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Sample records for field isolate reveals

  1. Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations

    PubMed Central

    McBride, Carolyn S.; Singer, Michael C.

    2010-01-01

    Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early

  2. 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

  3. 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

    2016-01-01

    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. PMID:26754154

  4. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia

    PubMed Central

    Winter, David J.; Pacheco, M. Andreína; Vallejo, Andres F.; Schwartz, Rachel S.; Arevalo-Herrera, Myriam; Herrera, Socrates

    2015-01-01

    Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. PMID:26709695

  5. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia.

    PubMed

    Winter, David J; Pacheco, M Andreína; Vallejo, Andres F; Schwartz, Rachel S; Arevalo-Herrera, Myriam; Herrera, Socrates; Cartwright, Reed A; Escalante, Ananias A

    2015-12-01

    Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. PMID:26709695

  6. Transverse Magnetic Field Propellant Isolator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2000-01-01

    An alternative high voltage isolator for electric propulsion and ground-based ion source applications has been designed and tested. This design employs a transverse magnetic field that increases the breakdown voltage. The design can greatly enhance the operating range of laboratory isolators used for high voltage applications.

  7. Prevalence of Clostridium botulinum in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates

    PubMed Central

    Hielm, Sebastian; Björkroth, Johanna; Hyytiä, Eija; Korkeala, Hannu

    1998-01-01

    The distribution of Clostridium botulinum serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay. C. botulinum type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310 C. botulinum type E spores kg−1, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in C. botulinum type E was high. A numerical analysis of SmaI-XmaI macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters. PMID:9797260

  8. Velocity field of isolated turbulent puffs

    NASA Astrophysics Data System (ADS)

    Ghaem-Maghami, E.; Johari, H.

    2010-11-01

    The velocity field of isolated turbulent puffs was measured using the particle image velocimetry technique and was compared with the steady jet flow field. Puffs were generated by injecting air through a 5 mm diameter nozzle into a flow chamber with a weak coflow. Isolated puffs with a Reynolds number of 5000 were examined in the range of 40-75 diameters downstream of the nozzle. The injection time was varied in order to assess the effects of injection volume and equivalent stroke ratio on the puff structure. The results from phase-locked measurements indicate that as the injection volume increased, puffs elongated in the axial direction and became similar to starting jets in the range considered. The largest scaled fluctuating velocities and turbulent shear stress within the puffs were twice the steady jet values. Inspection of the vorticity field revealed the presence of vorticity throughout the puff volume. Entrainment takes place on the portion of the puff closest to the nozzle and the entrainment rate is greater for the puffs with the smaller injection volume. This is consistent with the observations of rapid mixing and combustion of puffs in previous studies.

  9. 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.

  10. 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.

  11. Amplified Fragment Length Polymorphism Reveals Specific Epigenetic Distinctions between Mycobacterium avium Subspecies paratuberculosis Isolates of Various Isolation Types▿

    PubMed Central

    O'Shea, B.; Khare, S.; Klein, P.; Roussel, A.; Adams, L. G.; Ficht, T. A.; Rice-Ficht, A. C.

    2011-01-01

    Amplified fragment length polymorphism (AFLP) was employed as a genetic analysis tool for the study of the genetic relatedness of Mycobacterium avium subsp. paratuberculosis isolates harvested from bovine fecal samples and from bovine or human tissues. This analysis revealed genetic differences between these two isolate types that were confirmed through cluster analysis. Dendrogram analysis separated these two isolate types based on the isolation scheme (tissue-associated versus fecal M. avium subsp. paratuberculosis isolates). Further sequence analysis of unique genetic regions from each isolation type revealed no genetic sequence differences. However, Clustal DNA alignments identified AFLP restriction enzyme sites that were undigested in the tissue-associated isolates. AFLP analysis also disclosed that the same AFLP restriction sites were digested in all of the fecal isolates. Sequence analysis further revealed a consensus sequence upstream of the undigested restriction sites for possible methyltransferase recognition in the tissue-associated M. avium subsp. paratuberculosis isolates. PMID:21471350

  12. Molecular characterization of the Israeli B. bigemina vaccine strain and field isolates.

    PubMed

    Molad, T; Erster, O; Fleiderovitz, L; Roth, A; Leibovitz, B; Wolkomirsky, R; Mazuz, M L; Behar, A; Markovics, A

    2015-09-15

    The present study demonstrated the genetic character of the Israeli Babesia bigemina vaccine strain and field isolates, based on rap-1a and rap-1c gene sequences. The RAP-1a of blood-derived Israeli B. bigemina field isolates shared 100% amino acid sequence identity. However, comparison of RAP-1c from various Israeli B. bigemina field isolates revealed that the total sequence identity among the field isolates ranged from 98.2 to 100%. High identity was observed when RAP-1a sequences from the Israeli vaccine strain and field isolates were compared with RAP-1a from Egypt, Syria, Mexico and South Africa, while, the Israeli RAP-1c sequences showed the highest identity to the Mexican isolate JG-29 and to the PR isolate from Puerto-Rico. Based on sequence variations between the rap-1a of the vaccine strain and that of the field isolate, and between the rap-1c of the vaccine strain and that of the field isolates, nPCR-RFLP procedures were developed that enable, for the first time differentiation between the Israeli B. bigemina vaccine strain and field-infection isolates. These assays could serve as fast and sensitive methods for detection and differentiation between Israeli B. bigemina vaccine strains and field isolates, as well as for epidemiological investigations. PMID:26154404

  13. Velocity Field of Isolated Turbulent Puffs

    NASA Astrophysics Data System (ADS)

    Ghaem-Maghami, Elham; Johari, Hamid

    2006-11-01

    The velocity field of isolated turbulent puffs was investigated by the PIV technique. Particular attention was paid to the entrainment pattern of isolated puffs. Puffs were generated by injecting seeded air through a 5 mm diameter nozzle into a flow chamber with a weak co-flow. Puffs with a Reynolds number of 5,000 were examined in the range of 35 -- 75 diameters downstream of the nozzle. The injection time was varied in order to assess the effect of injection volume and impulse on the puff structure. The results indicate that as the injection volume increased, puffs elongated in the axial direction. The largest mean and fluctuating velocities were within the central portion of the puff. The maximum turbulent shear stress within the puff was as much as 2.5 times the steady jet value. The vorticity field showed the presence of vorticity throughout the puff volume. The ratio of volume flow rate at the puff center to the steady jet volume flux at the same location was largest for the smallest injection volume. The majority of entrainment into the puff occurs below the puff center while the puff cap pushes out into surrounding fluid.

  14. Magnetic field decay in isolated neutron stars

    NASA Technical Reports Server (NTRS)

    Goldreich, Peter; Reisenegger, Andreas

    1992-01-01

    Three mechanisms that promote the loss of magnetic flux from an isolated neutron star - Ohmic decay, ambipolar diffusion, and Hall drift - are investigated. Equations of motions are solved for charged particles in the presence of a magnetic field and a fixed background of neutrons, while allowing for the creation and destruction of particles by weak interactions. Although these equations apply to normal neutrons and protons, the present interpretations of their solutions are extended to cover cases of neutron superfluidity and proton superconductivity. The equations are manipulated to prove that, in the presence of a magnetic force, the charged particles cannot be simultaneously in magnetostatic equilibrium and chemical equilibrium with the neutrons. The application of the results to real neutron stars is discussed.

  15. 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. PMID:26984225

  16. Pulsed-field gel electrophoresis for epidemiologic studies of Campylobacter hyointestinalis isolates.

    PubMed Central

    Salama, S M; Tabor, H; Richter, M; Taylor, D E

    1992-01-01

    Campylobacter hyointestinalis was isolated from five members of the same family who had previously consumed raw milk. Pulsed-field gel electrophoresis of genomic DNAs from the five strains, after digestion with restriction endonuclease SalI, revealed that three strains had identical genome patterns and therefore appeared to be related, whereas the other two had completely different genome patterns and appeared to be unrelated. We report here for the first time the isolation of C. hyointestinalis from family members who had consumed raw milk. Our study also demonstrates the usefulness of pulsed-field gel electrophoresis for epidemiologic studies of this unusual campylobacter. Images PMID:1500503

  17. Characterization of a Borna disease virus field isolate which shows efficient viral propagation and transmissibility.

    PubMed

    Watanabe, Yohei; Ibrahim, Madiha S; Hagiwara, Katsuro; Okamoto, Minoru; Kamitani, Wataru; Yanai, Hideyuki; Ohtaki, Naohiro; Hayashi, Yohei; Taniyama, Hiroyuki; Ikuta, Kazuyoshi; Tomonaga, Keizo

    2007-04-01

    To investigate the biological characteristics of field isolates of Borna disease virus (BDV), as well as to understand BDV infections outside endemic countries, we isolated the virus from brain samples of a heifer with Borna disease in Japan. We demonstrate that the brain lysate contained replication products of BDV and induced viral propagation in rat glioma cells, suggesting that a replication-competent BDV existed in the bovine brain. This field strain of BDV, named Bo/04w, showed efficient viral release and transmissibility and also displayed a distinct pattern of expression of viral phosphoprotein (P) during infection, as compared with laboratory-adapted BDV strains. Interestingly, we found the level of P to be significantly low in cells infected with Bo/04w, and the transcription of this isolate to be more efficient than that of laboratory strain of BDV. These results indicated that the field isolate may regulate the expression of P at an optimal level in infected cells. We also confirmed that Bo/04w maintains biological significance in neonatal gerbil brain. Sequencing revealed that despite the biological differences, the field isolate is closely related genetically to the laboratory strains of BDV. We discuss here the sequence similarities between BDV isolates from endemic and nonendemic countries. PMID:17306587

  18. 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

  19. Methanococcus thermolithotrophicus Isolated from North Sea Oil Field Reservoir Water

    PubMed Central

    Nilsen, R. K.; Torsvik, T.

    1996-01-01

    Methanococcus thermolithotrophicus ST22 was isolated from produced water of a North Sea oil field, on mineral medium with H(inf2)-CO(inf2) as the sole source of carbon and energy. The isolate grew at 17 to 62(deg)C, with an optimum at 60(deg)C. The pH range was 4.9 to 9.8, with optimal growth at pH 5.1 to 5.9; these characteristics reflected its habitat. Strain ST22 was quickly identified and distinguished from the type strain by immunoblotting. PMID:16535247

  20. Molecular characterisation of Aspergillus flavus isolates from peanut fields in India using AFLP

    PubMed Central

    Singh, Diwakar; Radhakrishnan, T.; Kumar, Vinod; Bagwan, N.B.; Basu, M.S.; Dobaria, J.R.; Mishra, Gyan P.; Chanda, S.V.

    2015-01-01

    Aflatoxin contamination of peanut, due to infection by Aspergillus flavus, is a major problem of rain-fed agriculture in India. In the present study, molecular characterisation of 187 Aspergillus flavus isolates, which were sampled from the peanut fields of Gujarat state in India, was performed using AFLP markers. On a pooled cluster analysis, the markers could successfully discriminate among the ‘A’, ‘B’ and ‘G’ group A. flavus isolates. PCoA analysis also showed equivalent results to the cluster analysis. Most of the isolates from one district could be clustered together, which indicated genetic similarity among the isolates. Further, a lot of genetic variability was observed within a district and within a group. The results of AMOVA test revealed that the variance within a population (84%) was more than that between two populations (16%). The isolates, when tested by indirect competitive ELISA, showed about 68.5% of them to be atoxigenic. Composite analysis between the aflatoxin production and AFLP data was found to be ineffective in separating the isolate types by aflatoxigenicity. Certain unique fragments, with respect to individual isolates, were also identified that may be used for development of SCAR marker to aid in rapid and precise identification of isolates. PMID:26413047

  1. Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1.

    PubMed

    Vaz, P K; Horsington, J; Hartley, C A; Browning, G F; Ficorilli, N P; Studdert, M J; Gilkerson, J R; Devlin, J M

    2016-03-01

    Recombination in alphaherpesviruses allows evolution to occur in viruses that have an otherwise stable DNA genome with a low rate of nucleotide substitution. High-throughput sequencing of complete viral genomes has recently allowed natural (field) recombination to be studied in a number of different alphaherpesviruses, however, such studies have not been applied to equine herpesvirus 1 (EHV-1) or equine herpesvirus 4 (EHV-4). These two equine alphaherpesviruses are genetically similar, but differ in their pathogenesis and epidemiology. Both cause economically significant disease in horse populations worldwide. This study used high-throughput sequencing to determine the full genome sequences of EHV-1 and EHV-4 isolates (11 and 14 isolates, respectively) from Australian or New Zealand horses. These sequences were then analysed and examined for evidence of recombination. Evidence of widespread recombination was detected in the genomes of the EHV-4 isolates. Only one potential recombination event was detected in the genomes of the EHV-1 isolates, even when the genomes from an additional 11 international EHV-1 isolates were analysed. The results from this study reveal another fundamental difference between the biology of EHV-1 and EHV-4. The results may also be used to help inform the future safe use of attenuated equine herpesvirus vaccines. PMID:26691326

  2. Antimicrobial susceptibility testing of Spanish field isolates of Brachyspira hyodysenteriae.

    PubMed

    Hidalgo, A; Carvajal, A; García-Feliz, C; Osorio, J; Rubio, P

    2009-08-01

    This study is the first conducted in Spain to evaluate antimicrobial susceptibility of field isolates of Brachyspira hyodysenteriae. One hundred and eight isolates of the bacterium, recovered from different Spanish swine farms between 2000 and 2007, were investigated. The minimum inhibitory concentrations (MIC) of erythromycin, tylosin, tiamulin, valnemulin, clindamycin and lincomycin were determined using a broth microdilution technique. Most of the isolates showed poor susceptibility to erythromycin (MIC(90)>256 microg/ml), tylosin (MIC(90)>256 microg/ml), clindamycin (MIC(90)>4 microg/ml) and lincomycin (MIC(90)=128 microg/ml). Reduced susceptibility to tiamulin and valnemulin was observed with a MIC>2 microg/ml in 17.6% and 7.41% of the B. hyodysenteriae isolates, respectively. Moreover, a survival analysis permitted the detection of an increasing trend in the MIC values for almost all the antimicrobials used in the treatment of swine dysentery when comparing recent isolates (from 2006 to 2007) with those recovered in earlier years (between 2000 and 2004). PMID:19084246

  3. Formation, evolution and properties of isolated field elliptical galaxies

    NASA Astrophysics Data System (ADS)

    Niemi, Sami-Matias; Heinämäki, Pekka; Nurmi, Pasi; Saar, Enn

    2010-06-01

    We study the properties, evolution and formation mechanisms of isolated field elliptical (IfE) galaxies. We create a `mock' catalogue of IfE galaxies from the Millennium Simulation Galaxy Catalogue, and trace their merging histories. The formation, identity and assembly redshifts of simulated isolated and non-isolated elliptical galaxies are studied and compared. Observational and numerical data are used to compare age, mass and the colour-magnitude relation. Our results, based on simulation data, show that almost 7 per cent of all elliptical galaxies brighter than -19mag in B band can be classified as IfE galaxies. Results also show that isolated elliptical galaxies have a rather flat luminosity function; a number density of ~3 × 10-6h3Mpc-3mag-1, throughout their B-band magnitudes. IfE galaxies show bluer colours than non-isolated elliptical galaxies and they appear younger, in a statistical sense, according to their mass-weighted age. IfE galaxies also form and assemble at lower redshifts compared to non-isolated elliptical galaxies. About 46 per cent of IfE galaxies have undergone at least one major merging event in their formation history, while the same fraction is only ~33 per cent for non-isolated ellipticals. Almost all (~98 per cent) isolated elliptical galaxies show merging activity during their evolution, pointing towards the importance of mergers in the formation of IfE galaxies. The mean time of the last major merging is at z ~ 0.6 or 6Gyr ago for isolated ellipticals, while non-isolated ellipticals experience their last major merging significantly earlier at z ~ 1.1 or 8Gyr ago. After inspecting merger trees of simulated IfE galaxies, we conclude that three different, yet typical, formation mechanisms can be identified: solitude, coupling and cannibalism. Our results also predict a previously unobserved population of blue, dim and light galaxies that fulfil observational criteria to be classified as IfE galaxies. This separate population comprises

  4. Phylogenetic analysis of bluetongue virus serotype 4 field isolates from Argentina.

    PubMed

    Legisa, D; Gonzalez, F; De Stefano, G; Pereda, A; Dus Santos, M J

    2013-03-01

    Bluetongue is an insect-transmitted viral disease of ruminant species, which represents a major barrier to the international trade of animals and their products. Bluetongue virus (BTV) has a genome composed of ten linear segments of dsRNA, which code for at least ten different viral proteins. In South America, serological evidence for the presence of BTV has been found in Peru, Argentina, Brazil, Ecuador and Chile. Brazil and Argentina are the only South American countries where BTV has been isolated. In Brazil, only one BTV isolate, serotype 12, has been reported, whereas in Argentina five BTV serotype 4 isolates have been obtained from cattle without clinical signs. Three of these five isolates were isolated during 1999-2001, whereas two of them were obtained as part of the present work. This study describes sequence comparisons and phylogenetic analyses of segment (Seg)-2, Seg-3, Seg-6, Seg-7 and Seg-10 of the first Argentinian field isolates of BTV. The analysis of Seg-2 and Seg-6 resulted in a single cluster of Argentinian sequences into the serotype 4 clade. In addition, the Argentinian sequences grouped within the nucleotype A clade, along with reference strains. The analysis of Seg-3, Seg-7 and Seg-10 showed that the Argentinian isolates grouped into the western topotype, indicating that the circulating virus had an African/European origin. Phylogenetic analysis revealed that the Argentinian sequences present a South American genetic identity, suggesting an independent lineage evolution. PMID:23152367

  5. 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

  6. Genetic diversity of Clavispora lusitaniae isolated from Agave fourcroydes Lem, as revealed by DNA fingerprinting.

    PubMed

    Pérez-Brito, Daisy; Magaña-Alvarez, Anuar; Lappe-Oliveras, Patricia; Cortes-Velazquez, Alberto; Torres-Calzada, Claudia; Herrera-Suarez, Teófilo; Larqué-Saavedra, Alfonso; Tapia-Tussell, Raul

    2015-01-01

    This study characterized Clavispora lusitaniae strains isolated from different stages of the processing and early fermentation of a henequen (Agave fourcroydes) spirit produced in Yucatan, Mexico using a molecular technique. Sixteen strains identified based on morphological features, obtained from different substrates, were typed molecularly. Nine different versions of the divergent D1/D2 domain of the large-subunit ribosomal DNA sequence were identified among the C. lusitaniae strains. The greatest degree of polymorphism was found in the 90-bp structural motif of the D2 domain. The MSP-PCR technique was able to differentiate 100% of the isolates. This study provides significant insight into the genetic diversity of the mycobiota present during the henequen fermentation process, especially that of C. lusitaniae, for which only a few studies in plants have been published. The applied MSP-PCR markers were very efficient in revealing olymorphisms between isolates of this species. PMID:25557477

  7. Babesia canis: evidence for genetic diversity among isolates revealed by restriction fragment length polymorphism analysis.

    PubMed

    Citard, T; Mähl, P; Boulouis, H J; Chavigny, C; Druilhe, P

    1995-09-01

    The genetic diversity of B. canis was investigated by restriction fragment length polymorphism analysis. For this purpose, we identified a Babesia canis specific DNA probe named pS8. This 1.2 kbp probe can detect as low as 20 pg of B. canis DNA. Results suggest that the pS8 probe is distributed in multiple copies throughout the genome though is probably not itself internally repetitious, i.e. not structured into blocks of tandem units. This probe reveals discrete hybridizing fragments in B. canis enzyme-digested genomic DNA. RFLP patterns obtained with the pS8 probe revealed a large genetic diversity between various isolates and led us to distinguish several clones derived from a single isolate. Results suggest that for a single isolate, the fingerprints obtained reflect those of a few quantitatively dominant clones. This technique can now be routinely applied and provides a convenient tool for the characterization and the identification of B. canis isolates, strains and clones. PMID:8533020

  8. Comparative “-omics” in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors

    PubMed Central

    Lluch-Senar, Maria; Cozzuto, Luca; Cano, Jaime; Delgado, Javier; Llórens-Rico, Verónica; Pereyre, Sabine; Bebear, Cécile; Serrano, Luis

    2015-01-01

    The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of clinical isolates of this bacterium have been described (types 1 and 2), differing in the sequence of the P1 adhesin gene. Here, we have sequenced the genomes of 23 clinical isolates of M. pneumoniae. Studying SNPs, non-synonymous mutations, indels and genome rearrangements of these 23 strains and 4 previously sequenced ones, has revealed new subclasses in the two main groups, some of them being associated with the country of isolation. Integrative analysis of in vitro gene essentiality and mutation rates enabled the identification of several putative virulence factors and antigenic proteins; revealing recombination machinery, glycerol metabolism and peroxide production as possible factors in the genetics and physiology of these pathogenic strains. Additionally, the transcriptomes and proteomes of two representative strains, one from each of the two main groups, have been characterized to evaluate the impact of mutations on RNA and proteins levels. This study has revealed that type 2 strains show higher expression levels of CARDS toxin, a protein recently shown to be one of the major factors of inflammation. Thus, we propose that type 2 strains could be more toxigenic than type 1 strains of M. pneumoniae. PMID:26335586

  9. Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India.

    PubMed

    Gowda, Malali; Shirke, Meghana D; Mahesh, H B; Chandarana, Pinal; Rajamani, Anantharamanan; Chattoo, Bharat B

    2015-09-01

    The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40 Mb genome of B157 and 43 Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes. PMID:26484270

  10. Comprehensive antibiotic susceptibility profiling of Chilean Piscirickettsia salmonis field isolates.

    PubMed

    Henríquez, P; Kaiser, M; Bohle, H; Bustos, P; Mancilla, M

    2016-04-01

    Antibiotics have been extensively used against infections produced by Piscirickettsia salmonis, a fish pathogen and causative agent of piscirickettsiosis and one of the major concerns for the Chilean salmon industry. Therefore, the emergence of resistant phenotypes is to be expected. With the aim of obtaining a landscape of the antimicrobial resistance of P. salmonis in Chile, the susceptibility profiles for quinolones, florfenicol and oxytetracycline (OTC) of 292 field isolates derived from main rearing areas, different hosts and collected over 5 years were assessed. The results allowed for the determination of epidemiological cut-off values that were used to characterize the pathogen population. This work represents the first large-scale field study addressing the antimicrobial susceptibility of P. salmonis, providing evidence of the existence of resistant types with a high incidence of resistance to quinolones. Remarkably, despite the amounts and frequency of therapies, our results disclosed that the issue of resistance to florfenicol and OTC is still in the onset. PMID:26660665

  11. Spore-Forming Thermophilic Sulfate-Reducing Bacteria Isolated from North Sea Oil Field Waters

    PubMed Central

    Rosnes, Jan Thomas; Torsvik, Terje; Lien, Torleiv

    1991-01-01

    Thermophilic sulfate-reducing bacteria were isolated from oil field waters from oil production platforms in the Norwegian sector of the North Sea. Spore-forming rods dominated in the enrichments when lactate, propionate, butyrate, or a mixture of aliphatic fatty acids (C4 through C6) was added as a carbon source and electron donor. Representative strains were isolated and characterized. The isolates grew autotrophically on H2-CO2 and heterotrophically on fatty acids such as formate, propionate, butyrate, caproate, valerate, pyruvate, and lactate and on alcohols such as methanol, ethanol, and propanol. Sulfate, sulfite, and thiosulfate but not nitrate could be used as an electron acceptor. The temperature range for growth was 43 to 78°C; the spores were extremely heat resistant and survived 131°C for 20 min. The optimum pH was 7.0. The isolates grew well in salt concentrations ranging from 0 to 800 mmol of NaCl per liter. Sulfite reductase P582 was present, but cytochrome c and desulfoviridin were not found. Electron micrographs revealed a gram-positive cell organization. The isolates were classified as a Desulfotomaculum sp. on the basis of spore formation, general physiological characteristics, and submicroscopic organization. To detect thermophilic spore-forming sulfate-reducing bacteria in oil field water, polyvalent antisera raised against antigens from two isolates were used. These bacteria were shown to be widespread in oil field water from different platforms. The origin of thermophilic sulfate-reducing bacteria in the pore water of oil reservoirs is discussed. Images PMID:16348538

  12. Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate.

    PubMed

    Hadrys, Heike; Simon, Sabrina; Kaune, Barbara; Schmitt, Oliver; Schöner, Anja; Jakob, Wolfgang; Schierwater, Bernd

    2012-01-01

    Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution. PMID:22685537

  13. Archaeoglobus fulgidus Isolated from Hot North Sea Oil Field Waters

    PubMed Central

    Beeder, Janiche; Nilsen, Roald Kåre; Rosnes, Jan Thomas; Torsvik, Terje; Lien, Torleiv

    1994-01-01

    A hyperthermophilic sulfate reducer, strain 7324, was isolated from hot (75°C) oil field waters from an oil production platform in the Norwegian sector of the North Sea. It was enriched on a complex medium and isolated on lactate with sulfate. The cells were nonmotile, irregular coccoid to disc shaped, and 0.3 to 1.0 μm wide. The temperature for growth was between 60 and 85°C with an optimum of 76°C. Lactate, pyruvate, and valerate plus H2 were utilized as carbon and energy sources with sulfate as electron acceptor. Lactate was completely oxidized to CO2. The cells contained an active carbon monoxide dehydrogenase but no 2-oxoglutarate dehydrogenase activity, indicating that lactate was oxidized to CO2 via the acetyl coenzyme A/carbon monoxide dehydrogenase pathway. The cells produced small amounts of methane simultaneously with sulfate reduction. F420 was detected in the cells which showed a blue-green fluorescence at 420 nm. On the basis of morphological, physiological, and serological features, the isolate was classified as an Archaeoglobus sp. Strain 7324 showed 100% DNA-DNA homology with A. fulgidus Z, indicating that it belongs to the species A. fulgidus. Archaeoglobus sp. has been selectively enriched and immunomagnetically captured from oil field waters from three different platforms in the North Sea. Our results show that strain 7324 may grow in oil reservoirs at 70 to 85°C and contribute to hydrogen sulfide formation in this environment. Images PMID:16349231

  14. Incipient fault detection and isolation of sensors and field devices

    NASA Astrophysics Data System (ADS)

    Ferreira, Paulo Brasko

    The purpose of this research is to develop a robust fault detection and isolation method, for detecting faults in process sensors, actuators, controllers and other field devices. The approach to the solution to this problem is summarized below. A novel approach for the validation of control system components and sensors was developed in this research. The process is composed of detecting a system anomaly, isolating the faulty component (such as sensors, actuators, and controllers), computing its deviation from expected value for a given system's normal condition, and finally reconstructing its output when applicable. A variant of the Group Method of Data Handling (GMDH) was developed in this research for generating analytical redundancy from relationships among different system components. A rational function approximation was used for the data-driven modeling scheme. This analytical redundancy is necessary for detecting system anomalies and isolating faulty components. A rule-base expert system was developed in order to isolate the faulty component. The rule-based was established from model-simulated data. A fuzzy-logic estimator was implemented to compute the magnitude of the loop component fault so that the operator or the controller might take corrective actions. This latter engine allows the system to be operated in a normal condition until the next scheduled shutdown, even if a critical component were detected as degrading. The effectiveness of the method developed in this research was demonstrated through simulation and by implementation to an experimental control loop. The test loop consisted of a level control system, flow, pressure, level and temperature measuring sensors, motor-operated valves, and a pump. Commonly observed device faults were imposed in different system components such as pressure transmitters, pumps, and motor-operated valves. This research has resulted in a framework for system component failure detection and isolation, allowing easy

  15. Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections

    USGS Publications Warehouse

    Jarvi, S.I.; Farias, M.E.M.; Atkinson, C.T.

