generation and propagation of gravitational waves emitted by coalescing binaries and/or merging galactic nuclei.

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.

Application of pulsed field gel electrophoresis to the 1993 epidemic of whooping cough in the UK.

PubMed Central

Syedabubakar, S. N.; Matthews, R. C.; Preston, N. W.; Owen, D.; Hillier, V.

1995-01-01

The purpose of this study was to DNA fingerprint the majority (64%) of isolates received at the Pertussis Reference Laboratory during the 1993 whooping cough epidemic by pulsed field gel electrophoresis of Xba I-generated restriction digests. Two DNA restriction patterns, types 1 and 3, predominated (40% and 23%, respectively, of 180 isolates) but type 2, identified in a previous study was notably absent. Twenty-one new DNA types occurred (24% of isolates), some being atypical as bands 155-230 kb were no longer conserved, but there was no statistically significant difference in their incidence in the upswing (June-September) compared to the downswing (October-December) phase of the epidemic. There was a relatively high proportion of new types, compared to type 1, at the peak (September). About 50% of isolates received were from the North Western Region, where 44% of isolates were DNA type 1. Whereas only 1 out of 10 isolates from Scotland were of this type, suggesting some geographic variation. Statistically significant findings included a higher proportion of isolates from female patients (P < 0.01), most marked in the 12-24 months age group (P < 0.05); a higher proportion of infants under 12 months requiring hospital admission compared to older children (P < 0.05); and a greater number of isolates from unvaccinated children (P < 0.01). Analysis of serotype according to four age groups (under 3 months, 3-12 months, 12-24 months and above 2 years) showed statistically significant differences (P < 0.05) with a noticeably lower proportion (38%) of serotype 1,3 in 3-12 months age group and higher prevalence (74%) of serotype 1,3 in the 12-24 months age group. There was no correlation between DNA type and serotype. Images Fig. 2 PMID:7641824

A pulsed field gel electrophoresis (PFGE) study that suggests a major world-wide clone of Salmonella enterica serovar Enteritidis.

PubMed

Pang, Jen-Chieh; Chiu, Tsai-Hsin; Helmuth, Reiner; Schroeter, Andreas; Guerra, Beatriz; Tsen, Hau-Yang

2007-05-30

Since human infections by Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) have been increasing world-wide over the past years and epidemiological studies have implicated the consumption of meat, poultry, eggs and egg products, elucidation of the predominant subtypes for this Salmonella spp. is important. In this study, 107 poultry and food isolates of Salmonella Enteritidis obtained from Germany were analyzed by pulsed field gel electrophoresis (PFGE), and the subtypes were compared with those of the 124 human isolates obtained in Taiwan. Results showed that for these 107 poultry and food isolates, when XbaI, SpeI and NotI were used for chromosomal DNA digestion followed by PFGE analysis, a total of 19, 20 and 19 PFGE patterns, respectively, were identified. Of them, 51 (47.7%), 52 (48.6%) and 42 (39.3%) strains belong to a single pattern of X3, S3 and N3, respectively, and 34 strains belong to a pattern combination of X3S3N3, which was the major subtype. When PFGE patterns of these 107 German isolates were compared with those of the 124 human isolates obtained in Taiwan, pattern combination of X3S3N3 was found as the most common pattern shared by isolates from both areas. PT4 is a major phage type for German and Taiwan isolates. Although most of the X3S3N3 strains are of this phage type, some strains of other PFGE patterns are also of this phage type. Since strains used in this study were unrelated, i.e., they were isolated from different origins in areas geographically far apart from each other, the PFGE study suggests a major world-wide clone of S. enterica serovar Enteritidis.

Isoflavones isolated from red clover (Trifolium pratense) inhibit smooth muscle contraction of the isolated rat prostate gland.

PubMed

Brandli, A; Simpson, J S; Ventura, S

2010-09-01

This study investigated whether red clover contains any bioactive constituents which may affect contractility of rat prostatic smooth muscle in an attempt to determine whether its medicinal use in the treatment of benign prostatic hyperplasia is supported by pharmacological effects. A commercially available red clover extract was chemically fractionated and various isoflavones (genistein, formononetin and biochanin A) were isolated from these fractions and their effects on contractility were examined on preparations of the isolated rat prostate gland. Contractile effects of the isolated fractions were compared with commercially available isoflavones (genistein, formononetin and biochanin A). Pharmacological tools were used to investigate the mechanism of action modifying smooth muscle contraction. Crude red clover extract (Trinovin) inhibited electrical field stimulation induced contractions of the rat prostate across a range of frequencies with an IC(50) of approximately 68 microg/ml. Contractions of the rat prostate elicited by exogenous administration of acetylcholine, noradrenaline or adenosine 5'-triphosphate (ATP) were also inhibited. Chromatographic separation, and final purification by high performance liquid chromatography (HPLC) permitted the isolation of the isoflavones: daidzein, calycosin, formononetin, prunetin, pratensin, biochanin A and genistein. Genistein, formononetin and biochanin A (100 microM) from either commercial sources or isolated from red clover extract inhibited electrical field stimulation induced contractions of the isolated rat prostate. It is concluded that isoflavones contained in red clover are able to inhibit prostatic smooth muscle contractions in addition to their antiproliferative effects. However, the high concentrations required to observe these smooth muscle relaxant effects mean that a therapeutic benefit from this mechanism is unlikely at doses used clinically. Crown Copyright 2010. Published by Elsevier GmbH. All rights reserved.

Recombination between vaccine and field strains of canine parvovirus is revealed by isolation of virus in canine and feline cell cultures.

PubMed

Mochizuki, Masami; Ohshima, Takahisa; Une, Yumi; Yachi, Akiko

2008-12-01

Canine parvovirus type 2 (CPV) is a pathogen that causes severe hemorrhagic gastroenteritis with a high fatality rate in pups worldwide. Since CPV emerged in the late 1970s, its origin has been explored with the conclusion that CPV originated from feline panleukopenia virus or a closely related virus. Both high mutation rate and recombination are assumed to be key factors in the evolution of parvoviruses. Here we provide evidence for natural recombination in CPV isolated from dogs in cell culture. Antigenic and genetic properties of isolates from 10 diseased pups were elucidated. Six pups had been vaccinated beforehand with live combined vaccine containing original antigenic type CPV (CPV-2). Six isolates recovered from 4 vaccinated pups in cell cultures were found to contain either CPV-2 or CPV-2-like viruses. The other isolates, including all those from non-vaccinated pups, were CPV-2b viruses. Antigenic typing of two CPV-2-like isolates, 03-029/M and 1887/f, with a monoclonal antibody panel suggested they were a mixture of CPV-2 and CPV-2a (03-029/M) and a recombinant of CPV-2 and CPV-2b (1887/f). Genetic analysis of the VP1 gene indicated that isolate 03-029/M was a mixture of CPV-2, CPV-2a and a recombinant of CPV-2 and CPV-2a viruses, while isolate 1887/f was composed of a recombinant of CPV-2 and CPV-2b viruses. This is the first demonstration of natural CPV recombination in the field and suggests that recombination in the evolution of CPV is a more frequent and important process than previously believed.

Prevalence and characterization of multi-drug resistant Salmonella Enterica serovar Gallinarum biovar Pullorum and Gallinarum from chicken

PubMed Central

Parvej, Md. Shafiullah; Nazir, K. H. M. Nazmul Hussain; Rahman, M. Bahanur; Jahan, Mueena; Khan, Mohammad Ferdousur Rahman; Rahman, Marzia

2016-01-01

Aim: Salmonella is an important zoonotic pathogen responsible for animal and human diseases. The aim of the present study was to determine the prevalence and stereotyping of Salmonella isolates isolated from apparently healthy poultry. Furthermore, the clonal relatedness among the isolated Salmonella serovars was assessed. Materials and Methods: A total of 150 cloacal swab samples from apparently healthy chickens were collected, and were subjected for the isolation and identification of associated Salmonella organisms. The isolated colonies were identified and characterized on the basis of morphology, cultural characters, biochemical tests, slide agglutination test, polymerase chain reaction, and pulsed-field gel electrophoresis (PFGE). Antibiotic sensitivity patterns were also investigated using commonly used antibiotics. Results: Of the 150 samples, 11 (7.33%) produced characteristics pink colony with black center on XLD agar medium, and all were culturally and biochemically confirmed to be Salmonella. All possessed serovar-specific gene SpeF and reacted uniformly with group D antisera, suggesting that all of the isolates were Salmonella Enterica serovar Gallinarum, biovar Pullorum and/or Gallinarum. Antimicrobial susceptibility testing revealed that 54.54% of the isolated Salmonella Enterica serovars were highly sensitive to ciprofloxacin, whereas the 81.81% isolates were resistant to amoxycillin, doxycycline, kanamycin, gentamycin, and tetracycline. Pulsed-field gel electrophoresis of the XbaI-digested genomic DNA exhibited identical banding patterns, suggesting that the multidrug resistant Salmonella Enterica serovars occurring in commercial layers are highly clonal in Bangladesh. Conclusion: The present study was conducted to find out the prevalence of poultry Salmonella in layer chicken and to find out the clonal relationship among them. The data in this study suggest the prevalence of Salmonella Enterica, which is multidrug resistant and highly clonal for commercial layers of Bangladesh. PMID:27051187

Relationship Between Soil Type and N2O Reductase Genotype (nosZ) of Indigenous Soybean Bradyrhizobia: nosZ-minus Populations are Dominant in Andosols

PubMed Central

Shiina, Yoko; Itakura, Manabu; Choi, Hyunseok; Saeki, Yuichi; Hayatsu, Masahito; Minamisawa, Kiwamu

2014-01-01

Bradyrhizobium japonicum strains that have the nosZ gene, which encodes N2O reductase, are able to mitigate N2O emissions from soils (15). To examine the distribution of nosZ genotypes among Japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosZ and nodC genotypes. The 1556 resultant isolates were classified into the nosZ+/nodC+ genotype (855 isolates) and nosZ−/nodC+ genotype (701 isolates). The 11 soil samples in which nosZ− isolates significantly dominated (P < 0.05; the χ2 test) were all Andosols (a volcanic ash soil prevalent in agricultural fields in Japan), whereas the 17 soil samples in which nosZ+ isolates significantly dominated were mainly alluvial soils (non-volcanic ash soils). This result was supported by a principal component analysis of environmental factors: the dominance of the nosZ− genotype was positively correlated with total N, total C, and the phosphate absorption coefficient in the soils, which are soil properties typical of Andosols. Internal transcribed spacer sequencing of representative isolates showed that the nosZ+ and nosZ− isolates of B. japonicum fell mainly into the USDA110 (BJ1) and USDA6 (BJ2) groups, respectively. These results demonstrated that the group lacking nosZ was dominant in Andosols, which can be a target soil type for an N2O mitigation strategy in soybean fields. We herein discussed how the nosZ genotypes of soybean bradyrhizobia depended on soil types in terms of N2O respiration selection and genomic determinants for soil adaptation. PMID:25476067

Relationship between soil type and N₂O reductase genotype (nosZ) of indigenous soybean bradyrhizobia: nosZ-minus populations are dominant in Andosols.

PubMed

Shiina, Yoko; Itakura, Manabu; Choi, Hyunseok; Saeki, Yuichi; Hayatsu, Masahito; Minamisawa, Kiwamu

2014-01-01

Bradyrhizobium japonicum strains that have the nosZ gene, which encodes N2O reductase, are able to mitigate N2O emissions from soils (15). To examine the distribution of nosZ genotypes among Japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosZ and nodC genotypes. The 1556 resultant isolates were classified into the nosZ+/nodC+ genotype (855 isolates) and nosZ-/nodC+ genotype (701 isolates). The 11 soil samples in which nosZ- isolates significantly dominated (P < 0.05; the χ(2) test) were all Andosols (a volcanic ash soil prevalent in agricultural fields in Japan), whereas the 17 soil samples in which nosZ+ isolates significantly dominated were mainly alluvial soils (non-volcanic ash soils). This result was supported by a principal component analysis of environmental factors: the dominance of the nosZ- genotype was positively correlated with total N, total C, and the phosphate absorption coefficient in the soils, which are soil properties typical of Andosols. Internal transcribed spacer sequencing of representative isolates showed that the nosZ+ and nosZ- isolates of B. japonicum fell mainly into the USDA110 (BJ1) and USDA6 (BJ2) groups, respectively. These results demonstrated that the group lacking nosZ was dominant in Andosols, which can be a target soil type for an N2O mitigation strategy in soybean fields. We herein discussed how the nosZ genotypes of soybean bradyrhizobia depended on soil types in terms of N2O respiration selection and genomic determinants for soil adaptation.

Pathogenicity of three isolates of Rhizoctonia sp. from wheat and peanut on hard red winter wheat

USDA-ARS?s Scientific Manuscript database

Rhizoctonia-induced root diseases can significantly affect wheat and peanut production where these two field crops are grown in rotation. Hence, this study characterized two isolates of Rhizoctonia spp. from wheat [R. cerealis (RC) and R. solani (RSW)] and one from peanut [R. solani (RSP) ] for cul...

An untypeable Shigella flexneri strain associated with an outbreak in California.

PubMed

Trevejo, R T; Abbott, S L; Wolfe, M I; Meshulam, J; Yong, D; Flores, G R

1999-07-01

Eleven Shigella flexneri (group B) isolates were recovered from epidemiologically linked patrons and food handlers from a restaurant-associated outbreak of shigellosis. Six isolates available for pulsed-field gel electrophoresis were identical. All strains agglutinated in group B and subgroup factor 6 sera but not in group 1 through group 6 sera.

Formulations of Bacillus subtilis BY-2 suppress Sclerotinia sclerotiorum on oilseed rape in the field

USDA-ARS?s Scientific Manuscript database

We are developing a collection of Bacillus strains, isolated from different environments, for use in controlling Sclerotinia sclerotiorum on oilseed rape in China and elsewhere. Strain BY-2, isolated from internal tissues of an oilseed rape root, was demonstrated to be Bacillus subtilis based on bi...

Overcoming Isolation as a Woman in the Male-Dominated Superintendency

ERIC Educational Resources Information Center

McCooley, Melissa Ann

2017-01-01

The purpose of this hermeneutical phenomenological study was to explore the attributes associated with the leadership of women superintendents and how they overcome isolation in a predominantly male-dominated field. Through a feminist lens, I explored the manner in which women serve as superintendents, particularly, the manner in which they…

Evidence for an American origin of the genes for symbiosis in R. lusitanum

USDA-ARS?s Scientific Manuscript database

RAPD analysis was used to investigate the diversity of 179 bean isolates recovered from six field sites in the Arcos de Valdevez region of northwestern Portugal. The isolates were divided into 6 groups based on the fingerprint patterns that were obtained. Representatives for each group were select...

Evaluation of the Abington isolate of the gypsy moth nuclear polyhedrosis virus against a formulation of Gypchek in small field plots

Treesearch

R. E. Webb; M. Shapiro; J. D. Podgwaite; D. D. Cohen; R. L. Ridgway

1991-01-01

The "Abington" isolate of the nuclear polyhedrosis virus (NPV) of the gypsy moth (Lymantria dispar L.) was compared with a formulation of Gypchek against a natural gypsy moth population in the Swallow Falls State Forest in Garrett County, MD.

Occultifur kilbournensis f.a. sp. nov., a new member of the Cystobasidiales associated with maize (Zea mays) cultivation

USDA-ARS?s Scientific Manuscript database

During a study of microorganisms associated with maize (Zea mays) cultivation, yeasts were isolated from overwintered stalks, cobs and surrounding soil, which were collected from an agricultural field in south-central Illinois, USA. Predominant among isolates were two species of Cryptococcus (Cr. fl...

First report of Streptomyces stelliscabiei causing potato common scab in Michigan

USDA-ARS?s Scientific Manuscript database

Streptomyces scabies has been reported as the predominant cause of potato scab in Michigan. In a 2007 survey of common scab in Michigan, however, isolates were collected from a field that did not fit the description for S. scabies. Tests using species-specific PCR primers indicated isolates were S. ...

Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov.

PubMed

Murase, Jun; Kawasaki, Michio; De Jonckheere, Johan F

2010-08-01

A heterolobosean amoeba strain 6_5F was isolated from an Italian rice field soil. Although 18S rRNA gene sequence analysis demonstrated that the new isolate was closely related to Stachyamoeba sp. ATCC 50324, further molecular analysis and morphological observation showed distinct differences amongst the two. The 5.8S rRNA gene was successfully amplified and sequenced for strain 6_5F but not for strain ATCC 50324. Trophozoites of strain ATCC 50324 transform into flagellate forms in the late stage of incubation before encystment, while strain 6_5F do not show flagellate forms under different conditions of the flagellation test. Light and electron microscopic observation showed the structural difference of cysts of strain 6_5F from strain ATCC 50324 and also from the type strain Stachyamoeba lipophora. The results show that the strain 6_5F is distinct from Stachyamoeba spp. and we propose a new genus and species for this isolate, Vrihiamoeba italica gen. nov., sp. nov. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

Development and application of induced-strain actuators for building structures

NASA Astrophysics Data System (ADS)

Morita, Koichi; Fujita, Takafumi; Ise, Shiro; Kawaguchi, Ken-ichi; Kamada, Takayoshi; Fujitani, Hideo

2001-07-01

Induced strain actuator (ISA) can change their own shapes according to external electric/magnetic fields, and vice versa. Recently these materials have been widely used for the small/precision. The objectives in this study are to develop smart members for building and to realize the smart, comfortable and safe structures. The research items are 1) Semi-active isolation of structures using piezoelectric actuator, 2) Using ISA as sensor materials and 3) Improvement of Acoustic Environment. Semi-active base isolation system with controllable friction damper using piezoelectric actuators is proposed. Simulation study was carried out, and by semi-active isolation, it could be realized to reduce response displacement of the structure to 50% of values of the passive isolation. ISA materials can act as sensors because they cause change of electric or magnetic fields under deformation. PVDF sensors are suitable for membrane structures. We evaluate performance of PVDF sensors for membrane structures by experiment. Polymer based ISA films or distributed ISA devices can control vibration mode of plane members. Applications to music halls or dwelling partition walls are expected. Results of experimental studies of noise control are discussed.

Fungal degradation of an acetolactate synthase (ALS) inhibitor pyrazosulfuron-ethyl in soil.

PubMed

Sondhia, Shobha; Waseem, Uzma; Varma, R K

2013-11-01

Owing to reported phytotoxicity of some sulfonylurea class of herbicides in number of sensitive crops and higher persistence in soil, present study was conducted to isolate and identify pyrazosulfuron-ethyl degrading fungi from soil of rice field. Penicillium chrysogenum and Aspergillus niger, were isolated and identified from rhizospere soil of rice field, as potent pyrazosulfuron-ethyl degrading fungi. Degradation of pyrazosulfuron-ethyl by P. chrysogenum and A. niger, yielded transformation products/metabolites which were identified and characterized by LC/MS/MS. The rate of dissipation of pyrazosulfuron-ethyl was found higher in soil of rice field and soil inoculated with P. chrysogenum. This showed important route of degradation of pyrazosulfuron-ethyl by microbes apart from chemical degradation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Transmission Nonreciprocity in a Mutually Coupled Circulating Structure

NASA Astrophysics Data System (ADS)

He, Bing; Yang, Liu; Jiang, Xiaoshun; Xiao, Min

2018-05-01

Breaking Lorentz reciprocity was believed to be a prerequisite for nonreciprocal transmissions of light fields, so the possibility of nonreciprocity by linear optical systems was mostly ignored. We put forward a structure of three mutually coupled microcavities or optical fiber rings to realize optical nonreciprocity. Although its couplings with the fields from two different input ports are constantly equal, such system transmits them nonreciprocally either under the saturation of an optical gain in one of the cavities or with the asymmetric couplings of the circulating fields in different cavities. The structure made up of optical fiber rings can perform nonreciprocal transmissions as a time-independent linear system without breaking Lorentz reciprocity. Optical isolation for inputs simultaneously from two different ports and even approximate optical isolator operations are implementable with the structure.

Laser-driven Ion Acceleration using Nanodiamonds

NASA Astrophysics Data System (ADS)

D'Hauthuille, Luc; Nguyen, Tam; Dollar, Franklin

2016-10-01

Interactions of high-intensity lasers with mass-limited nanoparticles enable the generation of extremely high electric fields. These fields accelerate ions, which has applications in nuclear medicine, high brightness radiography, as well as fast ignition for inertial confinement fusion. Previous studies have been performed with ensembles of nanoparticles, but this obscures the physics of the interaction due to the wide array of variables in the interaction. The work presented here looks instead at the interactions of a high intensity short pulse laser with an isolated nanodiamond. Specifically, we studied the effect of nanoparticle size and intensity of the laser on the interaction. A novel target scheme was developed to isolate the nanodiamond. Particle-in-cell simulations were performed using the EPOCH framework to show the sheath fields and resulting energetic ion beams.

Molecular characterization of Group A streptococcal isolates causing scarlet fever and pharyngitis among young children: a retrospective study from a northern Taiwan medical center.

PubMed

Wu, Po-Chuang; Lo, Wen-Tsung; Chen, Shyi-Jou; Wang, Chih-Chien

2014-08-01

Little information is available on the differences in frequency of pyrogenic exotoxin genes between strains of group A streptococci that cause scarlet fever and those that cause pharyngotonsillitis in children in Taiwan. This study retrospectively monitored the presence of pyrogenic exotoxin genes, the emm typing, and the susceptibility of macrolide drugs in Streptococcus pyogenes isolated from children diagnosed with scarlet fever and pharyngotonsillitis in northern Taiwan. Isolates of S. pyogenes were recovered from children with scarlet fever (n = 21) and acute pharyngotonsillitis (n = 29) during 2000-2011. The isolates were characterized according to the presence of spe genes and emm typing. Antibiograms were determined by the disk diffusion method and agar dilution test. Polymerase chain reaction was used to detect the presence of erm genes in isolates that showed nonsusceptibility to erythromycin. All isolates underwent additional genotyping by pulsed-field gel electrophoresis. In isolates from patients with scarlet fever, the frequencies of pyrogenic exotoxin genes were 9.5% for speA, 81.0% for speB, 4.8% for speC, and 71.4% for speF. In isolates from patients with pharyngotonsillitis, the frequencies were 17.2% for speA, 72.4% for speB, 13.8% for speC, and 69.0% for speF. There were no significant differences in frequencies of the exotoxin genes between the two groups of isolates. Eight emm sequence types were identified from all group A streptococci isolates. The most common types were emm12 followed by emm1 and emm4. The erythromycin resistant rate was 4/50 (8%). The ermB gene was detected in only one isolate from a patient with pharyngotonsillitis. Pulsed-field gel electrophoresis had a total of three sets of clustered strains, which showed >80% homology and belonged to the same emm type. There were no significant differences in frequencies of the spe genes between S. pyogenes isolates from patients with scarlet fever and patients with pharyngotonsillitis. The most common emm type was emm12. Low erythromycin resistance in S. pyogenes was observed. Copyright © 2013. Published by Elsevier B.V.

Larval development assays reveal the presence of sub-populations showing high- and low-level resistance in a monepantel (Zolvix®)-resistant isolate of Haemonchus contortus.