    2008-01-01

    Background: The relatively recent introduction of a highly efficient mosquito vector and an avian pathogen (Plasmodium relictum) to an isolated island ecosystem with nai??ve, highly susceptible avian hosts provides a unique opportunity to investigate evolution of virulence in a natural system. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct impacts on virulence. Toward further understanding of how host-parasite and parasite-parasite relationships may impact virulence, this study characterizes within-host diversity of malaria parasite populations based on genetic analysis of the trap (thrombospondin-related anonymous protein) gene in isolates originating from Hawaii, Maui and Kauai Islands. Methods: A total of 397 clones were produced by nested PCR amplification and cloning of a 1664 bp fragment of the trap gene from two malarial isolates, K1 (Kauai) and KV115 (Hawaii) that have been used for experimental studies, and from additional isolates from wild birds on Kauai, Maui and Hawaii Islands. Diversity of clones was evaluated initially by RFLP-based screening, followed by complete sequencing of 33 selected clones. Results: RFLP analysis of trap revealed a minimum of 28 distinct RFLP haplotypes among the 397 clones from 18 birds. Multiple trap haplotypes were detected in every bird evaluated, with an average of 5.9 haplotypes per bird. Overall diversity did not differ between the experimental isolates, however, a greater number of unique haplotypes were detected in K1 than in KV115. We detected high levels of clonal diversity with clear delineation between isolates K1 and KV115 in a haplotype network. The patterns of within-host haplotype clustering are consistent with the possibility of a clonal genetic structure and rapid within-host mutation after infection. Conclusion: Avian malaria (P. relictum) and Avipoxvirus are the significant infectious diseases currently affecting the native Hawaiian avifauna. This

  16. Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections

    PubMed Central

    Jarvi, Susan I; Farias, Margaret EM; Atkinson, Carter T

    2008-01-01

    Background The relatively recent introduction of a highly efficient mosquito vector and an avian pathogen (Plasmodium relictum) to an isolated island ecosystem with naïve, highly susceptible avian hosts provides a unique opportunity to investigate evolution of virulence in a natural system. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct impacts on virulence. Toward further understanding of how host-parasite and parasite-parasite relationships may impact virulence, this study characterizes within-host diversity of malaria parasite populations based on genetic analysis of the trap (thrombospondin-related anonymous protein) gene in isolates originating from Hawaii, Maui and Kauai Islands. Methods A total of 397 clones were produced by nested PCR amplification and cloning of a 1664 bp fragment of the trap gene from two malarial isolates, K1 (Kauai) and KV115 (Hawaii) that have been used for experimental studies, and from additional isolates from wild birds on Kauai, Maui and Hawaii Islands. Diversity of clones was evaluated initially by RFLP-based screening, followed by complete sequencing of 33 selected clones. Results RFLP analysis of trap revealed a minimum of 28 distinct RFLP haplotypes among the 397 clones from 18 birds. Multiple trap haplotypes were detected in every bird evaluated, with an average of 5.9 haplotypes per bird. Overall diversity did not differ between the experimental isolates, however, a greater number of unique haplotypes were detected in K1 than in KV115. We detected high levels of clonal diversity with clear delineation between isolates K1 and KV115 in a haplotype network. The patterns of within-host haplotype clustering are consistent with the possibility of a clonal genetic structure and rapid within-host mutation after infection. Conclusion Avian malaria (P. relictum) and Avipoxvirus are the significant infectious diseases currently affecting the native Hawaiian avifauna. This study

  17. Molecular characterisation of virulence graded field isolates of myxoma virus

    PubMed Central

    2010-01-01

    Background Myxoma virus (MV) has been endemic in Europe since shortly after its deliberate release in France in 1952. While the emergence of more resistant hosts and more transmissible and attenuated virus is well documented, there have been relatively few studies focused on the sequence changes incurred by the virus as it has adapted to its new host. In order to identify regions of variability within the MV genome to be used for phylogenetic studies and to try to investigate causes of MV strain attenuation we have molecularly characterised nine strains of MV isolated in Spain between the years 1992 and 1995 from wide ranging geographic locations and which had been previously graded for virulence by experimental infection of rabbits. Results The findings reported here show the analysis of 16 genomic regions accounting for approximately 10% of the viral genomes. Of the 20 genes analysed 5 (M034L, M069L, M071L, M130R and M135R) were identical in all strains and 1 (M122R) contained only a single point mutation in an individual strain. Four genes (M002L/R, M009L, M036L and M017L) showed insertions or deletions that led to disruption of the ORFs. Conclusions The findings presented here provide valuable tools for strain differentiation and phylogenetic studies of MV isolates and some clues as to the reasons for virus attenuation in the field. PMID:20187925

  18. Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

    PubMed Central

    Periwal, Vinita; Patowary, Ashok; Vellarikkal, Shamsudheen Karuthedath; Gupta, Anju; Singh, Meghna; Mittal, Ashish; Jeyapaul, Shamini; Chauhan, Rajendra Kumar; Singh, Ajay Vir; Singh, Pravin Kumar; Garg, Parul; Katoch, Viswa Mohan; Katoch, Kiran; Chauhan, Devendra Singh; Sivasubbu, Sridhar; Scaria, Vinod

    2015-01-01

    The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical isolates sequenced and assembled in this study, to understand its pangenome architecture. We predicted genes for all the 96 strains and clustered their respective CDSs into homologous gene clusters (HGCs) to reveal a hard-core, soft-core and accessory genome component of MTBC. The hard-core (HGCs shared amongst 100% of the strains) was comprised of 2,066 gene clusters whereas the soft-core (HGCs shared amongst at least 95% of the strains) comprised of 3,374 gene clusters. The change in the core and accessory genome components when observed as a function of their size revealed that MTBC has an open pangenome. We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates. We report PCR validation on 9 candidate genes depicting 7 genes completely absent from H37Rv and H37Ra whereas 2 genes shared partial homology with them accounting to probable insertion and deletion events. The pangenome approach is a promising tool for studying strain specific genetic differences occurring within species. We also suggest that since selecting appropriate target genes for typing purposes requires the expected target gene be present in all isolates being typed, therefore estimating the core-component of the species becomes a subject of prime importance. PMID:25853708

  19. Long term field evaluation reveals HLB resistance in Citrus relatives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus huanglongbing (HLB) is a destructive disease with no known cure. To identify sources of HLB resistance in the subfamily Aurantioideae to which citrus belongs, we conducted a six-year field trial under natural disease challenge conditions in an HLB endemic region. The study included 65 Citrus ...

  20. Concentration- and time-response characteristics of plaque isolates of Agrotis ipsilon multiple nucleopolyhedrovirus derived from a field isolate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plaque isolates derived from the Illinois field isolate of Agrotis ipsilon multiple nucleopolyhedrovirus are distinguished by the presence or absence of a small deletion in the baculovirus egt (ecdysteroid UDP-glucosyltransferase) coding sequence. Dose-response and time-response bioassays were perf...

  1. Experimental hybridization and backcrossing reveal forces of reproductive isolation in Microbotryum

    PubMed Central

    2013-01-01

    Background Hybridization and reproductive isolation are central to the origin and maintenance of species, and especially for sympatric species, gene flow is often inhibited through barriers that depend upon mating compatibility factors. The anther-smut fungi (genus Microbotryum) serve as models for speciation in the face of sympatry, and previous studies have tested for but not detected assortative mating. In addition, post-mating barriers are indicated by reduced fitness of hybrids, but sources of those barriers (i.e. ecological maladaptation or genetic incompatibilities) have not yet been detected. Here, backcrossing experiments, specifically controlling for the fungal species origins of the mating compatibility factors, were used to investigate reproductive isolation in the recently-derived species Microbotryum lychnidis-dioicae and Microbotryum silenes-dioicae. Results Assortative mating was detected during backcrossing and was manifested by the preferential conjugation of the hybrid-produced gametes with non-hybrid gametes containing mating compatibility factors from the same parental species. Patterns of post-mating performance supported either a level of extrinsic isolation mechanism, where backcross progeny with a higher proportion of the pathogen genome adapted to the particular host environment were favored, or an infection advantage attributed to greater genetic contribution to the hybrid from the M. lychnidis-dioicae genome. Conclusion The use of controlled backcrossing experiments reveals significant species-specific mating type effects on conjugations between recently-derived sister species, which are likely to play important roles in both maintaining species separation and the nature of hybrids lineages that emerge in sympatry between Microbotryum species. PMID:24112452

  2. An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis

    PubMed Central

    Karhemo, Piia-Riitta; Ravela, Suvi; Laakso, Marko; Ritamo, Ilja; Tatti, Olga; Mäkinen, Selina; Goodison, Steve; Stenman, Ulf-Håkan; Hölttä, Erkki; Hautaniemi, Sampsa; Valmu, Leena; Lehti, Kaisa; Laakkonen, Pirjo

    2012-01-01

    Details of metastasis, the deadliest aspect of cancer, are unclear. Cell surface proteins play central roles in adhesive contacts between the tumor cell and the stroma during metastasis. We optimized a fast, small-scale isolation of biotinylated cell surface proteins to reveal novel metastasis-associated players froman isogenic pair of human MDA-MB-435 cancer cells with opposite metastatic phenotypes. Isolated proteins were trypsin digested and analyzed using LC–MS/MS followed by quantitation with the Progenesis LC–MS software. Sixteen proteins displayed over twofold expression differences between the metastatic and non-metastatic cells. Interestingly, overexpression of most of them (14/16) in the metastatic cells indicates a gain of novel surface protein profile as compared to the non-metastatic one. All five validated, differentially expressed proteins showed higher expression in the metastatic cells in culture, and four of these were further validated in vivo. Moreover, we analyzed the expression of two of the identified proteins, CD109 and ITGA6 in 3-dimensional cultures of six melanoma cell lines. Both proteins marked the surface of cells derived from melanoma metastasis over cells derived from primary melanoma. These unbiased identification and validation of both known and novel metastasis-associated proteins indicate a reliable approach for the identification of differentially expressed surface proteins. PMID:22813880

  3. Genetic characterization of Toxoplasma gondii isolates from Portugal, Austria and Israel reveals higher genetic variability within the type II lineage.

    PubMed

    Verma, S K; Ajzenberg, D; Rivera-Sanchez, A; Su, C; Dubey, J P

    2015-06-01

    This study compared genetic diversity of Toxoplasma gondii isolates from Portugal, Austria and Israel. For this, we genotyped 90 T. gondii isolates (16 from Portugal, 67 from Austria and 7 from Israel) using 10 nested PCR-restriction length polymorphism (RFLP) genetic markers and 15 microsatellite (MS) markers. By PCR-RFLP typing, 7 isolates from Portugal chickens were identified as type II (ToxoDB #1 or #3), 4 were type III (ToxoDB #2) and the remaining 4 isolates have unique genotype pattern were designated as ToxoDB #254. One mouse virulent isolate from a bovine fetus (Bos taurus) in Portugal was type I (ToxoDB #10) at all loci and designated as TgCowPr1. All 67 isolates from Austria and 7 from Israel were type II (ToxoDB #1 or #3). By MS typing, many additional genetic variations were revealed among the type II and type III isolates. Phylogenetic analysis showed that isolates from the same geographical locations tend to cluster together, and there is little overlapping of genotypes among different locations. This study demonstrated that the MS markers can provide higher discriminatory power to reveal association of genotypes with geographical locations. Future studies of the type II strains in Europe by these MS markers will be useful to reveal transmission patterns of the parasite. PMID:25677825

  4. Generation of isolated sub-40-attosecond pulse with a multicycle chirped laser and a static electric field

    NASA Astrophysics Data System (ADS)

    Mohebbi, Masoud

    2016-02-01

    We numerically investigate the high-order harmonic generation and isolated attosecond pulse generation in a waveform that linearly produced by chirped laser pulse, chirp-free laser pulse, and static electric field. When a chirp-free laser pulse is added to the produced field of the chirped driving pulse and the static electric field, the plateau harmonic yield is enhanced by two orders. The spectral modulation is also significantly decreased, and the bandwidth of XUV spectrum is further broadened. An intense and a clean isolated 38-as pulse can be produced from the intense broadband XUV supercontinuum. After proper phase compensation, an isolated sub-8-attosecond pulse can be obtained. Furthermore, quantum time-frequency analysis reveals that the selection of the short quantum path can be achieved in this scheme.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. Magnetite reveals ambient field strength at low temperatures

    NASA Astrophysics Data System (ADS)

    Smirnov, Alexei V.; Tarduno, John A.

    Magnetite (Fe3O4) is the most important and oldest known magnetic mineral on Earth (Figure l). We have come a long way from the magnetite loadstone compasses of ancient China; magnetite and titanomagnetite have been established as the principal carriers of geologically important remanent magnetizations in rocks, the study of which led to the plate tectonic paradigm. We now recognize that magnetite plays an important role in the biosphere. Some organisms contain intra-cellular particles of Fe3O4 that they use for spatial orientation and navigation. When preserved in rocks, these particles—called "magnetofossils"— can provide important insight into the origin and development of life here, and perhaps, on other planets [e.g., Thomas-Keprta et al., 2000]. Magnetite is now used in the medical field and in nanotechnology research. Nanoparticles of magnetite are used as a contrasting agent in magnetic resonance imaging and are being developed to deliver site-specific drugs for the treatment of cancer [Alexiou et al., 2000]. Such applications add to a long list of industrial uses of magnetite that range from magnetic ink to magnetic recording media.

  7. A Natural Electromagnetic Fields Effect on Healthy Volunteers During Long-Term Experiment with Isolation

    NASA Astrophysics Data System (ADS)

    Gurfinkel, Yury I.; Mikhailov, Valery M.; Ushakov, Boris B.

    2008-06-01

    There were investigated four healthy volunteers at the age of 37, 40, 41 and 48 during the baseline 240-d isolation period starting from July 3, 1999 in the frame of SFINCSS-99 - "SIMULATION OF FLIGHT OF INTERNATIONAL CREW ON SPACE STATION". Before a starting of experiment with long-term isolation were carried out measurements of magnetic properties of module and sleeping places. With the regularity of 3 times a week each subject made records of no less then 3 video episodes with the total length of one minute minimum at the same time between 1 and 2 p.m. Applying vital non-invasive computer capillaroscopy of nailbed has allowed quantitatively estimating a capillary blood velocity (CBV). The microcirculation parameters obtained during experiment were compared to local indexes of geomagnetic activity. About 1500 episodes were recorded on laser disks and analyzed. Parameters of microcirculation were compared with other physiological parameters monitored in the experiment. CBV investigation during the most intensive magnetic storm for the period of isolation (A-index- 44) show, that CBV at all volunteers was considerably slowed down. The greatest delay of blood flow velocity revealed at the subject which the factor of shielding of a constant magnetic field at the level of the sleeping berth has made 2,0. CBV at the subject has made 498 ± 46 μm/s with (- 65,8 % from base line). Least delay of a CBV is revealed at the subject which the factor of shielding of a constant magnetic field at the level of the sleeping berth has made 3, 15 (-12 % from base line).

  8. Novosphingobium colocasiae sp. nov., isolated from a taro field.

    PubMed

    Chen, Wen-Ming; Chen, Jhen-Ci; Huang, Cheng-Wen; Young, Chiu-Chung; Sheu, Shih-Yi

    2016-02-01

    A novel bacterial strain, designated Teta-03T, was isolated from a taro field in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain Teta-03T were aerobic, Gram-stain-negative, rod-shaped and non-motile and formed bright yellow colonies. Growth occurred at 10-37 °C (optimum, 20 °C), with 0-1.0 % (w/v) NaCl (optimum, 0 %) and at pH 3.0-9.0 (optimum, pH 7.0-8.0). The major fatty acids (>10 %) of strain Teta-03T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, an uncharacterized glycolipid and an uncharacterized aminolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.0 mol%. On the basis of 16S rRNA gene sequence analysis, strain Teta-03T was shown to belong to the genus Novosphingobium and showed highest similarity to Novosphingobium barchaimii LL02T (96.8 %). Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Teta-03T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium colocasiae sp. nov. is proposed. The type strain is Teta-03T ( = LMG 27385T = KCTC 32255T). PMID:26582085

  9. 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. PMID:19882104

  10. Sensitivity of Eimeria field isolates in the United States: responses of nicarbazin-containing anticoccidials.

    PubMed

    Bafundo, K W; Cervantes, H M; Mathis, G F

    2008-09-01

    A series of studies were conducted to assess the drug sensitivity of 26 coccidial field isolates to the anticoccidial effects of nicarbazin (NIC) and narasin + NIC (NAR + NIC). Isolates were collected from typical broiler farms in the United States from 2003 to 2006, propagated once in the absence of anticoccidial medication, and then used to inoculate broilers that were fed nonmedicated rations or those containing NIC 125 ppm or NAR + NIC 80 ppm. Results of these sensitivity trials indicated that 81% of these coccidial isolates were sensitive to the effects of NIC, but only 22% of these coccidia were controlled by NAR + NIC. Studies conducted to evaluate performance responses to these drugs demonstrated that birds fed NIC gained more weight and utilized feed more efficiently than those receiving NAR + NIC. The results of 2 floor pen tests, conducted to confirm the results of the above sensitivity trials, demonstrated that NIC provided a greater level of protection from coccidiosis than NAR + NIC. Lower lesion scores and improved performance were recorded for birds receiving NIC compared with NAR + NIC. Results of these studies revealed that changes in the susceptibility of Eimeria spp. to the activity of NAR + NIC are evident. These changes appear to be associated with the reduction in ionophore sensitivity that has been documented in most areas of the world. PMID:18753443

  11. A Molecular Surveillance Reveals the Prevalence of Vibrio cholerae O139 Isolates in China from 1993 to 2012

    PubMed Central

    Zhang, Ping; Zhou, Haijian; Diao, Baowei; Li, Fengjuan; Du, Pengcheng; Li, Jie; Morris, J. Glenn

    2014-01-01

    Vibrio cholerae serogroup O139 was first identified in 1992 in India and Bangladesh, in association with major epidemics of cholera in both countries; cases were noted shortly thereafter in China. We characterized 211 V. cholerae O139 isolates that were isolated at multiple sites in China between 1993 and 2012 from patients (n = 92) and the environment (n = 119). Among clinical isolates, 88 (95.7%) of 92 were toxigenic, compared with 47 (39.5%) of 119 environmental isolates. Toxigenic isolates carried the El Tor CTX prophage and toxin-coregulated pilus A gene (tcpA), as well as the Vibrio seventh pandemic island I (VSP-I) and VSP-II. Among a subset of 42 toxigenic isolates screened by multilocus sequence typing (MLST), all were in the same sequence type as a clinical isolate (MO45) from the original Indian outbreak. Nontoxigenic isolates, in contrast, generally lacked VSP-I and -II, and fell within13 additional sequence types in two clonal complexes distinct from the toxigenic isolates. In further pulsed-field gel electrophoresis (PFGE) (with NotI digestion) studies, toxigenic isolates formed 60 pulsotypes clustered in one group, while the nontoxigenic isolates formed 43 pulsotypes which clustered into 3 different groups. Our data suggest that toxigenic O139 isolates from widely divergent geographic locations, while showing some diversity, have maintained a relatively tight clonal structure across a 20-year time span. Nontoxigenic isolates, in contrast, exhibited greater diversity, with multiple clonal lineages, than did their toxigenic counterparts. PMID:24452176

  12. Genomic View of Bipolar Disorder Revealed by Whole Genome Sequencing in a Genetic Isolate

    PubMed Central

    Georgi, Benjamin; Craig, David; Kember, Rachel L.; Liu, Wencheng; Lindquist, Ingrid; Nasser, Sara; Brown, Christopher; Egeland, Janice A.; Paul, Steven M.; Bućan, Maja

    2014-01-01

    Bipolar disorder is a common, heritable mental illness characterized by recurrent episodes of mania and depression. Despite considerable effort to elucidate the genetic underpinnings of bipolar disorder, causative genetic risk factors remain elusive. We conducted a comprehensive genomic analysis of bipolar disorder in a large Old Order Amish pedigree. Microsatellite genotypes and high-density SNP-array genotypes of 388 family members were combined with whole genome sequence data for 50 of these subjects, comprising 18 parent-child trios. This study design permitted evaluation of candidate variants within the context of haplotype structure by resolving the phase in sequenced parent-child trios and by imputation of variants into multiple unsequenced siblings. Non-parametric and parametric linkage analysis of the entire pedigree as well as on smaller clusters of families identified several nominally significant linkage peaks, each of which included dozens of predicted deleterious variants. Close inspection of exonic and regulatory variants in genes under the linkage peaks using family-based association tests revealed additional credible candidate genes for functional studies and further replication in population-based cohorts. However, despite the in-depth genomic characterization of this unique, large and multigenerational pedigree from a genetic isolate, there was no convergence of evidence implicating a particular set of risk loci or common pathways. The striking haplotype and locus heterogeneity we observed has profound implications for the design of studies of bipolar and other related disorders. PMID:24625924

  13. A New Record of Pseudallescheria boydii Isolated from Crop Field Soil in Korea

    PubMed Central

    Babu, A. Giridhar; Kim, Sang Woo; Yadhav, Dil Raj; Adhikari, Mahesh; Kim, Changmu; Lee, Hyang Burm

    2014-01-01

    Pseudallescheria boydii KNU13-2 was isolated from crop field soil and identified by analysis of internal transcribed spacer regions of rDNA and morphological characteristics. In the literature, P. boydii has been mentioned as a human pathogen. This is the first record of P. boydii isolated from crop field soil in Korea. PMID:25606013

  14. Drug responsiveness of field isolates of chicken Coccidia.

    PubMed

    Mathis, G F; McDougald, L R

    1982-01-01

    Coccidia were isolated from litter samples collected in poultry houses in Georgia and other southeastern states and from intestinal scrapings from chickens submitted to diagnostic laboratories. The most common species of coccidia encountered were E. tenella, E. acervulina, and E. maxima. Each of the 41 isolates was tested for sensitivity to eight commercial anticoccidial drugs. Most of the isolates were resistant to some of the drugs judged by the parameters of percent weight gain, percent lesion score reduction, and a sensitivity index score. There was a high frequency of resistance to clopidol, amprolium/ethopabate, nequinate, zoalene, and sulfaquinoxaline. A very small percentage of the isolates tested were resistant to nicarbazin, robenidine, or halofuginone. PMID:7088782

  15. Identification and onion pathogenicity of Burkholderia cepacia complex isolates from the onion rhizosphere and onion field soil.

    PubMed

    Jacobs, Janette L; Fasi, Anthony C; Ramette, Alban; Smith, James J; Hammerschmidt, Raymond; Sundin, George W

    2008-05-01

    Burkholderia cepacia complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on B. cepacia complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative B. cepacia complex isolates were recovered on Pseudomonas cepacia azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative B. cepacia complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and recA sequences and restriction fragment length polymorphism analysis of the recA sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species B. cepacia (160), B. cenocepacia (480), B. ambifaria (623), and B. pyrrocinia (27). The majority of isolates identified as B. cepacia (85%), B. cenocepacia (90%), and B. ambifaria (76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of recA sequences from representative B. cepacia complex type and panel strains, along with isolates collected in this study, revealed that the B. cenocepacia isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple B. cepacia complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source

  16. Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field.

    PubMed

    Sheu, Shih-Yi; Chen, Zih-Han; Young, Chiu-Chung; Chen, Wen-Ming

    2016-04-01

    A bacterial strain, designated shin9-1T, was isolated from a water sample taken from a water convolvulus field in Taiwan and characterized using a polyphasic taxonomical approach. Cells of strain shin9-1T were aerobic, Gram-stain-negative, rod-shaped and surrounded by a thick capsule and formed cream-coloured colonies. Growth occurred at 10-45 °C (optimum, 30 °C), with 0-3.0 % NaCl (optimum, 0.5 %) and at pH 7.0-9.0 (optimum, pH 7.0). Strain shin9-1T did not form nodules on a legume plant, Macroptilium atropurpureum, and the nodulation genes nodA, nodC and the nitrogenase reductase gene nifH were not detected by PCR. Phylogenetic analyses based on 16S rRNA and three housekeeping gene sequences (recA, atpD and rpoB) showed that strain shin9-1T belonged to the genus Rhizobium. Strain shin9-1T had the highest level of 16S rRNA gene sequence similarity with respect to Rhizobium daejeonense L61T (97.6 %). The major fatty acid of strain shin9-1T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and several uncharacterized lipids. The DNA G+C content was 58.3 mol%. The DNA-DNA relatedness of strain shin9-1T with respect to recognized species of the genus Rhizobium was less than 70 %. Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium. On the basis of the phylogenetic inference and phenotypic data, strain shin9-1T should be classified as a representative of a novel species, for which the name Rhizobium ipomoeae sp. nov. is proposed. The type strain is shin9-1T ( = LMG 27163T = KCTC 32148T). PMID:26739022

  17. Clonal diversity of Acinetobacter baumannii clinical isolates revealed by a snapshot study

    PubMed Central

    2013-01-01

    Background Acinetobacter baumannii is a notorious opportunistic pathogen mainly associated with hospital-acquired infections. Studies on the clonal relatedness of isolates could lay the foundation for effective infection control. A snapshot study was performed to investigate the clonal relatedness of A. baumannii clinical isolates in our local settings. Results Among 82 non-repetitive Acinetobacter spp. clinical isolates that were recovered during a period of four days in 13 hospitals in Sichuan, Southwest China, 67 isolates were identified as A. baumannii. Half of the 67 A. baumannii isolates were non-susceptible to carbapenems. blaOXA-23 was the only acquired carbapenemase gene detected, present in 40 isolates including five carbapenem-susceptible ones. The isolates belonged to 62 pulsotypes determined by PFGE and 31 sequence types (ST) by multi-locus sequence typing. Forty-three isolates belonged to the globally-disseminated clonal complex 92, among which ST75, ST92 and ST208 were the most common sequence types. Conclusions Clinical isolates of A. baumannii were diverse in clonality in this snapshot study. However, most of the isolates belonged to the globally-distributed clonal complex CC92. ST75, ST92 and ST208 were the most common types in our region. In particular, ST208 might be an emerging lineage carrying blaOXA-23. PMID:24144168

  18. Subthalamic local field potentials in Parkinson's disease and isolated dystonia: An evaluation of potential biomarkers.