PubMed

Raza, Ali; Lamb, Jane; Chambers, Michael; Hunt, Peter W; Kotze, Andrew C

2016-04-15

Resistance to the amino-acetonitrile derivative monepantel has been reported in several species of gastrointestinal nematodes over recent years. We were interested in the use of in vitro assays with free-living worm life-stages to detect resistance to this drug. We therefore used larval development and larval migration assays to examine dose response relationships for the drug against two susceptible and one resistant isolate of Haemonchus contortus. The resistant isolate was established by laboratory propagation of the survivors of a field treatment with Zolvix(®) that had originally resulted in a drug efficacy of over 99%. Drug efficacy against this field-derived laboratory-propagated resistant isolate in vivo was approximately 15%. The larval development assay proved able to discriminate between the susceptible and resistant isolates, with larvae of the resistant isolate showing an ability to develop at higher drug concentrations than the two susceptible isolates. The resistant isolate showed the presence of two distinct subpopulations, separated by a plateau in the dose-response curve. Sub-population 1 (approximately 40% of the total population) showed a low level of resistance with an IC50 increased approximately 7-fold compared to the baseline susceptible isolate, while sub-population 2 (the remaining 60% of the total population) showed an IC50 increased over 1000-fold compared to the baseline susceptible isolate. This level of resistance is unusually high for any gastrointestinal nematode species in drug dose-response in vitro assays. In contrast, the migration assay could not discriminate between the three isolates, with migration not reduced to zero at any of the drug concentrations tested. This study demonstrates that a larval development assay is able to detect resistance to monepantel in H. contortus, and that resistance can exist in two distinct forms. This suggests that at least two separate monepantel resistance mechanisms are acting within the worm isolate studied here, with one or more mechanisms conferring a much higher level of resistance than the other(s). Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Optical Gating with Asymmetric Field Ratios for Isolated Attosecond Pulse Generation

DTIC Science & Technology

2015-09-01

field intensity at t = tc. 0 15 30 45 60 75 90 0.0 1:3 1:2 1:1 2:1 3:1 1 2 2 Field ratio Sc alin g f act or Polarization angle θ1 (deg) APG ADOG...of using field asymmetry is low compared to that of using field ellipticity. 0.0 0.2 0.4 0.6 0.8 1.0 5 10 15 20 25 Sc alin g f act or Field

Chemically synthesized silver nanoparticles as cell lysis agent for bacterial genomic DNA isolation

NASA Astrophysics Data System (ADS)

Goswami, Gunajit; Boruah, Himangshu; Gautom, Trishnamoni; Jyoti Hazarika, Dibya; Barooah, Madhumita; Boro, Robin Chandra

2017-12-01

Silver nanoparticles (AgNPs) have seen a recent spurt of use in varied fields of science. In this paper, we showed a novel application of AgNP as a promising microbial cell-lysis agent for genomic DNA isolation. We utilized chemically synthesized AgNPs for lysing bacterial cells to isolate their genomic DNA. The AgNPs efficiently lysed bacterial cells to yield good quality DNA that could be subsequently used for several molecular biology works.

Regional Spread of CTX-M-2-Producing Proteus mirabilis with the Identical Genetic Structure in Japan.

PubMed

Kato, Karin; Matsumura, Yasufumi; Yamamoto, Masaki; Nagao, Miki; Takakura, Shunji; Ichiyama, Satoshi

2017-07-01

In this study, we analyzed the molecular epidemiology of extended-spectrum β-lactamase (ESBL)-producing Proteus mirabilis isolates collected from the central region of Japan. Between 2005 and 2012, 820 clinical P. mirabilis isolates were obtained from ten acute care hospitals in Japan. We characterized ESBL confirmatory test-positive isolates by sequencing the ESBL genes and their flanking regions, detecting plasmid replicons, and performing pulsed-field gel electrophoresis (PFGE). Ninety-six isolates (12%) were positive according to the ESBL confirmatory test; all these isolates possessed bla CTX-M-2 with the same flanking structure of upstream ΔISEcp1 and a downstream region identical to downstream bla KLUA-1 . IncT was the prevalent, and only, replicon found in 63 isolates. PFGE analysis detected eight clusters with more than one isolate, among which three included 56 isolates and six included isolates from multiple hospitals. CTX-M-2-producing P. mirabilis with an identical genetic structure flanking bla CTX-M-2 is dominant in this Japanese region, and there is evidence for the clonal spread of isolates.

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.

Characterization of Salmonella Typhimurium isolates associated with septicemia in swine.

PubMed

Bergeron, Nadia; Corriveau, Jonathan; Letellier, Ann; Daigle, France; Quessy, Sylvain

2010-01-01

Salmonella Typhimurium is frequently isolated from pigs and may also cause enteric disease in humans. In this study, 33 isolates of S. Typhimurium associated with septicemia in swine (CS) were compared to 33 isolates recovered from healthy animals at slaughter (WCS). The isolates were characterized using phenotyping and genotyping methods. For each isolate, the phage type, antimicrobial resistance, and pulsed-field gel electrophoresis (PFGE) DNA profiles were determined. In addition, the protein profiles of each isolate grown in different conditions were studied by Coomassie Blue-stained sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot. Various phage types were identified. The phage type PT 104 represented 36.4% of all isolates from septicemic pigs. Resistance to as many as 12 antimicrobial agents, including some natural resistances, was found in isolates from CS and WCS. Many genetic profiles were identified among the PT 104 phage types. Although it was not possible to associate one particular protein with septicemic isolates, several highly immunogenic proteins, present in all virulent isolates and in most isolates from clinically healthy animals, were identified. These results indicated that strains associated with septicemia belong to various genetic lineages that can also be recovered from asymptomatic animals at the time of slaughter.

High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.

PubMed

Chen, Eric C H; Morin, Emmanuelle; Beaudet, Denis; Noel, Jessica; Yildirir, Gokalp; Ndikumana, Steve; Charron, Philippe; St-Onge, Camille; Giorgi, John; Krüger, Manuela; Marton, Timea; Ropars, Jeanne; Grigoriev, Igor V; Hainaut, Matthieu; Henrissat, Bernard; Roux, Christophe; Martin, Francis; Corradi, Nicolas

2018-01-22

Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

EFFECTOF ISOLATION WALL USING SCRAP TIRE ON GROUND VIBRATION REDUCTION

NASA Astrophysics Data System (ADS)

Kashimoto, Takahiko; Kashimoto, Yusuke; Hayakawa, Kiyoshi; Matsui, Tamotsu; Fujimoto, Hiroaki

Some countermeasure methods against the environmental ground vibration caused by some traffic vibrations have been proposed so far. The authors have developed a new type ground vibration isolation wall using scrap tire, and evaluated its effectiveness on the ground vibration reduction by full scale field tests. In this paper, the authors discussed and examined the effectiveness of the developed countermeasure method by two field tests. The one concerns on the effect of scrap tire as soft material of vibration isolation wall, and the other on the effect of the developed countermeasure method practically applied in a residential area close to monorail traffic. As the results, it was elucidated that the ground vibration of 2-3 dB was reduced in case of two times volume of the soft material, the conversion ratio of the vibration energy of the soft material to the kinetic energy was higher than that of the core material of PHC pile, the vibration acceleration of 0.19 - 1.26 gal was reduced by the developed countermeasure method in case of the monorail traffic, and the vibration reduction measured behind the isolation wall agreed well with the proposed theoretical value, together with confirming the effectiveness of the ground vibration isolation wall using scrap tire as the countermeasure method against the environmental ground vibration.

Molecular characterization of enterohemorrhagic Escherichia coli O157:H7 isolates dispersed across Japan by pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analysis.

PubMed

Pei, Yingxin; Terajima, Jun; Saito, Yasunori; Suzuki, Reiko; Takai, Nobuko; Izumiya, Hidemasa; Morita-Ishihara, Tomoko; Ohnishi, Makoto; Miura, Masashi; Iyoda, Sunao; Mitobe, Jiro; Wang, Binyou; Watanabe, Haruo

2008-01-01

We identified seven distinct subtypes of enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates that were derived from sporadic cases and outbreaks from multiple prefectures in Japan in 2005. A surveillance system utilizing pulsed-field gel electrophoresis (PFGE), PulseNet Japan, was used. Some strains showed indistinguishable PFGE patterns using another restriction enzyme (BlnI or SpeI) in each subtype of EHEC O157:H7 isolates that were routinely subtyped by the XbaI PFGE pattern. In order to examine the genotypic relatedness of these strains, we carried out a multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA). By using the MLVA system, we found that three of seven subtypes of EHEC O157:H7 strains that were isolated from sporadic cases dispersed across multiple prefectures within a few months showed indistinguishable PFGE patterns and identical MLVA types. Strains belonging to the other four subtypes of EHEC O157:H7 in the PFGE analysis were further classified into different clusters of EHEC O157:H7. Therefore, compared to PFGE, MLVA showed greater discriminatory power with respect to analysis of the isolates in this study.

A Single, Plastic Population of Mycosphaerella pinodes Causes Ascochyta Blight on Winter and Spring Peas (Pisum sativum) in France

PubMed Central

Guibert, Michèle; Leclerc, Aurélie; Andrivon, Didier; Tivoli, Bernard

2012-01-01

Plant diseases are caused by pathogen populations continuously subjected to evolutionary forces (genetic flow, selection, and recombination). Ascochyta blight, caused by Mycosphaerella pinodes, is one of the most damaging necrotrophic pathogens of field peas worldwide. In France, both winter and spring peas are cultivated. Although these crops overlap by about 4 months (March to June), primary Ascochyta blight infections are not synchronous on the two crops. This suggests that the disease could be due to two different M. pinodes populations, specialized on either winter or spring pea. To test this hypothesis, 144 pathogen isolates were collected in the field during the winter and spring growing seasons in Rennes (western France), and all the isolates were genotyped using amplified fragment length polymorphism (AFLP) markers. Furthermore, the pathogenicities of 33 isolates randomly chosen within the collection were tested on four pea genotypes (2 winter and 2 spring types) grown under three climatic regimes, simulating winter, late winter, and spring conditions. M. pinodes isolates from winter and spring peas were genetically polymorphic but not differentiated according to the type of cultivars. Isolates from winter pea were more pathogenic than isolates from spring pea on hosts raised under winter conditions, while isolates from spring pea were more pathogenic than those from winter pea on plants raised under spring conditions. These results show that disease developed on winter and spring peas was initiated by a single population of M. pinodes whose pathogenicity is a plastic trait modulated by the physiological status of the host plant. PMID:23023742

Prevalence and Diversity of Salmonella Serotypes in Ecuadorian Broilers at Slaughter Age

PubMed Central

Cevallos, María; Ron-Garrido, Lenin; Bertrand, Sophie; De Zutter, Lieven

2016-01-01

Salmonella is frequently found in poultry and represent an important source for human gastrointestinal infections worldwide. The aim of this study was to investigate the prevalence, genotypes and antimicrobial resistance of Salmonella serotypes in broilers from Ecuador. Caeca content from 388 at random selected broiler batches were collected in 6 slaughterhouses during 1 year and analyzed by the ISO 6579/Amd1 protocol for the isolation for Salmonella. Isolates were serotyped and genotypic variation was acceded by pulsed field gel electrophoresis. MIC values for sulfamethoxazole, gentamicin, ciprofloxacin, ampicillin, cefotaxime, ceftazidime, tetracycline, streptomycin, trimethropim, chloramphenicol, colistin, florfenicol, kanamycin and nalidixic acid were obtained. Presence of blaCTX-M, blaTEM, blaSHV and blaCMY; and mcr-1 plasmid genes was investigated in resistant strains to cefotaxime and colistin respectively. Prevalence at batch level was 16.0%. The most common serotype was S. Infantis (83.9%) followed by S. Enteritidis (14.5%) and S. Corvallis (1.6%). The pulsed field gel electrophoresis analysis showed that S. Corvallis, S. Enteritidis and S. Infantis isolates belonged to 1, 2 and 12 genotypes respectively. S. Infantis isolates showed high resistance rates to 12 antibiotics ranging from 57.7% (kanamycin) up to 98.1% (nalidixic acid and sulfamethoxazole). All S. Enteritidis isolates showed resistance to colistin. High multiresistant patterns were found for all the serotypes. The blaCTX-M gene was present in 33 S. Infantis isolates while mcr-1 was negative in 10 colistin resistant isolates. This study provides the first set of scientific data on prevalence and multidrug-resistant Salmonella coming from commercial poultry in Ecuador. PMID:27414038

Genetic characterization of H9N2 avian influenza viruses isolated from poultry in Poland during 2013/2014.

PubMed

Świętoń, Edyta; Jóźwiak, Michał; Minta, Zenon; Śmietanka, Krzysztof

2018-02-01

The study presents molecular characterization of H9N2 avian influenza (AI) isolates from field outbreaks in turkeys that occurred in Poland in 2013-2014. Sequences of all gene segments of one isolate from 2013 (A/turkey/Poland/14/2013(H9N2)) and two isolates from 2014 (A/turkey/Poland/08/2014(H9N2), A/turkey/Poland/09/2014(H9N2)) were obtained and analyzed in search of the phylogenetic relationship and molecular markers of zoonotic potential or increased pathogenicity. All gene segments were shown to originate from the wild bird reservoir and the close relationship of the analyzed isolates proved the link between the outbreaks in 2013 and 2014. However, remarkable molecular differences between isolates from 2013 to 2014 were identified, including mutation in the HA cleavage site (CS) leading to conversion from the PAASNR*GLF to the PAASKR*GLF motif and truncation of the PB1-F2 protein. Additionally, T97I substitution in the PA protein in A/turkey/Poland/08/2014 was detected which can be responsible for enhanced activity of viral polymerase in mammalian cells. However, experimental infection of mice with both isolates from 2014 showed their low pathogenicity, and no statistically significant differences in virus replication were observed between the viruses. Nevertheless, these findings indicate the dynamic evolution of H9N2 in the field emphasizing the need for monitoring of the situation in terms of H9N2 AI in Europe.

Biofilm formation in Haemophilus parasuis: relationship with antibiotic resistance, serotype and genetic typing.

PubMed

Zhang, Jianmin; Xu, Chenggang; Shen, Haiyan; Li, Jingyi; Guo, Lili; Cao, Guojie; Feng, Saixiang; Liao, Ming

2014-10-01

Biofilms are surface-associated microbial communities, which are encased in self-synthesized extracellular environment. Biofilm formation may trigger drug resistance and inflammation, resulting in persistent infections. Haemophilus parasuis is the etiological agent of a systemic disease, Glässer's disease, characterized by fibrinous polyserositis, arthritis and meningitis in pigs. The purpose of this study was to examine the correlation between biofilm and antibiotic resistance among the clinical isolates of H. parasuis. In the present study, we tested biofilm-forming ability of 110 H. parasuis isolates from various farms using polystyrene microtiter plate assays. Seventy-three isolates of H. parasuis (66.4%) showed biofilm formation and most of them performed weak biofilm-forming ability (38/73). All isolates were tested for antimicrobial susceptibility to 18 antimicrobial agents by the broth microdilution method. H. parasuis isolates showed very high resistance (>90%) to sulfanilamide, nalidixic acid, and trimethoprim. Resistance to eight antibiotics such as penicillin (41.1% vs 8.1%), ampicillin (31.5% vs 8.1%), amoxicillin (28.8% vs 5.4%), gentamicin (46.6% vs 24.3%), cefazolin (19.2% vs 2.7%), doxycycline (19.2% vs 8.1%), cefotaxime (11% vs 2.7%), and cefaclor (13.7% vs 5.4%) was comparatively higher among biofilm producers than non-biofilm producers. Pulsed-field gel electrophoresis (PFGE) analyses could distinguish various isolates. Our data indicated that H. parasuis field isolates were able to form biofilms in vitro. In addition, biofilm positive strains had positive correlation with resistance to β-lactams antibiotics. Thus, biofilm formation may play important roles during H. parasuis infections. Copyright © 2014. Published by Elsevier Ltd.

Development of a Selective Culture Medium for Primary Isolation of the Main Brucella Species▿

PubMed Central

De Miguel, M. J.; Marín, C. M.; Muñoz, P. M.; Dieste, L.; Grilló, M. J.; Blasco, J. M.

2011-01-01

Bacteriological diagnosis of brucellosis is performed by culturing animal samples directly on both Farrell medium (FM) and modified Thayer-Martin medium (mTM). However, despite inhibiting most contaminating microorganisms, FM also inhibits the growth of Brucella ovis and some B. melitensis and B. abortus strains. In contrast, mTM is adequate for growth of all Brucella species but only partially inhibitory for contaminants. Moreover, the performance of both culture media for isolating B. suis has never been established properly. We first determined the performance of both media for B. suis isolation, proving that FM significantly inhibits B. suis growth. We also determined the susceptibility of B. suis to the antibiotics contained in both selective media, proving that nalidixic acid and bacitracin are highly inhibitory, thus explaining the reduced performance of FM for B. suis isolation. Based on these results, a new selective medium (CITA) containing vancomycin, colistin, nystatin, nitrofurantoin, and amphotericin B was tested for isolation of the main Brucella species, including B. suis. CITA's performance was evaluated using reference contaminant strains but also field samples taken from brucella-infected animals or animals suspected of infection. CITA inhibited most contaminant microorganisms but allowed the growth of all Brucella species, to levels similar to those for both the control medium without antibiotics and mTM. Moreover, CITA medium was more sensitive than both mTM and FM for isolating all Brucella species from field samples. Altogether, these results demonstrate the adequate performance of CITA medium for the primary isolation of the main Brucella species, including B. suis. PMID:21270216

Studies on the Control of Ascochyta Blight in Field Peas (Pisum sativum L.) Caused by Ascochyta pinodes in Zhejiang Province, China

PubMed Central

Liu, Na; Xu, Shengchun; Yao, Xiefeng; Zhang, Guwen; Mao, Weihua; Hu, Qizan; Feng, Zhijuan; Gong, Yaming

2016-01-01

Ascochyta blight, an infection caused by a complex of Ascochyta pinodes, Ascochyta pinodella, Ascochyta pisi, and/or Phoma koolunga, is a destructive disease in many field peas (Pisum sativum L.)-growing regions, and it causes significant losses in grain yield. To understand the composition of fungi associated with this disease in Zhejiang Province, China, a total of 65 single-pycnidiospore fungal isolates were obtained from diseased pea samples collected from 5 locations in this region. These isolates were identified as Ascochyta pinodes by molecular techniques and their morphological and physiological characteristics. The mycelia of ZJ-1 could penetrate pea leaves across the stomas, and formed specific penetration structures and directly pierced leaves. The resistance level of 23 available pea cultivars was tested against their representative isolate A. pinodes ZJ-1 using the excised leaf-assay technique. The ZJ-1 mycelia could penetrate the leaves of all tested cultivars, and they developed typical symptoms, which suggested that all tested cultivars were susceptible to the fungus. Chemical fungicides and biological control agents were screened for management of this disease, and their efficacies were further determined. Most of the tested fungicides (11 out of 14) showed high activity toward ZJ-1 with EC50 < 5 μg/mL. Moreover, fungicides, including tebuconazole, boscalid, iprodione, carbendazim, and fludioxonil, displayed more than 80% disease control efficacy under the recorded conditions. Three biocontrol strains of Bacillus sp. and one of Pantoea agglomerans were isolated from pea-related niches and significantly reduced the severity of disease under greenhouse and field conditions. To our knowledge, this is the first study on ascochyta blight in field peas, and results presented here will be useful for controlling the disease in this area. PMID:27148177

Imaging Plasmonic Fields with Atomic Spatiotemporal Resolution

NASA Astrophysics Data System (ADS)

Li, Jianxiong; Saydanzad, Erfan; Thumm, Uwe

2018-06-01

We propose a scheme for the reconstruction of plasmonic near fields at isolated nanoparticles from infrared-streaked extreme-ultraviolet photoemission spectra. Based on quantum-mechanically modeled spectra, we demonstrate and analyze the accurate imaging of the IR-streaking-pulse-induced transient plasmonic fields at the surface of gold nanospheres and nanoshells with subfemtosecond temporal and subnanometer spatial resolution.

Using Charge Distributions to "Immerse" Your Classroom in an Electric Field

ERIC Educational Resources Information Center

Gaffney, Jon D. H.; Richards, Evan; Foote, Kathleen; Beichner, Robert J.

2013-01-01

Because electric fields are both invisible and three dimensional, they can be quite difficult to introduce to students. Simple diagrams are unable to convey the complexity or depth of the field, and computer simulations in isolation do not provide a familiar spatial context for students to understand what they see. Through "immersing"…

Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from Bermuda

PubMed Central

Akpaka, Patrick Eberechi; Kissoon, Shivnarine; Wilson, Clyde; Jayaratne, Padman; Smith, Ashley; Golding, George R.

2017-01-01

Molecular characteristics of vancomycin resistant enterococci isolates from Bermuda Island is currently unknown. This study was conducted to investigate phenotypic and genotypic characteristics of VRE isolates from Bermuda Island using the chromogenic agar, E-tests, polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Eighteen E. faecium isolates were completely analyzed and were all resistant to vancomycin, susceptible to linezolid and quinupristin/dalfopristin, positive for vanA and esp genes. The MLST analysis confirmed most isolates were of the sequence types linked to clonal complex 17 (CC17) that is widely associated with outbreaks in hospitals. Infection control measures, antibiotic stewardship, and surveillance activities will continue to be a priority in hospital on the Island. PMID:28267763

Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from Bermuda.

PubMed

Akpaka, Patrick Eberechi; Kissoon, Shivnarine; Wilson, Clyde; Jayaratne, Padman; Smith, Ashley; Golding, George R

2017-01-01

Molecular characteristics of vancomycin resistant enterococci isolates from Bermuda Island is currently unknown. This study was conducted to investigate phenotypic and genotypic characteristics of VRE isolates from Bermuda Island using the chromogenic agar, E-tests, polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Eighteen E. faecium isolates were completely analyzed and were all resistant to vancomycin, susceptible to linezolid and quinupristin/dalfopristin, positive for vanA and esp genes. The MLST analysis confirmed most isolates were of the sequence types linked to clonal complex 17 (CC17) that is widely associated with outbreaks in hospitals. Infection control measures, antibiotic stewardship, and surveillance activities will continue to be a priority in hospital on the Island.

Generation of an isolated sub-40-as pulse using two-color laser pulses: Combined chirp effects

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

Feng, Liqiang; Chu, Tianshu; Institute for Computational Sciences and Engineering, Laboratory of New Fiber Materials and Modern Textile, the Growing Base for State Key Laboratory, Qingdao University, Qingdao, 266071

2011-11-15

In this paper, we theoretically discuss the combined chirp effects on the isolated attosecond generation when a model Ar is exposed to an intense 5-fs, 800-nm fundamental chirped pulse combined with a weak 10-fs, 1200-nm controlling chirped pulse. It shows that for the case of the chirp parameters {beta}{sub 1} = 6.1 (corresponding to the 800-nm field) and {beta}{sub 2} = 4.0 (corresponding to the 1200-nm field), both the harmonic cutoff energy and the supercontinuum can be remarkably extended resulting in a 663-eV bandwidth. Moreover, due to the introduction of the chirps, the short quantum path is selected to contributemore » to the harmonic spectrum. Finally, by superposing a properly selected harmonic spectrum in the supercontinuum region, an isolated pulse as short as 31 as (5 as) is generated without (with) phase compensation.« less

MCNP study for epithermal neutron irradiation of an isolated liver at the Finnish BNCT facility.

PubMed

Kotiluoto, P; Auterinen, I

2004-11-01

A successful boron neutron capture treatment (BNCT) of a patient with multiple liver metastases has been first given in Italy, by placing the removed organ into the thermal neutron column of the Triga research reactor of the University of Pavia. In Finland, FiR 1 Triga reactor with an epithermal neutron beam well suited for BNCT has been extensively used to irradiate patients with brain tumors such as glioblastoma and recently also head and neck tumors. In this work we have studied by MCNP Monte Carlo simulations, whether it would be beneficial to treat an isolated liver with epithermal neutrons instead of thermal ones. The results show, that the epithermal field penetrates deeper into the liver and creates a build-up distribution of the boron dose. Our results strongly encourage further studying of irradiation arrangement of an isolated liver with epithermal neutron fields.

Expression of cardiac neural crest and heart genes isolated by modified differential display.

PubMed

Martinsen, Brad J; Groebner, Nathan J; Frasier, Allison J; Lohr, Jamie L

2003-08-01

The invasion of the cardiac neural crest (CNC) into the outflow tract (OFT) and subsequent outflow tract septation are critical events during vertebrate heart development. We have performed four modified differential display screens in the chick embryo to identify genes that may be involved in CNC, OFT, secondary heart field, and heart development. The screens included differential display of RNA isolated from three different axial segments containing premigratory cranial neural crest cells; of RNA from distal outflow tract, proximal outflow tract, and atrioventricular tissue of embryonic chick hearts; and of RNA isolated from left and right cranial tissues, including the early heart fields. These screens have resulted in the identification of the five cDNA clones presented here, which are expressed in the cardiac neural crest, outflow tract and developing heart in patterns that are unique in heart development.