    PubMed

    Wang, Doris D; de Hemptinne, Coralie; Miocinovic, Svjetlana; Qasim, Salman E; Miller, Andrew M; Ostrem, Jill L; Galifianakis, Nicholas B; San Luciano, Marta; Starr, Philip A

    2016-05-01

    Local field potentials (LFP) recorded from the subthalamic nucleus in patients with Parkinson's disease (PD) demonstrate prominent oscillations in the beta (13-30Hz) frequency range, and reduction of beta band spectral power by levodopa and deep brain stimulation (DBS) is correlated with motor symptom improvement. Several features of beta activity have been theorized to be specific biomarkers of the parkinsonian state, though these have rarely been studied in non-parkinsonian conditions. To compare resting state LFP features in PD and isolated dystonia and evaluate disease-specific biomarkers, we recorded subthalamic LFPs from 28 akinetic-rigid PD and 12 isolated dystonia patients during awake DBS implantation. Spectral power and phase-amplitude coupling characteristics were analyzed. In 26/28 PD and 11/12 isolated dystonia patients, the LFP power spectrum had a peak in the beta frequency range, with similar amplitudes between groups. Resting state power did not differ between groups in the theta (5-8Hz), alpha (8-12Hz), beta (13-30Hz), broadband gamma (50-200Hz), or high frequency oscillation (HFO, 250-350Hz) bands. Analysis of phase-amplitude coupling between low frequency phase and HFO amplitude revealed significant interactions in 19/28 PD and 6/12 dystonia recordings without significant differences in maximal coupling or preferred phase. Two features of subthalamic LFPs that have been proposed as specific parkinsonian biomarkers, beta power and coupling of beta phase to HFO amplitude, were also present in isolated dystonia, including focal dystonias. This casts doubt on the utility of these metrics as disease-specific diagnostic biomarkers. PMID:26884091

  19. Genetic relationships among Enterococcus faecalis isolates from different sources as revealed by multilocus sequence typing.

    PubMed

    Chen, X; Song, Y Q; Xu, H Y; Menghe, B L G; Zhang, H P; Sun, Z H

    2015-08-01

    Enterococcus faecalis is part of the natural gut flora of humans and other mammals; some isolates are also used in food production. So, it is important to evaluate the genetic diversity and phylogenetic relationships among E. faecalis isolates from different sources. Multilocus sequence typing protocol was used to compare 39 E. faecalis isolates from Chinese traditional food products (including dairy products, acidic gruel) and 4 published E. faecalis isolates from other sources including human-derived isolates employing 5 housekeeping genes (groEL, clpX, recA, rpoB, and pepC). A total of 23 unique sequence types were identified, which were grouped into 5 clonal complexes and 10 singletons. The value of standardized index of association of the alleles (IA(S)=0.1465) and network structure indicated a high frequency of intraspecies recombination across these isolates. Enterococcus faecalis lineages also exhibited clearly source-clustered distributions. The isolates from dairy source were clustered together. However, the relationship between isolates from acidic gruel and one isolate from a human source was close. The MLST scheme presented in this study provides a sharable and continuously growing sequence database enabling global comparison of strains from different sources, and will further advance our understanding of the microbial ecology of this important species. PMID:26074239

  20. Improvement of device isolation using field implantation for GaN MOSFETs

    NASA Astrophysics Data System (ADS)

    Jiang, Ying; Wang, Qingpeng; Zhang, Fuzhe; Li, Liuan; Shinkai, Satoko; Wang, Dejun; Ao, Jin-Ping

    2016-03-01

    Gallium nitride (GaN) metal-oxide-semiconductor field-effect transistors (MOSFETs) with boron field implantation isolation and mesa isolation were fabricated and characterized. The process of boron field implantation was altered and subsequently conducted after performing high-temperature ohmic annealing and gate oxide thermal treatment. Implanted regions with high resistivity were achieved. The circular MOSFET fabricated in the implanted region showed an extremely low current of 6.5 × 10-12 A under a gate voltage value up to 10 V, thus demonstrating that the parasitic MOSFET in the isolation region was eliminated by boron field implantation. The off-state drain current of the rectangular MOSFET with boron field implantation was 5.5 × 10-11 A, which was only one order of magnitude higher than the 6.6 × 10-12 A of the circular device. By contrast, the rectangular MOSFET with mesa isolation presented an off-state drain current of 3.2 × 10-9 A. The field isolation for GaN MOSFETs was achieved by using boron field implantation. The implantation did not reduce the field-effect mobility. The isolation structure of both mesa and implantation did not influence the subthreshold swing, whereas the isolation structure of only the implantation increased the subthreshold swing. The breakdown voltage of the implanted region with 5 μm spacing was up to 901.5 V.

  1. Characterization of Isolates of Meloidogyne from Rice-Wheat Production Fields in Nepal

    PubMed Central

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

    2007-01-01

    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. PMID:19259491

  2. 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. PMID:19259491

  3. Planetary science. Low-altitude magnetic field measurements by MESSENGER reveal Mercury's ancient crustal field.

    PubMed

    Johnson, Catherine L; Phillips, Roger J; Purucker, Michael E; Anderson, Brian J; Byrne, Paul K; Denevi, Brett W; Feinberg, Joshua M; Hauck, Steven A; Head, James W; Korth, Haje; James, Peter B; Mazarico, Erwan; Neumann, Gregory A; Philpott, Lydia C; Siegler, Matthew A; Tsyganenko, Nikolai A; Solomon, Sean C

    2015-05-22

    Magnetized rocks can record the history of the magnetic field of a planet, a key constraint for understanding its evolution. From orbital vector magnetic field measurements of Mercury taken by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft at altitudes below 150 kilometers, we have detected remanent magnetization in Mercury's crust. We infer a lower bound on the average age of magnetization of 3.7 to 3.9 billion years. Our findings indicate that a global magnetic field driven by dynamo processes in the fluid outer core operated early in Mercury's history. Ancient field strengths that range from those similar to Mercury's present dipole field to Earth-like values are consistent with the magnetic field observations and with the low iron content of Mercury's crust inferred from MESSENGER elemental composition data. PMID:25953822

  4. Sequence comparison of porcine respiratory coronavirus isolates reveals heterogeneity in the S, 3, and 3-1 genes.

    PubMed Central

    Vaughn, E M; Halbur, P G; Paul, P S

    1995-01-01

    Four new porcine respiratory coronavirus (PRCV) isolates were genetically characterized. Subgenomic mRNA patterns and the nucleotide sequences of the 5' ends of the S genes, the open reading frame (ORF) 3/3a genes, and the ORF 3-1/3b genes of these PRCV isolates were determined and compared with those of other PRCV and transmissible gastroenteritis virus (TGEV) isolates. The S, ORF 3/3a, and ORF 3-1/3b genes are under intense study because of their possible roles in determining tissue tropism and virulence. Northern (RNA) blot analysis of subgenomic mRNAs revealed that mRNA 2, which encodes for the S gene, of the PRCV isolates migrated faster than the mRNA 2 of TGEV. The PRCV isolates AR310 and LEPP produced eight subgenomic mRNA species, the same number as produced by the virulent Miller strain of TGEV. However, the PRCV isolates IA1894 and ISU-1 produced only seven subgenomic mRNA species. All four of the PRCV isolates were found to have a large in-frame deletion in the 5' end of the S gene; however, the size and location of the deletion varied. Analysis of the ORF 3/3a gene nucleotide sequences from the four PRCV isolates also showed a high degree of variability in this area. The ORF 3 gene of the PRCV isolates AR310 and LEPP was preceded by a CTAAAC leader RNA-binding site, and the ORF 3 gene was predicted to yield a protein of 72 amino acids, the same size as that of the virulent Miller strain of TGEV. The PRCV isolates AR310 and LEPP are the first PRCV isolates found to have an intact ORF 3 gene. The ORF 3a gene of the PRCV isolate IA1894 was preceded by a CTAAAC leader RNA-binding site and was predicted to yield a truncated protein of 54 amino acids due to a 23-nucleotide deletion. The CTAAAC leader RNA-binding site and ATG start codon of ORF 3 gene of the PRCV isolate ISU-1 were removed because of a 168-nucleotide deletion. Analysis of the ORF 3-1/3b gene nucleotide sequences from the four PRCV nucleotides isolates also showed variability. PMID:7707547

  5. Studies of resistance to anticoccidials in Eimeria field isolates and pure Eimeria strains.

    PubMed

    Stephen, B; Rommel, M; Daugschies, A; Haberkorn, A

    1997-04-01

    Ten Eimeria field isolates from North Germany were studied in battery tests for sensitivity to selected anticoccidials. A high percentage of the Eimeria field isolates (9 out of 10) showed resistance to anticoccidials, mostly multiple resistance. Partial or complete resistance to maduramicin was found in 7 field isolates, to monensin in 6, to salinomycin in 5, to nicarbazin in 8, to halofuginone in 7, to robenidine and toltrazuril in 1, and to diclazuril in 2 field isolates. Multiple resistance had developed in 7 of the 10 isolates. Cross-resistance between maduramicin, monensin, and salinomycin occurred in 5 Eimeria isolates. One isolate showed cross-resistance between diclazuril and toltrazuril. From the resistant isolates 15 pure E. acerculina and 5 pure E. brunetti strains were obtained by single oocyst infections. Seven of the E. acerculina and 4 of the E. brunetti strains showed resistance or partial resistance that was also present in the original isolate. Ten of 11 resistant strains were multiply resistant. PMID:9187026

  6. Polyploid genome of Camelina sativa revealed by isolation of fatty acid synthesis genes

    PubMed Central

    2010-01-01

    Background Camelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD) 2 and fatty acid elongase (FAE) 1, which revealed unexpected complexity in the C. sativa genome. Results In C. sativa, Southern analysis indicates the presence of three copies of both FAD2 and FAE1 as well as LFY, a known single copy gene in other species. All three copies of both CsFAD2 and CsFAE1 are expressed in developing seeds, and sequence alignments show that previously described conserved sites are present, suggesting that all three copies of both genes could be functional. The regions downstream of CsFAD2 and upstream of CsFAE1 demonstrate co-linearity with the Arabidopsis genome. In addition, three expressed haplotypes were observed for six predicted single-copy genes in 454 sequencing analysis and results from flow cytometry indicate that the DNA content of C. sativa is approximately three-fold that of diploid Camelina relatives. Phylogenetic analyses further support a history of duplication and indicate that C. sativa and C. microcarpa might share a parental genome. Conclusions There is compelling evidence for triplication of the C. sativa genome, including a larger chromosome number and three-fold larger measured genome size than other Camelina relatives, three isolated copies of FAD2, FAE1, and the KCS17-FAE1 intergenic region, and three expressed haplotypes observed for six predicted single-copy genes. Based on these results, we propose that C. sativa be considered an allohexaploid. The characterization of fatty acid synthesis pathway genes will allow for the future manipulation of oil composition of this emerging biofuel crop; however, targeted manipulations of oil composition and general development of C. sativa should

  7. The association of serotype and pulsed-field gel electrophoresis genotype in isolates of Streptococcus pneumoniae isolated in Israel.

    PubMed

    Bar-Meir, M; Naaman, G; Assous, M; Korenman, Z; Valinsky, L; Picard, E

    2015-05-01

    The relationship between Streptococcus pneumoniae isolates causing invasive infections in children admitted to a single center in central Israel was examined by pulsed-field gel electrophoresis (PFGE) and serotyping. Although there was a close correlation between serotype and PFGE clone, the genetic diversity varied by serotype, with some genotypes comprising multiple serotypes. Additionally, clones C and D were associated with higher penicillin minimum inhibitory concentrations. Serotyping alone may be insufficient for epidemiological mapping of pneumococcal isolates in the era of pneumococcal conjugate polysaccharide vaccines. PMID:25749648

  8. Intergenic Sequence Comparison of Escherichia coli Isolates Reveals Lifestyle Adaptations but Not Host Specificity▿

    PubMed Central

    White, A. P.; Sibley, K. A.; Sibley, C. D.; Wasmuth, J. D.; Schaefer, R.; Surette, M. G.; Edge, T. A.; Neumann, N. F.

    2011-01-01

    Establishing the risk of human infection is one of the goals of public health. For bacterial pathogens, the virulence and zoonotic potential can often be related to their host source. Escherichia coli bacteria are common contaminants of water associated with human recreation and consumption, and many strains are pathogenic. In this study, we analyzed three promoter-containing intergenic regions from 284 diverse E. coli isolates in an attempt to identify molecular signatures associated with specific host types. Promoter sequences controlling production of curli fimbriae, flagella, and nutrient import yielded a phylogenetic tree with isolates clustered by established phylogenetic grouping (A, B1, B2, and D) but not by host source. Virulence genes were more prevalent in groups B2 and D isolates and in human isolates. Group B1 isolates, primarily from nonhuman sources, were the most genetically similar, indicating that they lacked molecular adaptations to specific host environments and were likely host generalists. Conversely, B2 isolates, primarily from human sources, displayed greater genetic distances and were more likely to be host adapted. In agreement with these hypotheses, prevalence of σS activity and the rdar morphotype, phenotypes associated with environmental survival, were significantly higher in B1 isolates than in B2 isolates. Based on our findings, we speculate that E. coli host specificity is not defined by genome-wide sequence changes but, rather, by the presence or absence of specific genes and associated promoter elements. Furthermore, the requirements for colonization of the human gastrointestinal tract may lead to E. coli lifestyle changes along with selection for increased virulence. PMID:21908635

  9. 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). PMID:27498502

  10. 520-d Isolation and confinement simulating a flight to Mars reveals heightened immune responses and alterations of leukocyte phenotype.

    PubMed

    Yi, B; Rykova, M; Feuerecker, M; Jäger, B; Ladinig, C; Basner, M; Hörl, M; Matzel, S; Kaufmann, I; Strewe, C; Nichiporuk, I; Vassilieva, G; Rinas, K; Baatout, S; Schelling, G; Thiel, M; Dinges, D F; Morukov, B; Choukèr, A

    2014-08-01

    During interplanetary exploration, chronic stress caused by long term isolation and confinement in the spacecraft is one of the major concerns of physical and psychological health of space travelers. And for human on Earth, more and more people live in an isolated condition, which has become a common social problem in modern western society. Collective evidences have indicated prolonged chronic stress could bring big influence to human immune function, which may lead to a variety of health problems. However, to what extent long-term isolation can affect the immune system still remains largely unknow. A simulated 520-d Mars mission provided an extraordinary chance to study the effect of prolonged isolation. Six healthy males participated in this mission and their active neuroendocrine and immune conditions were studied with saliva and blood samples from all participants on chosen time points during the isolation period. As a typical neuroendocrine parameter, stress hormone cortisol was measured in the morning saliva samples. Immune phenotype changes were monitored through peripheral leukocyte phenotype analysis. Using an ex vivo viral infection simulation assay we assessed the immune response changes characterized by the ability to produce representative endogenous pro-inflammatory cytokines. The results of this study revealed elevated cortisol levels, increased lymphocyte amount and heightened immune responses, suggesting that prolonged isolation acting as chronic stressors are able to trigger leukocyte phenotype changes and poorly controlled immune responses. PMID:24704568

  11. A New Record of Volutella ciliata Isolated from Crop Field Soil in Korea

    PubMed Central

    Babu, Anam Giridhar; Kim, Sang Woo; Yadav, Dil Raj; Adhikari, Mahesh; Kim, Changmu; Lee, Hyang Burm

    2015-01-01

    During a survey of fungal species in South Korea, a species of Volutella ciliata was isolated and described based on the analysis of the internal transcribed spacer region of its rDNA and its morphological characteristics. This is the first record of Volutella ciliata isolated from crop field soil in Korea. PMID:25892918

  12. Flat Field Determinations Using AN Isolated Point Source

    NASA Astrophysics Data System (ADS)

    Bohlin, R. C.; Grogin, Norman

    2015-08-01

    The traditional method of measuring ACS flat fields (FF) involves a complicated analysis of multiple observations of a region of the 47 Tuc globular cluster at overlapping field positions. The analysis of the dithered 47 Tuc images suffers from source crowding and possible systematics related to the CTE correction and the high density of sources. New programs 13167 and 13602 avoid these problems by observing a single bright star at several locations around the field of view (FOV) in F435W and F814W. A discrepancy of ~3% with a 10σ level of significance exists between the two FF measurement techniques and is currently unexplained.

  13. Species-wide survey reveals the various flavors of intraspecific reproductive isolation in yeast.

    PubMed

    Hou, Jing; Fournier, Téo; Schacherer, Joseph

    2016-08-01

    Exploring the origin and extent of reproductive isolation within the same species is valuable to capture early events to the onset of speciation. In multiple genetic models, reproductive isolation was recently observed at the intraspecific scale, indicating that the raw potential for speciation segregates readily within populations, which could be a rule rather than an exception in a broad context. We briefly recapitulate the molecular evidence of intrinsic post-zygotic isolation in major model organisms including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and their close relatives. We then focus on recent advances in yeast and review the genetic basis of post-zygotic isolation within and between multiple members of the Saccharomyces genus, especially in Saccharomyces cerevisiae We discuss the role of various mechanisms involved in the onset of reproductive isolation including DNA sequence divergence, chromosomal rearrangement, cytonuclear as well as nuclear-nuclear genetic incompatibilities and provide a comparative view along a continuum of genetic differentiation, which encompasses intraspecific populations, recent delineating nascent species as well as closely related sister species in the same subphylum. PMID:27288348

  14. Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity.

    PubMed

    Shimelash, Daniel; Hussien, Temam; Fininsa, Chemeda; Forbes, Greg; Yuen, Jonathan

    2016-08-01

    Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93 % of the samples analyzed but the vast majority of these were Ia. The remaining 7 % represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7 % of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here. PMID:26873223

  15. Genotypic Analysis of Klebsiella pneumoniae Isolates in a Beijing Hospital Reveals High Genetic Diversity and Clonal Population Structure of Drug-Resistant Isolates

    PubMed Central

    Yi, Yong; Woo, Patrick C. Y.; Liu, Cui Hua

    2013-01-01

    Background The genetic diversity and the clinical relevance of the drug-resistant Klebsiella pneumoniae isolates from hospital settings are largely unknown. We thus conducted this prospective study to analyze the molecular epidemiology of K. pneumoniae isolates from patients being treated in the 306 Hospital in Beijing, China for the period of November 1, 2010–October 31, 2011. Methodology/Principal Findings Antibiotic susceptibility testing, PCR amplification and sequencing of the drug resistance-associated genes, and multilocus sequence typing (MLST) were conducted. A total of 163 isolates were analyzed. The percentage of MDR, XDR and PDR isolates were 63.8% (104), 20.9 (34), and 1.8% (3), respectively. MLST results showed that 60 sequence types (STs) were identified, which were further separated by eBURST into 13 clonal complexes and 18 singletons. The most dominant ST was ST15 (10.4%). Seven new alleles and 24 new STs were first identified in this study. Multiple logistic regression analysis revealed that certain clinical characteristics were associated with those prevalent STs such as: from ICU, from medical ward, from community acquired infection, from patients without heart disease, from patients with treatment success, susceptible to extended spectrum cephalosporin, susceptible to cephamycins, susceptible to fluoroquinolones, and with MDR. Conclusions/Significance Our data indicate that certain drug-resistant K. pneumoniae clones are highly prevalent and are associated with certain clinical characteristics in hospital settings. Our study provides evidence demonstrating that intensive nosocomial infection control measures are urgently needed. PMID:23437318

  16. Multilocus analysis reveals large genetic diversity in Kluyveromyces marxianus strains isolated from Parmigiano Reggiano and Pecorino di Farindola cheeses.

    PubMed

    Fasoli, Giuseppe; Barrio, Eladio; Tofalo, Rosanna; Suzzi, Giovanna; Belloch, Carmela

    2016-09-16

    In the present study, we have analysed the genetic diversity in Kluyveromyces marxianus isolated from Parmigiano Reggiano and Pecorino di Farindola cheesemaking environment. Molecular typing methods inter-RTL fingerprint and mtDNA RFLPs, as well as, sequence diversity and heterozygosity in the intergenic region between KmSSB1 and KmRIO2 genes and analysis of the mating locus were applied to 54 K. marxianus strains. Inter-RTL fingerprint revealed a large degree of genetic heterogeneity and clustering allowed differentiation of K. marxianus strains from different geographical origins. In general, inter-LTR profiles were more discriminating than RFLPs of mtDNA; however our results also indicate that both techniques could be complementary unveiling different degrees of genetic diversity. Sequence analysis of the intergenic region between KmSSB1 and KmRIO2 genes revealed 26 variable positions in which a double peak could be observed in the sequence chromatogram. Further analysis revealed the presence of heterozygous strains in the K. marxianus population isolated from Parmigiano Reggiano. On the other hand, all strains isolated from Pecorino di Farindola were homozygous. Two very different groups of haplotypes could be observed as well as mixtures between them. Phylogenetic reconstruction divided K. marxianus dairy strains into two separate populations. A few heterozygous strains in an intermediate position between them could also be observed. Mating type locus analysis revealed a large population of diploid strains containing both MATa and MATα alleles and few haploid strains, most of them presenting the MATα allele. Different scenarios explaining the presence and maintaining of homozygous and heterozygous diploids as well as hybrids between them in the Parmigiano Reggiano K. marxianus population are proposed. A principal component analysis supported the large differences between K. marxianus isolated from Parmigiano Reggiano and Pecorino di Farindola. PMID:27294555

  17. Life-Threatening Hypercalcemia Revealing Diffuse and Isolated Acute Sarcoid-Like Myositis: A New Entity? (A Case-Series).

    PubMed

    Mageau, Arthur; Rigolet, Aude; Benali, Khadija; Chauchard, Maria; Ladjeroud, Salima; Mahe, Isabelle; Maisonobe, Thierry; Chauveheid, Marie-Paule; Papo, Thomas; Sacre, Karim

    2016-03-01

    Up to 50% patients with sarcoidosis display extra-pulmonary disease. However, initial and isolated (ie, without lung disease) acute muscular involvement associated with pseudo-malignant hypercalcemia is very uncommon. We report on 3 cases of life-threatening hypercalcemia revealing florid and isolated acute sarcoid-like myositis.All patients complained of fatigue, progressive general muscle weakness, and weight loss. Laboratory tests showed a severe life-threatening hypercalcemia (>3.4 mmol/L). Hypercalcemia was associated with increased serum level of 1,25-(OH)2 vitamin D and complicated with acute renal failure. One patient displayed acute pancreatitis due to hypercalcemia.In all cases, PET-scan, performed for malignancy screening, incidentally revealed an intense, diffuse, and isolated muscular fluorodeoxyglucose (FDG) uptake consistent with diffuse non-necrotizing giant cells granulomatous myositis demonstrated by muscle biopsy. Of note, creatine phosphokinase blood level was normal in all cases. No patients displayed the usual thoracic features of sarcoidosis.All patients were treated with high dose steroids and achieved rapid, complete, and sustained remission. A review of English and French publications in Medline revealed 5 similar published cases.Steroid-sensitive acute sarcoid-like myositis causing high calcitriol levels and life-threatening hypercalcemia should be recognized as a separate entity. PMID:26962842

  18. Global multilocus sequence typing analysis of Mycoplasma bovis isolates reveals two main population clusters.

    PubMed

    Rosales, R S; Churchward, C P; Schnee, C; Sachse, K; Lysnyansky, I; Catania, S; Iob, L; Ayling, R D; Nicholas, R A J

    2015-03-01

    Mycoplasma bovis is a major bovine pathogen associated with bovine respiratory disease complex and is responsible for substantial economic losses worldwide. M. bovis is also associated with other clinical presentations in cattle, including mastitis, otitis, arthritis, and reproductive disorders. To gain a better understanding of the genetic diversity of this pathogen, a multilocus sequence typing (MLST) scheme was developed and applied to the characterization of 137 M. bovis isolates from diverse geographical origins, obtained from healthy or clinically infected cattle. After in silico analysis, a final set of 7 housekeeping genes was selected (dnaA, metS, recA, tufA, atpA, rpoD, and tkt). MLST analysis demonstrated the presence of 35 different sequence types (STs) distributed in two main clonal complexes (CCs), defined at the double-locus variant level, namely, CC1, which included most of the British and German isolates, and CC2, which was a more heterogeneous and geographically distant group of isolates, including European, Asian, and Australian samples. Index of association analysis confirmed the clonal nature of the investigated M. bovis population, based on MLST data. This scheme has demonstrated high discriminatory power, with the analysis showing the presence of genetically distant and divergent clusters of isolates predominantly associated with geographical origins. PMID:25540400

  19. Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type-specific adaptation.

    PubMed

    Bruchmann, Sebastian; Muthukumarasamy, Uthayakumar; Pohl, Sarah; Preusse, Matthias; Bielecka, Agata; Nicolai, Tanja; Hamann, Isabell; Hillert, Roger; Kola, Axel; Gastmeier, Petra; Eckweiler, Denitsa; Häussler, Susanne

    2015-11-01

    Health-care-associated infections by multi-drug-resistant bacteria constitute one of the greatest challenges to modern medicine. Bacterial pathogens devise various mechanisms to withstand the activity of a wide range of antimicrobial compounds, among which the acquisition of carbapenemases is one of the most concerning. In Klebsiella pneumoniae, the dissemination of the K. pneumoniae carbapenemase is tightly connected to the global spread of certain clonal lineages. Although antibiotic resistance is a key driver for the global distribution of epidemic high-risk clones, there seem to be other adaptive traits that may explain their success. Here, we exploited the power of deep transcriptome profiling (RNA-seq) to shed light on the transcriptomic landscape of 37 clinical K. pneumoniae isolates of diverse phylogenetic origins. We identified a large set of 3346 genes which was expressed in all isolates. While the core-transcriptome profiles varied substantially between groups of different sequence types, they were more homogenous among isolates of the same sequence type. We furthermore linked the detailed information on differentially expressed genes with the clinically relevant phenotypes of biofilm formation and bacterial virulence. This allowed for the identification of a diminished expression of biofilm-specific genes within the low biofilm producing ST258 isolates as a sequence type-specific trait. PMID:26261087

  20. Genetic diversity of Toxoplama gondii isolates from cats from Egypt reveals new genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cats are important in the epidemiology of Toxoplasma gondii because they are the only hosts that excrete environmentally resistant oocysts in feces. In the present study, 115 viable T. gondii isolates from tissues of cats from Egypt were genotyped using 10 PCR-restriction fragment length polymorphis...

  1. Kodamaea ohmeri isolates from patients in a university hospital: identification, antifungal susceptibility, and pulsed-field gel electrophoresis analysis.

    PubMed

    Lee, Jin Sol; Shin, Jong Hee; Kim, Mi-Na; Jung, Sook-In; Park, Kyung Hwa; Cho, Duck; Kee, Seung Jung; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

    2007-03-01

    Data on clinical isolates of Kodamaea (Pichia) ohmeri, an emerging fungal pathogen, are scarce. Over the past 5 years, we identified yeast isolates from nine patients with fungemia as K. ohmeri by using the API 20C system. Here, we reanalyzed these isolates first by sequencing the internal transcribed spacer 2 (ITS2) regions and then by growing the isolates on CHROMagar Candida medium and subjecting them to pulsed-field gel electrophoresis (PFGE). Based on their ITS2 sequences, six of the nine isolates were confirmed as K. ohmeri, while the others were identified as Candida haemulonii (n = 2) and Candida parapsilosis (n = 1). PFGE karyotyping of the K. ohmeri isolates revealed similar major bands, and their colonies showed a characteristic color change from pink to blue when grown on CHROMagar Candida medium for more than 48 h. For K. ohmeri, the ranges of MICs of fluconazole, voriconazole, caspofungin, and micafungin were 2 to 32 mug/ml, 0.03 to 0.5 mug/ml, 0.125 to 0.25 mug/ml, and 0.03 to 0.06 mug/ml, respectively. Restriction endonuclease analysis of genomic NotI-digested DNA (REAG-N) from isolates from different patients produced unique patterns, suggesting that the fungemia had occurred sporadically. This study determined that ITS2 sequence data, PFGE karyotypes, and CHROMagar Candida chromogenic culture medium are reliable diagnostic tools for identifying K. ohmeri while REAG-N is useful for genotyping the clinical isolates of K. ohmeri. PMID:17251396

  2. Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. Comparative full genome analysis revealed E1: A226V shift in 2007 Indian Chikungunya virus isolates.

    PubMed

    Santhosh, S R; Dash, P K; Parida, M M; Khan, M; Tiwari, M; Lakshmana Rao, P V

    2008-07-01

    The resurgence of Chikungunya virus (CHIKV) in the form of unprecedented explosive epidemic after a gap of 32 years in India is a point of major public health concern. In 2007 again there was outbreak in Kerala, India, affecting more than 25,000 cases with many reported mortalities. To understand the molecular basis of this high virulence and its implication in large-scale epidemic, a detailed systematic serological, virological and molecular investigation was undertaken with the epidemic samples of Kerala-2007. The comparative analysis of full genome sequence of Chikungunya virus isolate of 2007 with 2006 revealed three unique substitutions in structural and non-structural genes of 2007 isolate [two in E1 region (V14A and A226V) and one in Nsp1 (M184T)]. Our finding further substantiates the association of A226V shift in E1 gene with evolutionary success possibly due to adaptation in the mosquito vector with progression of epidemic, as observed in Reunion Island. This A226V shift which was absent in all 2006 Indian isolates, is found to be present in the four 2007 isolates, analysed in this study. These unique molecular features of the 2007 isolates with the progression of the epidemic from 2005 to 2007 demonstrate their high evolutionary and epidemic potential and thereby suggesting possible implication in higher magnitude and virulence of this outbreak. PMID:18384900

  4. Isolates of Cryptococcus neoformans from infected animals reveal genetic exchange in unisexual, alpha mating type populations.

    PubMed

    Bui, Tien; Lin, Xiaorong; Malik, Richard; Heitman, Joseph; Carter, Dee

    2008-10-01

    Sexual reproduction and genetic exchange are important for the evolution of fungal pathogens and for producing potentially infective spores. Studies to determine whether sex occurs in the pathogenic yeast Cryptococcus neoformans var. grubii have produced enigmatic results, however: basidiospores are the most likely infective propagules, and clinical isolates are fertile and genetically diverse, consistent with a sexual species, but almost all populations examined consist of a single mating type and have little evidence for genetic recombination. The choice of population is critical when looking for recombination, particularly when significant asexual propagation is likely and when latency may complicate assessing the origin of an isolate. We therefore selected isolates from infected animals living in the region of Sydney, Australia, with the assumption that the relatively short life spans and limited travels of the animal hosts would provide a very defined population. All isolates were mating type alpha and were of molecular genotype VNI or VNII. A lack of linkage disequilibrium among loci suggested that genetic exchange occurred within both genotype groups. Four diploid VNII isolates that produced filaments and basidium-like structures when cultured in proximity to an a mating type strain were found. Recent studies suggest that compatible alpha-alpha unions can occur in C. neoformans var. neoformans populations and in populations of the sibling species Cryptococcus gattii. As a mating type strains of C. neoformans var. grubii have never been found in Australia, or in the VNII molecular type globally, the potential for alpha-alpha unions is evidence that alpha-alpha unisexual mating maintains sexual recombination and diversity in this pathogen and may produce infectious propagules. PMID:18552280

  5. German Francisella tularensis isolates from European brown hares (Lepus europaeus) reveal genetic and phenotypic diversity

    PubMed Central

    2013-01-01

    Background Tularemia is a zoonotic disease caused by Francisella tularensis that has been found in many different vertebrates. In Germany most human infections are caused by contact with infected European brown hares (Lepus europaeus). The aim of this study was to elucidate the epidemiology of tularemia in hares using phenotypic and genotypic characteristics of F. tularensis. Results Cultivation of F. tularensis subsp. holarctica bacteria from organ material was successful in 31 of 52 hares that had a positive PCR result targeting the Ft-M19 locus. 17 isolates were sensitive to erythromycin and 14 were resistant. Analysis of VNTR loci (Ft-M3, Ft-M6 and Ft-M24), INDELs (Ftind33, Ftind38, Ftind49, RD23) and SNPs (B.17, B.18, B.19, and B.20) was shown to be useful to investigate the genetic relatedness of Francisella strains in this set of strains. The 14 erythromycin resistant isolates were assigned to clade B.I, and 16 erythromycin sensitive isolates to clade B.IV and one isolate was found to belong to clade B.II. MALDI-TOF mass spectrometry (MS) was useful to discriminate strains to the subspecies level. Conclusions F. tularensis seems to be a re-emerging pathogen in Germany. The pathogen can easily be identified using PCR assays. Isolates can also be identified within one hour using MALDI-TOF MS in laboratories where specific PCR assays are not established. Further analysis of strains requires genotyping tools. The results from this study indicate a geographical segregation of the phylogenetic clade B.I and B.IV, where B.I strains localize primarily within eastern Germany and B.IV strains within western Germany. This phylogeographical pattern coincides with the distribution of biovar I (erythromycin sensitive) and biovar II (erythromycin resistance) strains. When time and costs are limiting parameters small numbers of isolates can be analysed using PCR assays combined with DNA sequencing with a focus on genetic loci that are most likely discriminatory among

  6. The Genotypic and Phenotypic Stability of Plasmodium falciparum Field Isolates in Continuous In Vitro Culture.

    PubMed

    Yeda, Redemptah; Ingasia, Luicer A; Cheruiyot, Agnes C; Okudo, Charles; Chebon, Lorna J; Cheruiyot, Jelagat; Akala, Hoseah M; Kamau, Edwin

    2016-01-01

    The Plasmodium falciparum in vitro culture system is critical for genotypic and phenotypic analyses of the parasites. For genotypic analysis, the genomic DNA can be obtained directly from the patient blood sample or from culture adapted parasites whereas for phenotypic analysis, immediate ex vivo or in vitro culture adapted parasites are used. However, parasite biology studies have not investigated whether culture adaptation process affects genotypic and/or phenotypic characteristics of the parasites in short- or long-term cultures. Here, we set out to study the dynamics and stability of parasite genetic and phenotypic profiles as field isolate parasites were adapted in continuous cultures. Parasites collected from three different patients presenting with uncomplicated malaria were adapted and maintained in drug-free continuous cultures. Aliquots from the continuous cultures were collected every 24-48 hours for analyses. Each aliquot was treated as a separate parasite sample. For genetic analysis, microsatellite (MS) typing and single nucleotide polymorphism (SNP) analyses of 23 drug resistance markers were done. The 50% inhibitory concentrations (IC50) for some of the samples were also established for four antimalarial drugs. Samples from each patient (parasite-line) were compared as they were passed through the continuous culture. Data revealed genotypic and phenotypic profiles for the three parasite-lines fluctuated from one generation to the next with no specific pattern or periodicity. With few exceptions, multilocus analysis revealed samples from each parasite-line had high genetic diversity with unique haplotypes. Interestingly, changes in MS and SNP profiles occurred simultaneously. The difference in the IC50s of samples in each parasite-line reached statistical significance. However, phenotypic changes did not correspond or correlate to genotypic changes. Our study revealed parasite genetic and phenotypic characteristics fluctuates in short- and long

  7. The Genotypic and Phenotypic Stability of Plasmodium falciparum Field Isolates in Continuous In Vitro Culture

    PubMed Central

    Yeda, Redemptah; Ingasia, Luicer A.; Cheruiyot, Agnes C.; Okudo, Charles; Chebon, Lorna J.; Cheruiyot, Jelagat; Akala, Hoseah M.; Kamau, Edwin

    2016-01-01

    The Plasmodium falciparum in vitro culture system is critical for genotypic and phenotypic analyses of the parasites. For genotypic analysis, the genomic DNA can be obtained directly from the patient blood sample or from culture adapted parasites whereas for phenotypic analysis, immediate ex vivo or in vitro culture adapted parasites are used. However, parasite biology studies have not investigated whether culture adaptation process affects genotypic and/or phenotypic characteristics of the parasites in short- or long-term cultures. Here, we set out to study the dynamics and stability of parasite genetic and phenotypic profiles as field isolate parasites were adapted in continuous cultures. Parasites collected from three different patients presenting with uncomplicated malaria were adapted and maintained in drug-free continuous cultures. Aliquots from the continuous cultures were collected every 24–48 hours for analyses. Each aliquot was treated as a separate parasite sample. For genetic analysis, microsatellite (MS) typing and single nucleotide polymorphism (SNP) analyses of 23 drug resistance markers were done. The 50% inhibitory concentrations (IC50) for some of the samples were also established for four antimalarial drugs. Samples from each patient (parasite-line) were compared as they were passed through the continuous culture. Data revealed genotypic and phenotypic profiles for the three parasite-lines fluctuated from one generation to the next with no specific pattern or periodicity. With few exceptions, multilocus analysis revealed samples from each parasite-line had high genetic diversity with unique haplotypes. Interestingly, changes in MS and SNP profiles occurred simultaneously. The difference in the IC50s of samples in each parasite-line reached statistical significance. However, phenotypic changes did not correspond or correlate to genotypic changes. Our study revealed parasite genetic and phenotypic characteristics fluctuates in short- and long

  8. Lack of an effect of static magnetic field on calcium efflux from isolated chick brains

    SciTech Connect

    Bellossi, A.

    1986-01-01

    /sup 45/Ca2+ efflux from neonatal isolated chick brains was measured. The brains were exposed to uniform or nonuniform static magnetic fields. The field intensity ranged from 200-900 mT. The exposure took place during incubation and/or when efflux was being measured. No difference appeared in the /sup 45/Ca2+ efflux between controls and exposed brains.

  9. Genetic and antigenic typing of border disease virus (BDV) isolates from Italy reveals the existence of a novel BDV group.

    PubMed

    Giammarioli, Monica; La Rocca, Severina Anna; Steinbach, Falko; Casciari, Cristina; De Mia, Gian Mario

    2011-01-27

    Border disease virus belongs to the Pestivirus genus, within the family Flaviviridae. Genetic analysis of pestiviruses isolated from sheep in continental Europe have led to the proposal that BDV isolates are segregated into at least seven clusters. In 2005 the molecular analysis of an Italian caprine BDV strain provided evidence for the presence of an atypical pestivirus, which may represent the first member of a putative novel pestivirus sub-group. To further build on this study, ovine pestivirus strains were isolated from small ruminant flocks and characterized both genetically and antigenically. A defined section of the 5'UTR and the complete N(pro) coding region were amplified and used for phylogenetic analysis. This revealed that these pestiviruses belong to the BDV species but differed significantly from all previously described ovine pestiviruses providing evidence for the presence of a novel genetic group. Four of the five isolates were also typed antigenically with a panel of pestivirus specific mAbs directed against NS2/3, E(rns) and E2 proteins. The four isolates reacted with a distinct set of mAbs, in particular against the BDV-E2 and the BDV-E(rns) epitopes. The isolates were greatly reactive for E(rns) and NS2/3 mAbs, which are otherwise typical for BVDV-2, and one E2 mAb that typically stains BVDV-1. The Italian pestiviruses analysed in this study, according to their antigenic and genetic properties, clustered into a novel phylogenetic group, that we propose to term BDV-7. PMID:20656426

  10. Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates

    PubMed Central

    2012-01-01

    Background While Staphylococcus epidermidis is commonly isolated from healthy human skin, it is also the most frequent cause of nosocomial infections on indwelling medical devices. Despite its importance, few genome sequences existed and the most frequent hospital-associated lineage, ST2, had not been fully sequenced. Results We cultivated 71 commensal S. epidermidis isolates from 15 skin sites and compared them with 28 nosocomial isolates from venous catheters and blood cultures. We produced 21 commensal and 9 nosocomial draft genomes, and annotated and compared their gene content, phylogenetic relatedness and biochemical functions. The commensal strains had an open pan-genome with 80% core genes and 20% variable genes. The variable genome was characterized by an overabundance of transposable elements, transcription factors and transporters. Biochemical diversity, as assayed by antibiotic resistance and in vitro biofilm formation, demonstrated the varied phenotypic consequences of this genomic diversity. The nosocomial isolates exhibited both large-scale rearrangements and single-nucleotide variation. We showed that S. epidermidis genomes separate into two phylogenetic groups, one consisting only of commensals. The formate dehydrogenase gene, present only in commensals, is a discriminatory marker between the two groups. Conclusions Commensal skin S. epidermidis have an open pan-genome and show considerable diversity between isolates, even when derived from a single individual or body site. For ST2, the most common nosocomial lineage, we detect variation between three independent isolates sequenced. Finally, phylogenetic analyses revealed a previously unrecognized group of S. epidermidis strains characterized by reduced virulence and formate dehydrogenase, which we propose as a clinical molecular marker. PMID:22830599

  11. Ex Vivo Stretch Reveals Altered Mechanical Properties of Isolated Dystrophin-Deficient Hearts

    PubMed Central

    Barnabei, Matthew S.; Metzger, Joseph M.

    2012-01-01

    Duchenne muscular dystrophy (DMD) is a progressive and fatal disease of muscle wasting caused by loss of the cytoskeletal protein dystrophin. In the heart, DMD results in progressive cardiomyopathy and dilation of the left ventricle through mechanisms that are not fully understood. Previous reports have shown that loss of dystrophin causes sarcolemmal instability and reduced mechanical compliance of isolated cardiac myocytes. To expand upon these findings, here we have subjected the left ventricles of dystrophin-deficient mdx hearts to mechanical stretch. Unexpectedly, isolated mdx hearts showed increased left ventricular (LV) compliance compared to controls during stretch as LV volume was increased above normal end diastolic volume. During LV chamber distention, sarcomere lengths increased similarly in mdx and WT hearts despite greater excursions in volume of mdx hearts. This suggests that the mechanical properties of the intact heart cannot be modeled as a simple extrapolation of findings in single cardiac myocytes. To explain these findings, a model is proposed in which disruption of the dystrophin-glycoprotein complex perturbs cell-extracellular matrix contacts and promotes the apparent slippage of myocytes past each other during LV distension. In comparison, similar increases in LV compliance were obtained in isolated hearts from β-sarcoglycan-null and laminin-α2 mutant mice, but not in dysferlin-null mice, suggesting that increased whole-organ compliance in mdx mice is a specific effect of disrupted cell-extracellular matrix contacts and not a general consequence of cardiomyopathy via membrane defect processes. Collectively, these findings suggest a novel and cell-death independent mechanism for the progressive pathological LV dilation that occurs in DMD. PMID:22427904

  12. Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism

    PubMed Central

    Millar, Scott B.; Sanderson, Theo; Otto, Thomas D.; Lu, Woon Chan; Krishna, Sanjeev; Rayner, Julian C.; Cox-Singh, Janet

    2015-01-01

    Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology. PMID:25830531

  13. Analysis of Molecular Epidemiology of Chilean Salmonella enterica Serotype Enteritidis Isolates by Pulsed-Field Gel Electrophoresis and Bacteriophage Typing

    PubMed Central

    Fernandez, Jorge; Fica, Alberto; Ebensperger, German; Calfullan, Hector; Prat, Soledad; Fernandez, Alda; Alexandre, Marcela; Heitmann, Ingrid

    2003-01-01

    Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype

  14. Analysis of molecular epidemiology of Chilean Salmonella enterica serotype enteritidis isolates by pulsed-field gel electrophoresis and bacteriophage typing.

    PubMed

    Fernandez, Jorge; Fica, Alberto; Ebensperger, German; Calfullan, Hector; Prat, Soledad; Fernandez, Alda; Alexandre, Marcela; Heitmann, Ingrid

    2003-04-01

    Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype

  15. Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.

    PubMed

    Du, Juan; Ngo, Hien T T; Won, KyungHwa; Kim, Ki-Young; Jin, Feng-Xie; Yi, Tae-Hoo

    2015-08-01

    Strain THG-EP9T, a Gram-stain-negative, aerobic, motile, rod-shaped bacterium was isolated from field-grown eggplant (Solanum melongena) rhizosphere soil collected in Pyeongtaek, Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-EP9T had closest similarity with Chryseobacterium ginsenosidimutans THG 15T (97.3 % 16S rRNA gene sequence similarity), Chryseobacterium soldanellicola PSD1-4T (97.2%), Chryseobacterium zeae JM-1085T (97.2%) and Chryseobacterium indoltheticum LMG 4025T (96.8%). DNA-DNA hybridization showed 5.7% and 9.1% DNA reassociation with Chryseobacterium ginsenosidimutans KACC 14527T and Chryseobacterium soldanellicola KCTC 12382T, respectively. Chemotaxonomic data revealed that strain THG-EP9T possesses menaquinone-6 as the only respiratory quinone and iso-C15 : 0 (29.0%), C16 : 0 (12.5%) and iso-C17 : 0 3-OH (11.9 %) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified glycolipids, six unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 35.3 mol%. These data corroborated the affiliation of strain THG-EP9T to the genus Chryseobacterium. Thus, the isolate represents a novel species of this genus, for which the name Chryseobacterium solani sp. nov. is proposed, with THG-EP9T ( = KACC 17652T = JCM 19456T) as the type strain. PMID:25878202

  16. 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. PMID:24899019

  17. Multilocus Sequence Typing Scheme versus Pulsed-Field Gel Electrophoresis for Typing Mycobacterium abscessus Isolates

    PubMed Central

    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

    2014-01-01

    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. PMID:24899019

  18. Isolated magnetic field structures in Mercury's magnetosheath as possible analogues for terrestrial magnetosheath plasmoids and jets

    NASA Astrophysics Data System (ADS)

    Karlsson, Tomas; Liljeblad, Elisabet; Kullen, Anita; Raines, Jim M.; Slavin, James A.; Sundberg, Torbjörn

    2016-09-01

    We have investigated MESSENGER magnetic field data from the Mercury magnetosheath and near solar wind, to identify isolated magnetic field structures (defined as clear, isolated changes in the field magnitude). Their properties are studied in order to determine if they may be considered as analogues to plasmoids and jets known to exist in Earth's magnetosheath. Both isolated decreases of the magnetic field absolute value ('negative magnetic field structures') and increases ('positive structures') are found in the magnetosheath, whereas only negative structures are found in the solar wind. The similar properties of the solar wind and magnetosheath negative magnetic field structures suggests that they are analogous to diamagnetic plasmoids found in Earth's magnetosheath and near solar wind. The latter have earlier been identified with solar wind magnetic holes. Positive magnetic field structures are only found in the magnetosheath, concentrated to a region relatively close to the magnetopause. Their proximity to the magnetopause, their scale sizes, and the association of a majority of the structures with bipolar magnetic field signatures identify them as flux transfer events (which generally are associated with a decrease of plasma density in the magnetosheath). The positive magnetic field structures are therefore not likely to be analogous to terrestrial paramagnetic plasmoids but possibly to a sub-population of magnetosheath jets. At Earth, a majority of magnetosheath jets are associated with the quasi-parallel bow shock. We discuss some consequences of the findings of the present investigation pertaining to the different nature of the quasi-parallel bow shock at Mercury and Earth.

  19. Trichoderma Biodiversity of Agricultural Fields in East China Reveals a Gradient Distribution of Species

    PubMed Central

    Chen, Jing; Mao, Li-Juan; Feng, Xiao-Xiao; Zhang, Chu-Long; Lin, Fu-Cheng

    2016-01-01

    We surveyed the Trichoderma (Hypocreales, Ascomycota) biodiversity in agricultural fields in four major agricultural provinces of East China. Trichoderma strains were identified based on molecular approaches and morphological characteristics. In three sampled seasons (spring, summer and autumn), 2078 strains were isolated and identified to 17 known species: T. harzianum (429 isolates), T. asperellum (425), T. hamatum (397), T. virens (340), T. koningiopsis (248), T. brevicompactum (73), T. atroviride (73), T. fertile (26), T. longibrachiatum (22), T. pleuroticola (16), T. erinaceum (16), T. oblongisporum (2), T. polysporum (2), T. spirale (2), T. capillare (2), T. velutinum (2), and T. saturnisporum (1). T. harzianum, T. asperellum, T. hamatum, and T. virens were identified as the dominant species with dominance (Y) values of 0.057, 0.052, 0.048, and 0.039, respectively. The species amount, isolate numbers and the dominant species of Trichoderma varied between provinces. Zhejiang Province has shown the highest diversity, which was reflected in the highest species amount (14) and the highest Shannon–Wiener diversity index of Trichoderma haplotypes (1.46). We observed that relative frequencies of T. hamatum and T. koningiopsis under rice soil were higher than those under wheat and maize soil, indicating the preference of Trichoderma to different crops. Remarkable seasonal variation was shown, with summer exhibiting the highest biodiversity of the studied seasons. These results show that Trichoderma biodiversity in agricultural fields varies by region, crop, and season. Zhejiang Province (the southernmost province in the investigated area) had more T. hamatum than Shandong Province (the northernmost province), not only in isolate amounts but also in haplotype amounts. Furthermore, at haplotype level, only T. hamatum showed a gradient distribution from south to north in correspondence analysis among the four dominant species. The above results would contribute to the

  20. Intense Isolated Ultrashort Attosecond Pulse Generation in a Multi-Cycle Three-Colour Laser Field

    NASA Astrophysics Data System (ADS)

    Zhang, Gang-Tai

    2014-12-01

    An efficient method for generating an intense isolated ultrashort attosecond pulse is presented theoretically. By adding a 267 nm controlling pulse to a multi-cycle two-colour field, not only the spectral cutoff and the yields of the harmonic spectrum are evidently enhanced, but also the selection of the single quantum path is realised. Then a high-efficiency supercontinuum with a 504 eV bandwidth and smooth structure is obtained, which enables the production of an intense isolated 30 as pulse. In addition, the influences of the laser parameters on the supercontinuum and isolated attosecond pulse are investigated.

  1. Differentiation of field isolates and vaccine strains of infectious laryngotracheitis virus by DNA sequencing.

    PubMed

    Chacón, Jorge Luis; Ferreira, Antonio J Piantino

    2009-11-12

    Two different regions of the infected cell protein 4 (ICP4) gene of infectious laryngotracheitis virus (ILTV) were amplified and sequenced for characterization of field isolates and tissue culture-origin (TCO) and chicken embryo-origin (CEO) vaccine strains. Phylogenetic analysis of the two regions showed differences in nucleotide and amino acid sequences between field isolates and attenuated vaccines. The PCR-RFLP results were identical to those obtained by DNA sequencing and validated their use to differentiate ILTV strains. The approach using the sequencing of the two fragments of the ICP4 gene showed to be an efficient and practical procedure to differentiate between field isolates and vaccine strains of ILTV. PMID:19747995

  2. Inhibition of NO synthesis or endothelium removal reveals a vasoconstrictor effect of insulin on isolated arterioles.

    PubMed

    Schroeder, C A; Chen, Y L; Messina, E J

    1999-03-01

    In this study we tested the hypothesis that insulin may differentially affect isolated arterioles from red (RGM) and white gastrocnemius muscles (WGM) because of their differences in function and metabolic profile. We also determined whether the responses of these arterioles are endothelium dependent and mediated by either prostaglandins or nitric oxide (NO). Arterioles were isolated, pressurized to 85 mmHg, equilibrated in Krebs bicarbonate-buffered solution (pH 7.4) gassed with 10% O2 (5% CO2-85% N2), and studied in a no-flow state. Control diameters for first-order arterioles from RGM averaged 77 +/- 8 micrometers and from WGM averaged 77 +/- 5 micrometers. Cumulative dose-response curves to insulin (10 microU/ml, 100 microU/ml, 1 mU/ml, and 10 mU/ml) were obtained in arterioles before and after endothelium removal or administration of either indomethacin (Indo, 10(-5) M) or NG-nitro-L-arginine (L-NNA, 10(-4) M). Insulin evoked concentration-dependent increases in control diameter of intact RGM and WGM arterioles of 6-26% and 9-28%, respectively. Indo was without any effect on insulin-induced dilation in RGM and WGM arterioles. Insulin-evoked dilation in both RGM and WGM arterioles was completely inhibited and converted to vasoconstriction by endothelium removal and administration of L-NNA. These results indicate that in endothelium-intact arterioles from RGM and WGM, insulin evokes an endothelium-dependent dilation that is equivalent and mediated by NO. In contrast, in the absence of a functional endothelium, insulin evokes arteriolar constriction. The finding that insulin can constrict arterioles, at physiological concentrations, suggests that insulin may play a more significant role in the regulation of vascular tone and total peripheral resistance than previously appreciated. PMID:10070063

  3. Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association

    PubMed Central

    2013-01-01

    Background In spite of its association with gastroenteritis and inflammatory bowel diseases, the isolation of Campylobacter concisus from both diseased and healthy individuals has led to controversy regarding its role as an intestinal pathogen. One proposed reason for this is the presence of high genetic diversity among the genomes of C. concisus strains. Results In this study the genomes of six C. concisus strains were sequenced, assembled and annotated including two strains isolated from Crohn’s disease patients (UNSW2 and UNSW3), three from gastroenteritis patients (UNSW1, UNSWCS and ATCC 51562) and one from a healthy individual (ATCC 51561). The genomes of C. concisus BAA-1457 and UNSWCD, available from NCBI, were included in subsequent comparative genomic analyses. The Pan and Core genomes for the sequenced C. concisus strains consisted of 3254 and 1556 protein coding genes, respectively. Conclusion Genes were identified with specific conservation in C. concisus strains grouped by phenotypes such as invasiveness, adherence, motility and diseased states. Phylogenetic trees based on ribosomal RNA sequences and concatenated host-related pathways for the eight C. concisus strains were generated using the neighbor-joining method, of which the 16S rRNA gene and peptidoglycan biosynthesis grouped the C. concisus strains according to their pathogenic phenotypes. Furthermore, 25 non-synonymous amino acid changes with 14 affecting functional domains, were identified within proteins of conserved host-related pathways, which had possible associations with the pathogenic potential of C. concisus strains. Finally, the genomes of the eight C. concisus strains were compared to the nine available genomes of the well-established pathogen Campylobacter jejuni, which identified several important differences in the respiration pathways of these two species. Our findings indicate that C. concisus strains are genetically diverse, and suggest the genomes of this bacterium contain

  4. Comparison of the complete genome sequence of two closely related isolates of ‘Candidatus Phytoplasma australiense’ reveals genome plasticity

    PubMed Central

    2013-01-01

    Background ‘Candidatus Phytoplasma australiense’ is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a NZ isolate was sequenced in an effort to understand its pathogenicity and ecology. Comparison with a closely related Australian isolate enabled us to examine mechanisms of genomic rearrangement. Results The complete genome sequence of a strawberry lethal yellows (SLY) isolate of ‘Candidatus Phytoplasma australiense’ was determined. It is a circular genome of 959,779 base pairs with 1126 predicted open reading frames. Despite being 80 kbp larger than another ‘Ca. Phytoplasma australiense’ isolate PAa, the variation between housekeeping genes was generally less than 1% at a nucleotide level. The difference in size between the two isolates was largely due to the number and size of potential mobile units (PMUs), which contributed to some changes in gene order. Comparison of the genomes of the two isolates revealed that the highly conserved 5′ UTR of a putative DNA-directed RNA polymerase seems to be associated with insertion and rearrangement events. Two types of PMUs have been identified on the basis of the order of three to four conserved genes, with both PMUs appearing to have been present in the last common ancestor of ‘Ca. Phytoplasma asteris’ and ‘Ca. Phytoplasma australiense’. Comparison with other phytoplasma genomes showed that modification methylases were, in general, species-specific. A putative methylase (xorIIM) found in ‘Ca. Phytoplasma australiense’ appeared to have no analogue in any other firmicute, and we believe has been introduced by way of lateral gene transfer. A putative retrostransposon (ltrA) analogous to that found in OY-M was present in both isolates, although all examples in PAa appear to be fragments. Comparative analysis identified highly conserved 5′ and 3′ UTR regions of ltrA, which may

  5. Generation of an isolated few-attosecond pulse in optimized inhomogeneous two-color fields

    NASA Astrophysics Data System (ADS)

    Chou, Yi; Li, Peng-Cheng; Ho, Tak-San; Chu, Shih-I.