A predication model for combustion modes of the scramjet-powered aerospace vehicle based on the nonlinear features of the isolator flow field

NASA Astrophysics Data System (ADS)

Yang, Qingchun; Wang, Hongxin; Chetehouna, Khaled; Gascoin, Nicolas

2017-01-01

The supersonic combustion ramjet (scramjet) engine remains the most promising airbreathing engine cycle for hypersonic flight, particularly the high-performance dual-mode scramjet in the range of flight Mach number from 4 to 7, because it can operates under different combustion modes. Isolator is a very key component of the dual-mode scramjet engine. In this paper, nonlinear characteristics of combustion mode transition is theoretically analyzed. The discontinuous sudden changes of static pressure and Mach number are obtained as the mode transition occurs, which emphasizing the importance of predication and control of combustion modes. In this paper, a predication model of different combustion modes is developed based on these these nonlinear features in the isolator flow field. it can provide a valuable reference for control system design of the scramjet-powered aerospace vehicle.

High-Resolution Genotyping of Streptococcus pyogenes Serotype M1 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis

PubMed Central

Desai, Meeta; Efstratiou, Androulla; George, Robert; Stanley, John

1999-01-01

We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise “identical” M1 isolates as members of a clone complex. PMID:10325352

Molecular and genetic analyses of geographic variation in isolates of Phoma macrostoma used for biological weed control.

PubMed

Zhou, Lecong; Bailey, K L; Chen, C Y; Keri, Mario

2005-01-01

Molecular and genetic approaches were used to evaluate the genetic relatedness among isolates of the fungus Phoma macrostoma Montagne originating from Canada and Europe and to other species in the genus Phoma. Distinct differences were observed in genetic variation among nine species of the genus Phoma. Randomly amplified polymorphic DNA (RAPD) revealed the presence of intraspecific genetic variation among the isolates of P. macrostoma, with the isolates being used for biological weed control being distributed in a distinct phylogenetic cluster. Additional variation within the biocontrol isolate cluster in P. macrostoma was revealed by pulsed field gel electrophoresis (PFGE), which showed that biocontrol isolates generated two different chromosomal profiles, however the profiles did not relate to their Canadian ecozone origin. Mating studies showed that biocontrol isolates of P. macrostoma from Canada did not produce sexual reproductive structures and were incapable of crossing. These studies also confirmed that no obvious differentiation exists among the biocontrol isolates of P. macrostoma from Canadian Ecozones 3 and 4.

Impacts of varying light regimes on phycobiliproteins of Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 isolated from diverse habitats.

PubMed

Kannaujiya, Vinod K; Sinha, Rajeshwar P

2015-11-01

The adaptability of cyanobacteria in diverse habitats is an important factor to withstand harsh conditions. In the present investigation, the impacts of photosynthetically active radiation (PAR; 400-700 nm), ultraviolet-B (UV-B; 280-315 nm), and PAR + UV-B radiations on two cyanobacteria viz., Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 inhabiting diverse habitats such as hot springs and rice fields, respectively, were studied. Cell viability was about 14 % in Nostoc sp. HKAR-2 and <10 % in Nostoc sp. HKAR-11 after 48 h of UV-B exposure. PAR had negligible negative impact on the survival of both cyanobacteria. The continuous exposure of UV-B and PAR + UV-B showed rapid uncoupling, bleaching, fragmentation, and degradation in both phycocyanin (C-PC) and phycoerythrin (C-PE) subunits of phycobiliproteins (PBPs). Remarkable bleaching effect of C-PE and C-PC was not only observed with UV-B or PAR + UV-B radiation, but longer period (24-48 h) of exposure with PAR alone also showed noticeable negative impact. The C-PE and C-PC subunits of the rice field isolate Nostoc sp. HKAR-11 were severely damaged in comparison to the hot spring isolate Nostoc sp. HKAR-2 with rapid wavelength shifting toward shorter wavelengths denoting the bleaching of both the accessory light harvesting pigments. The results indicate that PBPs of the hot spring isolate Nostoc sp. HKAR-2 were more stable under various light regimes in comparison to the rice field isolate Nostoc sp. HKAR-11 that could serve as a good source of valuable pigments to be used in various biomedical and biotechnological applications.

Infection dynamics and acute phase response of an Actinobacillus pleuropneumoniae field isolate of moderate virulence in pigs.

PubMed

Gómez-Laguna, Jaime; Islas, Armando; Muñoz, Dennis; Ruiz, Alvaro; Villamil, Aura; Carrasco, Librado; Quezada, Manuel

2014-10-10

Actinobacillus pleuropneumoniae, the causative agent of porcine contagious pleuropneumonia (PCP), causes significant economic losses associated mainly with growth stunting of animals. Although serotypes can be distinguished according to their virulence, most of the studies are focused in A. pleuropneumoniae infections with virulent serotypes. There is little information regarding the role of acute phase proteins (APPs) and proinflammatory cytokines in infections with isolates of mild or moderate virulence. Thus, the present study aims to evaluate the kinetics of infection with an A. pleuropneumoniae serotype 6 (Ap6) field isolate of moderate virulence and the changes in the serum concentration of specific antibodies and different APPs and proinflammatory cytokines. Control animals showed no clinical signs or lesions throughout the study. Infected animals showed increased rectal temperature, respiratory distress and depression from 24hpi, and typical gross and microscopic lesions of PCP from 6hpi onwards. Ap6 was isolated from nasal swabs of four out of five inoculated animals at 24hpi, and from nasal swabs, tonsil and lung samples from all inoculated animals at 72hpi. Specific antibodies against Ap6 or changes in the serum concentration of IL-1β, IL-10 and TNF-α were not detected throughout the study. The serum concentration of IL-6 increased from 6hpi as well as serum A amyloid, C-reactive protein and haptoglobin from 24hpi onwards. Our results highlight the onset of the acute phase response after the infection with a field isolate of A. pleuropneumoniae of moderate virulence from 24hpi onwards which may be of interest in the study of the pathogenesis of this disease. Copyright © 2014 Elsevier B.V. All rights reserved.

Diversity of soil fungi in North 24 Parganas and their antagonistic potential against Leucinodes orbonalis Guen. (Shoot and fruit borer of brinjal).

PubMed

Pal, Sujoy; Ghosh, Swapan Kumar

2014-12-01

Soil samples were collected from agricultural fields and gardens in North 24 Parganas, West Bengal, and fungi species were isolated from them. Thirty-one fungal species were isolated with 19 found in agricultural soil and 28 in garden soil. Twenty-eight out of 31 were identified using cultural and microscopic characters, and three were unidentified. The diversity of isolated fungi was calculated by Simpson's diversity index. The garden soil possessed more fungal colonies (750) than agricultural soil (477). In agricultural soil, the dominant fungi were Aspergillus niger, Rhizopus oryzae, and Penicillium expansum, and the dominant fungi of garden soil were A. niger and Fusarium moniliforme. Simpson's diversity index indicated that garden soil had more fungal diversity (0.939) than agricultural soil (0.896). The entomopathogenic capacity of the isolated fungi was tested against the brinjal shoot and fruit borer (Leucinodes orbonalis Guen) which is the major insect pest of brinjal. The isolated fungi were screened against larva of L. orbonalis for their entomopathogenic potential. Beauveria bassiana, A. niger, and P. expansum showed appreciable antagonism to L. orbonalis, and their lethal doses with 50 % mortality (LD50s) were 4.0 × 10(7), 9.06 × 10(7), and 1.50 × 10(8) spore/mL, respectively, and their times taken to reach 50 % mortality (LT50s) were 9.77, 10.56, and 10.60 days, respectively. This work suggests the restriction of chemical pesticide application in agricultural fields to increase fungal diversity. The entomopathogenic efficacy of B. bassiana could be used in agricultural fields to increase fugal diversity and protect the brinjal crop.

Survey of indigenous entomopathogenic fungi and evaluation of their pathogenicity against the carmine spider mite, Tetranychus cinnabarinus (Boisd.), and the whitefly, Bemisia tabaci (Genn.) biotype B.

PubMed

Topuz, Emine; Erler, Fedai; Gumrukcu, Emine

2016-12-01

The carmine spider mite, Tetranychus cinnabarinus, and the silverleaf whitefly, Bemisia tabaci, are serious pests of both field- and greenhouse-grown crops in south-western Turkey. Control of these pests has been heavily dependent upon chemical pesticides. The objectives of this study were to investigate the occurrence of indigenous entomopathogenic fungi (EPF) in field populations of T. cinnabarinus and B. tabaci, and to evaluate their pathogenicity against these pests. For this purpose, a survey of EPF isolated from field-collected samples of both pests was carried out in Antalya in 2010 and 2011 using the dilution plating method. Four indigenous Beauveria bassiana isolates (TUR1-B, TUR2-B, FIN1-B, FIN2-B) were recovered. In pathogenicity bioassays with T. cinnabarinus and B. tabaci biotype B, all the isolates tested were pathogenic to some of the biological stages of both pests to varying degrees. FIN1-B and TUR1-B caused mortalities of up to 50 and 45%, respectively, in adults of T. cinnabarinus, and of over 79 and 37%, respectively, in pupae of B. tabaci with 10 7 conidia mL -1 suspensions under laboratory conditions 10 days after inoculation. FIN2-B and TUR2-B had mortalities of 19.45 and 12.28%, respectively, in adults of T. cinnabarinus, and of 6.78 and 8.18%, respectively, in pupae of B. tabaci. None of the isolates had an effect on eggs of either species and larvae of the mite. Overall results suggest that isolates FIN1-B and TUR1-B have potential for management of T. cinnabarinus and B. tabaci. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Molecular epidemiology of duck hepatitis a virus types 1 and 3 in China, 2010-2015.

PubMed

Wen, X; Zhu, D; Cheng, A; Wang, M; Chen, S; Jia, R; Liu, M; Sun, K; Zhao, X; Yang, Q; Wu, Y; Chen, X

2018-02-01

Duck hepatitis A virus (DHAV) is the most common aetiologic agent of duck virus hepatitis (DVH), causing substantial economic losses in the duck industry worldwide. In China, officially approved DHAV-1 live-attenuated vaccines have been used widely to vaccinate breeder ducks since 2013. However, following the reports of DVH outbreaks, it has become necessary to assess the epidemiological situation of this virus in China. We conducted molecular epidemiological analyses of 32 DHAV field isolates while analysing the samples from ducks suspected of having hepatitis collected from commercial duck farms in China between May 2010 and December 2015. Considerable changes were observed in the epidemiology of DHAV-1 and DHAV-3 in China over time. A higher number of DHAV-1 strains were isolated during 2010-2012, coinciding with the widespread use of officially approved DHAV-1 live vaccine strains beginning in 2013. In contrast, a higher rate of DHAV-3 causing DHAV infections was observed between 2013 and 2015. Phylogenetic analyses based on the full-length VP1 gene were performed on these field isolates and using reference strains available in GenBank. DHAV-1 field isolates were evaluated in two groups: one group closely related to prototype strains and circulating in China between 2010 and 2012 and another group exhibiting genetic and serological differences from prototype strains. All DHAV-3 strains isolated in this study were grouped as monophyletic, which has become the predominant viral type, particularly in Shandong and Sichuan provinces, since 2013. In conclusion, these data provide updated information on the genetic and serological diversity of DHAV-1 and DHAV-3, and our findings may serve as a foundation for the prevention of, and vaccine development for, DHAV in China. © 2017 Blackwell Verlag GmbH.

Pathogenic and Saprophytic Leptospira Species in Water and Soils from Selected Urban Sites in Peninsular Malaysia

PubMed Central

Benacer, Douadi; Woh, Pei Yee; Mohd Zain, Siti Nursheena; Amran, Fairuz; Thong, Kwai Lin

2013-01-01

Leptospira species were studied in water and soils from selected urban sites in Malaysia. A total of 151 water (n=121) and soil (n=30) samples were collected from 12 recreational lakes and wet markets. All samples were filtered and inoculated into semi-solid Ellinghausen and McCullough modified by Johnson and Harris (EMJH) media supplemented with additional 5-fluorouracil. The cultures were then incubated at 30°C and observed under a dark field microscope with intervals of 10 days. A PCR assay targeting the rrs gene was used to confirm the genus Leptospira among the isolates. Subsequently, the pathogenic status of the isolates was determined using primer sets G1/G2 and Sapro1/Sapro2, which target the secY and rrs genes, respectively. The isolates were identified at serogroup level using the microscopic agglutination test (MAT) while their genetic diversity was assessed by pulsed field gel electrophoresis (PFGE). Based on dark field microscopy, 23.1% (28/121) water and 23.3% (7/30) soil cultures were positive for Leptospira spp. Of the 35 positive cultures, only 8 were pure and confirmed as Leptospira genus by PCR assay. Two out of 8 isolates were confirmed as pathogenic, 5 were saprophytic and one was intermediate. These 8 isolates were negative for the 25 reference hyperimmune rabbit sera tested in the MAT. PFGE showed that all 8 of these environmental Leptospira spp. were genetically diverse. In conclusion, the presence of pathogenic Leptospira spp. in the urban Malaysian environment may indicate and highlight the importance of water screening, especially in recreational lakes, in order to minimize any chance of Leptospira infection. PMID:23363618

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.

Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

USDA-ARS?s Scientific Manuscript database

Pulsed-field gel electrophoresis (PFGE) is the most applied and effective genetic typing method for epidemiological studies and investigation of foodborne outbreaks caused by different pathogens, including Staphylococcus aureus. The technique relies on analysis of large DNA fragments generated by th...

Detection of the Velocity Shear Effect on the Spatial Distributions of the Galactic Satellites in Isolated Systems

NASA Astrophysics Data System (ADS)

Lee, Jounghun; Choi, Yun-Young

2015-02-01

We report a detection of the effect of the large-scale velocity shear on the spatial distributions of the galactic satellites around the isolated hosts. Identifying the isolated galactic systems, each of which consists of a single host galaxy and its satellites, from the Seventh Data Release of the Sloan Digital Sky Survey and reconstructing linearly the velocity shear field in the local universe, we measure the alignments between the relative positions of the satellites from their isolated hosts and the principal axes of the local velocity shear tensors projected onto the plane of sky. We find a clear signal that the galactic satellites in isolated systems are located preferentially along the directions of the minor principal axes of the large-scale velocity shear field. Those galactic satellites that are spirals, are brighter, are located at distances larger than the projected virial radii of the hosts, and belong to the spiral hosts yield stronger alignment signals, which implies that the alignment strength depends on the formation and accretion epochs of the galactic satellites. It is also shown that the alignment strength is quite insensitive to the cosmic web environment, as well as the size and luminosity of the isolated hosts. Although this result is consistent with the numerical finding of Libeskind et al. based on an N-body experiment, owing to the very low significance of the observed signals, it remains inconclusive whether or not the velocity shear effect on the satellite distribution is truly universal.

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

Epidemiological Characteristics and Clinical Treatment Outcome of Typhoid Fever in Ningbo, China, 2005-2014: Pulsed-Field Gel Electorophoresis Results Revealing Great Proportion of Common Transmission Sources.

PubMed

Song, Qifa; Yang, Yuanbin; Lin, Wenping; Yi, Bo; Xu, Guozhang

2017-09-25

We aimed to describe the molecular epidemiological characteristics and clinical treatment outcome of typhoid fever in Ningbo, China during 2005-2014. Eighty-eight Salmonella Typhi isolates were obtained from 307 hospitalized patients. Three prevalent pulsed-field gel electrophoresis (PFGE) patterns of 54 isolates from 3 outbreaks were identified. Overall, there were 64 (72.7%) isolates from clustered cases and 24 (27.3%) isolates from sporadic cases. Resistance to nalidixic acid (NAL) (n = 47; 53.4%) and ampicillin (AMP) (n = 40; 45.4%) and rare resistance to tetracycline (TET) (n = 2; 2.3%) and gentamicin (GEN) (n = 2; 2.3%) were observed. No isolates resistant to cefotaxime (CTX), chloramphenicol (CL), ciprofloxacin (CIP), and trimethoprim-sulfamethoxazole (SXT) were found. The occurrence of reduced sensitivity to CIP was 52.3% (n = 46). The medians of fever clearance time in cases with and without complications were 7 (interquartile range (IQR): 4-10) and 5 (IQR: 3-7) days (P = 0.001), respectively, when patients were treated with CIP or levofloxacin (LEV) and/or third-generation cephalosporins (CEP). Rates of serious complications were at low levels: peritonitis (2.3%), intestinal hemorrhage (6.8%), and intestinal perforation (1.1%). The present study revealed a long-term clustering trend with respect to PFGE patterns, occasional outbreaks, and the rapid spread of AMP resistance and decreased CIP susceptibility among S. Typhi isolates in recent years.

Fungi Associated with the Hemlock Woolly Adelgid, Adelges tsugae, and Assessment of Entomopathogenic Isolates for Management

PubMed Central

Reid, W.R.; Parker, B.L.; Gouli, S.Y.; Skinner, M.; Gouli, V.V.; Teillon, H.B.

2010-01-01

Fungi associated with the hemlock wooly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), were collected throughout the eastern USA and southern China. Twenty fungal genera were identified, as were 79 entomopathogenic isolates, including: Lecanicillium lecanii (Zimmermann) (Hypocreales: Insertae sedis), Isaria farinosa (Holm: Fries.) (Cordycipitaceae), Beauveria bassiana (Balasamo) (Hyphomycetes), and Fusarium spp (Nectriaceae). The remaining fungal genera associated with insect cadavers were similar for both the USA and China collections, although the abundance of Acremonium (Hypocreaceae) was greater in China. The entomopathogenic isolates were assayed for efficacy against Myzus persicae (Sulzer) (Homoptera: Aphididae) and yielded mortality ranging from 3 to 92%. Ten isolates demonstrating the highest efficacy were further assessed for efficacy against field-collected A. tsugae under laboratory conditions. Overall, two B. bassiana, one L. lecanii, and a strain of Metarhizium anisopliae (Metchnikoff) (Hypocreales: Clavicipitaceae), demonstrated significantly higher efficacy against A. tsugae than the others. Isolates were further evaluated for conidial production, germination rate and colony growth at four temperatures representative of field conditions. All isolates were determined to be mesophiles with optimal temperature between 25–30° C. In general, conidial production increased with temperature, though two I. farinosa produced significantly more conidia at cooler temperatures. When efficacy values were compared with conidial production and temperature tolerances, Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF) 1080, 5170, and 5798 had characteristics comparable to the industrial B. bassiana strain GHA. PMID:20672977

Community structures and antagonistic activities of the bacteria associated with surface-sterilized pepper plants grown in different field soils.

PubMed

Kang, Sin Ae; Han, Jae Woo; Kim, Beom Seok

2016-12-01

Endophytic bacteria may act individually or in consortia in controlling certain plant diseases. In this study, pepper plants (Capsicum annuum L. cv. Nokkwang) were cultivated in glasshouse conditions using field soils collected from two different geographic locations, Deokso (DS) and Gwangyang (GY) in Korea. Community structure and antifungal activity of pepper endophytic bacteria were analyzed using culture-independent (PCR-DGGE) and culture-dependent (plating) methods, respectively. Dissimilarities were observed between DGGE profiles of DS and GY samples at all plant tissues. However, sequencing of the major DGGE bands revealed an enrichment of Firmicutes in the leaves of plants propagated in either soil. Similar results were observed with the culturable assays. Firmicutes dominated the isolates from both leaf samples, DS leaf (100 %) and GY leaf (83.3 %), although the genus compositions of DS leaf and GY leaf isolates were different. We assessed the antifungal activity of each isolate recovered to better understand the potential role that these endophytic bacteria may play. Of the 27 representative isolates from DS plant samples, 17 isolates (63.0 %) had antagonistic activity against at least one of the fungi tested. Seventeen isolates from GY plant samples (58.6 %) displayed antagonistic properties. The results show that the endophytic communities differ in the same plant species when propagated in different soils. Exploring the internal tissues of plants growing in diverse soil environments could be a way to find potential candidates for biocontrol agents.

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.

An Untypeable Shigella flexneri Strain Associated with an Outbreak in California

PubMed Central

Trevejo, Rosalie T.; Abbott, Sharon L.; Wolfe, Mitchell I.; Meshulam, Jerry; Yong, David; Flores, George R.

1999-01-01

Eleven Shigella flexneri (group B) isolates were recovered from epidemiologically linked patrons and food handlers from a restaurant-associated outbreak of shigellosis. Six isolates available for pulsed-field gel electrophoresis were identical. All strains agglutinated in group B and subgroup factor 6 sera but not in group 1 through group 6 sera. PMID:10364614

EFFECTS OF REVERSE OSMOSIS ISOLATION ON REACTIVITY OF NATURALLY OCCURRING DISSOLVED ORGANIC MATTER IN PHYSICOCHEMICAL PROCESSES. (R828045)

EPA Science Inventory

A field reverse osmosis system was used to isolate dissolved organic matter (DOM) from two lacustrine and two riverine surface water sources. The rejection of DOM was on the order of 99% and did not vary significantly with pressure. A simple mass balance model using a single m...

Relative susceptibility of oaks to seven species of Phytophthora isolated from oak forest soils

Treesearch

Y. Balci; S. Balci; W.L. MacDonald; K.W. Gottschalk

2008-01-01

Isolates of Phytophthora cambivora, P. cinnamomi, P. citricola, P. europaea, P. quercetorum and two unidentified species were tested for their pathogenicity to eastern US oak species by root and stem inoculations. Experiments were conducted during two different periods and included 1-, 2- and 20- year-old oaks grown under greenhouse and field...

Comparison of helper component-protease RNA silencing suppression activity, subcellular localization, and aggregation of three Korean isolates of Turnip mosaic virus

USDA-ARS?s Scientific Manuscript database

In 2014, we performed a nationwide survey in Korean radish fields to investigate the distribution of Turnip mosaic virus (TuMV). Brassica chinensis sap-inoculated with TuMV-infected radish tissue showed different symptom severity with three isolates. In order to investigate variation among Korean Tu...

DOE's Notification of Planned Change to the EPA 40 CFR Part 194 Certification of the Waste Isolation Pilot Plant: Remote-Handled Transuranic Waste Characterization Plan

EPA Pesticide Factsheets

The U.S. Department of Energy's Carlsbad Field Office (DOE/CBFO) provided the U.S. Environmental Protection Agency (EPA) this Notification of Planned Change to accept remote-handled (RH) transuranic (TRU) waste at the Waste Isolation Pilot Plant (WIPP).

Phenotypic and molecular characterisation of efficient nitrogen-fixing Azotobacter strains from rice fields for crop improvement.

PubMed

Sahoo, Ranjan K; Ansari, Mohammad W; Dangar, Tushar K; Mohanty, Santanu; Tuteja, Narendra

2014-05-01

Biological nitrogen fixation (BNF) is highly effective in the field and potentially useful to reduce adverse effects chemical fertilisers. Here, Azotobacter species were selected via phenotypic, biochemical and molecular characterisations from different rice fields. Acetylene reduction assay of Azotobacter spp. showed that Azotobacter vinelandii (Az3) fixed higher amount of nitrogen (121.09 nmol C2H4 mg(-1) bacteria h(-1)). Likewise, its plant growth functions, viz. siderophore, hydrogen cyanide, salicylic acid, IAA, GA3, zeatin, NH3, phosphorus solubilisation, ACC deaminase and iron tolerance, were also higher. The profile of gDNA, plasmid DNA and cellular protein profile depicted inter-generic and inter-specific diversity among the isolates of A. vinelandii. The PCR-amplified genes nifH, nifD and nifK of 0.87, 1.4 and 1.5 kb , respectively, were ascertained by Southern blot hybridisation in isolates of A. vinelandii. The 16S rRNA sequence from A. vinelandii (Az3) was novel, and its accession number (JQ796077) was received from NCBI data base. Biofertiliser formulation of novel A. vinelandii isolates along with commercial one was evaluated in rice (Oriza sativa L. var. Khandagiri) fields. The present finding revealed that treatment T4 (Az3) (A. vinelandii) are highly efficient to improved growth and yield of rice crop.

Field detection of avian influenza virus in wild birds: evaluation of a portable rRT-PCR system and freeze-dried reagents

USGS Publications Warehouse

Takekawa, John Y.; Iverson, Samuel A.; Schultz, Annie K.; Hill, Nichola J.; Cardona, Carol J.; Boyce, Walter M.; Dudley, Joseph P.

2010-01-01

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAIV) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds is often conducted in remote regions, but results are often delayed because of limited local analytical capabilities, difficulties with sample transportation and permitting, or problems keeping samples cold in the field. In response to these challenges, the performance of a portable real-time, reverse transcriptase-polymerase chain reaction (rRT-PCR) unit (RAPID(Registered), Idaho Technologies, Salt Lake City, UT) that employed lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies) was compared to virus isolation combined with real-time RT-PCR conducted in a laboratory. This study included both field and experimental-based sampling. Field samples were collected from migratory shorebirds captured in northern California, while experimental samples were prepared by spiking fecal material with an H6N2 AIV isolate. Results indicated that the portable rRT-PCR unit had equivalent specificity to virus isolation with no false positives, but sensitivity was compromised at low viral titers. Use of portable rRT-PCR with lyophilized reagents may expedite surveillance results, paving the way to a better understanding of wild bird involvement in HPAIV H5N1 transmission.

In vitro activity of tylvalosin against Spanish field strains of Mycoplasma hyopneumoniae.

PubMed

Tavío, M M; Poveda, C; Assunção, P; Ramírez, A S; Poveda, J B

2014-11-29

Mycoplasma hyopneumoniae is involved in the porcine enzootic pneumonia and respiratory disease complex; therefore, the search for new treatment options that contribute to the control of this organism is relevant. The minimal inhibitory concentrations (MICs) and minimal bactericidal concentrations of tylvalosin and 19 other antimicrobial agents against 20 Spanish field isolates of M. hyopneumoniae were determined using the broth microdilution method, with the type strain (J) as a control strain. Tylvalosin had MIC50 and MIC90 values of 0.016 and 0.06 µg/ml, respectively, and was the second-most effective of the assayed antibiotics, after valnemulin. Tiamulin, tylosin and lincomycin were also among the antibiotics with the lowest MIC50 and MIC90 values against the 20 field isolates (0.06-0.25 µg/ml). However, resistance to tylosin and spiramycin, which like tylvalosin, are 16-membered macrolides, was observed. The MIC50 and MIC90 values for ciprofloxacin and enrofloxacin ranged from 0.125 to 1 µg/ml; the corresponding values ranged from 2 to 4 µg/ml for oxytetracyline, which was the most active tetracycline. Furthermore, tylvalosin and valnemulin exhibited the highest bactericidal activities. In conclusion, the macrolide tylvalosin and the pleuromutilin valnemulin exhibited the highest in vitro antimicrobial activities against M. hyopneumoniae field isolates in comparison with the other tested antibiotics. British Veterinary Association.

Pseudomonas syringae pv. phaseolicola isolated from weeds in bean crop fields.

PubMed

Fernández-Sanz, A M; Rodicio, M R; González, A J

2016-04-01

Pseudomonas syringae pv. phaseolicola, the causative agent of halo blight in common bean (Phaseolus vulgaris L.), was isolated from weeds associated with bean crops in Spain. The bacterium was recovered from Fumaria sp, Mercurialis annua, Solanum nigrum and Sonchus oleraceus. Ps. s. pv. phaseolicola had previously been isolated from leguminous plants and S. nigrum, but to our knowledge, this is the first time it was recovered from the other three species. The isolates were phenotypically and genetically characterized, and they were compared with isolates recovered from common beans. Five different genotypic profiles were detected by PmeI-PFGE, two of them being of new description. Weed isolates were as pathogenic on bean plants as bean isolates, but they were not pathogenic on S. nigrum. Regarding the survival of the pathogen in weeds, Ps. s. pv. phaseolicola was isolated from So. oleraceus 11 weeks after the end of the bean crop. These results strongly support the idea of weeds as a potential source of inoculum for halo blight in bean. It has traditionally been considered that the main source of inoculum of Pseudomonas syringae pv. phaseolicola causing halo blight disease in Phaseolus vulgaris are the bean seeds, and that the host range of the bacterium is almost restricted to leguminous plants. In this study, the bacterium was recovered from four nonleguminous weed species collected in bean fields, and its permanence in weeds for at least 11 weeks after the harvesting of the beans was demonstrated. We have also proved that the strains isolated from weeds were pathogenic on bean plants. Accordingly, the host range of Ps. s. pv. phaseolicola could be broader than previously thought and weeds appear to be acting as a reservoir of the pathogen until the next crop. © 2016 The Society for Applied Microbiology.

Arbuscular mycorrhiza of Arnica montana under field conditions--conventional and molecular studies.

PubMed

Ryszka, Przemysław; Błaszkowski, Janusz; Jurkiewicz, Anna; Turnau, Katarzyna

2010-11-01

Two distinct populations of Arnica montana, an endangered medicinal plant, were studied under field conditions. The material was investigated using microscopic and molecular methods. The analyzed plants were always found to be mycorrhizal. Nineteen arbuscular mycorrhizal fungal DNA sequences were obtained from the roots. They were related to Glomus Group A, but most did not match any known species. Some showed a degree of similarity to fungi colonizing liverworts. Conventional analysis of spores isolated from soil samples allowed to identify different fungal taxa: Glomus macrocarpum, Glomus mosseae, Acaulospora lacunosa, and Scutellospora dipurpurescens. Their spores were also isolated from trap cultures.

On the Propagation and Interaction of Spherical Blast Waves

NASA Technical Reports Server (NTRS)

Kandula, Max; Freeman, Robert

2007-01-01

The characteristics and the scaling laws of isolated spherical blast waves have been briefly reviewed. Both self-similar solutions and numerical solutions of isolated blast waves are discussed. Blast profiles in the near-field (strong shock region) and the far-field (weak shock region) are examined. Particular attention is directed at the blast overpressure and shock propagating speed. Consideration is also given to the interaction of spherical blast waves. Test data for the propagation and interaction of spherical blast waves emanating from explosives placed in the vicinity of a solid propellant stack are presented. These data are discussed with regard to the scaling laws concerning the decay of blast overpressure.

Fungi isolated from flue-cured tobacco inoculated in the field with storage fungi.

PubMed

Welty, R E

1971-03-01

Flue-cured tobacco inoculated in the field with A. amstelodami, A. flavus, A. ochraceus, A. repens, A. ruber, and a species of Penicillium was rarely invaded by these fungi. Regardless of inoculum, the predominant fungi reisolated from green tissue were species of Alternaria and Cladosporium. After curing, A. repens, A. niger, and species of Alternaria and a species of Penicillium were the most commonly isolated fungi. The fungus used as inoculum was not the predominant fungus reisolated from green or cured tissue. Conditions during handling and storage prior to marketing probably determine when storage fungi become associated with the leaf and which species becomes predominant.

Nonreciprocal optical isolation via graphene based photonic crystals

NASA Astrophysics Data System (ADS)

Roshan Entezar, S.; Karimi Habil, M.

2018-03-01

The transmission properties of a one-dimensional photonic crystal containing graphene mono-layers are studied using the transfer matrix method. It is shown that the structure can be used as a polarization-selective nonreciprocal device which discriminates between the two circularly polarized waves with different handedness impinging in the same direction. This structure may be utilized in designing optical isolators for the circularly polarized waves due to the gyrotropic behavior of the graphene mono-layers under the perpendicularly applied external magnetic field. Moreover, the effect of an external magnetic field and the chemical potential of the graphene mono-layers on the band gap of the structure are investigated.

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

Multifunctional magneto-metasurface for terahertz one-way transmission and magnetic field sensing.

PubMed

Chen, Sai; Fan, Fei; He, Xiaotong; Chen, Meng; Chang, Shengjiang

2015-11-01

A magneto-metasurface is demonstrated for one-way transmission of terahertz (THz) waves and magnetic field sensing. Due to the magneto-optical effect and the asymmetric structure of the transmission system, magnetoplasmon mode splitting for forward and backward THz waves and one-way transmission has been observed in this magneto-metasurface. Significantly, the resonance of the magneto-metasurface has been found that can remain at 0.750 THz at a temperature of 218 K, performing as a stable isolator with an isolation of larger than 30 dB within a magnetic field disturbance from 0.23 to 0.35 T. Also, since the resonance of the magneto-metasurface can be tuned by the different external magnetic fields at a temperature that is higher or lower than 218 K, the magneto-metasurface can work as a highly sensitive magnetic field sensor. The sensitivity of this device reaches S=513.05  GHz·T(-1) when T=230  K. This multifunctional magneto-metasurface has broad potential in THz application systems.

Bacteria in midguts of field-collected Anopheles albimanus block Plasmodium vivax sporogonic development.

PubMed

Gonzalez-Ceron, Lilia; Santillan, Frida; Rodriguez, Mario H; Mendez, Domingo; Hernandez-Avila, Juan E

2003-05-01

Bacterial infections were investigated in midguts of insectary and field-collected Anopheles albimanus Weidemann from southern Mexico. Serratia marcescens, Enterobacter cloacae and Enterobacter amnigenus 2, Enterobacter sp., and Serratia sp. were isolated in field samples obtained in 1998, but only Enterobacter sp. was recovered in field samples of 1997 and no bacteria were isolated from insectary specimens. These bacteria were offered along with Plasmodium vivax infected blood to aseptic insectary An. albimanus, and the number of infected mosquitoes as well as the oocyst densities assessed after 7d. Plasmodium vivax infections in mosquitoes co-infected with En. amnigenus 2, En. cloacae, and S. marcensces were 53, 17, and 210 times, respectively, lower than in control mosquitoes, and the mean oocyst density in mosquitoes co-infected with En. cloacae was 2.5 times lower than in controls. Mortality was 13 times higher in S. marcensces-infected mosquitoes compared with controls. The overall midgut bacterial infection in mosquito field populations may influence P. vivax transmission, and could contribute to explain the annual variations in malaria incidence observed in the area.

Efficacy of a biopesticide for control of aflatoxins in corn.

PubMed

Dorner, Joe W

2010-03-01

A 2-year study was carried out to determine the efficacy of a biopesticide in reducing aflatoxin contamination in corn. The biopesticide, afla-guard, delivers a nontoxigenic strain of Aspergillus flavus to the field where it competes with naturally occurring toxigenic strains of the fungus. Afla-guard was applied to entire fields in two areas of Texas at either 11.2 or 22.4 kg/ha. Specific nontreated fields in close proximity to treated fields were designated as controls. Samples of corn were collected at harvest and analyzed for aflatoxins and density of toxigenic and nontoxigenic isolates of A. flavus. Aflatoxin concentrations were generally quite low in 2007, but the mean concentration in treated samples (0.5 ppb) was reduced by 85% compared with controls (3.4 ppb). In 2008, samples from treated and control fields averaged 1.5 and 12.4 ppb, respectively, an 88% reduction. There were no significant differences between the two afla-guard application rates. In conjunction with the reductions in aflatoxin contamination, treatments produced significant reductions in the incidence of toxigenic isolates of A. flavus in corn.

ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants.

PubMed

Bal, Himadri Bhusan; Das, Subhasis; Dangar, Tushar K; Adhya, Tapan K

2013-12-01

Beneficial plant-associated bacteria play a key role in supporting and/or promoting plant growth and health. Plant growth promoting bacteria present in the rhizosphere of crop plants can directly affect plant metabolism or modulate phytohormone production or degradation. We isolated 355 bacteria from the rhizosphere of rice plants grown in the farmers' fields in the coastal rice field soil from five different locations of the Ganjam district of Odisha, India. Six bacteria producing both ACC deaminase (ranging from 603.94 to 1350.02 nmol α-ketobutyrate mg(-1)  h(-1) ) and indole acetic acid (IAA; ranging from 10.54 to 37.65 μM ml(-1) ) in pure cultures were further identified using polyphasic taxonomy including BIOLOG((R)) , FAME analysis and the 16S rRNA gene sequencing. Phylogenetic analyses of the isolates resulted into five major clusters to include members of the genera Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Seed inoculation of rice (cv. Naveen) by the six individual PGPR isolates had a considerable impact on different growth parameters including root elongation that was positively correlated with ACC deaminase activity and IAA production. The cultures also had other plant growth attributes including ammonia production and at least two isolates produced siderophores. Study indicates that presence of diverse rhizobacteria with effective growth-promoting traits, in the rice rhizosphere, may be exploited for a sustainable crop management under field conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of a hybridization window that facilitates sizeable reductions of pollen-mediated gene flow in spring wheat.

PubMed

Willenborg, Christian J; Brûlé-Babel, Anita L; Van Acker, Rene C

2010-06-01

Transgenic wheat (Triticum aestivum L.) with improved agronomic traits is currently being field-tested. Gene flow in space is well-documented, but isolation in time has not received comparable attention. Here, we report the results of a field experiment that investigated reductions in intraspecific gene flow associated with temporal isolation of flowering between T. aestivum conspecifics. Pollen-mediated gene flow (PMGF) between an imazamox-resistant (IR) volunteer wheat population and a non-IR spring wheat crop was assessed over a range of volunteer emergence timings and plant population densities that collectively promoted flowering asynchrony. Natural hybridization events between the two populations were detected by phenotypically scoring plants in F(1) populations followed by verification with Mendelian segregation ratios in the F(1:2) lines. Based on the examination of >545,000 seedlings, we identified a hybridization window in spring wheat approximately 125 growing degree-days (GDD) in length. We found a sizeable reduction (two- to four-fold) in gene flow frequencies when flowering occurred outside of this window. The hybridization window identified in this research also will serve to temporally isolate neighboring wheat crops. However, strict control of volunteer populations or spatial isolation of neighbouring crops emerging within a 125 GDD hybridization window will be necessary to maintain low frequencies of PMGF in spring wheat fields. The model developed herein also is likely to be applicable to other wind-pollinated species.

Plant growth-promoting bacteria facilitate the growth of barley and oats in salt-impacted soil: implications for phytoremediation of saline soils.

PubMed

Chang, Pearl; Gerhardt, Karen E; Huang, Xiao-Dong; Yu, Xiao-Ming; Glick, Bernard R; Gerwing, Perry D; Greenberg, Bruce M

2014-01-01

Plant growth-promoting bacteria (PGPB) strains that contain the enzyme 1-amino-cyclopropane-1-carboxylate (ACC) deaminase can lower stress ethylene levels and improve plant growth. In this study, ACC deaminase-producing bacteria were isolated from a ) salt-impacted ( 50 dS/m) farm field, and their ability to promote plant growth of barley 1): and oats in saline soil was investigated in pouch assays (1% NaCI), greenhouse trials (9.4 dS/m), and field trials (6-24 dS/m). A mix of previously isolated PGPB strains UW3 (Pseudomonas sp.) and UW4 (P. sp.) was also tested for comparison. Rhizobacterial isolate CMH3 (P. corrugata) and UW3+UW4 partially alleviated plant salt stress in growth pouch assays. In greenhouse trials, CMH3 enhanced root biomass of barley and oats by 200% and 50%, respectively. UW3+UW4, CMH3 and isolate CMH2 also enhanced barley and oat shoot growth by 100%-150%. In field tests, shoot biomass of oats tripled when treated with UW3+UW4 and doubled with CHM3 compared with that of untreated plants. PGPB treatment did not affect salt uptake on a per mass basis; higher plant biomass led to greater salt uptake, resulting in decreased soil salinity. This study demonstrates a method for improving plant growth in marginal saline soils. Associated implications for salt

Magnetized Neutron Stars in the Interstellar Medium

NASA Astrophysics Data System (ADS)

Toropina, O. D.; Romanova, M. M.; Lovelace, R. V. E.

2014-09-01

We investigate the propagation of magnetized, isolated old neutron stars through the interstellar medium. We performed axisymmetric, non-relativistic magnetohydrodynamic simulations of the supersonic motion of neutron star with dipole magnetic field aligned with its velocity through the interstellar medium (ISM). We consider two cases: (1) where the accretion radius is larger than Alfvén radius, i.e. Racc>>RA and gravitational focusing is important; and (2) where Racc<

Electron series resonance in a magnetized 13.56 MHz symmetric capacitive coupled discharge

NASA Astrophysics Data System (ADS)

Joshi, J. K.; Binwal, S.; Karkari, S. K.; Kumar, Sunil

2018-03-01

A 13.56 MHz capacitive coupled radio-frequency (RF) argon discharge under transverse magnetic field has been investigated. The discharge is operated in a push-pull mode using a 1:1 isolation transformer with its centre tap grounded to a RF generator. The power delivered to the plasma has been calculated from phase-calibrated RF current/voltage waveforms measured on the secondary side of the isolation transformer. An equivalent electrical circuit of the discharge has been described to determine the net plasma impedance. It is found that in the presence of magnetic field, the discharge impedance exhibits a series resonance as the RF power level is increased gradually. However, in the un-magnetized case, the discharge remains entirely capacitive. A qualitative discussion has been given to explain the role of external magnetic field in achieving the series resonance.

Lethal effect of electric fields on isolated ventricular myocytes.

PubMed

de Oliveira, Pedro Xavier; Bassani, Rosana Almada; Bassani, José Wilson Magalhães

2008-11-01

Defibrillator-type shocks may cause electric and contractile dysfunction. In this study, we determined the relationship between probability of lethal injury and electric field intensity (E in isolated rat ventricular myocytes, with emphasis on field orientation and stimulus waveform. This relationship was sigmoidal with irreversible injury for E > 50 V/cm . During both threshold and lethal stimulation, cells were twofold more sensitive to the field when it was applied longitudinally (versus transversally) to the cell major axis. For a given E, the estimated maximum variation of transmembrane potential (Delta V(max)) was greater for longitudinal stimuli, which might account for the greater sensitivity to the field. Cell death, however, occurred at lower maximum Delta V(max) values for transversal shocks. This might be explained by a less steep spatial decay of transmembrane potential predicted for transversal stimulation, which would possibly result in occurrence of electroporation in a larger membrane area. For the same stimulus duration, cells were less sensitive to field-induced injury when shocks were biphasic (versus monophasic). Ours results indicate that, although significant myocyte death may occur in the E range expected during clinical defibrillation, biphasic shocks are less likely to produce irreversible cell injury.

An Experimental Study of the Ising Chain Statistics under the Magnetic Field

NASA Astrophysics Data System (ADS)

Takeda, Kazuyoshi; Wada, Masaru

1981-11-01

The first experimental study of the statistics of a quasi-one-dimensional Ising system under the magnetic field Hα, described by the Hamiltonian \\includegraphics{dummy.eps} has been performed, where J1 and J2 are the intra- and the inter-chain exchange constants, respectively. A single crystal of the compound (CH3)3NHCoCl3\\cdot2H2O has been used as a model sample of the ferromagnetic system with J1/kB{=}14.2 K and J2/kB{=}0.20 K. It has been revealed that the experimental values of the magnetic heat capacity under the field Hα>2J2/gzμB (≈0.8 kOe) applied along the spin preferential axis are excellently reproduced by the values calculated for the isolated Ising chain under the longitudinal field (α{=}z; gz{=}6.54). For the temperature higher than 7 K (≈J1/2kB), the experimental values of the magnetic heat capacity under the field along the spin hard axis have also agreed with the theoretical values for the isolated Ising chain under the transverse field (α{=}y; gy{=}3.90).

A histidine-rich protein 2-based malaria drug sensitivity assay for field use.

PubMed

Noedl, Harald; Attlmayr, Bernhard; Wernsdorfer, Walther H; Kollaritsch, Herwig; Miller, Robert S

2004-12-01

With the spread of antimalarial drug resistance, simple and reliable tools for the assessment of antimalarial drug resistance, particularly in endemic regions and under field conditions, have become more important than ever before. We therefore developed a histidine-rich protein 2 (HRP2)-based drug sensitivity assay for testing of fresh isolates of Plasmodium falciparum in the field. In contrast to the HRP2 laboratory assay, the field assay uses a procedure that further simplifies the handling and culturing of malaria parasites by omitting centrifugation, washing, the use of serum, and dilution with uninfected red blood cells. A total of 40 fresh Plasmodium falciparum isolates were successfully tested for their susceptibility to dihydroartemisinin, mefloquine, quinine, and chloroquine (50% inhibitory concentration [IC50] = 3.43, 61.89, 326.75, and 185.31 nM, respectively). Results very closely matched those obtained with a modified World Health Organization schizont maturation assay (R2 = 0.96, P < 0.001; mean log difference at IC50 = 0.054).

Genetic Variability and Distribution of Mating Type Alleles in Field Populations of Leptosphaeria maculans from France

PubMed Central

Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

2006-01-01

Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

Bacterial isolates from equine infections in western Canada (1998–2003)

PubMed Central

Clark, Chris; Greenwood, Sarah; Boison, Joe O.; Chirino-Trejo, Manuel; Dowling, Patricia M.

2008-01-01

All bacterial samples of equine origin submitted to the diagnostic laboratory at the Western College of Veterinary Medicine from January 1998 to December 2003 from either “in-clinic” or Field Service cases were accessed (1323 submissions). The most common bacterial isolates from specific presenting signs were identified, along with their in vitro antimicrobial susceptibility patterns. The most common site from which significant bacterial isolates were recovered was the respiratory tract, followed by wounds. Streptococcus zooepidemicus was the most common isolate from most infections, followed by Escherichia coli. Antimicrobial resistance was not common in the isolates and acquired antimicrobial resistance to multiple drugs was rare. The results are compared with previous published studies from other institutions and used to suggest appropriate antimicrobial treatments for equine infections in western Canada. PMID:18309745

[Molecular study of methicillin-resistant Staphylococcus haemolyticus in a Mexican hospital].

PubMed

Castro, Natividad; Loaiza-Loeza, María Salomé; Calderón-Navarro, Amparo; Sánchez, Alejandro; Silva-Sánchez, Jesús

2006-01-01

To perform the molecular characterization of methicillin-resistant Staphylococcus haemolyticus (MRSH) clinical isolates from patients in a Mexican hospital. Sixty three Staphylococcus ssp. isolates collected from September 2000 to October 2002 were analyzed. Antimicrobial susceptibility was determined by disk diffusion method and the presence of the mecA gene was detected by PCR technique. Isolates characterization was carried out by pulsed field gel electrophoresis (PFGE). The frequency of S. haemolyticus was 25.5% (18 of 63 clinical isolates), all S. haemolyticus isolates were methicillin-resistant and they were positive for the mecA gene. A major pattern (A) with 8 subtypes was identified. This clone was distributed during the 20 months period. Most of them were isolated from the surgery (55%) and pediatric services (27.5%). The methicillin-resistant S. haemolyticus permanence as pathogen in this hospital, suggest the implementation of control programs in order to decrease the prevalence of this multiresistant pathogen.

Drop-on-Demand Single Cell Isolation and Total RNA Analysis

PubMed Central

Moon, Sangjun; Kim, Yun-Gon; Dong, Lingsheng; Lombardi, Michael; Haeggstrom, Edward; Jensen, Roderick V.; Hsiao, Li-Li; Demirci, Utkan

2011-01-01

Technologies that rapidly isolate viable single cells from heterogeneous solutions have significantly contributed to the field of medical genomics. Challenges remain both to enable efficient extraction, isolation and patterning of single cells from heterogeneous solutions as well as to keep them alive during the process due to a limited degree of control over single cell manipulation. Here, we present a microdroplet based method to isolate and pattern single cells from heterogeneous cell suspensions (10% target cell mixture), preserve viability of the extracted cells (97.0±0.8%), and obtain genomic information from isolated cells compared to the non-patterned controls. The cell encapsulation process is both experimentally and theoretically analyzed. Using the isolated cells, we identified 11 stem cell markers among 1000 genes and compare to the controls. This automated platform enabling high-throughput cell manipulation for subsequent genomic analysis employs fewer handling steps compared to existing methods. PMID:21412416

Microbiological Features of KPC-Producing Enterobacter Isolates Identified in a U.S. Hospital System

PubMed Central

Ahn, Chulsoo; Syed, Alveena; Hu, Fupin; O’Hara, Jessica A.; Rivera, Jesabel I.; Doi, Yohei

2014-01-01

Microbiological data regarding KPC-producing Enterobacter spp. are scarce. In this study, 11 unique KPC-producing Enterobacter isolates were identified among 44 ertapenem-non-susceptible Enterobacter isolates collected between 2009 and 2013 at a hospital system in Western Pennsylvania. All cases were healthcare-associated and occurred in medically complex patients. While pulsed-field gel electrophoresis (PFGE) showed diverse restriction patterns overall, multilocus sequence typing (MLST) identified Enterobacter cloacae isolates with sequence types (STs) 93 and 171 from two hospitals each. The levels of carbapenem minimum inhibitory concentrations were highly variable. All isolates remained susceptible to colistin, tigecycline, and the majority to amikacin and doxycycline. A blaKPC-carrying IncN plasmid conferring trimethoprim-sulfamethoxazole resistance was identified in three of the isolates. Spread of blaKPC in Enterobacter spp. appears to be due to a combination of plasmid-mediated and clonal processes. PMID:25053203

Vibrio cholerae O1 El Tor from southern Vietnam in 2010 was molecularly distinct from that present from 1999 to 2004.