    2015-08-01

    We present a numerical study for optimization of ultrabroad supercontinuum spectrum by controlling the waveforms of laser fields, with the ultimate goal to generate isolated ultrashort attosecond pulses. Specifically, we extend a derivative-free nonconvex optimization algorithm for maximization of the supercontinnum power spectrum near the high-order harmonic generation (HHG) cutoff. It is found that optimally shaped inhomogeneous two-color mid-infrared laser fields can greatly enhance and extend the high-order harmonic generation plateau. Wavelet time-frequency analysis and classical simulations show that the superposition of resulting hydrogen HHG supercontinuum effectively gives rise to a robust isolated 5-as pulse.

  6. Revealing giant internal magnetic fields due to spin fluctuations in magnetically doped colloidal nanocrystals.

    PubMed

    Rice, William D; Liu, Wenyong; Baker, Thomas A; Sinitsyn, Nikolai A; Klimov, Victor I; Crooker, Scott A

    2016-02-01

    Strong quantum confinement in semiconductors can compress the wavefunctions of band electrons and holes to nanometre-scale volumes, significantly enhancing interactions between themselves and individual dopants. In magnetically doped semiconductors, where paramagnetic dopants (such as Mn(2+), Co(2+) and so on) couple to band carriers via strong sp-d spin exchange, giant magneto-optical effects can therefore be realized in confined geometries using few or even single impurity spins. Importantly, however, thermodynamic spin fluctuations become increasingly relevant in this few-spin limit. In nanoscale volumes, the statistical fluctuations of N spins are expected to generate giant effective magnetic fields Beff, which should dramatically impact carrier spin dynamics, even in the absence of any applied field. Here we directly and unambiguously reveal the large Beff that exist in Mn(2+)-doped CdSe colloidal nanocrystals using ultrafast optical spectroscopy. At zero applied magnetic field, extremely rapid (300-600 GHz) spin precession of photoinjected electrons is observed, indicating Beff ∼ 15 -30 T for electrons. Precession frequencies exceed 2 THz in applied magnetic fields. These signals arise from electron precession about the random fields due to statistically incomplete cancellation of the embedded Mn(2+) moments, thereby revealing the initial coherent dynamics of magnetic polaron formation, and highlighting the importance of magnetization fluctuations on carrier spin dynamics in nanomaterials. PMID:26595331

  7. Respiratory neuron characterization reveals intrinsic bursting properties in isolated adult turtle brainstems (Trachemys scripta).

    PubMed

    Johnson, Stephen M; Hedrick, Michael S; Krause, Bryan M; Nilles, Jacob P; Chapman, Mark A

    2016-04-01

    It is not known whether respiratory neurons with intrinsic bursting properties exist within ectothermic vertebrate respiratory control systems. Thus, isolated adult turtle brainstems spontaneously producing respiratory motor output were used to identify and classify respiratory neurons based on their firing pattern relative to hypoglossal (XII) nerve activity. Most respiratory neurons (183/212) had peak activity during the expiratory phase, while inspiratory, post-inspiratory, and novel pre-expiratory neurons were less common. During synaptic blockade conditions, ∼10% of respiratory neurons fired bursts of action potentials, with post-inspiratory cells (6/9) having the highest percentage of intrinsic burst properties. Most intrinsically bursting respiratory neurons were clustered at the level of the vagus (X) nerve root. Synaptic inhibition blockade caused seizure-like activity throughout the turtle brainstem, which shows that the turtle respiratory control system is not transformed into a network driven by intrinsically bursting respiratory neurons. We hypothesize that intrinsically bursting respiratory neurons are evolutionarily conserved and represent a potential rhythmogenic mechanism contributing to respiration in adult turtles. PMID:25462012

  8. Scanning Electron Microscopy Reveals Two Distinct Classes of Erythroblastic Island Isolated from Adult Mammalian Bone Marrow.

    PubMed

    Yeo, Jia Hao; McAllan, Bronwyn M; Fraser, Stuart T

    2016-04-01

    Erythroblastic islands are multicellular clusters in which a central macrophage supports the development and maturation of red blood cell (erythroid) progenitors. These clusters play crucial roles in the pathogenesis observed in animal models of hematological disorders. The precise structure and function of erythroblastic islands is poorly understood. Here, we have combined scanning electron microscopy and immuno-gold labeling of surface proteins to develop a better understanding of the ultrastructure of these multicellular clusters. The erythroid-specific surface antigen Ter-119 and the transferrin receptor CD71 exhibited distinct patterns of protein sorting during erythroid cell maturation as detected by immuno-gold labeling. During electron microscopy analysis we observed two distinct classes of erythroblastic islands. The islands varied in size and morphology, and the number and type of erythroid cells interacting with the central macrophage. Assessment of femoral marrow isolated from a cavid rodent species (guinea pig, Cavis porcellus) and a marsupial carnivore species (fat-tailed dunnarts, Sminthopsis crassicaudata) showed that while the morphology of the central macrophage varied, two different types of erythroblastic islands were consistently identifiable. Our findings suggest that these two classes of erythroblastic islands are conserved in mammalian evolution and may play distinct roles in red blood cell production. PMID:26898901

  9. A Novel Strategy to Isolate Ubiquitin Conjugates Reveals Wide Role for Ubiquitination during Neural Development*

    PubMed Central

    Franco, Maribel; Seyfried, Nicholas T.; Brand, Andrea H.; Peng, Junmin; Mayor, Ugo

    2011-01-01

    Ubiquitination has essential roles in neuronal development and function. Ubiquitin proteomics studies on yeast and HeLa cells have proven very informative, but there still is a gap regarding neuronal tissue-specific ubiquitination. In an organism context, direct evidence for the ubiquitination of neuronal proteins is even scarcer. Here, we report a novel proteomics strategy based on the in vivo biotinylation of ubiquitin to isolate ubiquitin conjugates from the neurons of Drosophila melanogaster embryos. We confidently identified 48 neuronal ubiquitin substrates, none of which was yet known to be ubiquitinated. Earlier proteomics and biochemical studies in non-neuronal cell types had identified orthologs to some of those but not to others. The identification here of novel ubiquitin substrates, those with no known ubiquitinated ortholog, suggests that proteomics studies must be performed on neuronal cells to identify ubiquitination pathways not shared by other cell types. Importantly, several of those newly found neuronal ubiquitin substrates are key players in synaptogenesis. Mass spectrometry results were validated by Western blotting to confirm that those proteins are indeed ubiquitinated in the Drosophila embryonic nervous system and to elucidate whether they are mono- or polyubiquitinated. In addition to the ubiquitin substrates, we also identified the ubiquitin carriers that are active during synaptogenesis. Identifying endogenously ubiquitinated proteins in specific cell types, at specific developmental stages, and within the context of a living organism will allow understanding how the tissue-specific function of those proteins is regulated by the ubiquitin system. PMID:20861518

  10. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil

    SciTech Connect

    Hjort, K.; Bergstrom, M.; Adesina, M.F.; Jansson, J.K.; Smalla, K.; Sjoling, S.

    2009-09-01

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal-restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal-restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF{sup 103} of the isolate, Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  11. Genetic polymorphisms associated with sulphadoxine-pyrimethamine drug resistance among Plasmodium falciparum field isolates in malaria endemic areas of Assam

    PubMed Central

    Sharma, J; Dutta, P; Khan, SA; Soni, M; Dey, D; Mahanta, J

    2015-01-01

    Background: The emergence of antimalarial drug resistance malaria parasite is widespread in North eastern region of India. During January 2012-December 2013, we conducted active surveillance for detection of antifolate resistance-associated genetic polymorphisms in Plasmodium falciparum malaria parasite from different malaria endemic areas of Assam. Materials and Methods: A total of 281 field samples were collected from suspected malaria patients of which 106 malaria P. falciparum positive cases were detected in microscopic slide examination. A nested PCR was done for amplification of a 648 bp portion of the dhfr gene and 710 bp portion of the dhps gene. Results: Mutation analysis revealed existence of three different haplotypes of the P. falciparum dhfr gene of which ANRNI was highly prevalent (90%). Triple mutant haplotypes AIRNI (N51I + C59R + S108N) of the dhfr gene associated with pyrimethamine resistance were prevalent in Chirang district of Assam. Whereas, dhps mutation study revealed that triple mutant haplotype AGEAA (S436A + A437G + K540E) associated with Sulphadoxine resistance was found among 26% of P. falciparum field isolates. However, P. falciparum dhfr-dhps two locus mutation analysis showed that there were a total of nine dhfr-dhps genotypes. Conclusion: It was noticed that 93.62% (88/94) isolates had mutations in the sequences of both enzymes, which is an indication of prevalence of high grade of Sulphadoxine — pyrimethamine resistance in P. falciparum malaria parasites in Assam. PMID:25511211

  12. Porcine reproductive and respiratory syndrome virus field isolates differ in in vitro interferon phenotypes.

    PubMed

    Lee, Sang-Myeong; Schommer, Susan K; Kleiboeker, Steven B

    2004-12-01

    Type I interferons (IFN-alpha and -beta) play an important role in the innate host defense against viral infection by inducing antiviral responses. In addition to direct antiviral activities, type I IFN serves as an important link between the innate and adaptive immune response through multiple mechanisms. Therefore, the outcome of a viral infection can be affected by IFN induction and the IFN sensitivity of a virus. North American porcine reproductive and respiratory syndrome virus (PRRSV) field isolates were studied with regard to IFN-alpha sensitivity and induction in order to understand the role of type I IFN in PRRSV pathogenesis. PRRSV isolates were differentially sensitive to porcine recombinant IFN-alpha (rIFN-alpha) and varied in their ability to induce IFN-alpha in porcine alveolar macrophages (PAM) cultures as measured by a porcine IFN-alpha specific ELISA on cell culture supernatants. Fifty-two plaques were purified from three PRRSV isolates (numbers 3, 7, and 12) and tested for IFN sensitivity and IFN induction. Plaque-derived populations were composed of heterogeneous populations in terms of IFN-inducing capacity and sensitivity to rIFN-alpha. When macrophages infected with isolates 3, 7, or 12 were treated with polycytidylic acid (polyI:C), IFN-alpha production was enhanced. Cells infected with isolate 3 and treated with polyI:C showed the most consistent and strongest enhancement of IFN-alpha production. It was demonstrated that the relatively low concentrations of IFN-alpha produced by isolate 3 contributed to the enhanced IFN-alpha synthesis in response to polyI:C. Isolates 7 and 12 significantly suppressed the enhanced IFN-alpha production by isolate 3 in polyI:C treated cells. To determine if suppression was at the level of IFN-alpha transcription, quantitative RT-PCR was performed for IFN-alpha mRNA and compared to GAPDH and cyclophilin mRNA quantification. However, the relative number of IFN-alpha transcript copies did not correlate with IFN

  13. Molecular epidemiologic analysis of Vibrio cholerae O1 isolates by pulsed-field gel electrophoresis.

    PubMed Central

    Mahalingam, S; Cheong, Y M; Kan, S; Yassin, R M; Vadivelu, J; Pang, T

    1994-01-01

    Isolates of Vibrio cholerae O1 El Tor from two well-defined cholera outbreaks in Malaysia were analyzed by using pulsed-field gel electrophoresis (PFGE). Isolates from sporadic cases occurring during the same time period were also studied. Digestion of chromosomal DNA from these isolates of V. cholerae O1 with restriction endonucleases NotI (5'-GCGGCCGC-3') and SfiI (5'-GGCCNNNN-3'), followed by PFGE, produced restriction endonuclease analysis (REA) patterns consisting of 13 to 24 bands (ranging in size from 46 to 398 kbp). Analysis of the REA patterns generated by PFGE after digestion with NotI and SfiI suggested the clonal nature and close genetic identity of the isolates obtained during each of the two outbreaks (Dice coefficient, 0.93 to 1.0). Although they had very similar REA patterns, the two outbreak clones were not identical. Isolates of V. cholerae O1 from sporadic cases, on the other hand, appeared to be much more heterogeneous (five different REA patterns detected in the five isolates tested; Dice coefficient, 0.31 to 0.81) than those obtained during the two outbreaks. We conclude that PFGE of V. cholerae O1 chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for molecular typing of V. cholerae isolates for epidemiological purposes. Images PMID:7883885

  14. Genetic variability among Schistosoma japonicum isolates from different endemic regions in China revealed by sequences of three mitochondrial DNA genes.

    PubMed

    Zhao, G H; Mo, X H; Zou, F C; Li, J; Weng, Y B; Lin, R Q; Xia, C M; Zhu, X Q

    2009-05-26

    The present study examined sequence variation in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 3 (cox3), NADH dehydrogenase subunits 4 and 5 (nad4 and nad5), among Schistosoma japonicum isolates from different endemic regions in China, and their phylogenetic relationships were re-constructed. A portion of the cox3 gene (pcox3), a portion of the nad4 and nad5 genes (pnad4 and pnad5) were amplified separately from individual trematodes by polymerase chain reaction (PCR) and the amplicons were subjected to direct sequencing. In the mountainous areas, sequence variations between parasites from Yunnan and those from Sichuan were 0.3% for pcox3, 0.0-0.1% for pnad4, and 0.0-0.2% for pnad5. In the lake/marshland areas, sequence variations between male and female parasites among different geographical locations were 0.0-0.3% for pcox3, 0.0-0.7% for pnad4, and 0.0-1.6% for pnad5. Sequence variations between S. japonicum from mountainous areas and those from lake/marshland areas were 0.0-0.5% for pcox3, 0.0-0.7% for pnad4, and 0.0-1.6% for pnad5. Phylogenetic analyses based on the combined sequences of pcox3, pnad4 and pnad5 revealed that S. japonicum isolates from mountainous areas (Yunnan and Sichuan provinces) clustered together. For isolates from the lake/marshland areas, isolates from Anhui and Jiangsu provinces clustered together and was sister to samples from Jiangxi province, while isolates from Hubei and Zhejiang province clustered together. However, isolates from different geographical locations in Hunan province were in different clades. These findings demonstrated the usefulness and attributes of the three mtDNA sequences for population genetic studies of S. japonicum, and have implications for studying population biology, molecular epidemiology, and genetic structure of S. japonicum, as well as for the effective control of schistosomiasis. PMID:19303214

  15. Isolated attosecond pulse generation with the chirped two-color laser field

    NASA Astrophysics Data System (ADS)

    Tai, Huiqin; Li, Fang; Wang, Zhe

    2016-07-01

    We propose a scheme to generate isolated attosecond pulse using a linearly chirped two-color laser field, which includes a fundamental laser field and a weak infrared control laser field in the multicycle regime. The fundamental laser field consists of one linearly up-chirped and one linearly down-chirped pulses. The control pulse is chirped free. We compare the attosecond pulse generated in the chirped two-color field and the chirp-free field. It is found that an IAP can be generated even without carrier envelop phase stabilization in the chirped two-color laser field with a duration of 40 fs. We also discuss the influence of the relative intensity, relative phase, time delay, and chirping parameters on the generation of IAPs.

  16. Evaluation of Marek's disease field isolates by the "best fit" pathotyping assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although determination of pathotype is central to the study of Marek's disease field isolates, methods are not standardized and results from different laboratories may not compare well to the original Avian Disease and Oncology Laboratory (ADOL) assay. This study was designed to investigate the vali...

  17. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Minimum Land, Isolation, Field, and Seed Standards. 201.76 Section 201.76 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) FEDERAL SEED ACT FEDERAL SEED ACT...

  18. 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.

  19. Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

    PubMed Central

    Koton, Yael; Gordon, Michal; Chalifa-Caspi, Vered; Bisharat, Naiel

    2015-01-01

    In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically

  20. Genetic clustering of recent classical swine fever virus isolates from Karnataka, India revealed the emergence of subtype 2.2 replacing subtype 1.1.

    PubMed

    Shivaraj, D B; Patil, S S; Rathnamma, D; Hemadri, D; Isloor, S; Geetha, S; Manjunathareddy, G B; Gajendragad, M R; Rahman, H

    2015-09-01

    The phylogenetic analysis of 11 CSFV isolates from Karnataka, India obtained during the year 2012-13 was undertaken to obtain the most reliable genetic typing of the CSFV isolates based on E2, NS5B and 5'UTR genomic regions. The study indicated that all the 11 CSFV isolates belonged to subgroup 2.2. The most reliable classification was obtained with sequence data from the NS5B region which separated all the isolates based on the history of outbreak and geographic origin. Analysis of full length E2 amino acid sequences revealed different genetic makeup of Indian 2.2 isolates compared to 2.2 isolates from different countries. The group 2.2 viruses are gradually spreading as confirmed by frequent detection/ isolation of group 2.2 viruses in the recent years and replacing the subgroup 1.1 viruses, which were hitherto predominantly involved in CSF outbreaks in India. PMID:26396984

  1. Ca3 fingerprinting of Candida albicans bloodstream isolates from the United States, Canada, South America, and Europe reveals a European clade.

    PubMed

    Pujol, Claude; Pfaller, Michael; Soll, David R

    2002-08-01

    It was previously demonstrated by a cluster analysis that 26 unrelated U.S. isolates of Candida albicans separated into three distinct groups (groups I, II, and III) while South African isolates separated into four distinct groups (groups I, II, III, and SA). To verify the absence or underrepresentation of SA isolates in North America, and to identify which groups are represented in Europe and South America, collections of bloodstream isolates from each geographical locale were analyzed by cluster analyses based on genetic fingerprinting with the Ca3 probe. The results verify that North America is almost devoid of SA isolates (2%). However, the results reveal a new clade, designated group E, relatively specific to Europe. While 26% of a European collection of 46 isolates was composed of group E isolates, only 2% of the 164 North American isolates, 5% of 22 South American isolates, and 1% of 361 South African isolates were composed of group E isolates. The North American collection proved to be the least-diverse collection in regard to group representation. In a comparison of collections from the Northeast, Midwest, and Southwest regions of the United States, Canada, and South America, it was demonstrated that both the U.S. Southwest and the South American collections were devoid of group II isolates. Together these results identify for the first time a European-specific clade and demonstrate clear distinctions in the representations of the five demonstrated clades (groups I, II, III, SA, and E) in different geographical locales. PMID:12149321

  2. Simulation of Intense Isolated Attosecond Pulse Generation with a Two-color Laser Field

    NASA Astrophysics Data System (ADS)

    Eilanlou, Abdolreza Amani; Ishikawa, Kenichi L.; Nabekawa, Yasuo; Takahashi, Hiroyuki; Midorikawa, Katsumi

    A numerical analysis by solving the time-dependent Schrödinger equation on a neon atom within the single-active electron approximation shows that a two-color laser field synthesized from a sub-12-fs fundamental field and a detuned second harmonic field with a wavelength shorter than 380nm is suitable for generating an intense isolated attosecond pulse (IAP). We have also investigated the effects of carrier-envelope phase variation on the obtained IAP and have compared the results to those obtained from a 5-fs fundamental field alone with the same peak field amplitude to show that a more intense IAP can be generated by the two-color laser field which is useful for nonlinear experiments in the extreme ultraviolet spectral range.

  3. 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

  4. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

    PubMed Central

    Wang, Yun; Butler, Robert R.; Reddy, N. Rukma; Skinner, Guy E.; Larkin, John W.

    2015-01-01

    Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance. PMID:26519392

  5. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing.

    PubMed

    Schill, Kristin M; Wang, Yun; Butler, Robert R; Pombert, Jean-François; Reddy, N Rukma; Skinner, Guy E; Larkin, John W

    2016-01-01

    Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance. PMID:26519392

  6. Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil.

    PubMed

    Kumari, Prabla; Bandyopadhyay, Saumya; Das, Subrata K

    2013-07-01

    A novel aerobic soil actinobacterium (strain MB10(T)) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0-11.0 and at 16-37 °C; optimum growth was observed at 28 °C and pH 7.0-9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10(T) were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10(T) clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145(T). However, DNA-DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145(T), the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, it is proposed that strain MB10(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10(T) ( = JCM 16837(T) = DSM 23396(T)). PMID:23203624

  7. Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.

    PubMed

    Zhang, Shi-Ying; Xiao, Wei; Xia, Yun-Sheng; Wang, Yong-Xia; Cui, Xiao-Long; Zhang, Nai-Ming

    2015-05-01

    A Gram-stain negative, aerobic, rod-shaped bacterial strain, YN2-31A(T), was isolated from rice-field soil, Taoyuan Village, Yunnan province of China. The bacterium was observed to grow at 20-45 °C (optimum 28 °C), at pH 5.0-10.0 (optimum 7.0), and in the presence of 0-2% (w/v) NaCl (optimum 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2-31A(T) is most closely related to Arenimonas daejeonensis DSM 18060(T) (96.1%), Arenimonas malthae DSM 21305(T) (95.9%), Arenimonas donghaensis DSM 18148(T) (95.1%), Arenimonas composti DSM 18010(T) (94.8%) and Arenimonas maotaiensis JCM 19710(T) (94.8%). The major cellular fatty acids (>10%) were found to be iso-C(18:1) ω9c, iso-C(15:0), Sum In Feature 3 (C(16:1) ω7c/C(16:1) ω6c), and C(16:0). The major ubiquinone was identified as Q-8 and the major cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The genomic DNA G+C content was determined to be 72.3 mol%. The results of the phylogenetic, genetic, phenotypic and chemotaxonomic analyses suggest that strain YN2-31A(T) represents a novel species of the genus Arenimonas, for which the name Arenimonas taoyuanensis sp. nov. is proposed. The type strain is YN2-31A(T) (=DSM 26777(T) = CCTCC AB2012964(T)). PMID:25731739

  8. Combinations of Macrolide Resistance Determinants in Field Isolates of Mannheimia haemolytica and Pasteurella multocida▿

    PubMed Central

    Desmolaize, Benoit; Rose, Simon; Wilhelm, Cornelia; Warrass, Ralf; Douthwaite, Stephen

    2011-01-01

    Respiratory tract infections in cattle are commonly associated with the bacterial pathogens Mannheimia haemolytica and Pasteurella multocida. These infections can generally be successfully treated in the field with one of several groups of antibiotics, including macrolides. A few recent isolates of these species exhibit resistance to veterinary macrolides with phenotypes that fall into three distinct classes. The first class has type I macrolide, lincosamide, and streptogramin B antibiotic resistance and, consistent with this, the 23S rRNA nucleotide A2058 is monomethylated by the enzyme product of the erm(42) gene. The second class shows no lincosamide resistance and lacks erm(42) and concomitant 23S rRNA methylation. Sequencing of the genome of a representative strain from this class, P. multocida 3361, revealed macrolide efflux and phosphotransferase genes [respectively termed msr(E) and mph(E)] that are arranged in tandem and presumably expressed from the same promoter. The third class exhibits the most marked drug phenotype, with high resistance to all of the macrolides tested, and possesses all three resistance determinants. The combinations of erm(42), msr(E), and mph(E) are chromosomally encoded and intermingled with other exogenous genes, many of which appear to have been transferred from other members of the Pasteurellaceae. The presence of some of the exogenous genes explains recent reports of resistance to additional drug classes. We have expressed recombinant versions of the erm(42), msr(E), and mph(E) genes within an isogenic Escherichia coli background to assess their individually contributions to resistance. Our findings indicate what types of compounds might have driven the selection for these resistance determinants. PMID:21709086

  9. Isolation of chromatin from dysfunctional telomeres reveals an important role for Ring1b in NHEJ-mediated chromosome fusions.

    PubMed

    Bartocci, Cristina; Diedrich, Jolene K; Ouzounov, Iliana; Li, Julia; Piunti, Andrea; Pasini, Diego; Yates, John R; Lazzerini Denchi, Eros

    2014-05-22

    When telomeres become critically short, DNA damage response factors are recruited at chromosome ends, initiating a cellular response to DNA damage. We performed proteomic isolation of chromatin fragments (PICh) in order to define changes in chromatin composition that occur upon onset of acute telomere dysfunction triggered by depletion of the telomere-associated factor TRF2. This unbiased purification of telomere-associated proteins in functional or dysfunctional conditions revealed the dynamic changes in chromatin composition that take place at telomeres upon DNA damage induction. On the basis of our results, we describe a critical role for the polycomb group protein Ring1b in nonhomologous end-joining (NHEJ)-mediated end-to-end chromosome fusions. We show that cells with reduced levels of Ring1b have a reduced ability to repair uncapped telomeric chromatin. Our data represent an unbiased isolation of chromatin undergoing DNA damage and are a valuable resource to map the changes in chromatin composition in response to DNA damage activation. PMID:24813883

  10. Isolation and proteomic analysis of the SYP61 compartment reveal its role in exocytic trafficking in Arabidopsis.

    PubMed

    Drakakaki, Georgia; van de Ven, Wilhelmina; Pan, Songqin; Miao, Yansong; Wang, Junqi; Keinath, Nana F; Weatherly, Brent; Jiang, Liwen; Schumacher, Karin; Hicks, Glenn; Raikhel, Natasha

    2012-02-01

    The endomembrane system is a complex and dynamic intracellular trafficking network. It is very challenging to track individual vesicles and their cargos in real time; however, affinity purification allows vesicles to be isolated in their natural state so that their constituent proteins can be identified. Pioneering this approach in plants, we isolated the SYP61 trans-Golgi network compartment and carried out a comprehensive proteomic analysis of its contents with only minimal interference from other organelles. The proteome of SYP61 revealed the association of proteins of unknown function that have previously not been ascribed to this compartment. We identified a complete SYP61 SNARE complex, including regulatory proteins and validated the proteome data by showing that several of these proteins associated with SYP61 in planta. We further identified the SYP121-complex and cellulose synthases, suggesting that SYP61 plays a role in the exocytic trafficking and the transport of cell wall components to the plasma membrane. The presence of proteins of unknown function in the SYP61 proteome including ECHIDNA offers the opportunity to identify novel trafficking components and cargos. The affinity purification of plant vesicles in their natural state provides a basis for further analysis and dissection of complex endomembrane networks. The approach is widely applicable and can afford the study of several vesicle populations in plants, which can be compared with the SYP61 vesicle proteome. PMID:21826108

  11. Isolation and proteomic analysis of the SYP61 compartment reveal its role in exocytic trafficking in Arabidopsis

    PubMed Central

    Drakakaki, Georgia; van de Ven, Wilhelmina; Pan, Songqin; Miao, Yansong; Wang, Junqi; Keinath, Nana F; Weatherly, Brent; Jiang, Liwen; Schumacher, Karin; Hicks, Glenn; Raikhel, Natasha

    2012-01-01

    The endomembrane system is a complex and dynamic intracellular trafficking network. It is very challenging to track individual vesicles and their cargos in real time; however, affinity purification allows vesicles to be isolated in their natural state so that their constituent proteins can be identified. Pioneering this approach in plants, we isolated the SYP61 trans-Golgi network compartment and carried out a comprehensive proteomic analysis of its contents with only minimal interference from other organelles. The proteome of SYP61 revealed the association of proteins of unknown function that have previously not been ascribed to this compartment. We identified a complete SYP61 SNARE complex, including regulatory proteins and validated the proteome data by showing that several of these proteins associated with SYP61 in planta. We further identified the SYP121-complex and cellulose synthases, suggesting that SYP61 plays a role in the exocytic trafficking and the transport of cell wall components to the plasma membrane. The presence of proteins of unknown function in the SYP61 proteome including ECHIDNA offers the opportunity to identify novel trafficking components and cargos. The affinity purification of plant vesicles in their natural state provides a basis for further analysis and dissection of complex endomembrane networks. The approach is widely applicable and can afford the study of several vesicle populations in plants, which can be compared with the SYP61 vesicle proteome. PMID:21826108

  12. Sub-pixel porosity revealed by x-ray scatter dark field imaging

    NASA Astrophysics Data System (ADS)

    Revol, V.; Jerjen, I.; Kottler, C.; Schütz, P.; Kaufmann, R.; Lüthi, T.; Sennhauser, U.; Straumann, U.; Urban, C.