PubMed

Nguyen, V H; Pham, H T; Diep, T T; Phan, C D H; Nguyen, T Q; Nguyen, N T N; Ngo, T C; Nguyen, T V; Do, Q K; Phan, H C; Nguyen, B M; Ehara, M; Ohnishi, M; Yamashiro, T; Nguyen, L T P; Izumiya, H

2016-04-01

The Vibrio cholerae O1 (VCO1) El Tor biotype appeared during the seventh cholera pandemic starting in 1961, and new variants of this biotype have been identified since the early 1990s. This pandemic has affected Vietnam, and a large outbreak was reported in southern Vietnam in 2010. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem-repeat analyses (MLVA) were used to screen 34 VCO1 isolates from the southern Vietnam 2010 outbreak (23 patients, five contact persons, and six environmental isolates) to determine if it was genetically distinct from 18 isolates from outbreaks in southern Vietnam from 1999 to 2004, and two isolates from northern Vietnam (2008). Twenty-seven MLVA types and seven PFGE patterns were identified. Both analyses showed that the 2008 and 2010 isolates were distinctly clustered and separated from the 1999-2004 isolates.

Efficacy of oral moxidectin against susceptible and resistant isolates of Dirofilaria immitis in dogs.

PubMed

McTier, Tom L; Six, Robert H; Pullins, Aleah; Chapin, Sara; McCall, John W; Rugg, Douglas; Maeder, Steven J; Woods, Debra J

2017-11-09

Monthly topical and sustained-release injectable formulations of moxidectin are currently marketed; however, an oral formulation, while approved at a dose of 3 μg/kg, is not currently marketed in the United States. Although resistance of heartworms to all macrocyclic lactone (ML) heartworm preventives (ivermectin, milbemycin, selamectin and moxidectin) has been demonstrated, to date no data have been reported on the effectiveness of oral moxidectin against recent isolates of Dirofilaria immitis. A total of nine studies were conducted to determine the efficacy of moxidectin against a range of older and recently sourced heartworm isolates. Dogs (groups of three to eight) were inoculated with 50 D. immitis infective larvae (L3) from nine different isolates (MP3, Michigan, JYD-34, ZoeMO-2012, ZoeKy-2013, ZoeLA-2013, GCFL-2014, AMAL-2014 and ZoeAL-2015) and treated 28-30 days later with single oral doses of 3 μg/kg of moxidectin. Additionally, one group of dogs that was inoculated with JYD-34 was treated monthly for 3 consecutive months beginning 30 days post inoculation. Dogs were held for approximately 4 months after the initial (or only) treatment and then necropsied for recovery of adult heartworms. A single dose of 3 μg/kg of moxidectin was 100% effective in preventing the development of five of nine heartworm isolates (MP3, Michigan, ZoeKy, GCFL and ZoeAL isolates), confirming their susceptibility to oral moxidectin at this dose. MP3 and Michigan are isolates sourced from the field more than 9 years ago, while ZoeKy, ZoeAL and GCFL were isolated from the field within the past 2 to 3 years. Against JYD-34, ZoeMO, ZoeLA and AMAL isolates, a single dose of 3 μg/kg of moxidectin was not completely effective, with efficacies of 19%, 82%, 54% and 62%, respectively, demonstrating resistance of these heartworm isolates to oral moxidectin at this dosage. Three consecutive monthly doses of 3 μg/kg of moxidectin were also incompletely effective against the JYD-34 isolate, with an efficacy of 44%. JYD-34 was originally isolated in 2010, while ZoeMO, ZoeLA and AMAL were isolated within the past 2 to 3 years. A single oral dose (3 μg/mg) of moxidectin was 100% effective in preventing the development of ML-susceptible heartworm isolates while being incompletely effective against ML-resistant isolates.

Characterization of Salmonella Typhimurium isolates associated with septicemia in swine

PubMed Central

Bergeron, Nadia; Corriveau, Jonathan; Letellier, Ann; Daigle, France; Quessy, Sylvain

2010-01-01

Salmonella Typhimurium is frequently isolated from pigs and may also cause enteric disease in humans. In this study, 33 isolates of S. Typhimurium associated with septicemia in swine (CS) were compared to 33 isolates recovered from healthy animals at slaughter (WCS). The isolates were characterized using phenotyping and genotyping methods. For each isolate, the phage type, antimicrobial resistance, and pulsed-field gel electrophoresis (PFGE) DNA profiles were determined. In addition, the protein profiles of each isolate grown in different conditions were studied by Coomassie Blue-stained sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot. Various phage types were identified. The phage type PT 104 represented 36.4% of all isolates from septicemic pigs. Resistance to as many as 12 antimicrobial agents, including some natural resistances, was found in isolates from CS and WCS. Many genetic profiles were identified among the PT 104 phage types. Although it was not possible to associate one particular protein with septicemic isolates, several highly immunogenic proteins, present in all virulent isolates and in most isolates from clinically healthy animals, were identified. These results indicated that strains associated with septicemia belong to various genetic lineages that can also be recovered from asymptomatic animals at the time of slaughter. PMID:20357952

Enzyme Mini-Test for Field Identification of Leishmania isolates from U.S. Military Personnel.

DTIC Science & Technology

1984-08-15

was noted that L. m. peruviana has an extensive distribution which includes Venezuela, Dominican Republic, Peru , Panama, Belize and possibly 10 Costa...isolates from human hosts (6 from Dominican Republic, 5 from Venezuela, 3 from Belize, 1 each from Peru , 14 Panama, Costa Rica and Mexico). These isolates...L147, LV24 547 OWC LMJ Man R. Beach Kenya LRC-L137 551 OWC LMJ Rodent R. Beach Kenya NLB095 552 OWC LMJ Sandfly R. Beach Kenya NLB144 558 OWC LMJ Man

Effects of nematicides on cotton root mycobiota.

PubMed

Baird, R E; Carling, D E; Watson, C E; Scruggs, M L; Hightower, P

2004-02-01

Baseline information on the diversity and population densities of fungi collected from soil debris and cotton (Gossypium hirsutum L.) roots was determined. Samples were collected from Tifton, GA, and Starkville, MS containing cotton field soil treated with the nematicides 1,3-dichloroproprene (fumigant) and aldicarb (granules). A total of 10,550 and 13,450 fungal isolates were collected from these two study sites, respectively. Of this total, 34 genera of plant pathogenic or saprophytic species were identified. Pathogenic root fungi included Fusarium spp. (40% of all isolations), Macrophomina, Pythium, Rhizoctonia, and Sclerotium. Fusarium and Rhizoctonia were the most common fungal species identified and included F. oxysporum, F. verticillioides and F. solani, the three Fusarium species pathogenic on cotton plants. Population densities of Fusarium were not significantly different among locations or tissue types sampled. Macrophomina was isolated at greater numbers near the end of the growing seasons. Anastomosis groups of R. solani isolated from roots and soil debris included AG-3, -4, -7, 2-2, and -13 and anastomosis groups of binucleate Rhizoctonia included CAG-2, -3, and -5. Occurrences and frequency of isolations among sampling dates were not consistent. Fluctuations in the frequency of isolation of Rhizoctonia did not correspond with changes in frequency of isolation of the biological control fungus, Trichoderma. When individual or pooled frequencies of the mycobiota were compared to nematicide treatments, no specific trends occurred between treatments, application methods or rates. Results from this study show that use of 1,3-D and aldicarb in cotton fields does not significantly impact plant pathogenic fungi or saprophytic fungal populations. Thus cotton producers need not adjust seedling disease control measures when these two nematicides are used.

Epidemiology of antibiotic-resistant wound infections from six countries in Africa

PubMed Central

Bebell, Lisa M; Meney, Carron; Valeri, Linda

2017-01-01

Introduction Little is known about the antimicrobial susceptibility of common bacteria responsible for wound infections from many countries in sub-Saharan Africa. Methods We performed a retrospective review of microbial isolates collected based on clinical suspicion of wound infection between 2004 and 2016 from Mercy Ships, a non-governmental organisation operating a single mobile surgical unit in Benin, Congo, Liberia, Madagascar, Sierra Leone and Togo. Antimicrobial resistant organisms of interest were defined as methicillin-resistant Staphylococcus aureus (MRSA) or Enterobacteriaceae resistant to third-generation cephalosporins. Generalised mixed-effects models accounting for repeated isolates in a patient, potential clustering by case mix for each field service, age, gender and country were used to test the hypothesis that rates of antimicrobial resistance differed between countries. Results 3145 isolates from repeated field services in six countries were reviewed. In univariate analyses, the highest proportion of MRSA was found in Benin (34.6%) and Congo (31.9%), while the lowest proportion was found in Togo (14.3%) and Madagascar (14.5%); country remained a significant predictor in multivariate analyses (P=0.002). In univariate analyses, the highest proportion of third-generation cephalosporin-resistant Enterobacteriaceae was found in Benin (35.8%) and lowest in Togo (14.3%) and Madagascar (16.3%). Country remained a significant predictor for antimicrobial-resistant isolates in multivariate analyses (P=0.009). Conclusion A significant proportion of isolates from wound cultures were resistant to first-line antimicrobials in each country. Though antimicrobial resistance isolates were not verified in a reference laboratory and these data may not be representative of all regions of the countries studied, differences in the proportion of antimicrobial-resistant isolates and resistance profiles between countries suggest site-specific surveillance should be a priority and local antimicrobial resistance profiles should be used to guide empiric antibiotic selection. PMID:29588863

Phenotypic and genotypic profile of clinical and animal multidrug-resistant Salmonella enterica isolates from Mexico.

PubMed

Aguilar-Montes de Oca, S; Talavera-Rojas, M; Soriano-Vargas, E; Barba-León, J; Vázquez-Navarrete, J; Acosta-Dibarrat, J; Salgado-Miranda, C

2018-01-01

The objective of this study was to obtain a phenotypic and genotypic profile of Salmonella enterica including multidrug-resistant (MDR) isolates from food-producing animals and clinical isolates, as well as their genetic relatedness in two different States of Mexico (Jalisco and State of Mexico). A total of 243 isolates were evaluated in terms of antimicrobial resistance (AMR) and related genes through a disk diffusion method and PCR respectively; we found 16 MDR isolates, all of them harbouring the bla CMY gene but not qnr genes, these isolates represent less than 10% of the collection. The pulsed-field gel electrophoresis revealed a higher genotypic similitude within isolates of State of Mexico than Jalisco. A low percentage of Salmonella isolates were resistant to relevant antibiotics in human health, nevertheless, the AMR and involved genes were similar despite the different serovars and origin of the isolates. This investigation provided an insight of the current status of AMR of Salmonella isolates in two States of Mexico and pinpoint the genes involved in AMR and their epidemiological relationship, the information could help to determine an adequate therapy in human and veterinary medicine. © 2017 The Society for Applied Microbiology.

Relationship Between Broiler Body Weights, Eimeria maxima Gross Lesion Scores, and Microscores in Three Anticoccidial Sensitivity Tests.

PubMed

Barrios, Miguel A; Da Costa, Manuel; Kimminau, Emily; Fuller, Lorraine; Clark, Steven; Pesti, Gene; Beckstead, Robert

2017-06-01

Anticoccidial sensitivity tests (ASTs) serve to determine the efficacy of anticoccidial drugs against Eimeria field isolates in a controlled laboratory setting. The most commonly measured parameters are body weight gain, feed conversion ratio, gross intestinal lesion scores, and mortality. Due to the difficulty in reliably scoring gross lesion scores of Eimeria maxima , microscopic analysis of intestinal scrapings (microscores) can be used in the field to indicate the presence of this particular Eimeria. The goal of this study was to determine the relationship between E. maxima microscores and broiler body weights and gross E. maxima lesion scores in three ASTs. Day-old broiler chicks were raised for 12 days on a standard corn-soy diet. On Day 12, chicks were placed in Petersime batteries and treatment diets were provided. There were six birds per pen, four pens per treatment, and 12 treatments, for a total of 288 chicks per AST. The treatments were as follows: 1) nonmedicated, noninfected; 2) nonmedicated, infected; 3) lasalocid, infected; 4) salinomycin, infected; 5) diclazuril, infected; 6) monensin, infected; 7) decoquinate, infected; 8) narasin + nicarbazin, infected; 9) narasin, infected; 10) nicarbazin, infected; 11) robenidine, infected; and 12) zoalene, infected. On Day 14, chicks were challenged with an Eimeria field isolate by oral gavage. On Day 20, broilers were weighed, and gross lesion scores and microscores were classified from 0 to 4 depending on the severity of the gross lesion scores and E. maxima microscores. Data from three trials using different field isolates were statistically analyzed using a logarithmic regression model. There was no relationship (P = 0.1224) between microscores and body weight gain. There was a positive relationship between microscores and gross lesion scores (P = 0.004). However, there was also an interaction between isolate and treatment (P < 0.0001). Lastly, the interaction between isolate and gross lesion scores (P = 0.0041) demonstrates that the significance of the relationship between microscores and gross lesion scores may be dependent on pathogenicity of the challenge Eimeria or the amount of E. maxima in the inoculum.

Infection Courts in Watermelon Plants Leading to Seed Infestation by Fusarium oxysporum f. sp. niveum.

PubMed

Petkar, Aparna; Ji, Pingsheng

2017-07-01

Fusarium wilt incited by Fusarium oxysporum f. sp. niveum is a seed-transmitted disease that causes significant yield loss in watermelon production. The pathogen may infect watermelon seeds latently, which can be an important inoculum source and contribute to severe disease outbreak. However, information regarding infection courts of F. oxysporum f. sp. niveum leading to infestation of watermelon seeds is limited. To determine how seeds in watermelon fruit can be infested by F. oxysporum f. sp. niveum during the watermelon growing season, greenhouse and field experiments were conducted in 2014 and 2015 where watermelon flowers and immature fruit were inoculated with F. oxysporum f. sp. niveum. Seeds were extracted from mature watermelon fruit, and infestation of watermelon seeds was determined by isolation of F. oxysporum f. sp. niveum and further confirmed by real-time polymerase chain reaction (PCR) analysis. Inoculation of the pericarp of immature fruit resulted in 17.8 to 54.4% of infested seeds under field conditions and 0.6 to 12.8% of infested seeds under greenhouse conditions when seeds were not surface disinfested prior to isolation. Seed infestation was also detected in 0 to 4.5% of the seeds when seeds were surface disinfested prior to isolation. Inoculation of pistil resulted in 0 to 7.2% and 0 to 18.3% of infested seeds under greenhouse and field conditions when seeds were surface disinfested or not disinfested before isolation, respectively. Inoculation of peduncle resulted in 0.6 to 6.1% and 0 to 10.0% of infested seeds in the greenhouse and field experiments when seeds were surface disinfested or not disinfested before isolation, respectively. Seed infestation was also detected in all the experiments using real-time PCR assay when pericarp or pistil was inoculated, and in three of four experiments when peduncle was inoculated, regardless of whether seeds were surface disinfested or not disinfested. Pericarp and peduncle of immature watermelon fruit and pistil of watermelon flowers could be potential infection courts for F. oxysporum f. sp. niveum leading to infestation of seeds in asymptomatic watermelon fruit.

Characterization of antimicrobial resistance, molecular and phage types of Salmonella enterica serovar Typhi isolations.

PubMed

Demczuk, W H B; Finley, R; Nadon, C; Spencer, A; Gilmour, M; Ng, L-K

2010-10-01

Isolation rates in Canada of Salmonella enterica serovar Typhi increased from 0.29 to 0.55 isolations/100,000 population during 2000-2006. Although no ciprofloxacin resistance was detected, nalidixic acid resistance increased from 41% to 80%. Multidrug-resistant S. Typhi represented 18% of the strains tested. Pulsed-field gel electrophoresis (PFGE) analysis of 222 isolates resulted in 91 distinct patterns clustering into four major genetic similarity groups. The five most frequently occurring PFGE patterns accounted for 46% of the isolates. Drug-resistant isolates predominantly occurred in one PFGE similarity group. There were 39 phage types identified in 826 isolates analysed with 60% described by five phage types; 134 were untypable. The phage types associated with multidrug resistance were phage types 53, B1, D1, E1, E9, G3 and M1. Improved integration of epidemiological and laboratory case data will facilitate the protection of public health in Canada during an era of increasing travel and globalization.

[Campylobacter spp.: prevalence and pheno-genotypic characterization of isolates recovered from patients suffering from diarrhea and their pets in La Pampa Province, Argentina].

PubMed

Tamborini, Ana L; Casabona, Luis M; Viñas, María R; Asato, Valeria; Hoffer, Alicia; Farace, María I; Lucero, María C; Corso, Alejandra; Pichel, Mariana

2012-01-01

The prevalence of Campylobacter spp. was investigated in 327 patients suffering from diarrhea and in 36 animals (dogs, cats and chickens) owned by the patients that presented infection by Campylobacter in Santa Rosa, La Pampa, Argentina. Campylobacter spp. was isolated in 50/327 patients and in 12/36 animals, being Campylobacter jejuni the most common species. Resistance to ciprofloxacin (65 %) and tetracycline (32 %) was found among 35 isolates of human origin studied. Seven genetic subtypes were observed among 13 C. jejuni isolates by pulsed field gel electrophoresis. Two subtypes grouped isolates belonging to patients and their respective dogs whereas another subtype grouped one isolate of human origin and two isolates from the patient's chickens. The results of this investigation highlight the need to strengthen surveillance of Campylobacter spp. not only in poultry, which is recognized as the main reservoir, but also in pets, which were shown to be asymptomatic carriers of the pathogen.

Analysis of Design Parameters Effects on Vibration Characteristics of Fluidlastic Isolators

NASA Astrophysics Data System (ADS)

Deng, Jing-hui; Cheng, Qi-you

2017-07-01

The control of vibration in helicopters which consists of reducing vibration levels below the acceptable limit is one of the key problems. 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 is very important to obtain efficient vibration-suppressed. Aiming at getting the effect of design parameters on the property of fluidlastic isolator, a dynamic equation is set up based on the theory of dynamics. And the dynamic analysis is carried out. The influences of design parameters on the property of fluidlastic isolator are calculated. Dynamic analysis results have shown that fluidlastic isolator can reduce the vibration effectively. Analysis results also showed that the design parameters such as the fluid density, viscosity coefficient, stiffness (K1 and K2) and loss coefficient have obvious influence on the performance of isolator. The efficient vibration-suppressed can be obtained by the design optimization of parameters.

Molecular typing of Chinese Streptococcus pyogenes isolates.

PubMed

You, Yuanhai; Wang, Haibin; Bi, Zhenwang; Walker, Mark; Peng, Xianhui; Hu, Bin; Zhou, Haijian; Song, Yanyan; Tao, Xiaoxia; Kou, Zengqiang; Meng, Fanliang; Zhang, Menghan; Bi, Zhenqiang; Luo, Fengji; Zhang, Jianzhong

2015-06-01

Streptococcus pyogenes causes human infections ranging from mild pharyngitis and impetigo to serious diseases including necrotizing fasciitis and streptococcal toxic shock syndrome. The objective of this study was to compare molecular emm typing and pulsed field gel electrophoresis (PFGE) with multiple-locus variable-number tandem-repeat analysis (MLVA) for genotyping of Chinese S. pyogenes isolates. Molecular emm typing and PFGE were performed using standard protocols. Seven variable number tandem repeat (VNTR) loci reported in a previous study were used to genotype 169 S. pyogenes geographically-diverse isolates from China isolated from a variety of disease syndromes. Multiple-locus variable-number tandem-repeat analysis provided greater discrimination between isolates when compared to emm typing and PFGE. Removal of a single VNTR locus (Spy2) reduced the sensitivity by only 0.7%, which suggests that Spy2 was not informative for the isolates screened. The results presented support the use of MLVA as a powerful epidemiological tool for genotyping S. pyogenes clinical isolates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Transmissible gastroenteritis virus: plaques and a plaque neutralization test.

PubMed Central

Thomas, F C; Dulac, G C

1976-01-01

A plaquing system and plaque neutralization test in porcine thyroid cells were used to study different transmissible gastroenteritis isolates and hemagglutinating encephalomyelitis virus. Among transmissible gastroenteritis virus isolates, plaque size varied considerably and mixed size ranges sometimes occurred. The most recently isolated viruses produced smaller plaques than the laboratory viruses or hemagglutinating encephalomyelitis virus. All transmissible gastroenteritis virus isolates reacted in the plaque neutralization test with a transmissible gastroenteritis virus antiserum which showed no activity against hemagglutinating encephalomyelitis virus. Plaque neutralization results both from experimentally infected pigs and following a field outbreak demonstrated the reliability of this test and its greater sensitivity than the conventional tube test. Images Fig. 1. PMID:187296

Genetic diversity and structure of Phakopsora pachyrhizi infecting soybean in Nigeria

USDA-ARS?s Scientific Manuscript database

The genetic structure of Nigerian field populations of the soybean rust pathogen Phakopsora pachyrhizi was determined using 18 simple sequence repeat markers. A total of 113 fungal isolates was collected by hierarchical sampling infected leaves from soybean fields in three agroecological zones in 2...

First Complete Genome Sequence of Papaya ringspot virus-W Isolated from a Gourd in the United States.

PubMed

Ali, Akhtar

2017-01-12

In the United States, the Papaya ringspot virus was first reported from papaya in Florida in 1949. Here, we determined the first complete genome sequence (10,302 nucleotides) of a Papaya ringspot virus-W isolate, which was collected from a commercial field of gourd in Tulsa, OK. Copyright © 2017 Ali.

Comparative genomics analysis of field isolates of Aspergillus flavus and A. parasiticus to explain phenotypic variation in oxidative stress tolerance and host preference

USDA-ARS?s Scientific Manuscript database

Aflatoxin contamination of peanut and other crops is a major concern for producers globally, and has been shown to be exacerbated by drought stress. Previous transcriptomic and proteomic examination of the responses of isolates of Aspergillus flavus to drought-related oxidative stress in vitro have ...

Effector gene suites in some soil isolates of Fusarium oxysporum are not sufficient predictors of vascular wilt in tomato

USDA-ARS?s Scientific Manuscript database

This is the first study examining the distribution of fungal effector genes among soil populations of Fusarium oxysporum in a tomato field undergoing a wilt disease epidemic. 74 F. oxysporum soil isolates were assayed for known effector genes present in a Race 3 tomato wilt strain (FOL MN-25) obtain...

Characterizing virulence phenotypes among U.S. isolates of Magnaporthe oryzae using IRRI NILs, US germplasm, and NERICA lines

USDA-ARS?s Scientific Manuscript database

Rice blast disease, caused by Magnaporthe oryzae, is a major constraint to rice production in most rice production areas, including the Southern U.S. In continued efforts to evaluate the effectiveness of resistance (R) genes, a total of 33 field and 12 U.S. reference isolates of M. oryzae were eval...

Characterization of Puccinia graminis f.sp. tritici isolates derived from an unusual wheat stem rust outbreak in Germany in 2013

USDA-ARS?s Scientific Manuscript database

An unusual stem rust infestation occurred in German wheat fields in summer 2013. We analyzed 48 isolates derived from 16 Puccinia graminis f. sp. tritici (Pgt) samples and six races were identified: TKTTF, TKKTF, TKPTF, TKKTP, PKPTF, and MMMTF. Infection type and genotypic data confirm that none of ...

Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus

PubMed Central

Servín-Garcidueñas, Luis E.; Rogel, Marco A.; Ormeño-Orrillo, Ernesto; Zayas-del Moral, Alejandra; Sánchez, Federico

2016-01-01

We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, a nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus. Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island. PMID:26988045

In Vitro Susceptibilities of Mycoplasma putrefaciens Field Isolates▿

PubMed Central

Antunes, N. T.; Tavío, M. M.; Mercier, P.; Ayling, R. D.; Al-Momani, W.; Assunção, P.; Rosales, R. S.; Poveda, J. B.

2007-01-01

MICs were determined for 15 antimicrobial agents against 37 Mycoplasma putrefaciens isolates. The most effective antimicrobial drug classes were the fluoroquinolones, the tetracyclines, the lincosamide lincomycin, and the macrolides. The susceptibility profile of the isolates correlated with the geographic origin. This is the first report of decreased susceptibility to the macrolides, lincomycin, and the tetracyclines in M. putrefaciens strains. PMID:17638695

A dual-rating method for evaluating impact noise isolation of floor-ceiling assemblies.

PubMed

LoVerde, John J; Dong, D Wayland

2017-01-01

Impact Insulation Class (IIC), the single-number rating for evaluating the impact noise insulation of a floor-ceiling assembly, and the associated field testing ratings, are unsatisfactory because they do not have strong correlation with subjective reaction nor provide suitable detailed information for evaluation or design of floor-ceiling assemblies. Various proposals have been made for improving the method, but the data presented indicate that no single-number rating can adequately characterize the impact noise isolation of an assembly. For realistic impact noise sources and floor-ceiling assembly types, there are two frequency domains for impact noise, and the impact noise levels in the two domains can vary independently. Therefore, two ratings are required in order to satisfactorily evaluate the impact isolation provided by a floor-ceiling assembly. Two different ratings are introduced for measuring field impact isolation in the two frequency domains, using the existing impact source and measurement method. They are named low-frequency impact rating (LIR) and high-frequency impact rating (HIR). LIR and HIR are proposed to improve the current method for design and evaluation of floor-ceiling assemblies and also provide a better method for predicting subjective reaction.

Investigation of a Possible Link Between Vaccination and the 2010 Sheep Pox Epizootic in Morocco.

PubMed

Haegeman, A; Zro, K; Sammin, D; Vandenbussche, F; Ennaji, M M; De Clercq, K

2016-12-01

Sheep pox is endemic in most parts of Northern Africa and has the potential to cause severe economic problems. Live attenuated vaccines are used in Morocco, and in many other countries, to control the disease. Sheep pox virus (SPPV) re-appeared in 2010 causing a nodular clinical form previously not observed in Morocco. The severe clinical signs observed during the course of this outbreak and initial reports citing similarity in nucleotide sequence between the Moroccan vaccine strain and field isolates warranted a more in depth analysis of this epizootic. In this study, sequence analysis showed that isolates obtained from four provinces of eastern Morocco were identical, demonstrating that a single SPPV strain was responsible for the 2010 epizootic. In addition, the genome fragments sequenced and phylogenetic analyses undertaken as part of this study showed significant differences between field isolates and the Moroccan vaccine strain. New PCR methods were developed to differentiate between wild-type isolates and vaccine strains of SPPV. Using these methods, no trace of wild-type SPPV was found in the vaccine and no evidence was found to suggest that the vaccine strain was causing clinical disease. © 2015 Blackwell Verlag GmbH.

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.

Molecular Mechanisms of Fluoroquinolone Resistance in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients

PubMed Central

Jalal, Shah; Ciofu, Oana; Høiby, Niels; Gotoh, Naomasa; Wretlind, Bengt

2000-01-01

Twenty P. aeruginosa isolates were collected from six cystic fibrosis (CF) patients, aged 27 to 33, in 1994 (9 isolates) and 1997 (11 isolates) at the CF Center, Copenhagen, Denmark, and were typed by pulse-field gel electrophoresis (PFGE) or ribotyping. Five of the patients had isolates with the same PFGE or ribotyping patterns in 1997 as in 1994, and ciprofloxacin had a two- to fourfold higher MIC for the isolates collected in 1997 than those from 1994. Genomic DNA was amplified for gyrA, parC, mexR, and nfxB by PCR and sequenced. Eleven isolates had mutations in gyrA, seven isolates had mutations at codon 83 (Thr to Ile), and four isolates had mutations at codon 87 (Asp to Asn or Tyr). Sixteen isolates had mutations in nfxB at codon 82 (Arg to Leu). Increased amounts of OprN were found in six isolates and OprJ in eight isolates as determined by immunoblotting. No isolates had mutations in parC or mexR. Six isolates had mutations in efflux pumps without gyrA mutations. The average number of mutations was higher in isolates from 1997 than in those from 1994. The results also suggested that efflux resistance mechanisms are more common in isolates from CF patients than in strains from urine and wounds from non-CF patients, in which mutations in gyrA and parC dominate (S. Jalal and B. Wretlind, Microb. Drug Resist. 4:257–261, 1998). PMID:10681343

Successful strategy for the selection of new strawberry-associated rhizobacteria antagonistic to Verticillium wilt.

PubMed

Berg, G; Kurze, S; Buchner, A; Wellington, E M; Smalla, K

2000-12-01

In order to isolate and characterize new strawberry-associated bacteria antagonistic to the soil-borne pathogenic fungus Verticillium dahliae Kleb., rhizobacterial populations from two different strawberry species, Greenish Strawberry (Fragaria viridis) and Garden Strawberry (F. x ananassa) obtained after plating onto King's B and glycerol-arginine agar, were screened for in vitro antagonism toward V. dahliae. The proportion of isolates with antifungal activity determined in in vitro assay against V. dahliae was higher for the Garden Strawberry than for the Greenish Strawberry. From 300 isolates, 20 isolates with strong antifungal activity were selected characterized by physiological profiling and molecular fingerprinting methods. Diversity among the isolates was characterized with molecular fingerprints using amplified ribosomal DNA restriction analysis (ARDRA) and the more discriminating BOX-PCR fingerprint method. The physiological profiles were well correlated with molecular fingerprinting pattern analysis. Significant reduction of Verticillium wilt by bacterial dipping bath treatment was shown in the greenhouse and in fields naturally infested by V. dahliae. The relative increase of yield ranged from 117% (Streptomyces albidoflavus S1) to 344% (Pseudomonas fluorescens P10) in greenhouse trials, and 113% (Streptomyces albidoflavus S1) to 247% (Pseudomonas fluorescens P6) in field trials. Evaluation resulted in the selection of three effective biocontrol agents (Pseudomonas fluorescens P6, P10, and Streptomyces diastatochromogenes S9) antagonistic to the Verticillium wilt pathogen.

Isolation and characterization of antagonistic fungi against potato scab pathogens from potato field soils.

PubMed

Tagawa, Masahiro; Tamaki, Hideyuki; Manome, Akira; Koyama, Osamu; Kamagata, Yoichi

2010-04-01

Potato scab is a serious plant disease caused by several Streptomyces sp., and effective control methods remain unavailable. Although antagonistic bacteria and phages against potato scab pathogens have been reported, to the best of our knowledge, there is no information about fungi that are antagonistic to the pathogens. The aim of this study was to isolate fungal antagonists, characterize their phylogenetic positions, determine their antagonistic activities against potato scab pathogens, and highlight their potential use as control agents under lower pH conditions. Fifteen fungal stains isolated from potato field soils were found to have antagonistic activity against three well-known potato scab pathogens: Streptomyces scabiei, Streptomyces acidiscabiei, and Streptomyces turgidiscabiei. These 15 fungal strains were phylogenetically classified into at least six orders and nine genera based on 18S rRNA gene sequencing analysis. These fungal isolates were related to members of the genera Penicillium, Eupenicillium, Chaetomium, Fusarium, Cladosporium, Mortierella, Kionochaeta, Pseudogymnoascus, and Lecythophora. The antagonistic activities of most of the fungal isolates were highly strengthened under the lower pH conditions, suggesting the advantage of combining their use with a traditional method such as soil acidification. This is the first report to demonstrate that phylogenetically diverse fungi show antagonistic activity against major potato scab pathogens. These fungal strains could be used as potential agents to control potato scab disease.

Attosecond electronic recollision as field detector

NASA Astrophysics Data System (ADS)

Carpeggiani, P. A.; Reduzzi, M.; Comby, A.; Ahmadi, H.; Kühn, S.; Frassetto, F.; Poletto, L.; Hoff, D.; Ullrich, J.; Schröter, C. D.; Moshammer, R.; Paulus, G. G.; Sansone, G.

2018-05-01

We demonstrate the complete reconstruction of the electric field of visible–infrared pulses with energy as low as a few tens of nanojoules. The technique allows for the reconstruction of the instantaneous electric field vector direction and magnitude, thus giving access to the characterization of pulses with an arbitrary time-dependent polarization state. The technique combines extreme ultraviolet interferometry with the generation of isolated attosecond pulses.

A possible pole problem in the formula for klystron gap fields

NASA Technical Reports Server (NTRS)

Kosmahl, H. G.

1977-01-01

In isolated cases a pole may be encountered in a previously published solution for the fields in a klystron gap. Formulas, permitting the critical combinations of parameters to be defined, are presented. It is noted that the region of inaccuracy surrounding the pole is sufficiently small and that a 0.1% change in the field changing parameter is enough to avoid it.

A study on the social behavior and social isolation of the elderly Korea.

PubMed

Yi, Eun-Surk; Hwang, Hee-Joung

2015-06-01

This study aimed at presenting what factors are to predict the social isolation of the elderly as an element to prevent the problem of why various matters related to old people are inevitably taking place by carefully examining the meaning of social isolation and the conditions of social isolation that the South Korean senior citizens go through after working on previous studies. This section discusses the results obtained through document analysis. First, the aspects of the elderly's social isolation arising from the changes of the South Korean society are changes of family relationship, the social structure, the economic structure and the culture. Second, the social isolation and social activity of the elderly are problems (suicide, criminals, dementia, depression and medical costs) of the elderly, change trend of the elderly issues related to social isolation and prediction factors that personal and regional. Lastly, as a role and challenges of the field of rehabilitation exercise aimed at resolving social isolation should be vitalized such as the development and provision of various relationship-building programs.

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.

Novel diesel-oil-degrading bacteria and fungi from the Ecuadorian Amazon rainforest.

PubMed

Maddela, N R; Masabanda, M; Leiva-Mora, M

2015-01-01

Isolating new diesel-oil-degrading microorganisms from crude-oil contaminated sites and evaluating their degradation capacities are vitally important in the remediation of oil-polluted environments and crude-oil exploitation. In this research, new hydrocarbon-degrading bacteria and fungi were isolated from the crude-oil contaminated soil of the oil-fields in the Amazon rainforest of north-east Ecuador by using a soil enrichment technique. Degradation analysis was tracked by gas chromatography and a flame ionization detector. Under laboratory conditions, maximum degradability of the total n-alkanes reached up to 77.34 and 62.62 removal ratios after 30 days of incubation for the evaporated diesel oil by fungi (isolate-1) and bacteria (isolate-1), respectively. The 16S/18S rDNA sequence analysis indicated that the microorganisms were most closely (99-100%) related to Bacillus cereus (isolate-1), Bacillus thuringiensis (isolate-2), Geomyces pannorum (isolate-1), and Geomyces sp. (isolate-2). Therefore, these strains enable the degradation of hydrocarbons as the sole carbon source, and these findings will benefit these strains in the remediation of oil-polluted environments and oil exploitation.

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

A mutation in the 14 alpha-demethylase gene of Uncinula necator that correlates with resistance to a sterol biosynthesis inhibitor.

PubMed Central

Délye, C; Laigret, F; Corio-Costet, M F

1997-01-01

We investigated the molecular basis of resistance of the obligate biotrophic grape powdery mildew fungus Uncinula necator to sterol demethylation-inhibiting fungicides (DMIs). The sensitivity of 91 single-spore field isolates of U. necator to triadimenol was assessed by using a leaf disc assay. Resistance factors (RF) ranged from 1.8 to 26.0. The gene encoding the target of DMIs (eburicol 14 alpha-demethylase) from five sensitive and seven resistant isolates was cloned and sequenced. A single mutation, leading to the substitution of a phenylalanine residue for a tyrosine residue at position 136, was found in all isolates exhibiting an RF higher than 5. No mutation was found in sensitive or weakly resistant (RF, < 5) isolates. An allele-specific PCR assay was developed to detect the mutation. Among the 91 isolates tested, only isolates with RF higher than 5 carried the mutation. Three of the 19 resistant isolates and all sensitive and weakly resistant isolates did not possess the mutation. The mutation at codon 136 is thus clearly associated with high levels of resistance to triadimenol. PMID:9251183

Wideband Isolation by Frequency Conversion in a Josephson-Junction Transmission Line

NASA Astrophysics Data System (ADS)

Ranzani, Leonardo; Kotler, Shlomi; Sirois, Adam J.; DeFeo, Michael P.; Castellanos-Beltran, Manuel; Cicak, Katarina; Vale, Leila R.; Aumentado, José

2017-11-01

Nonreciprocal transmission and isolation at microwave frequencies are important in many practical applications. In particular, compact isolators are useful in protecting sensitive quantum circuits operating at cryogenic temperatures from amplifier backaction and other environmental noise such as black-body radiation from higher temperature stages. However, the size of commercial cryogenic isolators limits the ability to measure multiple quantum circuits because of space constraints in typical dilution refrigerator systems. Furthermore, isolators usually require the use of ferrite components that cannot be integrated at the chip level and, since they also need large biasing magnetic fields, are incompatible with superconducting quantum circuits. In this work we show one way to accomplish isolation in a superconducting chip-scale device, a traveling-wave unidirectional frequency converter based on a parametrically pumped superconducting Josephson-junction transmission line, demonstrating better than 4.8 dB of inferred signal isolation from 6.6 to 11.4 GHz, with a maximum of 12 dB at 9.5 GHz. By using frequency diplexing techniques a conventional isolator could be implemented over this bandwidth.

A study on the social behavior and social isolation of the elderly Korea

PubMed Central

Yi, Eun-Surk; Hwang, Hee-Joung

2015-01-01

This study aimed at presenting what factors are to predict the social isolation of the elderly as an element to prevent the problem of why various matters related to old people are inevitably taking place by carefully examining the meaning of social isolation and the conditions of social isolation that the South Korean senior citizens go through after working on previous studies. This section discusses the results obtained through document analysis. First, the aspects of the elderly’s social isolation arising from the changes of the South Korean society are changes of family relationship, the social structure, the economic structure and the culture. Second, the social isolation and social activity of the elderly are problems (suicide, criminals, dementia, depression and medical costs) of the elderly, change trend of the elderly issues related to social isolation and prediction factors that personal and regional. Lastly, as a role and challenges of the field of rehabilitation exercise aimed at resolving social isolation should be vitalized such as the development and provision of various relationship-building programs. PMID:26171377

Determining the fertility status of Setaria infecting Magnaporthe grisea isolates with standard testers and identification of tolerant cultivar of Setaria italica.

PubMed

Karthikeyan, Veluswamy; Gnanamanickam, S S

2008-10-01

A total of 128 isolates of Setaria-infecting Magnaporthe grisea strains were obtained from different states of South India which includes sampling sites from Tamil Nadu, two from Karnataka, one from Andhra Pradesh and Kerala. Out of the selected 128 isolates 30 strains were tested with MAT1-1 and MAT1-2 fertile standard testers to determine their mating type. None of the 30 Setaria isolates produced perithecia with fertile testers. However, when monoconidial isolates were mated among themselves, isolates from the same field produced only barren perithecia and the tester isolates were able to mate readily with finger millet isolates. This is the first report of the mating-type studies on Setaria infecting Magnaporthe grisea with standard testers. This result indicates that the Setaria infecting population is infertile. In pathogenicity assay, it was found that 9 out of the 22 Setaria accessions were highly susceptible to Setaria strains of the blast fungus and seven cultivars/accessions were resistant to blast pathogen. Various virulence reactions were scored according to Standard Evaluation System.

[Examination of metallo-beta-lactamase-producing different types of Serratia marcescens detected in the same patient].

PubMed

Takamitsu, Ito; Fukui, Yasuo; Ono, Noriaki; Ikeda, Fumiaki; Kanayama, Akiko; Kobayashi, Intetsu

2013-03-01

Metallo-beta-lactamase (MBL) producing Serratia marcescens isolate was recovered from a study patient in September, 2007 in whom MBL non-producing S. marcescens had been isolated 2 months previously. Two S. marcescens isolates recovered from the study patient showed the same pulsed-field gel electrophoresis (PFGE) pattern. Seven S. marcescens isolates were recovered from other patients in our hospital during August, 2007 and November, 2007. Five of the seven isolates produced MBL. All of the MBL-producing isolates showed the same PFGE pattern and harbored plasmids of the same size and bla(IMP) genes. The bla(IMP) genes were easily transferred to Escherichia coli DH5alpha by transformation of a plasmid purified from the MBL-producing isolate. Those transformation experiments suggested that bla(IMP) genes were encoded by the plasmid. From these observations, it was speculated that the MBL non-producing S. marcescens isolate recovered from the study patient had acquired the plasmid which encoded bla(IMP) genes and a monoclone of MBL-producing S. marcescens spread horizontally in our hospital.

Differences in virulence genes and genome patterns of mastitis-associated Staphylococcus aureus among goat, cow, and human isolates in Taiwan.

PubMed

Chu, Chishih; Wei, Yajiun; Chuang, Shih-Te; Yu, Changyou; Changchien, Chih-Hsuan; Su, Yaochi

2013-03-01

A total of 117 mastitis-associated Staphylococcus aureus isolates from cow, goat, and human patients were analyzed for differences in antibiotic susceptibility, virulence genes, and genotypes using accessory gene regulator (agr) typing, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Multidrug-resistant (MDR) S. aureus were commonly found in all sources, though they were predominantly found in human and goat isolates. Almost 70% of the isolates were resistant to ampicillin and penicillin. Host-associated virulence genes were identified as follows: tst, a gene encoding toxic shock syndrome toxin, was found in goat isolates; lukED and lukM, genes encoding leukocidin, found in cow isolates; lukPV, a gene encoding leukocidin, found in human isolates; and eta, a gene encoding for exfoliative toxin, found in both human and cow isolates. All four types of hemolysin, α, β, γ, and δ, were identified in human isolates, three types (α, γ, and δ), were identified in cow isolates, and two types (α and δ) were identified in goat isolates. Agr-typing determined agr1 to be the main subtype in human and cow isolates. PFGE and MLST analysis revealed the presence of diverse genotypes among the three sources. In conclusion, mastitis-associated, genetically diverse strains of MDR S. aureus differed in virulence genes among human, cow, and goat isolates.

Clinical and molecular epidemiology of hospital Enterococcus faecalis isolates in eastern France.

PubMed

Mulin, Blandine; Bailly, Pascale; Thouverez, Michelle; Cailleaux, Vincent; Cornette, Christian; Dupont, Marie-Jeanne; Talon, Daniel

1999-03-01

OBJECTIVE: To report on the occurrence of Enterococcus faecalis hospital isolates obtained during 1 year in hospitals in the Franche-Comté region of France. METHODS: Clinical isolates of E. faecalis of different antibiotic susceptibility phenotypes from hospitalized patients were characterized by pulsed-field gel electrophoresis. Patients with positive cultures were investigated by three case-control studies to identify risk factors for colonization/infection. RESULTS: The crude incidence of colonization/infection was 2.37%, and 4-day and 7-day colonization rates after admission were 10.0% and 6.36%, respectively. The rates of high-level resistance to kanamycin (HLKR) and to gentamicin (HLGR) were 47.1% and 7.1%, respectively. No isolate was resistant to glycopeptides or produced beta-lactamase. The 209 hospital isolates obtained during the study yielded 98 major DNA patterns, of which two were major epidemic patterns including HLKR isolates. No single factor was significantly associated with colonization/infection by HLKR isolates. The length of hospitalization before isolation was associated with colonization by HLGR isolates. CONCLUSIONS: The isolation frequency of E. faecalis strains with acquired resistance to aminoglycoside antibiotics, and the wide dissemination of resistant strains with characteristics that allow them to persist and spread, argue for further large prospective surveys of clinical isolates of E. faecalis in hospitals.

Determination of staphylococcal exotoxins, SCCmec types, and genetic relatedness of Staphylococcus intermedius group isolates from veterinary staff, companion animals, and hospital environments in Korea

PubMed Central

Youn, Jung-Ho; Ahn, Kuk Ju; Lim, Suk-Kyung

2011-01-01

The Staphylococcus (S.) intermedius group (SIG) has been a main research subject in recent years. S. pseudintermedius causes pyoderma and otitis in companion animals as well as foodborne diseases. To prevent SIG-associated infection and disease outbreaks, identification of both staphylococcal exotoxins and staphylococcal cassette chromosome mec (SCCmec) types among SIG isolates may be helpful. In this study, it was found that a single isolate (one out of 178 SIG isolates examined) harbored the canine enterotoxin SEC gene. However, the S. intermedius exfoliative toxin gene was found in 166 SIG isolates although the S. aureus-derived exfoliative toxin genes, such as eta, etb and etd, were not detected. SCCmec typing resulted in classifying one isolate as SCCmec type IV, 41 isolates as type V (including three S. intermedius isolates), and 10 isolates as non-classifiable. Genetic relatedness of all S. pseudintermedius isolates recovered from veterinary staff, companion animals, and hospital environments was determined by pulsed-field gel electrophoresis. Strains having the same band patterns were detected in S. pseudintermedius isolates collected at 13 and 18 months, suggesting possible colonization and/or expansion of a specific S. pseudintermedius strain in a veterinary hospital. PMID:21897094

Determination of staphylococcal exotoxins, SCCmec types, and genetic relatedness of Staphylococcus intermedius group isolates from veterinary staff, companion animals, and hospital environments in Korea.

PubMed

Youn, Jung-Ho; Koo, Hye Cheong; Ahn, Kuk Ju; Lim, Suk-Kyung; Park, Yong Ho

2011-09-01

The Staphylococcus (S.) intermedius group (SIG) has been a main research subject in recent years. S. pseudintermedius causes pyoderma and otitis in companion animals as well as foodborne diseases. To prevent SIG-associated infection and disease outbreaks, identification of both staphylococcal exotoxins and staphylococcal cassette chromosome mec (SCCmec) types among SIG isolates may be helpful. In this study, it was found that a single isolate (one out of 178 SIG isolates examined) harbored the canine enterotoxin SEC gene. However, the S. intermedius exfoliative toxin gene was found in 166 SIG isolates although the S. aureus-derived exfoliative toxin genes, such as eta, etb and etd, were not detected. SCCmec typing resulted in classifying one isolate as SCCmec type IV, 41 isolates as type V (including three S. intermedius isolates), and 10 isolates as non-classifiable. Genetic relatedness of all S. pseudintermedius isolates recovered from veterinary staff, companion animals, and hospital environments was determined by pulsed-field gel electrophoresis. Strains having the same band patterns were detected in S. pseudintermedius isolates collected at 13 and 18 months, suggesting possible colonization and/or expansion of a specific S. pseudintermedius strain in a veterinary hospital.

Molecular diversity of serial Cryptococcus neoformans isolates from AIDS patients in the city of São Paulo, Brazil.

PubMed

Martins, Marilena A; Pappalardo, Mara C S M; Melhem, Márcia S C; Pereira-Chioccola, Vera L

2007-11-01

Despite highly active anti-retroviral therapy, cryptococcal meningoencephalitis is the second most prevalent neurological disease in Brazilian AIDS patients, being frequently a defining condition with several episodes. As knowledge of Cryptococcus neoformans isolates in the same episode is critical for understanding why some patients develop several episodes, we investigated the genotype characteristics of C. neoformans isolates in two different situations. By pulsed field gel electrophoresis and random amplified polymorphic DNA analysis, 54 isolates from 12 patients with AIDS and cryptococcosis were analyzed. Group 1 comprised 39 isolates from nine patients with a single episode and hospitalization. Group 2 comprised 15 isolates from three patients with two episodes and hospitalizations. Except for three patients from group 1 probably infected with a single C. neoformans isolate, the other nine patients probably were infected with multiple isolates selected in different collection periods, or the infecting isolate might have underwent mutation to adapt and survive the host immune system and/or the antifungal therapy. However, the three patients from group 2 presented genetic diversity among isolates collected in both hospitalizations, possibly having hosted the initial isolate in both periods. These data, emphasize that Cryptococcus diversity in infection can contribute to strategies of treatment and prevention of cryptococcosis.

Sampling scales define occupancy and underlying occupancy-abundance relationships in animals

Treesearch

Robin Steenweg; Mark Hebblewhite; Jesse Whittington; Paul Lukacs; Kevin McKelvey

2018-01-01

Occupancy-abundance (OA) relationships are a foundational ecological phenomenon and field of study, and occupancy models are increasingly used to track population trends and understand ecological interactions. However, these two fields of ecological inquiry remain largely isolated, despite growing appreciation of the importance of integration. For example, using...

Social Movements and Educational Research: Toward a United Field of Scholarship

ERIC Educational Resources Information Center

Niesz, Tricia; Korora, Aaron M.; Walkuski, Christy Burke; Foot, Rachel E.

2018-01-01

Background/Context: Educational research addressing social movements appears to be growing rapidly but, with a few exceptions, this body of literature has remained largely isolated in pockets stretched across myriad fields of educational scholarship. Awareness and dialogue across researchers is limited because social movement-focused educational…

Learning and Innovation Competence in Agricultural and Rural Development

ERIC Educational Resources Information Center

Pant, Laxmi Prasad

2012-01-01

Purpose: The fields of competence development and capacity development remain isolated in the scholarship of learning and innovation despite the contemporary focus on innovation systems thinking in agricultural and rural development. This article aims to address whether and how crossing the conventional boundaries of these two fields provide new…

Taxonomic complexity of powdery mildew pathogens found on lentil and pea in the US Pacific Northwest

USDA-ARS?s Scientific Manuscript database

Classification of powdery mildews found on lentil and pea in greenhouse and field production conditions in the US Pacific Northwest was investigated using morphological and molecular characters. Isolates collected from lentil plants grown in the greenhouse or field displayed morphologies in substant...

Distribution of Aspergillus section flavi in soils of maize fields in three agroecological zones of Nigeria

USDA-ARS?s Scientific Manuscript database

Fungal communities in soils of Nigerian maize fields were examined to determine distributions of aflatoxin-producing fungi and to identify endemic atoxigenic strains of potential value as biological control agents for limiting aflatoxin contamination in West African crops. Over 1,000 isolates belon...

A design study for a medium-scale field demonstration of the viscous barrier technology

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

Moridis, G.; Yen, P.; Persoff, P.

1996-09-01

This report is the design study for a medium-scale field demonstration of Lawrence Berkeley National Laboratory`s new subsurface containment technology for waste isolation using a new generation of barrier liquids. The test site is located in central California in a quarry owned by the Los Banos Gravel Company in Los Banos, California, in heterogeneous unsaturated deposits of sand, silt, and -ravel typical of many of the and DOE cleanup sites and particularly analogous to the Hanford site. The coals of the field demonstration are (a) to demonstrate the ability to create a continuous subsurface barrier isolating a medium-scale volume (30more » ft long by 30 ft wide by 20 ft deep, i.e. 1/10th to 1/8th the size of a buried tank at the Hanford Reservation) in the subsurface, and (b) to demonstrate the continuity, performance, and integrity of the barrier.« less

Infection rate of Leptospira interrogans in the field rodent, Apodemus agrarius, in Korea.

PubMed Central

Cho, M. K.; Kee, S. H.; Song, H. J.; Kim, K. H.; Song, K. J.; Baek, L. J.; Kim, H. H.; Oh, H. B.; Kim, Y. W.; Chang, W. H.

1998-01-01

Leptospirosis has significantly decreased in Korea since 1988, following the leptospiral vaccination programme initiated in 1988. Whether this wholly explains the decreased incidence is uncertain. As an initial step to answer this question, infection rates of Leptospira interrogans in field rodents, Apodemis agrarius, were examined and compared with previous data. Two hundred and twenty-two A. agrarius were captured during October-December 1996. Spirochaetes were isolated from 22 (9.9%) and leptospiral DNA was detected in an additional 6 rodents (12.6%). Subsequent microscopic agglutination tests (MAT) classified all these isolates as L. interrogans serogroup Icterohaemorrhagiae serovar lai. The above data did not significantly differ from previous surveys in 1984-7. There was no significant change of L. interrogans infection in field rodents following the introduction of the vaccination programme in Korea. Further studies are needed to determine the role of human vaccination in reducing incidence. PMID:10030719

Prevalence and clinical relevance of Staphylococcus warneri in the neonatal intensive care unit.

PubMed

Cimiotti, Jeannie P; Haas, Janet P; Della-Latta, Phyllis; Wu, Fann; Saiman, Lisa; Larson, Elaine L

2007-03-01

To describe the prevalence of Staphylococcus warneri on the hands of nurses and the clinical relevance of this organism among neonates in the neonatal intensive care unit (NICU). Prospective cohort study that examined the microbial flora on the hands of nurses and clinical isolates recovered from neonates during a 23-month period (March 1, 2001, through January 31, 2003). Two high-risk NICUs in New York City. All neonates hospitalized in the NICUs for more than 24 hours and all full-time nurses from the same NICUs who volunteered to participate. At baseline and then every 3 months, samples for culture were obtained from each nurse's cleaned dominant hand. Pulsed-field electrophoresis compared S. warneri isolates from neonates and staff. Samples for culture (n=834) were obtained from the hands of 119 nurses; 520 (44%) of the 1,195 isolates of coagulase-negative staphylococci recovered were identified as S. warneri. Of the 647 clinically relevant isolates recovered from neonates, 17 (8%) of the 202 isolates that were identified to species level were S. warneri. Pulsed-field electrophoresis revealed a common strain of S. warneri that was shared among the nurses and neonates. Furthermore, 117 (23%) of 520 S. warneri isolates from nurses' hands had minimum inhibitory concentrations for vancomycin of 4 mu g/mL, which indicate decreasing susceptibility. Our findings that S. warneri can be pathogenic in neonates, is a predominant species of coagulase-negative staphylococci cultured from the hands of nurses, and has decreased vancomycin susceptibility underscore the importance of continued surveillance for vancomycin resistance and pathogenicity in pediatric care settings.

Deduced sequences of the membrane fusion and attachment proteins of canine distemper viruses isolated from dogs and wild animals in Korea.

PubMed

Bae, Chae-Wun; Lee, Joong-Bok; Park, Seung-Yong; Song, Chang-Seon; Lee, Nak-Hyung; Seo, Kun-Ho; Kang, Young-Sun; Park, Choi-Kyu; Choi, In-Soo

2013-08-01

Canine distemper virus (CDV) causes highly contagious respiratory, gastrointestinal, and neurological diseases in wild and domestic animal species. Despite a broad vaccination campaign, the disease is still a serious problem worldwide. In this study, six field CDV strains were isolated from three dogs, two raccoon dogs, and one badger in Korea. The full sequence of the genes encoding fusion (F) and hemagglutinin (H) proteins were compared with those of other CDVs including field and vaccine strains. The phylogenetic analysis for the F and H genes indicated that the two CDV strains isolated from dogs were most closely related to Chinese strains in the Asia-1 genotype. Another four strains were closely related to Japanese strains in the Asia-2 genotype. The six currently isolated strains shared 90.2-92.1% and 88.2-91.8% identities with eight commercial vaccine strains in their nucleotide and amino acid sequences of the F protein, respectively. They also showed 90.1-91.4% and 87.8-90.7% identities with the same vaccine strains in their nucleotide and deduced amino acid sequences of the H protein, respectively. Different N-linked glycosylation sites were identified in the F and H genes of the six isolates from the prototype vaccine strain Onderstepoort. Collectively, these results demonstrate that at least two different CDV genotypes currently exist in Korea. The considerable genetic differences between the vaccine strains and wild-type isolates would be a major factor of the incomplete protection of dogs from CDV infections.

Identification of arsenobetaine in sole, lemon sole, flounder, dab, crab and shrimps by field desorption and fast atom bombardment mass spectrometry

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

Luten, J.B.; Riekwel-Booy, G.; Greef, M.C.

1983-01-01

Organo-arsenic has been isolated from sole, lemon sole, flounder, dab, crab and shrimps by extraction or ion-exchange in combination with thin-layer chromatography. An alkaline digestion of the samples, followed by a reduction with sodiumborohydride leads to the formation of trimethylarsine. Field desorption mass spectrometry (FDMS) can be used to identify arsenobetaine in the isolates. Sufficient purification by thin-layer chromatography is found to be a prerequisite for the detection of a protonated molecular ion of arsenobetaine. If this situation is not met acid enchanced FDMS or Fast Atom Bombardment mass spectrometry in high resolution can be used successfully.

Diagnosis of a new variant of soybean yellow mottle mosaic virus with extended host-range in India.

PubMed

Sandra, Nagamani; Kumar, Alok; Sharma, Prachi; Kapoor, Reetika; Jain, Rakesh Kumar; Mandal, Bikash

2015-12-01

Soybean yellow mottle mosaic virus (SYMMV, genus Carmovirus) was previously known to occur in South Korea and USA causing bright yellow mosaic in soybean. In this study, SYMMV (Car-Mb14 isolate) was isolated from mungbean (Vigna radiata) exhibiting mild mottling and puckering symptoms in the experimental field at Indian Agricultural Research Institute, New Delhi during 2012. The virus isolate, Car-Mb14 induced veinal mottling, mild mottling, chlorotic blotching, local and systemic necrosis in soybean, mungbean, blackgram, French bean and guar bean, respectively. The symptomatology of the present isolate of SYMMV was different from the previously reported South Korean isolate, as the later did not induce symptoms in any of the above legumes other than soybean. The present isolate was phylogenetically distinct and shared 90-93 % sequence identity in coat protein (CP) of 52 SYMMV isolates reported from Korea and USA. In order to know the serological relationships, the CP gene of the present isolate was over expressed as a 39 kDa protein in E. coli and an antiserum of 1:16,000 titer against the recombinant CP was produced. Serological cross reactivity analysis revealed that SYMMV was serologically related to blackgram mottle virus but not to cowpea mottle virus, the other legume infecting carmoviruses. The antiserum was used to detect prevalence of SYMMV in legume crops by ELISA. Out of 145 field samples of legumes (mungbean, blackgram, French bean and soybean) collected from different places in India, SYMMV was detected only in 16 samples of mungbean and one sample of blackgram. The natural infection of SYMMV in mungbean and blackgram was further confirmed based on CP gene sequence. This study provides evidence of occurrence of a new variant of SYMMV with distinct symptom phenotype and extended host-range in India.

Comparison of field-collected ascovirus isolates by DNA hybridization, host range, and histopathology.

PubMed

Hamm, J J; Styer, E L; Federici, B A

1998-09-01

Six field-collected ascovirus isolates obtained from five noctuid species in the continental United States were compared with respect to the general relatedness of their DNA, host range, and histopathology. Two isolates were from Spodoptera frugiperda, and the other four were from Autographa precationis, Heliothis virescens, Helicoverpa zea, and Trichoplusia ni. DNA-DNA hybridization studies showed that the six isolates belonged to three distinct viral species, with the isolates from S. frugiperda composing one species, those from A. precationis and H. virescens a second species, and those from H. zea and T. ni a third species. The host range and histopathology of each isolate was studied in eight noctuid species, S. frugiperda, Spodoptera ornithogalli, Spodoptera exigua, Spodoptera eridania, H. virescens, H. zea, A. precationis, and Feltia subterranea. Though some variation existed between the different isolates of each viral species, distinct patterns were apparent for each. The viral species from S. frugiperda had a host range that was limited primarily to Spodoptera species and both isolates of this virus only replicated and caused significant pathology in the fat body, whereas the viral species from A. precationis and H. virescens had a much broader host range that included most of the species tested, but also had a tissue tropism primarily restricted to the fat body. The viral species from T. ni and H. zea readily infected all the hosts tested, where the principal site of replication and significant pathology was the epidermis. In many test hosts, however, this viral species also replicated and caused significant pathology in the tracheal epithelium and to a lesser extent in the fat body. Aside from contributing to knowledge of ascovirus biology, these studies indicate that DNA hybridization profiles combined with studies of host range and tissue tropism can be used as characters for defining ascovirus species. Copyright 1998 Academic Press.

Pulsed-Field Gel Electrophoresis characterization of Listeria monocytogenes isolates from cheese manufacturing plants in São Paulo, Brazil.

PubMed

Barancelli, Giovana V; Camargo, Tarsila M; Gagliardi, Natália G; Porto, Ernani; Souza, Roberto A; Campioni, Fabio; Falcão, Juliana P; Hofer, Ernesto; Cruz, Adriano G; Oliveira, Carlos A F

2014-03-03

This study aimed to evaluate the occurrence of Listeria monocytogenes in cheese and in the environment of three small-scale dairy plants (A, B, C) located in the Northern region state of São Paulo, Brazil, and to characterize the isolates using conventional serotyping and PFGE. A total of 393 samples were collected and analyzed from October 2008 to September 2009. From these, 136 came from dairy plant A, where only L. seeligeri was isolated. In dairy plant B, 136 samples were analyzed, and L. innocua, L. seeligeri and L. welshimeri were isolated together with L. monocytogenes. In dairy plant C, 121 samples were analyzed, and L. monocytogenes and L. innocua were isolated. Cheese from dairy plants B and C were contaminated with Listeria spp, with L. innocua being found in Minas frescal cheese from both dairy plants, and L. innocua and L. monocytogenes in Prato cheese from dairy plant C. A total of 85 L. monocytogenes isolates were classified in 3 serotypes: 1/2b, 1/2c, and 4b, with predominance of serotype 4b in both dairy plants. The 85 isolates found in the dairy plants were characterized by genomic macrorestriction using ApaI and AscI with Pulsed Field Gel Electrophoresis (PFGE). Macrorestriction yielded 30 different pulsotypes. The presence of indistinguishable profiles repeatedly isolated during a 12-month period indicated the persistence of L. monocytogenes in dairy plants B and C, which were more than 100 km away from each other. Brine used in dairy plant C contained more than one L. monocytogenes lineage. The routes of contamination were identified in plants B and C, and highlighted the importance of using molecular techniques and serotyping to track L. monocytogenes sources of contamination, distribution, and routes of contamination in dairy plants, and to develop improved control strategies for L. monocytogenes in dairy plants and dairy products. Copyright © 2013 Elsevier B.V. All rights reserved.

Salmonella enterica isolated from wildlife at two Ohio rehabilitation centers.

PubMed

Jijón, Steffani; Wetzel, Amy; LeJeune, Jeffrey

2007-09-01

Between May and September 2004, fecal samples from various wildlife species admitted to two rehabilitation centers in Ohio were cultured for Salmonella enterica and Escherichia coli O157:H7. Eight of 71 (11%) samples, including specimens from three opossums (Didelphis virginiana), two gray squirrels (Sciurus carolinensis), a woodchuck (Marmota monax), a Harris hawk (Parabuteo unicinctus), and a screech owl (Otus asio) tested positive for Salmonella serovars Braenderup, Senftenberg, Oranienburg, and Kentucky. The Salmonella Oranienburg isolates were indistinguishable by pulsed-field gel electrophoresis. Most isolates were susceptible to commonly used antibiotics; however, the Salmonella Kentucky isolate was resistant to multiple beta-lactam antibiotics (amoxicillin/clavulanic acid and ampicillin), cefoxitin, and ceftiofur, a third-generation cephalosporin. Escherichia coli O157:H7 was not isolated from any sample. Transmission of Salmonella from wildlife may occur between animals at rehabilitation centers.

π -Stacking interactions in YFP, quantum mechanics and force field evaluations in the S0 and S1 states

NASA Astrophysics Data System (ADS)

Merabti, Karim Elhadj; Azizi, Sihem; Ridard, Jacqueline; Lévy, Bernard; Demachy, Isabelle

2017-08-01

We study the π -stacking interaction between the chromophore and Tyr203 in the Yellow Fluorescent Protein (YFP) in order to (i) evaluate the contribution of the internal interaction energy of the isolated Chromophore-Tyrosine complex (Eint) to the 26 nm red shift observed from GFP to YFP, (ii) compare the effects of Eint and of the proteic environment. To that end, we perform quantum mechanical and force field (ff) calculations of the isolated complex in S0 and S1 states on a large sample of geometries, together with molecular dynamics simulations and potential of mean force analysis. The calculated absorption wavelengths are found red shifted with respect to the isolated chromophore by 12-19 nm, that represents a large part of the GFP-YFP shift. We find that the effect of the protein is determinant on the dynamics of the complex while the error that results from using a classicalff is of limited effect.

Versatile variable temperature and magnetic field scanning probe microscope for advanced material research

NASA Astrophysics Data System (ADS)

Jung, Jin-Oh; Choi, Seokhwan; Lee, Yeonghoon; Kim, Jinwoo; Son, Donghyeon; Lee, Jhinhwan

2017-10-01

We have built a variable temperature scanning probe microscope (SPM) that covers 4.6 K-180 K and up to 7 T whose SPM head fits in a 52 mm bore magnet. It features a temperature-controlled sample stage thermally well isolated from the SPM body in good thermal contact with the liquid helium bath. It has a 7-sample-holder storage carousel at liquid helium temperature for systematic studies using multiple samples and field emission targets intended for spin-polarized spectroscopic-imaging scanning tunneling microscopy (STM) study on samples with various compositions and doping conditions. The system is equipped with a UHV sample preparation chamber and mounted on a two-stage vibration isolation system made of a heavy concrete block and a granite table on pneumatic vibration isolators. A quartz resonator (qPlus)-based non-contact atomic force microscope (AFM) sensor is used for simultaneous STM/AFM operation for research on samples with highly insulating properties such as strongly underdoped cuprates and strongly correlated electron systems.

Occurrence of plasmid-mediated quinolone resistance determinants and rmtB gene in Salmonella enterica serovar enteritidis and Typhimurium isolated from food-animal products in Tunisia.

PubMed

Al-Gallas, Nazek; Abbassi, Mohamed Salah; Gharbi, Becher; Manai, Molka; Ben Fayala, Mohamed N; Bichihi, Raghda; Al-Gallas, Amna; Ben Aissa, Ridha

2013-09-01

Four hundred and thirty Salmonella isolates, recovered from various food-animal products, were tested for nalidixic acid resistance, plasmid-mediated quinolone resistance, and genetic relationship. One hundred fifteen isolates (113 Salmonella serovar Enteritidis and two Salmonella serovar Typhimurium isolates) of 430 (26.7%) Salmonella isolates exhibited nalidixic acid resistance. Polymerase chain reaction screening for qnrA, qnrB, qnrS, qepA (encoding fluoroquinolones resistance) and rmtB (encoding aminoglycosides resistance) showed that 5 (1.16%) isolates were positive for qnr- and qepA-type genes, and the aac(6')-Ib-cr gene was observed in two (1.7%) Enteritidis isolates concomitantly with qnrA or qnrB. The co-occurrence of qepA and rmtB in one Typhimurium isolate is noteworthy. Pulsed-field gel electrophoresis revealed a high genetic homogeneity of nalidixic-resistant isolates and the persistence of clonal clusters over 4 years in different regions in Tunisia and from various food-animal products. To the best of our knowledge, this is the first report of co-occurrence of qepA and rmtB in a Salmonella strain.

Detection of asymptomatic renal Leptospira infection in abattoir slaughtered cattle in southeastern Georgia, United States

PubMed Central

Ilha, Marcia; Woldemeskel, Moges; Berghaus, Roy D; Pence, Mel E

2014-01-01

Objectives: Leptospirosis is one of the most widespread zoonotic infectious diseases affecting humans and animals. Several animal species, including cattle, can act as potential asymptomatic carriers facilitating zoonotic transmission of Leptospira. This study was conducted to assess the occurrence of asymptomatic renal Leptospira carriers among cattle slaughtered in southeastern Georgia, United States. Methods: A battery of diagnostic tests, including dark field microscopy, direct fluorescent antibody staining, polymerase chain reaction, and culture, were performed on a set of bovine kidneys (n = 37) collected from an abattoir in southeastern Georgia, United States. Virulence of a field isolate obtained from this study was tested in a hamster experimental model. Results: Motile spirochete-like structures were observed by dark field microscopy in 23 (59%) out of 37 kidney samples tested. In all, 29 samples (78%) were positive by direct fluorescent antibody staining. Only 11 (29.7%) samples by polymerase chain reaction and 3 (8.1%) by culture were positive for Leptospira sp. The isolates obtained by culture were confirmed as Leptospira borgpetersenii. Hamsters experimentally infected with one of the Leptospira field isolates obtained from this study did not show clinical signs but developed renal infection with interstitial nephritis and tubular necrosis. Conclusions: This study confirms that asymptomatic Leptospira renal infection is present among cattle in the region. Our findings underscore the need for future studies to assess the potential environmental contamination and transmission to humans in contact with infected cattle. PMID:26770734

Study on the effect of magnetic field treatment of newly isolated Paenibacillus sp.

PubMed

Li, Jie; Yi, Yanli; Cheng, Xilei; Zhang, Dageng; Irfan, Muhammad

2015-12-01

Symbiotic nitrogen fixation in plants occurs in roots with the help of some bacteria which help in soil nitrogen fertility management. Isolation of significant environment friendly bacteria for nitrogen fixation is very important to enhance yield in plants. In this study effect of different magnetic field intensity and treatment time was studied on the morphology, physiology and nitrogen fixing capacity of newly isolated Paenibaccilus sp. from brown soil. The bacterium was identified by 16S rDNA sequence having highest similarity (99%) with Paenibacillus sp as revealed by BLAST. Different magnetic intensities such as 100mT, 300mT and 500mT were applied with processing time of 0, 5, 10, 20 and 30 minutes. Of all these treatment 300mT with processing time of 10 minutes was found to be most suitable treatment. Results revealed that magnetic treatment improve the growth rate with shorter generation time leading to increased enzyme activities (catalase, peroxidase and superoxide dismutase) and nitrogen fixing efficiencies. High magnetic field intensity (500mT) caused ruptured cell morphology and decreased enzyme activities which lead to less nitrogen fixation. It is concluded that appropriate magnetic field intensity and treatment time play a vital role in the growth of soil bacteria which increases the nitrogen fixing ability which affects the yield of plant. These results were very helpful in future breading programs to enhance the yield of soybean.

Endoscopic retrograde cholangiopancreatography-associated AmpC Escherichia coli outbreak.

PubMed

Wendorf, Kristen A; Kay, Meagan; Baliga, Christopher; Weissman, Scott J; Gluck, Michael; Verma, Punam; D'Angeli, Marisa; Swoveland, Jennifer; Kang, Mi-Gyeong; Eckmann, Kaye; Ross, Andrew S; Duchin, Jeffrey

2015-06-01

We identified an outbreak of AmpC-producing Escherichia coli infections resistant to third-generation cephalosporins and carbapenems (CR) among 7 patients who had undergone endoscopic retrograde cholangiopancreatography at hospital A during November 2012-August 2013. Gene sequencing revealed a shared novel mutation in a bla CMY gene and a distinctive fumC/ fimH typing profile. To determine the extent and epidemiologic characteristics of the outbreak, identify potential sources of transmission, design and implement infection control measures, and determine the association between the CR E. coli and AmpC E. coli circulating at hospital A. We reviewed laboratory, medical, and endoscopy reports, and endoscope reprocessing procedures. We obtained cultures from endoscopes after reprocessing as well as environmental samples and conducted pulsed-field gel electrophoresis and gene sequencing on phenotypic AmpC isolates from patients and endoscopes. Cases were those infected with phenotypic AmpC isolates (both carbapenem-susceptible and CR) and identical bla CMY-2, fumC, and fimH alleles or related pulsed-field gel electrophoresis patterns. Thirty-five of 49 AmpC E. coli tested met the case definition, including all CR isolates. All cases had complicated biliary disease and had undergone at least 1 endoscopic retrograde cholangiopancreatography at hospital A. Mortality at 30 days was 16% for all patients and 56% for CR patients. Two of 8 reprocessed endoscopic retrograde cholangiopancreatography scopes harbored AmpC that matched case isolates by pulsed-field gel electrophoresis. Environmental cultures were negative. No breaches in infection control were identified. Endoscopic reprocessing exceeded manufacturer's recommended cleaning guidelines. Recommended reprocessing guidelines are not sufficient.

Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen

PubMed Central

Daverdin, Guillaume; Rouxel, Thierry; Gout, Lilian; Aubertot, Jean-Noël; Fudal, Isabelle; Meyer, Michel; Parlange, Francis; Carpezat, Julien; Balesdent, Marie-Hélène

2012-01-01

Modern agriculture favours the selection and spread of novel plant diseases. Furthermore, crop genetic resistance against pathogens is often rendered ineffective within a few years of its commercial deployment. Leptosphaeria maculans, the cause of phoma stem canker of oilseed rape, develops gene-for-gene interactions with its host plant, and has a high evolutionary potential to render ineffective novel sources of resistance in crops. Here, we established a four-year field experiment to monitor the evolution of populations confronted with the newly released Rlm7 resistance and to investigate the nature of the mutations responsible for virulence against Rlm7. A total of 2551 fungal isolates were collected from experimental crops of a Rlm7 cultivar or a cultivar without Rlm7. All isolates were phenotyped for virulence and a subset was genotyped with neutral genetic markers. Virulent isolates were investigated for molecular events at the AvrLm4-7 locus. Whilst virulent isolates were not found in neighbouring crops, their frequency had reached 36% in the experimental field after four years. An extreme diversity of independent molecular events leading to virulence was identified in populations, with large-scale Repeat Induced Point mutations or complete deletion of AvrLm4-7 being the most frequent. Our data suggest that increased mutability of fungal genes involved in the interactions with plants is directly related to their genomic environment and reproductive system. Thus, rapid allelic diversification of avirulence genes can be generated in L. maculans populations in a single field provided that large population sizes and sexual reproduction are favoured by agricultural practices. PMID:23144620

Isolation and Characterization of Strains CVO and FWKO B, Two Novel Nitrate-Reducing, Sulfide-Oxidizing Bacteria Isolated from Oil Field Brine

PubMed Central

Gevertz, Diane; Telang, Anita J.; Voordouw, Gerrit; Jenneman, Gary E.

2000-01-01

Bacterial strains CVO and FWKO B were isolated from produced brine at the Coleville oil field in Saskatchewan, Canada. Both strains are obligate chemolithotrophs, with hydrogen, formate, and sulfide serving as the only known energy sources for FWKO B, whereas sulfide and elemental sulfur are the only known electron donors for CVO. Neither strain uses thiosulfate as an energy source. Both strains are microaerophiles (1% O2). In addition, CVO grows by denitrification of nitrate or nitrite whereas FWKO B reduces nitrate only to nitrite. Elemental sulfur is the sole product of sulfide oxidation by FWKO B, while CVO produces either elemental sulfur or sulfate, depending on the initial concentration of sulfide. Both strains are capable of growth under strictly autotrophic conditions, but CVO uses acetate as well as CO2 as its sole carbon source. Neither strain reduces sulfate; however, FWKO B reduces sulfur and displays chemolithoautotrophic growth in the presence of elemental sulfur, hydrogen, and CO2. Both strains grow at temperatures between 5 and 40°C. CVO is capable of growth at NaCl concentrations as high as 7%. The present 16s rRNA analysis suggests that both strains are members of the epsilon subdivision of the division Proteobacteria, with CVO most closely related to Thiomicrospira denitrifcans and FWKO B most closely related to members of the genus Arcobacter. The isolation of these two novel chemolithotrophic sulfur bacteria from oil field brine suggests the presence of a subterranean sulfur cycle driven entirely by hydrogen, carbon dioxide, and nitrate. PMID:10831429

Molecular Analysis of Group A Streptococcal Isolates Associated with Scarlet Fever in Southern Taiwan between 1993 and 2002

PubMed Central

Yan, Jing-Jou; Liu, Ching-Chuan; Ko, Wen-Chien; Hsu, Shui-Yuan; Wu, Hsiu-Mei; Lin, Yee-Shin; Lin, Ming T.; Chuang, Woei-Jer; Wu, Jiunn-Jong

2003-01-01

Collected between 1993 and 2002 at a Taiwanese university hospital, 77 group A streptococcus isolates associated with scarlet fever were grouped by emm typing and pulsed-field gel electrophoresis. The predominance of an emm1 clone before 1996 and the presence of genetically diverse emm1 and emm4 strains thereafter were found. PMID:14532243

Effect of atmospheric carbon dioxide concentration on the cultivation of bovine Mycoplasma species.

PubMed

Lowe, J L; Fox, L K; Enger, B D; Progar, A Adams; Gay, J M

2018-05-01

Recommendations for bovine mycoplasma culture CO 2 concentrations are varied and were not empirically derived. The objective of this study was to determine whether the growth measures of bovine mycoplasma isolates differed when incubated in CO 2 concentrations of 10 or 5% or in candle jars (2.7 ± 0.2% CO 2 ). Growth of Mycoplasma bovis (n = 22), Mycoplasma californicum (n = 18), and other Mycoplasma spp. (n = 10) laboratory isolates was evaluated. Isolate suspensions were standardized to approximately 10 8 cfu/mL and serially diluted in pasteurized whole milk to achieve test suspensions of 10 2 and 10 6 cfu/mL. One hundred microliters of each test dilution was spread in duplicate onto the surface of a modified Hayflick's agar plate. Colony growth was enumerated on d 3, 5, and 7 of incubation. A mixed linear model included the fixed effects of CO 2 treatment (2.7, 5, or 10%), species, day (3, 5, or 7), and their interactions, with total colony counts as the dependent variable. Carbon dioxide concentration did not significantly affect overall mycoplasma growth differences, but differences between species and day were present. Colony counts (log 10 cfu/mL) of M. bovis were 2.6- and 1.6-fold greater than M. californicum and other Mycoplasma spp., respectively. Growth at 7 d of incubation was greater than d 3 and 5 for all species. These findings were confirmed using field isolates (n = 98) from a commercial veterinary diagnostic laboratory. Binary growth responses (yes/no) of the field isolates were not different between CO 2 treatments but did differ between species and day of incubation. On average, 57% of all field isolates were detected by 3 d of incubation compared with 93% on d 7. These results suggest that the range of suitable CO 2 culture conditions and incubation times for the common mastitis-causing Mycoplasma spp. may be broader than currently recommended. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

An efficient thermotolerant and halophilic biosurfactant-producing bacterium isolated from Dagang oil field for MEOR application

NASA Astrophysics Data System (ADS)

Wu, Langping; Richnow, Hans; Yao, Jun; Jain, Anil

2014-05-01

Dagang Oil field (Petro China Company Limited) is one of the most productive oil fields in China. In this study, 34 biosurfactant-producing strains were isolated and cultured from petroleum reservoir of Dagang oil field, using haemolytic assay and the qualitative oil-displacement test. On the basis of 16S rDNA analysis, the isolates were closely related to the species in genus Pseudomonas, Staphylococcus and Bacillus. One of the isolates identified as Bacillus subtilis BS2 were selected for further study. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties at 37ºC as well as at higher temperature of 55ºC. The biosurfactant produced by the strain BS2 could reduce the surface tension of the culture broth from 70.87 mN/m to 28.97 mN/m after 8 days of incubation at 37ºC and to 36.15 mN/m after 20 days of incubation at 55ºC, respectively. The biosurfactant showed stability at high temperature (up to 120ºC), a wide range of pH (2 to 12) and salt concentrations (up to 12%) offering potential for biotechnology. Fourier transform infrared (FT-IR) spectrum of extracted biosurfactant tentatively characterized the produced biosurfactant as glycolipid derivative. Elemental analysis of the biosurfactant by energy dispersive X-ray spectroscopy (EDS) reveals that the biosurfactant was anionic in nature. 15 days of biodegradation of crude oil suggested a preferential usage of n-alkane upon microbial metabolism of BS2 as a carbon substrate and consequently also for the synthesis of biosurfactants. Core flood studies for oil release indicated 9.6% of additional oil recovery over water flooding at 37ºC and 7.2% of additional oil recovery at 55 ºC. Strain BS2 was characterized as an efficient biosurfactant-producing, thermotolerant and halophillic bacterium and has the potential for application for microbial enhanced oil recovery (MEOR) through water flooding in China's oil fields even in situ as adapted to reservoir chemistry and temperature.

Does mass accretion lead to field decay in neutron stars

NASA Technical Reports Server (NTRS)

Shibazaki, N.; Murakami, T.; Shaham, Jacob; Nomoto, K.

1989-01-01

The recent discovery of cyclotron lines from gamma-ray bursts indicates that the strong magnetic fields of isolated neutron stars might not decay. The possible inverse correlation between the strength of the magnetic field and the mass accreted by the neutron star suggests that mass accretion itself may lead to the decay of the magnetic field. The spin and magnetic field evolution of the neutron star was calculated under the hypothesis of the accretion-induced field decay. It is shown that the calculated results are consistent with the observations of binary and millisecond radio pulsars.

[Molecular epidemiology of methicillin-resistant Staphylococcus aureus isolates with toxic shock syndrome toxin and staphylococcal enterotoxin C genes].

PubMed

Kim, Jae Seok; Kim, Han Sung; Song, Wonkeun; Cho, Hyoun Chan; Lee, Kyu Man; Kim, Eui Chong

2007-04-01

Many methicillin-resistant Staphylococcus aureus (MRSA) isolates in Korea possess a specific profile of staphylococcal enterotoxins in that the toxic shock syndrome toxin gene (tst) coexists with the staphylococcal enterotoxin C gene (sec). Because the analysis of staphylococcal cassette chromosome mec (SCCmec), a mobile genetic element mecA gene encoding methicillin resistance, showed that majority of these are SCCmec type II, these MRSA isolates with tst and sec may be genetically related with each other. This study was performed to investigate the genetic relatedness of tstand sec-harboring MRSA strains isolated in Korea by using pulsed-field gel electrophoresis (PFGE). A total of 59 strains of MRSA isolates of SCCmec type II possessing tst and sec were selected for PFGE and phylogenetic analyses. These isolates were collected from 13 health care facilities during nationwide surveillance of antimicrobial resistance in 2002. The 59 MRSA isolates were clustered into 11 PFGE types, including one major group of 26 strains (44.1%) isolated from 7 healthcare facilities. Seven PFGE types contained 2 or more isolates each, comprising 55 isolates in total. Most of SCCmec type II MRSA isolates containing tst and sec showed closely related PFGE patterns. Moreover, MRSA isolates collected from different healthcare facilities showed identical PFGE patterns. These findings suggested a clonal spread of MRSA strains possessing tst and sec in Korean hospitals.

Characterization of carbapenem nonsusceptible Pseudomonas aeruginosa in Denmark: a nationwide, prospective study.

PubMed

Hansen, Frank; Johansen, Helle Krogh; Østergaard, Claus; Arpi, Magnus; Hansen, Dennis Schrøder; Littauer, Pia; Holm, Anette; Heltberg, Ole; Schumacher, Helga; Fuursted, Kurt; Lykke, Mari-Ann Domar; Tønning, Birgitte; Hammerum, Anette M; Justesen, Ulrik Stenz

2014-02-01

From January 1st 2011 through June 30th 2011, 116 nonreplicate, noncystic fibrosis-related Pseudomonas aeruginosa isolates with reduced carbapenem susceptibility were collected from 12 out of 13 Danish departments of clinical microbiology. The presence of acquired β-lactamases was assessed with combination tablet-diffusion methodology and polymerase chain reaction. In addition, antimicrobial susceptibility testing, an efflux pump inhibitor assay, and pulsed-field gel electrophoresis (PFGE) were performed. Isolates producing acquired β-lactamases were further investigated by serotyping and multi locus sequence typing. Eight isolates produced the metallo-β-lactamase (MBL) VIM-2, and one isolate produced OXA-10 and VEB-1-like extended-spectrum beta-lactamase (ESBL). Phenotypic indications of derepressed AmpC and efflux pump were seen in 56 and 43 isolates, respectively. Overall, the results indicate that mutational factors related to permeability--often combined with derepressed, chromosomal AmpC--is the main factor behind carbapenem nonsusceptibility in Danish P. aeruginosa isolates. The ESBL producer and all the VIM producers belonged to international clones. PFGE revealed that most of the isolates were unrelated, but clonal spread was seen; the 116 isolates distributed in 97 PFGE types, with the largest cluster consisting of 4 isolates (including three isolates from the same hospital with 100% similarity). Thirty-two isolates were pair-wise related, while the remaining isolates were clonally unrelated, as were all nine ESBL/MBL producers.

Molecular epidemiology and clinical implications of metallo-β-lactamase-producing Pseudomonas aeruginosa isolated from urine.

PubMed

Sako, Shinichi; Kariyama, Reiko; Mitsuhata, Ritsuko; Yamamoto, Masumi; Wada, Koichiro; Ishii, Ayano; Uehara, Shinya; Kokeguchi, Susumu; Kusano, Nobuchika; Kumon, Hiromi

2014-01-01

We conducted a study on molecular epidemiology and clinical implications of metallo-beta-lactamase (MBL)-producing Pseudomonas aeruginosa isolated from urine. Over a 10-year period from 2001 through 2010, a total of 92 MBL-producing P. aeruginosa urine isolates were collected from patients (one isolate per patient) who were admitted to 5 hospitals in Okayama Prefecture, Japan. When cross-infection was suspected in the hospital, pulsed-field gel electrophoresis was performed. In the resulting dendrogram of 79 MBL-producing P. aeruginosa urine isolates, no identical isolates and 7 pairs of isolates with >80% similarity were found. The biofilm-forming capabilities of 92 MBL-producing P. aeruginosa urine isolates were significantly greater than those of 92 non-MBL-producing urine isolates in a medium of modified artificial urine. The imipenem resistance transferred in 16 of 18 isolates tested, and these frequencies were in the range of 10⁻³ to 10⁻⁹. All of 18 isolates tested belonged to internationally spread sequence type 235 and had 3 gene cassettes of antimicrobial resistance genes in the class 1 integron. The strong biofilm-forming capabilities of MBL-producing P. aeruginosa urine isolates could be seriously implicated in nosocomial infections. To prevent spread of the organism and transferable genes, effective strategies to inhibit biofilm formation in medical settings are needed.

Influence of the operatory field isolation technique on tooth-colored direct dental restorations.

PubMed

Cajazeira, Marlus Roberto Rodrigues; De Sabóia, Ticiana Medeiros; Maia, Lucianne Cople

2014-06-01

To evaluate, through a systematic review, the influence of the operatory field isolation technique on the longevity of dental restorations performed with tooth-colored materials. An electronic search of the scientific databases (MEDLINE, SCIRUS, VHL and SIGLE) and reference lists of the selected articles was conducted to identify randomized controlled clinical trials with a follow-up period of at least 12 months. The selected articles evaluated the effects of the operatory field isolation techniques (rubber dam or cotton rolls/saliva ejector) on the longevity of direct restorations performed with tooth-colored materials (e.g. resin composites, compomers and glass-ionomer cements) in primary or permanent posterior teeth. The selected studies were analyzed and categorized using a checklist proposed by the National Institute for Health and Clinical Excellence of the United Kingdom. 484 studies were identified on the scientific databases. After applying the exclusion criteria and removal of duplicates, a total of nine studies were considered as potentially eligible. From these, five studies were included in the final analysis by two evaluators. In four studies analyzed, the use of rubber dam did not influence the longevity of restorations in comparison to cotton rolls/saliva ejector. Only two studies were considered as low risk of bias.

Sexual and asexual states of some endophytic Phialocephala species of Picea.

PubMed

Tanney, Joey B; Douglas, Brian; Seifert, Keith A

2016-01-01

Unidentified DNA sequences in isolation-based or culture-free studies of conifer endophytes are a persistent problem that requires a field approach to resolve. An investigation of foliar endophytes of Picea glauca, P. mariana, P. rubens and Pinus strobus in eastern Canada, using a combined field, morphological, cultural and DNA sequencing approach, resulted in the frequent isolation of Phialocephala spp. and the first verified discovery of their mollisia-like sexual states in the field. Phialocephala scopiformis and Ph. piceae were the most frequent species isolated as endophytes from healthy conifer needles. Corresponding Mollisia or mollisioid sexual states for Ph. scopiformis, Ph. piceae and several undescribed species in a clade containing Ph. dimorphospora were collected in the sampling area and characterized by analysis of the nuc internal transcribed spacer rDNA (ITS) and gene for the largest subunit of RNA polymerase II (RPB1) loci. Four novel species and one new combination in a clade containing Ph. dimorphospora, the type of Phialocephala, are presented, accompanied by descriptions of apothecia and previously undocumented synanamorphs. An epitype culture and corresponding reference sequences for Phialocephala dimorphospora are proposed. The resulting ITS barcodes linked with robust taxonomic species concepts are an important resource for future research on forest ecosystems and endophytes. © 2016 by The Mycological Society of America.

Crystal growth and analysis of ohmic contact and magneto-optical isolator properties of cadmium manganese telluride

NASA Astrophysics Data System (ADS)

Prakasam, Mythili; Viraphong, Oudomsack; Teulé-Gay, Lionel; Decourt, Rodolphe; Veber, Philippe; Víllora, Encarnación G.; Shimamura, Kiyoshi

2011-03-01

Cd1-xMnxTe (x=0.1, 0.3, 0.5, 0.7 and 0.9) (CMT) single crystals were grown by the vertical Bridgman method. The optical studies reveal that with the increase in Mn concentration, the band gap values increase, which is attributed to s, p-d exchange interaction between the band carriers and Mn ions. Faraday rotation angle of the grown CMT (x=0.5) crystals were measured at the following wavelengths: 825, 1060 and 1575 nm. It was inferred that CMT exhibit larger Faraday effect (3-6 times larger than terbium-gallium garnet (TGG) currently used for optical isolators) making it as an efficient material for optical isolator at longer wavelengths. Field-cooled and zero field-cooled magnetizations of CMT were measured as a function of temperature and magnetic field. The spin-glass like behavior of CMT and their tendency to decrease in magnitude with increasing Mn concentration have been analyzed. The metal contacts on the Cd1-xMnxTe (x=0.1, 0.5, 0.7 and 0.9) crystals have been made with various metals and metal alloys to establish the ohmic contact. The detector characteristics of CMT have been tested using γ-rays with 511 keV (22 Na) and 59.5 keV (241 Am).

Background field Landau mode operators for the nucleon

NASA Astrophysics Data System (ADS)

Kamleh, Waseem; Bignell, Ryan; Leinweber, Derek B.; Burkardt, Matthias

2018-03-01

The introduction of a uniform background magnetic field breaks threedimensional spatial symmetry for a charged particle and introduces Landau mode effects. Standard quark operators are inefficient at isolating the nucleon correlation function at nontrivial field strengths. We introduce novel quark operators constructed from the twodimensional Laplacian eigenmodes that describe a charged particle on a finite lattice. These eigenmode-projected quark operators provide enhanced precision for calculating nucleon energy shifts in a magnetic field. Preliminary results are obtained for the neutron and proton magnetic polarisabilities using these methods.

Power system applications of fiber optic sensors

NASA Technical Reports Server (NTRS)

Johnston, A. R.; Jackson, S. P.; Kirkham, H.; Yeh, C.

1986-01-01

This document is a progress report of work done in 1985 on the Communications and Control for Electric Power Systems Project at the Jet Propulsion Laboratory. These topics are covered: Electric Field Measurement, Fiber Optic Temperature Sensing, and Optical Power transfer. Work was done on the measurement of ac and dc electric fields. A prototype sensor for measuring alternating fields was made using a very simple electroscope approach. An electronic field mill sensor for dc fields was made using a fiber optic readout, so that the entire probe could be operated isolated from ground. There are several instances in which more precise knowledge of the temperature of electrical power apparatus would be useful. This report describes a number of methods whereby the distributed temperature profile can be obtained using a fiber optic sensor. The ability to energize electronics by means of an optical fiber has the advantage that electrical isolation is maintained at low cost. In order to accomplish this, it is necessary to convert the light energy into electrical form by means of photovoltaic cells. JPL has developed an array of PV cells in gallium arsenide specifically for this purpose. This work is described.

In-Field Spatial Variability in the Degradation of the Phenyl-Urea Herbicide Isoproturon Is the Result of Interactions between Degradative Sphingomonas spp. and Soil pH

PubMed Central

Bending, Gary D.; Lincoln, Suzanne D.; Sørensen, Sebastian R.; Morgan, J. Alun W.; Aamand, Jens; Walker, Allan

2003-01-01

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field. PMID:12571001

Characterization of Genomic Island 3 and Genetic Variability of Chilean Field Strains of Brucella abortus▿

PubMed Central

Céspedes, Sandra; Salgado, Paulina; Valenzuela, Patricio; Vidal, Roberto; Oñate, Angel A.

2011-01-01

One of the capabilities developed by bacteria is the ability to gain large fragments of DNA from other bacteria or to lose portions of their own genomes. Among these exchangeable fragments are the genomic islands (GIs). Nine GIs have been identified in Brucella, and genomic island 3 (GI-3) is shared by two pathogenic species, B. melitensis and B. abortus. GI-3 encodes mostly unknown proteins. One of the aims of this study was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of B. abortus from Chile to determine whether these isolates are clonally related. Furthermore, we focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of B. abortus from Chile, showed that the strains were genetically homogeneous. To increase the power of genetic discrimination among these strains, we used multiple locus variable-number tandem-repeat (VNTR) analysis with 16 loci (MLVA-16). The results obtained by MLVA-16 showed that the strains of B. abortus were genetically heterogeneous and that most of them clustered according to their geographic origin. Of the genetic loci studied, panel 2B was the one describing the highest diversity in the analysis, as well as locus Bruce19 in panel 2A. In relation to the study of GI-3, our experimental analysis by TP-PCR identified and confirmed that GI-3 is present in all wild strains of B. abortus, demonstrating the high stability of gene cluster GI-3 in Chilean field strains. PMID:21543580

Nonreciprocal reflection-beam isolators for far-infrared use

NASA Technical Reports Server (NTRS)

Kanda, M.; May, W. G.

1973-01-01

Magnetoplasma reflection-beam isolators for submillimeter-wave use are discussed in theory and experiment. The basic device uses the Kerr transverse magnetooptic effect (plane of polarization of the EM wave in the plane of incidence, which is perpendicular to a dc magnetic field) in InSb near room temperature. When the semiconductor slab is covered with a thin dielectric layer acting as a matching transformer, improved performance is predicted and observed at 337 microns, and very efficient isolator performance is predicted for 118 microns. Physical arguments are presented to explain the nonreciprocal phenomenon and lead to better device design.

Magnetic techniques for the isolation and purification of proteins and peptides

PubMed Central

Safarik, Ivo; Safarikova, Mirka

2004-01-01

Isolation and separation of specific molecules is used in almost all areas of biosciences and biotechnology. Diverse procedures can be used to achieve this goal. Recently, increased attention has been paid to the development and application of magnetic separation techniques, which employ small magnetic particles. The purpose of this review paper is to summarize various methodologies, strategies and materials which can be used for the isolation and purification of target proteins and peptides with the help of magnetic field. An extensive list of realised purification procedures documents the efficiency of magnetic separation techniques. PMID:15566570

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.

Identification of VanN-type vancomycin resistance in an Enterococcus faecium isolate from chicken meat in Japan.

PubMed

Nomura, Takahiro; Tanimoto, Koichi; Shibayama, Keigo; Arakawa, Yoshichika; Fujimoto, Shuhei; Ike, Yasuyoshi; Tomita, Haruyoshi

2012-12-01

Five VanN-type vancomycin-resistant Enterococcus faecium strains were isolated from a sample of domestic chicken meat in Japan. All isolates showed low-level resistance to vancomycin (MIC, 12 mg/liter) and had the same pulsed-field gel electrophoresis profile. The vancomycin resistance was encoded on a large plasmid (160 kbp) and was expressed constitutively. The VanN-type resistance operon was identical to the first resistance operon to be reported, with the exception of a 1-bp deletion in vanT(N) and a 1-bp substitution in vanS(N).