    2011-08-01

    X-ray scatter dark field imaging based on the Talbot-Lau interferometer allows for the measurement of ultra-small angle x-ray scattering. The latter is related to the variations in the electron density in the sample at the sub- and micron-scale. Therefore, information on features of the object below the detector resolution can be revealed. In this article, it is demonstrated that scatter dark field imaging is particularly adapted to the study of a material's porosity. An interferometer, optimized for x-ray energies around 50 keV, enables the investigation of aluminum welding with conventional laboratory x-ray tubes. The results show an unprecedented contrast between the pool and the aluminum workpiece. Our conclusions are confirmed due to micro-tomographic three-dimensional reconstructions of the same object with a microscopic resolution.

  13. Sequence and phylogenetic analysis of highly pathogenic avian influenza H5N1 viruses isolated during 2006–2008 outbreaks in Pakistan reveals genetic diversity

    PubMed Central

    2012-01-01

    Background Since the first outbreak recorded in northern areas of Pakistan in early 2006, highly pathogenic avian influenza H5N1 viruses were isolated from commercial poultry and wild/domestic birds from different areas of Pakistan up to July 2008. Different isolates of H5N1 were sequenced to explore the genetic diversity of these viruses. Results Phylogenetic analysis revealed close clustering and highest sequence identity in all 8 genes to HPAI H5N1 isolates belonging to unified H5 clade 2.2, sub-lineage EMA-3 recovered from Afghanistan during the same time period. Two subgroups within Pakistani H5N1 viruses, from domestic and wild birds, were observed on the basis of their sequence homology and mutations. HPAI motif, preferred receptor specificity for α-(2, 3) linkages, potential N-linked glycosylation sites and an additional glycosylation site at the globular head of HA protein of four Pakistani H5N1 isolates. While, the amino acids associated with sensitivities to various antiviral drugs (Oseltamivir, Zanamivir, Amantadine) were found conserved for the Pakistani H5N1 isolates. Conspicuously, some important mutations observed at critical positions of antigenic sites (S141P, D155S, R162I & P181S) and at receptor binding pocket (A185T, R189K & S217P) of HA-1. A high sequence similarity between Pakistani HP H5N1 and LP H9N2 viruses was also observed. Avian like host specific markers with the exception of E627K in PB2, K356R in PA, V33I in NP, I28V in M2 and L107F in NS2 proteins were also observed. Conclusions Various point mutations in different genes of H5 viruses from Pakistan were observed during its circulation in the field. The outbreaks started in Khyber Pakhtoon Khawa (North West) province in 2006 and spread to the Southern regions over a period of time. Though migratory birds may have a role for this continued endemicity of clade 2.2 H5N1 viruses during 2006–2008 in Pakistan, the possibility of their transmission through legal or illegal poultry trade

  14. Imaging of action currents reveals the origin of biomagnetic fields in cardiac tissue

    NASA Astrophysics Data System (ADS)

    Holzer, Jenny R.; Sidorov, Veniamin; Fong, Luis; Baudenbacher, Franz

    2003-03-01

    The origin of the magnetocardiogram (MCG) and the relative information content between the MCG and the electrocardiogram (ECG) remain central questions in biomagnetism. To provide key insights to this question, we mapped excitation wave fronts in a thin layer of cardiac tissue of an isolated rabbit heart using high-resolution LTS-SQUID microscopy and epi-fluorescent imaging with sub-millimeter resolution. The combination of the two methods allows us to map the transmembrane potential (Vm) and the magnetic field over the same area. The leading edge of a propagating action potential can be defined as the wave front and can be identified by the difference in relative intensities of resting and depolarized tissue in the epi-fluorescence data. The corresponding magnetic field pattern was used to calculate the net action current, which shows a strong current component parallel to and overlying the Vm wave front. These electrically silent currents are a direct consequence of the cardiac bidomain with unequal anisotropies in the intra- and extracellular space and depend strongly on the angle of the wave front relative to the fiber orientation. We provide evidence that the MCG contains information not present in the ECG, and that it is necessary to reexamine the modeling and interpretation of the MCG.

  15. Trypanosoma (Herpetosoma) grosi: first isolation from Chinese striped field mouse (Apodemus agrarius).

    PubMed

    Guan, Guiquan; Niu, Qingli; Yang, Jifei; Li, Youquan; Gao, Jinliang; Luo, Jianxun; Yin, Hong

    2011-01-01

    A "lewisi-like" Trypanosoma parasite was isolated from the blood of Chinese striped field mice (Apodemus agrarius) trapped in the fields in the Gannan Tibet area, Gansu province, China. The parasite was successfully cultivated in vitro in HL-1 medium supplemented 20% fetal bovine serum (FBS). Full formed spheromastigote, metacyclic trypomastigote and trypomastigote structures were all visible in films made from the culture. A nucleotide fragment of 2159-bp length was amplified from genomic DNA of the parasite using specific primers for the 18S rRNA gene of trypanosomes. The alignment indicated that this parasite had higher identities with T. (Herpetosoma) grosi (more than 99.6%) than other Herpetosoma species (less than 98.5%), which suggest that the parasite should be classified as T. (Herpetosoma) grosi. This is the first time in China that an isolation of T. (Herpetosoma) grosi is reported although several strains of T. (Herpetosoma) lewisi have been isolated from rodents of family Muridae in various provinces. Thus, it was designated as T. (Herpetosoma) grosi Cha1 and deposited in the center of parasite strain collection and preservation in our laboratory for future study. In addition, this culture method will be used to isolate, maintain and study the long-term development of this parasite in vitro. PMID:21059401

  16. 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. PMID:9709014

  17. On the Generation of Intense Isolated Attosecond Pulses by Many-Cycle Laser Fields

    NASA Astrophysics Data System (ADS)

    Tzallas, Paris; Skantzakis, Emmanouil; Kruse, Jann E.; Charalambidis, Dimitrios

    Real-time observation of ultrafast dynamics in all states of matter requires temporal resolution on the atomic unit of time (24.189 asec) (1 asec = 1{0}^{-18} s). Tools for tracking such ultrafast dynamics are ultrashort light pulses. During the last decade, continuous efforts in ultrashort pulse engineering led to the development of light pulses width duration close to the atomic unit of time. Attosecond (asec) pulses have been synthesized by broadband coherent extreme ultraviolet (XUV) radiation generated by the interaction of gases or solids with an intense IR fs pulse. Asec pulse trains can be generated when the medium interacts with many-cycle driving IR fs laser fields. In this case, a broadband XUV frequency comb is emitted from the medium. The Fourier synthesis of a part of the comb results in an asec pulse train. Isolated asec pulses are generated when the medium is forced to emit XUV radiation only during few cycles of the driving laser field. This leads to the emission of a broadband quasicontinuum XUV radiation. The Fourier synthesis of the continuum part of the spectrum results in an isolated asec pulse. For the realization of studies of ultrafast dynamics, intense asec pulses are preferable. If the pulses are intense enough to induce a nonlinear process in a target system, they can be used for ultrafast dynamic studies in an XUV pump-probe configuration. Although trains of intense asec pulses are commonly produced nowadays, the generation of intense isolated asec pulses remains a challenge. Here, we review a recently developed approach for the generation of intense asec pulses using high-peak-power many-cycle laser fields. The approach is based on controlling, with asec precession, the response of the atomic dipole to an external many-cycle driving field in such a way as to emit an isolated asec XUV burst. This approach has been implemented by using the inteferometric polarization gating (IPG) technique. The bandwidth of the generated XUV radiation is

  18. 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.

  19. Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

    PubMed Central

    Wagner, Isaac D.; Varghese, Litty B.; Hemme, Christopher L.; Wiegel, Juergen

    2013-01-01

    Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances. PMID:23801987

  20. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    PubMed

    Latorre-Margalef, Neus; Avril, Alexis; Tolf, Conny; Olsen, Björn; Waldenström, Jonas

    2016-02-01

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. PMID:26655759

  1. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    PubMed Central

    Avril, Alexis; Tolf, Conny; Olsen, Björn

    2015-01-01

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. PMID:26655759

  2. [Production of a vaccine against enterotoxemia from Clostridium perfringens strains isolated in the field].

    PubMed

    Cherfaoui, S; Kadra, B

    1992-01-01

    We have isolated eight strains of C. perfringens from cases of enterotoxaemia. Five of these strains have revealed themselves toxic with respective types (type "A":2, type "C":2, type "D":1). In order to produce anti-enterotoxaemia vaccine, we have proceeded at the cultivation in fermenter of isolated strains and reference strains CWA 35, CWC and CWD AF. At the end of fermentation, we have evaluated the two following parameters: obtained biomass, and toxin titers. With the two classes of strains we reached an important biomass but toxins titers relatively weak comparatively to that which is usually required. It will be necessary then, to demonstrate the immunogen value of the produced vaccines by testing their efficacity. PMID:1309137

  3. Forecasting the Feasibility of Implementing Isolation Perimeters Between GM and non-GM Maize Fields Under Agricultural Conditions

    NASA Astrophysics Data System (ADS)

    Devos, Yann; Cougnon, Mathias; Thas, Olivier; De Clercq, Eva M.; Cordemans, Karl; Reheul, Dirk

    2008-10-01

    Although spatially isolating genetically modified (GM) maize fields from non-GM maize fields is a robust on-farm strategy to keep the adventitious presence of GM material in the harvests of neighboring non-GM maize fields due to cross-fertilizations below established labeling thresholds (and thus to ensure the spatial co-existence between maize cropping systems), the practical implementation of isolation perimeters attracted little research efforts. In this study, the feasibility of implementing isolation perimeters around GM maize fields is investigated. Using Geographic Information System datasets and Monte Carlo simulations, various scenarios differing in shares and spatial distributions of GM maize were tested for various isolation perimeters in six agricultural areas in Flanders. Factors that affect the feasibility of implementing isolation perimeters are discussed.

  4. Detection and Isolation Techniques for Methanogens from Microbial Mats (in the El Tatio Geyser Field, Chile)

    NASA Astrophysics Data System (ADS)

    Pearson, E. Z.; Franks, M. A.; Bennett, P.

    2010-12-01

    Isolating methanogenic archea from an extreme environment such as El Tatio (high altitude, arid climate) gives insight to the methanogenic taxas able to adapt and grow under extreme conditions. The hydrothermal waters at El Tatio geyser field demonstrate extreme geochemical conditions, with discharge water from springs and geysers at local boiling temperature (85° C) with high levels of arsenic and low DIC levels. Despite these challenges, many of El Tatio’s hundred plus hydrothermal features host extensive microbial mat communities, many showing evidence of methanogenesis. When trying to isolate methanogens unique to this area, various approaches and techniques were used. To detect the presence of methanogens in samples taken from the field, dissolved methane concentrations were determined via gas chromatography (GC) analysis. Samples were then selected for culturing and most probable number (MPN) enumeration, where growth was assessed using both methane production and observations of fluorescence under UV light. PCR was used to see if the archeal DNA was apparent directly from the field, and shotgun cloning was done to determine phylogenetic affiliation. Several culturing techniques were carried out in an attempt to isolate methanogens from samples that showed evidence of methanogenesis. The slant culturing method was used because of the increased surface area for colonization combined with the relative ease of keeping anaerobic. After a few weeks, when colonies were apparent, some were aseptically selected and inoculated to observe growth in a liquid media containing ampicillin to inhibit bacterial growth. Culturing techniques proved successful after inoculation, showing a slow growth of methanogens via GC and autofluorescence. Further PCR tests and subsequent sequencing were done to confirm and identify isolates.

  5. 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).

  6. Crystal field splitting on D<-->S transitions of atomic manganese isolated in solid krypton

    NASA Astrophysics Data System (ADS)

    Byrne, O.; Collier, M. A.; Ryan, M. C.; McCaffrey, J. G.

    2010-05-01

    Narrow excitation features present on the [Ar]3d64s1aD(J=9/2-1/2)6←[Ar]3d54s2aS1/26 transitions of manganese atoms isolated in solid Kr are analyzed within the framework of weak crystal field splitting. Use of the Wp optical lineshape function allowed identification of multiple zero-phonon lines for individual spin-orbit J states of the a aD6←aS6 transition recorded with laser-induced excitation spectroscopy. Excellent agreement exists between the predicted crystal field splitting patterns for the J levels of the aD6 state isolated in the «red» tetravacancy site of solid Kr. The tetrahedral crystal field of the «red» trapping site splits J >3/2 levels of the aDJ6 and aD7/24 states by approximately 30cm-1. This report represents the first definitive evidence of crystal field splitting, induced by the weak van der Waals interactions between a neutral metal atom and the rare gas atoms surrounding it in a well-defined solid-state site.

  7. Saccharopolyspora subtropica sp. nov., a thermophilic actinomycete isolated from soil of a sugar cane field.

    PubMed

    Wu, Hao; Liu, Bin; Pan, Shangli

    2016-05-01

    A novel thermophilic actinomycete, designated strain T3T, was isolated from a soil sample of a sugar cane field. The strain grew at 25-60 °C (optimum 37-50 °C), at pH 6.0-11.0 (optimum 7.0-9.0) and with 0-12.0 % (w/v) NaCl (optimum 0-7 %). The aerial mycelium was white and the vegetative mycelium was colourless to pale yellow. The substrate mycelium fragmented into rod-shaped elements after 4-5 days at 50 °C. The aerial mycelium formed flexuous chains of 5-20 spores per chain; the oval-shaped spores had spiny surfaces and were non-motile. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars consisted of arabinose, galactose and ribose. The cellular fatty acid profile consisted mainly of anteiso-C17 : 0, iso-C17 : 0 and iso-C16 : 0. The quinone system was composed predominantly of MK-9(H4). The phospholipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, phosphatidylmethylethanolamine and ninhydrin-positive glycophospholipids. The DNA G+C content of strain T3T was 71.3 mol%. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Saccharopolyspora. In the 16S rRNA gene tree of Saccharopolyspora it formed a distinct phyletic line and was related most closely to Saccharopolyspora thermophila 216T. However, the phenotypic characteristics of strain T3T were significantly different from those of S. thermophila 216T and DNA-DNA hybridization revealed a low level of relatedness (28.6-32.3 %) between them. Based on the phenotypic and phylogenetic data, strain T3T represents a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora subtropica sp. nov. is proposed. The type strain is T3T ( = DSM 46801T = CGMCC 4.7206T). PMID:26882893

  8. Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Hoang, Van-An; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Yang, Deok-Chun

    2014-09-01

    A novel Gram-staining-positive, aerobic bacterium, designed DCY80(T), was isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence analysis revealed that strain DCY80(T) belonged to the genus Brachybacterium (95.8-98.2 % similarity) and was most closely related to Brachybacterium faecium DSM 4810(T) (98.2 %). Colonies were circular, entire, low-convex, opaque and 0.5-1.0 mm in diameter after growth for 2 days on TSA at 30 °C. Growth occurred at 4-34 °C (optimum, 25 °C), at pH 5.0-10.0 (optimum, pH 6.5-7.0) and in the presence of 0-7.0 % NaCl. Strain DCY80(T) produced siderophores and was sensitive to penicillin G, erythromycin, cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin, carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels of DNA-DNA relatedness between strain DCY80(T) and B. faecium DSM 4810(T), B. paraconglomeratum KCTC 9916(T), B. saurashtrense DSM 23186(T) and B. conglomeratum KCTC 9915(T) were 46.9±0.5, 28.9±0.6, 20.4±0.9 and 17.3±0.4 %, respectively. The cell-wall peptidoglycan of strain DCY80(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. The menaquinones were MK-7 (85.8 %) and MK-8 (14.2 %). The major cellular fatty acids were anteiso-C15 : 0 (69.1 %) and anteiso-C17 : 0 (12.2 %). Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, two unidentified phospholipids and five unidentified polar lipids were found. On the basis of our phenotypic and genotypic analyses, strain DCY80(T) represents a novel species of the genus Brachybacterium, for which the name Brachybacterium ginsengisoli sp. nov. is proposed (type strain DCY80(T) = KCTC 29226(T) = JCM 19356(T)). PMID:24944333

  9. Phylogenetic and geographic analysis of fowl adenovirus field strains isolated from poultry in Poland.

    PubMed

    Niczyporuk, Jowita Samanta

    2016-01-01

    Fowl adenoviruses (FAdVs) are widely distributed in chickens in Poland and throughout the world. FAdV infections have been reported in the United States, Australia, Europe, and the Mediterranean basin. Detection of FAdVs strains is very important from the epidemiological point of view and for monitoring disease outbreaks and developing strategies for vaccine development. Several molecular epidemiology and phylogenetic studies have been performed, but the results obtained are still limited, because FAdV strains, even of the same serotype, have very diverse characteristics. Some strains are pathogenic and some are nonpathogenic. This report describes the successful isolation of 96 FAdV field strains from chickens in Poland. A PCR assay specific for the L1 loop region of the hexon gene was conducted, and the products were subjected to sequence analysis. The sequences were analysed using BLAST and Geneious 6.0 software and compared to adenovirus field and reference strain sequences from different parts of the world that are accessible in the NCBI GenBank database. The sequences of the adenovirus strains indicated that they belonged to five species, Fowl aviadenovirus A-E, represented by eight serotypes FAdV-1, FAdV-4, FAdV-5, FAdV-7, FAdV-8a, FAdV-8b, and FAdV-2/11 (FAdV-D). The relationships between FAdVs isolated in Poland and isolates from other regions of the world were determined. PMID:26446890

  10. 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.

  11. 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. PMID:26831160

  12. Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages

    PubMed Central

    Bobay, Louis-Marie; Smeesters, Pierre R.; Bousbata, Sabrina; Vermeersch, Marjorie; Perez-Morga, David; Drèze, Pierre-Alexandre; Rocha, Eduardo P. C.; Touchon, Marie

    2012-01-01

    Despite increasing interest in coagulase-negative staphylococci (CoNS), little information is available about their bacteriophages. We isolated and sequenced three novel temperate Siphoviridae phages (StB12, StB27, and StB20) from the CoNS Staphylococcus hominis and S. capitis species. The genome sizes are around 40 kb, and open reading frames (ORFs) are arranged in functional modules encoding lysogeny, DNA metabolism, morphology, and cell lysis. Bioinformatics analysis allowed us to assign a potential function to half of the predicted proteins. Structural elements were further identified by proteomic analysis of phage particles, and DNA-packaging mechanisms were determined. Interestingly, the three phages show identical integration sites within their host genomes. In addition to this experimental characterization, we propose a novel classification based on the analysis of 85 phage and prophage genomes, including 15 originating from CoNS. Our analysis established 9 distinct clusters and revealed close relationships between S. aureus and CoNS phages. Genes involved in DNA metabolism and lysis and potentially in phage-host interaction appear to be widespread, while structural genes tend to be cluster specific. Our findings support the notion of a possible reciprocal exchange of genes between phages originating from S. aureus and CoNS, which may be of crucial importance for pathogenesis in staphylococci. PMID:22923589

  13. Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages.

    PubMed

    Deghorain, Marie; Bobay, Louis-Marie; Smeesters, Pierre R; Bousbata, Sabrina; Vermeersch, Marjorie; Perez-Morga, David; Drèze, Pierre-Alexandre; Rocha, Eduardo P C; Touchon, Marie; Van Melderen, Laurence

    2012-11-01

    Despite increasing interest in coagulase-negative staphylococci (CoNS), little information is available about their bacteriophages. We isolated and sequenced three novel temperate Siphoviridae phages (StB12, StB27, and StB20) from the CoNS Staphylococcus hominis and S. capitis species. The genome sizes are around 40 kb, and open reading frames (ORFs) are arranged in functional modules encoding lysogeny, DNA metabolism, morphology, and cell lysis. Bioinformatics analysis allowed us to assign a potential function to half of the predicted proteins. Structural elements were further identified by proteomic analysis of phage particles, and DNA-packaging mechanisms were determined. Interestingly, the three phages show identical integration sites within their host genomes. In addition to this experimental characterization, we propose a novel classification based on the analysis of 85 phage and prophage genomes, including 15 originating from CoNS. Our analysis established 9 distinct clusters and revealed close relationships between S. aureus and CoNS phages. Genes involved in DNA metabolism and lysis and potentially in phage-host interaction appear to be widespread, while structural genes tend to be cluster specific. Our findings support the notion of a possible reciprocal exchange of genes between phages originating from S. aureus and CoNS, which may be of crucial importance for pathogenesis in staphylococci. PMID:22923589

  14. Full Genome Sequence Analysis of Two Isolates Reveals a Novel Xanthomonas Species Close to the Sugarcane Pathogen Xanthomonas albilineans

    PubMed Central

    Pieretti, Isabelle; Cociancich, Stéphane; Bolot, Stéphanie; Carrère, Sébastien; Morisset, Alexandre; Rott, Philippe; Royer, Monique

    2015-01-01

    Xanthomonas albilineans is the bacterium responsible for leaf scald, a lethal disease of sugarcane. Within the Xanthomonas genus, X. albilineans exhibits distinctive genomic characteristics including the presence of significant genome erosion, a non-ribosomal peptide synthesis (NRPS) locus involved in albicidin biosynthesis, and a type 3 secretion system (T3SS) of the Salmonella pathogenicity island-1 (SPI-1) family. We sequenced two X. albilineans-like strains isolated from unusual environments, i.e., from dew droplets on sugarcane leaves and from the wild grass Paspalum dilatatum, and compared these genomes sequences with those of two strains of X. albilineans and three of Xanthomonas sacchari. Average nucleotide identity (ANI) and multi-locus sequence analysis (MLSA) showed that both X. albilineans-like strains belong to a new species close to X. albilineans that we have named “Xanthomonas pseudalbilineans”. X. albilineans and “X. pseudalbilineans” share many genomic features including (i) the lack of genes encoding a hypersensitive response and pathogenicity type 3 secretion system (Hrp-T3SS), and (ii) genome erosion that probably occurred in a common progenitor of both species. Our comparative analyses also revealed specific genomic features that may help X. albilineans interact with sugarcane, e.g., a PglA endoglucanase, three TonB-dependent transporters and a glycogen metabolism gene cluster. Other specific genomic features found in the “X. pseudalbilineans” genome may contribute to its fitness and specific ecological niche. PMID:26213974

  15. Heterogeneity in the Infection Biology of Campylobacter jejuni Isolates in Three Infection Models Reveals an Invasive and Virulent Phenotype in a ST21 Isolate from Poultry

    PubMed Central

    Humphrey, Suzanne; Lacharme-Lora, Lizeth; Chaloner, Gemma; Gibbs, Kirsty; Humphrey, Tom; Williams, Nicola; Wigley, Paul

    2015-01-01

    Although Campylobacter is the leading cause of bacterial foodborne gastroenteritis in the world and the importance of poultry as a source of infection is well understood we know relatively little about its infection biology in the broiler chicken. Much of what we know about the biology of Campylobacter jejuni is based on infection of inbred or SPF laboratory lines of chickens with a small number of isolates used in most laboratory studies. Recently we have shown that both the host response and microbial ecology of C. jejuni in the broiler chicken varies with both the host-type and significantly between C. jejuni isolates. Here we describe heterogeneity in infection within a panel of C. jejuni isolates in two broiler chicken breeds, human intestinal epithelial cells and the Galleria insect model of virulence. All C. jejuni isolates colonised the chicken caeca, though colonisation of other parts of the gastrointestinal tract varied between isolates. Extra-intestinal spread to the liver varied between isolates and bird breed but a poultry isolate 13126 (sequence type 21) showed the greatest levels of extra-intestinal spread to the liver in both broiler breeds with over 70% of birds of the fast growing breed and 50% of the slower growing breed having C. jejuni in their livers. Crucially 13126 is significantly more invasive than other isolates in human intestinal epithelial cells and gave the highest mortality in the Galleria infection model. Taken together our findings suggest that not only is there considerable heterogeneity in the infection biology of C. jejuni in avian, mammalian and alternative models, but that some isolates have an invasive and virulent phenotype. Isolates with an invasive phenotype would pose a significant risk and increased difficulty in control in chicken production and coupled with the virulent phenotype seen in 13126 could be an increased risk to public health. PMID:26496441

  16. Heterogeneity in the Infection Biology of Campylobacter jejuni Isolates in Three Infection Models Reveals an Invasive and Virulent Phenotype in a ST21 Isolate from Poultry.

    PubMed

    Humphrey, Suzanne; Lacharme-Lora, Lizeth; Chaloner, Gemma; Gibbs, Kirsty; Humphrey, Tom; Williams, Nicola; Wigley, Paul

    2015-01-01

    Although Campylobacter is the leading cause of bacterial foodborne gastroenteritis in the world and the importance of poultry as a source of infection is well understood we know relatively little about its infection biology in the broiler chicken. Much of what we know about the biology of Campylobacter jejuni is based on infection of inbred or SPF laboratory lines of chickens with a small number of isolates used in most laboratory studies. Recently we have shown that both the host response and microbial ecology of C. jejuni in the broiler chicken varies with both the host-type and significantly between C. jejuni isolates. Here we describe heterogeneity in infection within a panel of C. jejuni isolates in two broiler chicken breeds, human intestinal epithelial cells and the Galleria insect model of virulence. All C. jejuni isolates colonised the chicken caeca, though colonisation of other parts of the gastrointestinal tract varied between isolates. Extra-intestinal spread to the liver varied between isolates and bird breed but a poultry isolate 13126 (sequence type 21) showed the greatest levels of extra-intestinal spread to the liver in both broiler breeds with over 70% of birds of the fast growing breed and 50% of the slower growing breed having C. jejuni in their livers. Crucially 13126 is significantly more invasive than other isolates in human intestinal epithelial cells and gave the highest mortality in the Galleria infection model. Taken together our findings suggest that not only is there considerable heterogeneity in the infection biology of C. jejuni in avian, mammalian and alternative models, but that some isolates have an invasive and virulent phenotype. Isolates with an invasive phenotype would pose a significant risk and increased difficulty in control in chicken production and coupled with the virulent phenotype seen in 13126 could be an increased risk to public health. PMID:26496441

  17. Global Genome and Transcriptome Analyses of Magnaporthe oryzae Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evolution

    PubMed Central

    Dong, Yanhan; Li, Ying; Zhao, Miaomiao; Jing, Maofeng; Liu, Xinyu; Liu, Muxing; Guo, Xianxian; Zhang, Xing; Chen, Yue; Liu, Yongfeng; Liu, Yanhong; Ye, Wenwu; Zhang, Haifeng; Wang, Yuanchao; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

    2015-01-01

    Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution, in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates. This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however, genetic variations among different isolates of M. oryzae remain largely unknown, particularly at genome and transcriptome levels. Here, we applied genomic and transcriptomic analytical tools to investigate M. oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars. A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15. Genome-wide expression profiling revealed the presence of two critical expression patterns of M. oryzae based on 64 known pathogenicity-related (PaR) genes. In addition, 134 candidate effectors with various segregation patterns were identified. Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves. Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity. Moreover, Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex (BIC) and their overexpression leads to suppression of defense-related gene expression in rice, suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host. Thus, our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M. oryzae field isolate 98-06, and reveal molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions. PMID:25837042

  18. Characterization of Listeria monocytogenes isolates from cattle and ground beef by pulsed-field gel electrophoresis.

    PubMed

    Foerster, Claudia; Vidal, Lorena; Troncoso, Miriam; Figueroa, Guillermo

    2012-01-01

    The aims of this study were to determine the occurrence of Listeria monocytogenes in cattle feces and ground beef, to characterize these strains by pulsed-field gel electrophoresis and to compare them to three listeria strains found in humans. Cattle from different origins (n = 250) and ground beef obtained from supermarkets (n = 40) were sampled. The results show low occurrence in cattle feces (0.4 %) but a higher presence in ground beef (37 %). An important part of the ground beef strains (80 %) had > 95 % similarity with a strain isolated from a human sporadic case and the ATCC 19115 used as control. The strain isolated from cattle feces had 93 % similarity to clone 009, previously associated with a listeriosis outbreak related to cheese. Cattle and ground beef can harbor virulent L. monocytogenes strains. Further studies in animals and animal products are needed to improve listeriosis control. PMID:23102469

  19. Membrane solid-phase extraction: Field application for isolation of polycyclic aromatic hydrocarbons from water samples

    SciTech Connect

    Furlong, E.T.; Koleis, J.C.; Gates, P.M.

    1995-12-31

    Solid-phase extraction (SPE) membranes (M-SPE) were used to isolate microgram-per-liter to nanogram-per-liter quantities of polycyclic aromatic hydrocarbons (PAH) in 4- to 8-liter ground-water samples from a crude-oil-contaminated ground-water site near Bemidji, Minnesota. The M-SPE method was evaluated (1) under laboratory conditions using reagent water fortified with individual PAH at 1.23 micrograms per liter, and (2) at the Bemidji site. At the site, ground-water samples were processed and PAH isolated using a M-SPE system connected directly to the well pump. Following sample isolation, all M-SPE samples were extracted using dichloromethane and analyzed by gas chromatography-mass spectrometry with selected-ion monitoring. Operationally, the M-SPE method provided a simple means to isolate PAH on site at the wellhead, particularly for anoxic water samples. Acceptable recoveries, ranging from 56 to over 100 percent, were observed for lower molecular weight PAH (naphthalene to pyrene) using the M-SPE method. Recoveries using M-SPE were somewhat lower, but reproducible, for higher molecular weight PAH (chrysene to benzo[ghi]perylene), ranging from 18 to 56 percent. M-SPE provides the capability to collect and field isolate PAH from a sufficiently large number of samples to identify environmental chemical processes occurring at individual compound concentrations of 50 to 1,200 nanograms per liter. Using M-SPE, the potential for facilitated transport of PAH by in situ-derived dissolved organic carbon (DOC) was evaluated at the site. Plots comparing DOC and PAH concentrations indicate that PAH concentrations increase exponentially with linear increases in DOC concentrations.

  20. Genetic Variability and Geographical Distribution of Mycotoxigenic Fusarium verticillioides Strains Isolated from Maize Fields in Texas

    PubMed Central

    Ortiz, Carlos S.; Richards, Casey; Terry, Ashlee; Parra, Joselyn; Shim, Won-Bo

    2015-01-01

    Maize is the dominant cereal crop produced in the US. One of the main fungal pathogens of maize is Fusarium verticillioides, the causative agent of ear and stalk rots. Significantly, the fungus produces a group of mycotoxins - fumonisins - on infested kernels, which have been linked to various illnesses in humans and animals. Nonetheless, durable resistance against F. verticillioides in maize is not currently available. In Texas, over 2.1 million acres of maize are vulnerable to fumonisin contamination, but understanding of the distribution of toxigenic F. verticillioides in maize-producing areas is currently lacking. Our goal was to investigate the genetic variability of F. verticillioides in Texas with an emphasis on fumonisin trait and geographical distribution. A total of 164 F. verticillioides cultures were isolated from 65 maize-producing counties. DNA from each isolate was extracted and analyzed by PCR for the presence of FUM1- a key fumonisin biosynthesis gene - and mating type genes. Results showed that all isolates are in fact F. verticillioides capable of producing fumonisins with a 1:1 mating-type gene ratio in the population. To further study the genetic diversity of the population, isolates were analyzed using RAPD fingerprinting. Polymorphic markers were identified and the analysis showed no clear correlation between the RAPD profile of the isolates and their corresponding geographical origin. Our data suggest the toxigenic F. verticillioides population in Texas is widely distributed wherever maize is grown. We also hypothesize that the population is fluid, with active movement and genetic recombination occurring in the field. PMID:26361468

  1. Genetic Variability and Geographical Distribution of Mycotoxigenic Fusarium verticillioides Strains Isolated from Maize Fields in Texas.

    PubMed

    Ortiz, Carlos S; Richards, Casey; Terry, Ashlee; Parra, Joselyn; Shim, Won-Bo

    2015-09-01

    Maize is the dominant cereal crop produced in the US. One of the main fungal pathogens of maize is Fusarium verticillioides, the causative agent of ear and stalk rots. Significantly, the fungus produces a group of mycotoxins - fumonisins - on infested kernels, which have been linked to various illnesses in humans and animals. Nonetheless, durable resistance against F. verticillioides in maize is not currently available. In Texas, over 2.1 million acres of maize are vulnerable to fumonisin contamination, but understanding of the distribution of toxigenic F. verticillioides in maize-producing areas is currently lacking. Our goal was to investigate the genetic variability of F. verticillioides in Texas with an emphasis on fumonisin trait and geographical distribution. A total of 164 F. verticillioides cultures were isolated from 65 maize-producing counties. DNA from each isolate was extracted and analyzed by PCR for the presence of FUM1- a key fumonisin biosynthesis gene - and mating type genes. Results showed that all isolates are in fact F. verticillioides capable of producing fumonisins with a 1:1 mating-type gene ratio in the population. To further study the genetic diversity of the population, isolates were analyzed using RAPD fingerprinting. Polymorphic markers were identified and the analysis showed no clear correlation between the RAPD profile of the isolates and their corresponding geographical origin. Our data suggest the toxigenic F. verticillioides population in Texas is widely distributed wherever maize is grown. We also hypothesize that the population is fluid, with active movement and genetic recombination occurring in the field. PMID:26361468

  2. 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

  3. Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta.

    PubMed

    Sánchez, Marta M; Fritze, Dagmar; Blanco, Ana; Spröer, Cathrin; Tindall, Brian J; Schumann, Peter; Kroppenstedt, Reiner M; Diaz, Pilar; Pastor, F I Javier

    2005-03-01

    A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10-40 degrees C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C(15 : 0). Comparison of 16S rRNA gene sequences showed that strain BP-23(T) fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97.4 %), Paenibacillus pabuli (97.1 %) and Paenibacillus amylolyticus (96.9 %). The DNA-DNA relatedness of strain BP-23(T) with respect to these three species was very low (32.7, 31.6 and 23.0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23(T) should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23(T) (=CECT 7022(T)=DSM 15478(T)). PMID:15774688

  4. Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field.

    PubMed

    Wu, Yue-Hong; Xu, Lin; Zhou, Peng; Wang, Chun-Sheng; Oren, Aharon; Xu, Xue-Wei

    2015-10-01

    A Gram-stain-negative, motile, aerobic bacterial strain, designated 22DY15T, was isolated from a deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise. The isolate was a short rod with a single flagellum and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory quinone. The major polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphoglycolipid, one aminolipid and three unidentified phospholipids. The principal fatty acid (>70 %) was C18 : 1ω7c. The genomic DNA G+C content was 64.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22DY15T represents a distinct lineage within the family Rhodobacteraceae. The closest relatives were species of the genera Aliiroseovarius (93.3–96.0 % 16S rRNA gene sequence similarity), Sulfitobacter (94.0–96.0 %) and Loktanella (92.0–95.9 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain 22DY15T could be differentiated from its most closely related genera. Therefore, it is proposed that strain 22DY15T represents a novel species in a new genus of the family Rhodobacteraceae, for which the name Brevirhabdus pacifica gen. nov., sp. nov. is proposed. The type strain of the type species is 22DY15T ( = JCM 19489T = DSM 27767T = CGMCC 1.12416T = MCCC 1K00276T). PMID:26198580

  5. Pathotyping of Vibrio isolates by multiplex PCR reveals a risk of virulent strain spreading in New Caledonian shrimp farms.

    PubMed

    Labreuche, Yannick; Pallandre, Laurane; Ansquer, Dominique; Herlin, José; Wapotro, Billy; Le Roux, Frédérique

    2012-01-01

    Two recurring syndromes threaten the viability of the shrimp industry in New Caledonia, which represents the second largest export business. The "Syndrome 93" is a cold season disease due to Vibrio penaeicida affecting all shrimp farms, while the "Summer Syndrome" is a geographically restricted vibriosis caused by a virulent lineage of Vibrio nigripulchritudo. Microbiological procedures for diagnosis of these diseases are time-consuming and do not have the ability to discriminate the range of virulence potentials of V. nigripulchritudo. In this study, we developed a multiplex PCR method to simultaneously detect these two bacterial species and allow for pathotype discrimination. The detection limits of this assay, that includes an internal amplification control to eliminate any false-negative results, were determined at 10 pg purified DNA and 200 cfu/ml. After confirming the effectiveness of our method using experimentally infected animals, its accuracy was compared to standard biochemical methods during a field survey using 94 samples collected over 3 years from shrimp farms encountering mortality events. The multiplex PCR showed very high specificity for the detection of V. penaeicida and V. nigripulchritudo (inclusivity and exclusivity 100%) and allowed us to detect the spreading of highly pathogenic isolates of V. nigripulchritudo to a farm adjoining the "Summer Syndrome area." This assay represents a simple, rapid, and cost-effective diagnostic tool for implementing timely risk management decisions but also understanding the seasonal and geographical distribution of these pathogens. PMID:22001997

  6. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000-2012.

    PubMed

    Cassiday, Pamela K; Skoff, Tami H; Jawahir, Selina; Tondella, M Lucia

    2016-03-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000-2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%-46% of isolates tested from 2000-2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000-2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis. PMID:26886905

  7. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000–2012

    PubMed Central

    Skoff, Tami H.; Jawahir, Selina; Tondella, M. Lucia

    2016-01-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000–2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%–46% of isolates tested from 2000–2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000–2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis. PMID:26886905

  8. Terribacillus saccharophilus gen. nov., sp. nov. and Terribacillus halophilus sp. nov., spore-forming bacteria isolated from field soil in Japan.

    PubMed

    An, Sun-Young; Asahara, Mika; Goto, Keiichi; Kasai, Hiroaki; Yokota, Akira

    2007-01-01

    Three strains, 002-048(T), RB589 and 002-051(T), isolated from field soil in Japan, were characterized using a polyphasic approach. The isolates were Gram-positive, strictly aerobic, non-motile rods that formed ellipsoidal, subterminal endospores. The chemotaxonomic characteristics of these isolates included the presence of meso-diaminopimelic acid as the cell-wall peptidoglycan, anteiso-C(15 : 0) and anteiso-C(17 : 0) as the major cellular fatty acids and MK-7 as the predominant menaquinone. The DNA G+C content was 44-46 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolates represented an independent lineage that is distinct from related taxa and exhibited less than 94.3 % sequence similarity with respect to those taxa. Moreover, a DNA-DNA hybridization analysis showed that the three isolates represented two species. On the basis of their phenotypic and phylogenetic distinctiveness, the isolates represent two species within a novel genus, for which the names Terribacillus saccharophilus gen. nov., sp. nov. and Terribacillus halophilus sp. nov. are proposed. The type strain of T. saccharophilus is 002-048(T) (=IAM 15309(T)=KCTC 13936(T)) and the type strain of T. halophilus is 002-051(T) (=IAM 15310(T)=KCTC 13937(T)). PMID:17220440

  9. Shipboard magnetic field "noise" reveals shallow heavy mineral sediment concentrations in Chesapeake Bay

    USGS Publications Warehouse

    Shah, Anjana K.; Vogt, Peter R.; Rosenbaum, Joseph G.; Newell, Wayne; Cronin, Thomas M.; Willard, Debra A.; Hagen, Rick A.; Brozena, John; Hofstra, Albert

    2012-01-01

    Shipboard magnetic field data collected over Chesapeake Bay exhibit low-amplitude, short-wavelength anomalies that most likely indicate shallow concentrations of heavy mineral sediments. Piston core layers and black sand beach samples exhibit enhanced magnetic susceptibilities and carry remanent magnetization, with mineralogical analyses indicating ilmenite and trace magnetite and/or maghemite and hematite. The anomalies are subtle and would be filtered as noise using traditional approaches, but can instead be highlighted using spectral methods, thus providing nearly continuous coverage along survey tracks. The distribution of the anomalies provides constraints on relevant sorting mechanisms. Comparisons to sonar data and previous grab samples show that two of three areas surveyed exhibit short-wavelength anomalies that are clustered over sand-covered areas, suggesting initial sorting through settling mechanisms. This is supported by a correlation between core magnetic susceptibility and grain size. Near the Choptank River, where sediment resuspension is wave-dominated, anomalies show a sharp decrease with seafloor depth that cannot be explained by signal attenuation alone. In Pocomoke Sound, where both tidal currents and wave-action impact sediment resuspension, anomalies show a more gradual decrease with depth. Near the mouth of the bay, where there is a higher influx of sediments from the continental shelf, short-wavelength anomalies are isolated and do not appear to represent heavy mineral sand concentrations. These combined observations suggest the importance of further sorting by erosional processes in certain parts of the bay. Additionally, comparisons of these data to cores sampling pre-Holocene sediments suggest that the sorting of heavy minerals in higher energy, shallow water environments provides a mechanism for correlations between core magnetic susceptibility and sea-level changes.

  10. Induction of avirulence in U.S. virulent field isolates of Magnaporthe oryzae by AVR-Pita 1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 in field isolates (TM2, ZN19, B2 and B8) that originally were virule...

  11. Characterization of Salmonella isolates from retail foods based on serotyping, pulse field gel electrophoresis, antibiotic resistance and other phenotypic properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sixteen Salmonella strains isolated from a variety of foods during 2000 and 2003, by the Florida State Department of Agriculture, were characterized by various genotypic and phenotypic tests. Among 16 isolates, 15 different serotypes were identified. Pulse-Field Gel Electrophoresis (PFGE) fingerpr...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Breakdown characteristics of an isolated conducting object in a uniform electric field

    NASA Technical Reports Server (NTRS)

    Grothaus, M. G.; Trost, T. F.

    1986-01-01

    A laboratory experiment was conducted to determine the physical processes involved in the electrical breakdown of a particular spark gap arrangement. The gap consists of an isolated conducting ellipsoid located midway between two large flat electrodes. Gradual increase of the applied electric field, E, in the gap produces corona on the ellipsoid tips followed by flashover in a leader-arc sequence. The leader phase consists of the abrupt formation of ionized channels which partially bridge the gap and then decay prior to the arc. Measurements of dE/dt and of current were made, and photographs were taken with an image converter. Experimental parameters are listed.

  14. Dynamic full field optical coherence tomography: subcellular metabolic contrast revealed in tissues by interferometric signals temporal analysis

    PubMed Central

    Apelian, Clement; Harms, Fabrice; Thouvenin, Olivier; Boccara, A. Claude

    2016-01-01

    We developed a new endogenous approach to reveal subcellular metabolic contrast in fresh ex vivo tissues taking advantage of the time dependence of the full field optical coherence tomography interferometric signals. This method reveals signals linked with local activity of the endogenous scattering elements which can reveal cells where other OCT-based techniques fail or need exogenous contrast agents. We benefit from the micrometric transverse resolution of full field OCT to image intracellular features. We used this time dependence to identify different dynamics at the millisecond scale on a wide range of organs in normal or pathological conditions. PMID:27446672

  15. Wide-field Ca2+ imaging reveals visually evoked activity in the retrosplenial area

    PubMed Central

    Murakami, Tomonari; Yoshida, Takashi; Matsui, Teppei; Ohki, Kenichi

    2015-01-01

    Due to recent advances of genetic manipulation, mouse brain has become a useful model for studying brain function, which demands whole brain functional mapping techniques in the mouse brain. In the present study, to finely map visual responsive areas in the mouse brain, we combined high-resolution wide-field optical imaging with transgenic mice containing the genetically encoded Ca2+ indicator, GCaMP3. With the high signal amplitude of GCaMP3 expressing in excitatory neurons, this system allowed neural activity to be observed with relatively fine spatial resolution and cell-type specificity. To evaluate this system, we examined whether non-visual areas exhibited a visual response over the entire surface of the mouse hemisphere. We found that two association areas, the retrosplenial area (RS) and secondary motor/anterior cingulate area (M2/AC), were significantly responsive to drifting gratings. Examination using gratings with distinct spatiotemporal frequency parameters revealed that the RS strongly responded to high-spatial and low-temporal frequency gratings. The M2/AC exhibited a response property similar to that of the RS, though it was not statistically significant. Finally, we performed cellular imaging using two-photon microscopy to examine orientation and direction selectivity of individual neurons, and found that a minority of neurons in the RS clearly showed visual responses sharply selective for orientation and direction. These results suggest that neurons in RS encode visual information of fine spatial details in images. Thus, the present study shows the usefulness of the functional mapping method using a combination of wide-field and two-photon Ca2+ imaging, which allows for whole brain mapping with high spatiotemporal resolution and cell-type specificity. PMID:26106292

  16. Isolation and purification of {sup 14}C-atrazine metabolites from field grown sugarcane and sorghum

    SciTech Connect

    Ash, S.G.; Larson, J.D.; Talaat, R.E.

    1996-10-01

    Sugarcane and sorghum plants were grown in separate field plots and treated with [2,4,6-{sup 14}C]-Atrazine (according to standard agricultural practices and at levels approximating the maximum usage rate) in partial fulfillment of EPA registration requirements. Sugarcane leaves were collected just before the final (fourth) test material application and at final harvest; canes were collected only at final harvest. Atrazine and a total of 20 metabolites of atrazine, accounting for 45.1% of the total radioactive residues, were isolated and characterized from prefourth application sugarcane leaves. Sorghum forage samples were collected 30 days after treatment (30 DAT), and at silage stage; mature fodder and grain were collected at final harvest. Two additional metabolites of atrazine were isolated and characterized from 30 DAT sorghum. Flowcharts describing the extraction and fractionation procedures used for isolation and purification of selected metabolites will be presented. The mass spectra as well as proposed metabolic pathways for these metabolites will be presented in an accompanying abstract.

  17. Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity

    PubMed Central

    2011-01-01

    Background Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isolates from blood, peri-anal, and wound sources were examined in an attempt to identify genetic features that could be correlated to each isolation source. Results Pulsed-field gel electrophoresis, multi-locus sequence typing and antibiotic resistance profiles demonstrated genotypic and phenotypic variation. Each isolate was sequenced to high-quality draft status, which allowed for comparative genomic analyses with existing A. baumannii genomes. A high resolution, whole genome alignment method detailed the phylogenetic relationships of sequenced A. baumannii and found no correlation between phylogeny and body site of isolation. This method identified genomic regions unique to both those isolates found on the surface of the skin or in wounds, termed colonization isolates, and those identified from body fluids, termed invasive isolates; these regions may play a role in the pathogenesis and spread of this important pathogen. A PCR-based screen of 74 A. baumanii isolates demonstrated that these unique genes are not exclusive to either phenotype or isolation source; however, a conserved genomic region exclusive to all sequenced A. baumannii was identified and verified. Conclusions The results of the comparative genome analysis and PCR assay show that A. baumannii is a diverse and genomically variable pathogen that appears to have the potential to cause a range of human disease regardless of the isolation source. PMID:21639920

  18. Multiphasic approach reveals genetic diversity of environmental and patient isolates of Mycobacterium mucogenicum and Mycobacterium phocaicum associated with an outbreak of bacteremias at a Texas hospital.

    PubMed

    Cooksey, Robert C; Jhung, Michael A; Yakrus, Mitchell A; Butler, W Ray; Adékambi, Toidi; Morlock, Glenn P; Williams, Margaret; Shams, Alicia M; Jensen, Bette J; Morey, Roger E; Charles, Nadege; Toney, Sean R; Jost, Kenneth C; Dunbar, Denise F; Bennett, Vickie; Kuan, Marcella; Srinivasan, Arjun

    2008-04-01

    Between March and May 2006, a Texas hospital identified five Mycobacterium mucogenicum bloodstream infections among hospitalized oncology patients using fluorescence high-performance liquid chromatography analysis of mycolic acids. Isolates from blood cultures were compared to 16 isolates from environmental sites or water associated with this ward. These isolates were further characterized by hsp65, 16S rRNA, and rpoB gene sequencing, hsp65 PCR restriction analysis, and molecular typing methods, including repetitive element PCR, random amplified polymorphic DNA PCR, and pulsed-field gel electrophoresis (PFGE) of large restriction fragments. Three of five patient isolates were confirmed as M. mucogenicum and were in a single cluster as determined by all identification and typing methods. The remaining two patient isolates were identified as different strains of Mycobacterium phocaicum by rpoB sequence analysis. One of these matched an environmental isolate from a swab of a hand shower in the patient's room, while none of the clinical isolates of M. mucogenicum matched environmental strains. Among the other 15 environmental isolates, 11 were identified as M. mucogenicum and 4 as M. phocaicum strains, all of which were unrelated by typing methods. Although the 16S rRNA gene sequences matched for all 14 M. mucogenicum isolates, there were two each of the hsp65 and rpoB sequevars, seven PCR typing patterns, and 12 PFGE patterns. Among the seven M. phocaicum isolates were three 16S rRNA sequevars, two hsp65 sequevars, two rpoB sequevars, six PCR typing patterns, and six PFGE patterns. This outbreak represents the first case of catheter-associated bacteremia caused by M. phocaicum and the first report of clinical isolates from a U.S. hospital. The investigation highlights important differences in the available typing methods for mycobacteria and demonstrates the genetic diversity of these organisms even within narrow confines of time and space. PMID:18310417

  19. Some Trends in Radioactive Waste Form Behavior Revealed in Long-Term Field Tests

    SciTech Connect

    Ojovan, M. I.; Ojovan, N. V.; Startceva, I. V.; Barinov, A. S.

    2002-02-25

    Results from long-term field tests with borosilicate glass, cement and bitumen waste forms containing actual intermediate-level radioactive waste are summarized and discussed in the paper. Leaching behavior of the waste forms was evaluated by monitoring the contamination of contacting water. Measured leach rates of the three waste-form materials were in a narrow range in shallow subsurface repositories, but varied in a wide range at an open testing site owing to weathering of bitumen and cement materials. The repositories were opened after 12-year testing for visual examination, sampling and analysis. All retrieved waste forms were in good physical condition. The study has not revealed any negative changes in the waste glass. Some ageing processes were detected in cement and bitumen waste forms, which can positively (bitumen) or negatively (cement) affect physical and containment properties of these waste materials. It has been established that a significant proportion of the radioactive inventory in the bitumen waste form became associated with the bitumen phase. Phase separation of this radioactive bitumen has shown, than the asphaltene fraction is responsible for the major part of the radioactivity retained by the bitumen.

  20. Coherent control of broadband isolated attosecond pulses in a chirped two-color laser field

    SciTech Connect

    Zou Pu; Zeng Zhinan; Zheng Yinghui; Lu Yingying; Liu Peng; Li Ruxin; Xu Zhizhan

    2010-03-15

    A theoretical investigation is presented that uses a strong two-color laser field composed of a linearly chirped fundamental (900 nm) and its subharmonic (1800-nm) laser pulses to control coherently the broadband isolated attosecond pulses in high-order harmonic generations. After the subharmonic field is added, the intrinsic chirp of harmonic emission can be reduced significantly, and consequently, the temporal synchronization of harmonic emission with different photon energies at the level of the single-atom response can be realized. In addition, the scheme is robust against the carrier envelope phase variation to produce a twin pulse of stable sub-100-as duration, and the relative intensity of the twin pulses can be changed just by adjusting the relative time delay of the two driving pulses, which is of benefit in general pump-probe experiments.

  1. Evaluation of the in vitro activity of flumequine against field isolates of Brachyspira hyodysenteriae.

    PubMed

    Aller-Morán, Luis Miguel; Martínez-Lobo, Francisco Javier; Rubio, Pedro; Carvajal, Ana

    2015-12-01

    Flumequine is a quinolone derivative used in veterinary medicine to treat enteric infections, mainly those caused by Gram negative bacteria and also some Gram positive. Some recent reports by field practitioners have suggested that its use in swine dysentery outbreaks can minimize the impact of this disease. This study aims to evaluate the in vitro anti-Brachyspira hyodysenteriae activity of flumequine. Forty eight field isolates of the bacterium were evaluated using a microdilution test. The lack of colon bioavailability studies of flumequine in pigs makes it difficult to establish the true efficacy of this antibiotic for swine dysentery control. Nonetheless, the relatively high values of MIC50 (50 μg/mL) and MBC50 (50 μg/mL) obtained suggest poor activity against B. hyodysenteriae. Flumequine activity in swine dysentery outbreaks could be related to its activity against other bacteria, different from B. hyodysenteriae, engaged in swine dysentery pathogenesis. PMID:26679795

  2. Crustal Velocity Field from InSAR and GPS reveals Internal Deformation of Western Tibet

    NASA Astrophysics Data System (ADS)

    Wang, H.; Wright, T. J.

    2010-12-01

    a compromise between solution roughness and data misfit. The resultant velocity field satisfies the InSAR and GPS data with an rms misfit of ~1 mm/yr. It reveals a series of focused strain zones within the plateau and low slip rate on the Karakoram fault. Although focused strain zones are predicted by block models, those that we observe appear to occur away from the major faults, in the interior of the plateau. At least one is associated with a possible postseismic transient (1996 Mw6.8). This is incompatible with block models, but consistent with continuum models of continental deformation modified by the short-term influence of the earthquake cycle. Finally, we augmented the GPS velocity field using existing InSAR rate maps for the whole Tibetan plateau. It shows that a continental-scale velocity fields can be constructed without complete InSAR coverage using our method.

  3. Comparative Genome Hybridization Reveals Substantial Variation among Clinical Isolates of Borrelia burgdorferi Sensu Stricto with Different Pathogenic Properties

    PubMed Central

    Terekhova, Darya; Iyer, Radha; Wormser, Gary P.; Schwartz, Ira

    2006-01-01

    Clinical and murine studies suggest that there is a differential pathogenicity of different genotypes of Borrelia burgdorferi, the spirochetal agent of Lyme disease. Comparative genome hybridization was used to explore the relationship between different genotypes. The chromosomes of all studied isolates were highly conserved (>93%) with respect to both sequence and gene order. Plasmid sequences were substantially more diverse. Plasmids lp54, cp26, and cp32 were present in all tested isolates, and their sequences and gene order were conserved. The majority of linear plasmids showed variation both in terms of presence among different isolates and in terms of sequence and gene order. The data strongly imply that all B. burgdorferi clinical isolates contain linear plasmids related to each other, but the structure of these replicons may vary substantially from isolate to isolate. These alterations include deletions and presumed rearrangements that are likely to result in unique plasmid elements in many isolates. There is a strong correlation between complete genome hybridization profiles and other typing methods, which, in turn, also correlate to differences in pathogenicity. Because there is substantially less variation in the chromosomal and circular plasmid portions of the genome, the major differences in open reading frame content and genomic diversity among isolates are linear plasmid driven. PMID:16923879

  4. Molecular analyses revealed genetic complexity in Citrus tristeza virus Dekopon isolate and its aphid-transmitted progeny

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An assessment was made of the disease potential of a Citrus tristeza virus (CTV) isolate designated Dekopon found in a hybrid mandarin variety topworked in a citrus planting in Fresno County, CA. After aphid transmissions (AT), parental and AT isolates were analyzed by SSCP, genotyping with multipl...

  5. Genetic characterization of Toxoplasma gondii isolates from Portugal, Austria, and Israel reveals higher genetic variability within the type II lineage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study compared genetic diversity of Toxoplasma gondii isolates from Portugal, Austria and Israel. For this, we genotyped 90 T. gondii isolates (16 from Portugal, 67 from Austria and 7 from Israel) using 10 nested PCR-restriction length polymorphism (RFLP) genetic markers and 15 microsatellite (...

  6. Socially flexible female choice and premating isolation in field crickets (Teleogryllus spp.).

    PubMed

    Bailey, N W; Macleod, E

    2014-01-01

    Social influences on mate choice are predicted to influence evolutionary divergence of closely related taxa, because of the key role mate choice plays in reproductive isolation. However, it is unclear whether females choosing between heterospecific and conspecific male signals use previously experienced social information in the same manner or to the same extent that they do when discriminating among conspecific mates only. We tested this using two field cricket sister species (Teleogryllus oceanicus and Teleogryllus commodus), in which considerable information is known about the role of male calling song in premating isolation, in addition to the influence of acoustic experience on the development of reproductive traits. We manipulated the acoustic experience of replicate populations of both species and found, unexpectedly, that experience of male calling song during rearing did not change how accurate females were in choosing a conspecific over a heterospecific male song during playback trials. However, females with acoustic experience were considerably less responsive to male song compared with naïve females. Our results suggest that variation in the acoustic environment affects mate choice in both species, but that it may have a limited impact on premating isolation. The fact that social flexibility during interspecific mate discrimination does not appear to operate identically to that which occurs during conspecific mate discrimination highlights the importance of considering the context in which animals exercise socially flexible mating behaviours. We suggest an explanation for why social flexibility might be context dependent and discuss the consequences of such flexibility for the evolution of reproductive isolation. PMID:24330452

  7. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662

  8. Subtype Analysis of Salmonella Isolated from Subclinically Infected Dairy Cattle and Dairy Farm Environments Reveals the Presence of Both Human- and Bovine-Associated Subtypes

    PubMed Central

    Rodriguez-Rivera, L.D.; Wright, E.M.; Siler, J.D.; Elton, M.; Cummings, K.J.; Warnick, L.D.; Wiedmann, M.

    2014-01-01

    While it is well established that clinically ill livestock represent a reservoir of Salmonella, the importance of subclinical shedders as sources of human salmonellosis is less well defined. The aims of this study were to assess the subtype diversity of Salmonella in healthy dairy cattle and associated farm environments and to compare the subtypes isolated from these sources with the Salmonella subtypes associated with clinical human cases in the same geographic area. A total of 1,349 Salmonella isolates from subclinical dairy cattle and farm environments (46 farms) were initially characterized by traditional or molecular serotyping and tested for antimicrobial susceptibility. A set of 381 representative isolates was selected for further characterization by pulsed-field gel electrophoresis (PFGE); these isolates represented unique combinations of sampling date, serovar, antimicrobial resistance pattern, farm of origin, and source, to avoid overrepresentation of subtypes that were re-isolated from a given source. These 381 isolates represented 26 Salmonella serovars; the most common serovars were Cerro [(38.8%, 148/381) isolated from 21 farms], Kentucky [16.3%; 10 farms], Typhimurium [9.4%; 7 farms], Newport [7.6%; 8 farms], and Anatum [6.3%; 6 farms]. Among the 381 isolates, 90 (23.6%) were resistant to between 1 and 11 antimicrobial agents, representing 50 different antimicrobial resistance patterns. Overall, 61 XbaI-PFGE types were detected among these 381 isolates, indicating considerable Salmonella diversity on dairy farms without evidence of clinical salmonellosis. Fourteen PFGE types, representing 12 serovars, exactly matched PFGE types from human isolates, suggesting that subclinically infected dairy cattle could be sources of human disease-associated Salmonella. PMID:24636164

  9. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina

    PubMed Central

    2013-01-01

    Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small

  10. QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

    PubMed Central

    2012-01-01

    Background Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. Results QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. Conclusions Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with

  11. Studies on the virulence of two field isolates of the classical Swine Fever virus genotype 2.3 rostock in wild boars of different age groups.

    PubMed

    Kaden, V; Lange, E; Polster, U; Klopfleisch, R; Teifke, J P

    2004-06-01

    The virulence of two isolates of the classical swine fever virus (CSFV) was studied in experimentally infected wild boars of different ages. The isolates, originating from wild boars shot in Mecklenburg-Western Pomerania (isolate '1829-NVP') and in Rhineland-Palatinate (isolate '11722-WIL'), belong to the genetic subgroup 2.3 Rostock. Clinical picture, transient viraemia, virus excretion and gross lesions at necropsy as well as a failure of virus detection at the end of the experiment revealed that this virus subtype was only moderately virulent. Whereas one subadult wild boar and both 7-week-old wild boar piglets infected intranasally became sick and died, only one of three 8-week-old animals which survived after contact infection remained CSFV positive until the end of the experiment [34 days post infection (dpi)], although neutralizing antibodies were present. This underlines the role of young boars in CSF epidemics. The isolate '11722-WIL' was shed by an infected adult wild boar and was transmitted to susceptible piglets. Interestingly, all animals which became sick and died also were found to be infected with a secondary pathogen. Therefore, we assume that after infection with moderately virulent CSFV simultaneous infections with other pathogens may be important for the clinical course and the outcome of the disease as well as for a spread of the virus in field. PMID:15330978

  12. Analysis of Clinical Isolates of Helicobacter pylori in Pakistan Reveals High Degrees of Pathogenicity and High Frequencies of Antibiotic Resistance

    PubMed Central

    Rasheed, Faisal; Campbell, Barry James; Alfizah, Hanafiah; Varro, Andrea; Zahra, Rabaab; Yamaoka, Yoshio; Pritchard, David Mark

    2014-01-01

    Background Antibiotic resistance in Helicobacter pylori contributes to failure in eradicating the infection and is most often due to point and missense mutations in a few key genes. Methods The antibiotic susceptibility profiles of H. pylori isolates from 46 Pakistani patients were determined by Etest. Resistance and pathogenicity genes were amplified, and sequences were analyzed to determine the presence of mutations. Results A high percentage of isolates (73.9%) were resistant to metronidazole (MTZ), with considerable resistance to clarithromycin (CLR; 47.8%) and amoxicillin (AML; 54.3%) also observed. Relatively few isolates were resistant to tetracycline (TET; 4.3%) or to ciprofloxacin (CIP; 13%). However, most isolates (n = 43) exhibited resistance to one or more antibiotics. MTZ-resistant isolates contained missense mutations in oxygen-independent NADPH nitroreductase (RdxA; 8 mutations found) and NADH flavin oxidoreductase (FrxA; 4 mutations found). In the 23S rRNA gene, responsible for CLR resistance, a new point mutation (A2181G) and 4 previously reported mutations were identified. Pathogenicity genes cagA, dupA, and vacA s1a/m1 were detected frequently in isolates which were also found to be resistant to MTZ, CLR, and AML. A high percentage of CagA and VacA seropositivity was also observed in these patients. Phylogenetic analysis of partial sequences showed uniform distribution of the 3′ region of cagA throughout the tree. Conclusions We have identified H. pylori isolates in Pakistan which harbor pathogenicity genes and worrying antibiotic resistance profiles as a result of having acquired multiple point and missense mutations. H. pylori eradication regimens should therefore be reevaluated in this setting. PMID:24827414

  13. 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

  14. Isolation and pathogenic analysis of virulent Marek's disease virus field strain in China.

    PubMed

    Cui, Ning; Su, Shuai; Sun, Peng; Zhang, Yankun; Han, Ni; Cui, Zhizhong

    2016-07-01

    Marek's disease (MD) has become increasingly common in China, resulting in considerable economic loss. The etiological agent is unclear. In this study, we isolated a field MD virus (MDV) strain, designated SX1301, from CVI988/Rispens-vaccinated chickens with tumors. Co-infection of avian leukosis virus, reticuloendotheliosis virus, and chicken infectious anemia virus was excluded by polymerase chain reaction, enzyme-linked immunosorbant assay, DNA blotting hybridization, and indirect immunofluorescence assay. As with most strains isolated in China, SX1301 had the same amino acid mutation of meq protein at positions 77(E), 80(Y), and 115(A) Animal experimental results showed development of lethal MD in 57% and MD tumor in 23% of the specific pathogen-free chickens inoculated with SX1301, with tumors mainly distributed in spleen, liver, and kidney. CVI988/Rispens protected 83% of chickens upon challenge with SX1301, with a mortality rate and tumor incidence of 10% and 7%, respectively. These results implicated SX1301 as a virulent MDV strain, with commercial MDV vaccine CVI988/Rispens unable to confer adequate protection against SX1301. There have been no reports of very virulent (vv) plus MDV in China, but frequently occurring virulent MDV may account for the repeated outbreaks of MD. Vaccines with greater efficacy are needed to protect against MDV. PMID:26976907

  15. The isolation of a field strain of Haemonchus contortus in Queensland showing multiple anthelmintic resistance.

    PubMed

    Green, P E; Forsyth, B A; Rowan, K J; Payne, G

    1981-02-01

    Following the apparent failure of levamisole to control infections of Haemonchus contortus in sheep at Lawes in south eastern Queensland, a strain of this parasite was isolated at the Animal Research Institute, Yeerongpilly. This strain was used to infect sheep at Yeerongpilly and the Merrindale Research Station, Victoria where four experiments to classify the resistance pattern of the parasite were carried out. Resistance to thiabendazole was first suspected in 1969, and these experiments confirmed that resistance to this drug was still present. They also showed that a strong degree of resistance had been developed to both levamisole and morantel tartrate. Other benzimidazole anthelmintics and also the organophosphorus compound naphthalophos were only moderately effective against the original isolate but rafoxanide, nitroxynil and phenothiazine were almost 100% effective. Other highly effective chemicals were disophenol and closantel. After passaging the strain for four generations with both levamisole and albendazole, resistance to both naphthalophos and the newer benzimidazole anthelmintics increased dramatically. This is the first report of a field strain of H. contortus exhibiting resistance to benzimidazole, non-benzimidazole and organophosphorus anthelmintics. PMID:7259650

  16. The magnetic field of the Large Magellanic Cloud revealed through Faraday rotation.

    PubMed

    Gaensler, B M; Haverkorn, M; Staveley-Smith, L; Dickey, J M; McClure-Griffiths, N M; Dickel, J R; Wolleben, M

    2005-03-11

    We have measured the Faraday rotation toward a large sample of polarized radio sources behind the Large Magellanic Cloud (LMC) to determine the structure of this galaxy's magnetic field. The magnetic field of the LMC consists of a coherent axisymmetric spiral of field strength approximately 1 microgauss. Strong fluctuations in the magnetic field are also seen on small (<0.5 parsec) and large (approximately 100 parsecs) scales. The large bursts of recent star formation and supernova activity in the LMC argue against standard dynamo theory, adding to the growing evidence for rapid field amplification in galaxies. PMID:15761149

  17. The genetic diversity of genus Bacillus and the related genera revealed by 16s rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    PubMed Central

    Cihan, Arzu Coleri; Tekin, Nilgun; Ozcan, Birgul; Cokmus, Cumhur

    2012-01-01

    Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%), the facultative thermophiles (14%) and the mesophiles (12%). These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16), Brevibacillus (13), Paenibacillus (1) and Thermoactinomycetes (2) were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4–100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6), B. lichenformis (3), B. subtilis (3), B. agri (3), B. smithii (2), T. vulgaris (2) and finally P. barengoltzii (1). In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies. PMID:24031834

  18. Optimization of infrared two-color multicycle field synthesis for intense-isolated-attosecond-pulse generation

    SciTech Connect

    Lan Pengfei; Takahashi, Eiji J.; Midorikawa, Katsumi

    2010-11-15

    We present the optimization of the two-color synthesis method for generating an intense isolated attosecond pulse (IAP) in the multicycle regime. By mixing an infrared assistant pulse with a Ti:sapphire main pulse, we show that an IAP can be produced using a multicycle two-color pulse with a duration longer than 30 fs. We also discuss the influence of the carrier-envelope phase (CEP) and the relative intensity on the generation of IAPs. By optimizing the wavelength of the assistant field, IAP generation becomes insensitive to the CEP slip. Therefore, the optimized two-color method enables us to relax the requirements of pulse duration and easily produce the IAP with a conventional multicycle laser pulse. In addition, it enables us to markedly suppress the ionization of the harmonic medium. This is a major advantage for efficiently generating intense IAPs from a neutral medium by applying the appropriate phase-matching and energy-scaling techniques.

  19. Isolation and Characterization of a Novel Facultative Anaerobic Filamentous Fungus from Japanese Rice Field Soil

    PubMed Central

    Tonouchi, Akio

    2009-01-01

    A novel filamentous fungus strain designated RB-1 was isolated into pure culture from Japanese rice field soil through an anaerobic role tube technique. The strain is a mitosporic fungus that grows in both aerobic and strict anaerobic conditions using various mono-, di-, tri-, and polysaccharides with acetate and ethanol productions. The amount of acetate produced was higher than that of ethanol in both aerobic and anaerobic cultures. The characteristic verrucose or punctuate conidia of RB-1 closely resembled those of some strains of the genus Thermomyces, a thermophilic or mesophilic anamorphic ascomycete. However, based on phylogenetic analysis with the small subunit (SSU) and large subunit (LSU) rDNA sequences, RB-1 was characterized as a member of the class Lecanoromycetes of the phylum Ascomycota. Currently, RB-1 is designated as an anamorphic ascomycete and is phylogenetically considered an incertae sedis within the class Lecanoromycetes. PMID:20148171

  20. Attosecond Lighthouses: How To Use Spatiotemporally Coupled Light Fields To Generate Isolated Attosecond Pulses

    NASA Astrophysics Data System (ADS)

    Vincenti, H.; Quéré, F.

    2012-03-01

    Under the effect of even simple optical components, the spatial properties of femtosecond laser beams can vary over the duration of the light pulse. We show how using such spatiotemporally coupled light fields in high harmonic generation experiments (e.g., in gases or dense plasmas) enables the production of attosecond lighthouses, i.e., sources emitting a collection of angularly well-separated light beams, each consisting of an isolated attosecond pulse. This general effect opens the way to a new generation of light sources, particularly suitable for attosecond pump-probe experiments, and provides a new tool for ultrafast metrology, for instance, giving direct access to fluctuations of the carrier-envelope relative phase of even the most intense ultrashort lasers.

  1. Isolated horizons, p-form matter fields, topology, and the black-hole/string correspondence principle

    SciTech Connect

    Liko, Tomas

    2009-04-15

    We study the mechanics of D-dimensional isolated horizons (IHs) for Einstein gravity in the presence of arbitrary p-form matter fields. This generalizes the analysis of Copsey and Horowitz to nonstationary spacetimes and therefore the local first law in D>4 dimensions to include nonmonopolar (dipole) charges. The only requirement for the local first law to hold is that the action has to be differentiable. The resulting conserved charges are all intrinsic to the horizon and are independent of the topology of the horizon cross sections. We explicitly calculate the local charges for five-dimensional black holes and black rings that are relevant within the context of superstring theory. We conclude with some comments on the black-hole/string correspondence principle and argue that IHs (or some other quasilocal variant) should play a fundamental role in superstring theory.

  2. Optimization of infrared two-color multicycle field synthesis for intense-isolated-attosecond-pulse generation

    NASA Astrophysics Data System (ADS)

    Lan, Pengfei; Takahashi, Eiji J.; Midorikawa, Katsumi

    2010-11-01

    We present the optimization of the two-color synthesis method for generating an intense isolated attosecond pulse (IAP) in the multicycle regime. By mixing an infrared assistant pulse with a Ti:sapphire main pulse, we show that an IAP can be produced using a multicycle two-color pulse with a duration longer than 30 fs. We also discuss the influence of the carrier-envelope phase (CEP) and the relative intensity on the generation of IAPs. By optimizing the wavelength of the assistant field, IAP generation becomes insensitive to the CEP slip. Therefore, the optimized two-color method enables us to relax the requirements of pulse duration and easily produce the IAP with a conventional multicycle laser pulse. In addition, it enables us to markedly suppress the ionization of the harmonic medium. This is a major advantage for efficiently generating intense IAPs from a neutral medium by applying the appropriate phase-matching and energy-scaling techniques.

  3. Isolation and identification of pathogenic microorganisms at wastewater-irrigated fields: ratios in air and wastewater

    SciTech Connect

    Teltsch, B.; Kedmi, S.; Bonnet, L.; Borenzstajn-Rotem, Y.; Katzenelson, E.

    1980-06-01

    Samples of air and corresponding wastewater samples were taken at wastewater spray-irrigated fields. The concentrations of salmonellae and enteroviruses present in these samples were determined and compared with those of coliforms, and the ratios between them were calculated. The most common Salmonella serotype in the air was Salmonella ohio, whereas in the wastewater, Salmonella anatum was the most common. Enteroviruses isolated and identified were poliovirus, echovirus, and coxsackievirus type B. From the ratios of salmonellas to coliforms and enteroviruses to coliforms in the air, as compared to these ratios in the wastewater, it was concluded that the suitability of coliforms as an indication of airborne contamination caused by spray irrigation is questionable.

  4. Magnetic-field-induced ferroelectric polarization reversal in magnetoelectric composites revealed by piezoresponse force microscopy

    NASA Astrophysics Data System (ADS)

    Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin

    2014-07-01

    Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results.

  5. Magnetic-field-induced ferroelectric polarization reversal in magnetoelectric composites revealed by piezoresponse force microscopy.

    PubMed

    Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin

    2014-08-01

    Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results. PMID:24953042

  6. Detection of beta2 and major toxin genes by PCR in Clostridium perfringens field isolates of domestic animals suffering from enteritis or enterotoxaemia.

    PubMed

    Sting, Reinhard

    2009-01-01

    The production of Clostridium (C.) perfringens toxins in the intestine is an important cause of enteritis and enterotoxaemia in livestock. In the present study, the alpha toxin and the genes encoding beta2 and epsilon toxin could be frequently detected by means of phenotypical and PCR examinations in these bacteria. The C. perfringens isolates originated from 1213 field samples taken from diseased or perished livestock located in the north-eastern administrative districts of Baden-Württemberg (Germany) from 2005 to 2008. The beta2 toxin gene of C perfringens was detected in all animal species examined, comprising pigs, the small ruminants sheep and goats, cattle, horses, rabbits, alpacas and lamas, and fallow deer. Among all the animal species included in this study, pigs attracted attention by a high quota of 74.2% (610 of 822) cpb2-positive C. perfringens isolates in comparison to the other animal species tested, revealing a quota of 20.8% (72 of 346). Beta2 toxigenic isolates could be predominantly cultivated from the faeces of young piglets. The beta toxin gene was detected in isolates from piglets and small ruminants only, amounting to 82.5% (33 of 40) in piglets in combination with the cpb2 gene. In this context, cpb2/cpb-positive C. perfringens isolates of piglets could be clearly detected more often in the intestine of perished animals (18 of 158) than in faeces (15 of 629). Furthermore, cpb2-bearing C. perfringens isolates were detected in cattle, horses, rabbits, alpacas and lamas, and fallow deer to a notable degree. The detection of C. perfringens isolates carrying the epsilon toxin gene was restricted to sheep and goats. Of a total of 242 small ruminants that succumbed to sudden death, 71 (29.3%) harboured epsilon toxin-positive C. perfringens isolates in their intestines. These cases clustered seasonally in the second quarter (April, May, and June) of the year. Neither the isolates bearing the beta2 nor beta toxin gene nor those carrying the epsilon

  7. Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection

    PubMed Central

    Azarian, Taj; Ali, Afsar; Johnson, Judith A.; Mohr, David; Prosperi, Mattia; Veras, Nazle M.; Jubair, Mohammed; Strickland, Samantha L.; Rashid, Mohammad H.; Alam, Meer T.; Weppelmann, Thomas A.; Katz, Lee S.; Tarr, Cheryl L.; Colwell, Rita R.

    2014-01-01

    ABSTRACT Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy. PMID:25538191

  8. Anti-Kibble-Zurek Behavior in Crossing the Quantum Critical Point of a Thermally Isolated System Driven by a Noisy Control Field.

    PubMed

    Dutta, Anirban; Rahmani, Armin; Del Campo, Adolfo

    2016-08-19

    We show that a thermally isolated system driven across a quantum phase transition by a noisy control field exhibits anti-Kibble-Zurek behavior, whereby slower driving results in higher excitations. We characterize the density of excitations as a function of the ramping rate and the noise strength. The optimal driving time to minimize excitations is shown to scale as a universal power law of the noise strength. Our findings reveal the limitations of adiabatic protocols such as quantum annealing and demonstrate the universality of the optimal ramping rate. PMID:27588838

  9. Towards phonon photonics: scattering-type near-field optical microscopy reveals phonon-enhanced near-field interaction.

    PubMed

    Hillenbrand, Rainer

    2004-08-01

    Diffraction limits the spatial resolution in classical microscopy or the dimensions of optical circuits to about half the illumination wavelength. Scanning near-field microscopy can overcome this limitation by exploiting the evanescent near fields existing close to any illuminated object. We use a scattering-type near-field optical microscope (s-SNOM) that uses the illuminated metal tip of an atomic force microscope (AFM) to act as scattering near-field probe. The presented images are direct evidence that the s-SNOM enables optical imaging at a spatial resolution on a 10nm scale, independent of the wavelength used (lambda=633 nm and 10 microm). Operating the microscope at specific mid-infrared frequencies we found a tip-induced phonon-polariton resonance on flat polar crystals such as SiC and Si3N4. Being a spectral fingerprint of any polar material such phonon-enhanced near-field interaction has enormous applicability in nondestructive, material-specific infrared microscopy at nanoscale resolution. The potential of s-SNOM to study eigenfields of surface polaritons in nanostructures opens the door to the development of phonon photonics-a proposed infrared nanotechnology that uses localized or propagating surface phonon polaritons for probing, manipulating and guiding infrared light in nanoscale devices, analogous to plasmon photonics. PMID:15231334

  10. 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

  11. Faraday isolator based on a TSAG single crystal with compensation of thermally induced depolarization inside magnetic field

    NASA Astrophysics Data System (ADS)

    Snetkov, Ilya; Palashov, Oleg

    2015-04-01

    A Faraday isolator based on a terbium scandium aluminum garnet (TSAG) single crystal with compensation of thermally induced depolarization inside magnetic field was demonstrated. An isolation ratio of 32 dB at 350 W cw laser radiation power was achieved. Thermally induced depolarization and thermal lens were studied and compared with similar thermal effects arising in the widely used terbium gallium garnet crystal (TGG) for the first time.

  12. Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand

    PubMed Central

    Coker, Olabisi Oluwabukola; Ngamphiw, Chumpol; Tongsima, Sissades; Regmi, Sanjib Mani; Clark, Taane G.; Ong, Rick Twee Hee; Teo, Yik-Ying; Prammananan, Therdsak; Palittapongarnpim, Prasit

    2016-01-01

    Genome sequencing plays a key role in understanding the genetic diversity of Mycobacterium tuberculosis (M.tb). The genotype-specific character of M. tb contributes to tuberculosis severity and emergence of drug resistance. Strains of M. tb complex can be classified into seven lineages. The Nonthaburi (NB) genotype, belonging to the Indo-Oceanic lineage (lineage 1), has a unique spoligotype and IS6110-RFLP pattern but has not previously undergone a detailed whole genome analysis. In addition, there is not much information available on the whole genome analysis of M. tb isolates from tuberculous meningitis (TBM) patients in public databases. Isolates CSF3053, 46-5069 and 43-13838 of NB genotype were obtained from the cerebrospinal fluids of TBM Thai patients in Siriraj Hospital, Bangkok. The whole genomes were subjected to high throughput sequencing. The sequence data of each isolate were assembled into draft genome. The sequences were also aligned to reference genome, to determine genomic variations. Single nucleotide polymorphisms (SNPs) were obtained and grouped according to the functions of the genes containing them. They were compared with SNPs from 1,601 genomes, representing the seven lineages of M. tb complex, to determine the uniqueness of NB genotype. Susceptibility to first-line, second-line and other antituberculosis drugs were determined and related to the SNPs previously reported in drug-resistant related genes. The assembled genomes have an average size of 4,364,461 bp, 4,154 genes, 48 RNAs and 64 pseudogenes. A 500 base pairs deletion, which includes ppe50, was found in all isolates. RD239, specific for members of Indo Oceanic lineage, and RD147c were identified. A total of 2,202 SNPs were common to the isolates and used to classify the NB strains as members of sublineage 1.2.1. Compared with 1,601 genomes from the seven lineages of M. tb complex, mutation G2342203C was found novel to the isolates in this study. Three mutations (T28910C, C1180580T

  13. Isolation and characterization of a low phytic acid rice mutant reveals a mutation in the rice orthologue of maize mik.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a forward genetics approach, we isolated two independent low phytic acid (lpa) rice mutants, N15-186 and N15-375. Both mutants are caused by single gene, recessive non-lethal mutations which result in approximately 75% (N15-186) and 43% (N15-375) reductions in seed phytic acid (inositol hexaki...

  14. Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants

    PubMed Central

    Panoutsopoulou, Kalliope; Hatzikotoulas, Konstantinos; Xifara, Dionysia Kiara; Colonna, Vincenza; Farmaki, Aliki-Eleni; Ritchie, Graham R. S.; Southam, Lorraine; Gilly, Arthur; Tachmazidou, Ioanna; Fatumo, Segun; Matchan, Angela; Rayner, Nigel W.; Ntalla, Ioanna; Mezzavilla, Massimo; Chen, Yuan; Kiagiadaki, Chrysoula; Zengini, Eleni; Mamakou, Vasiliki; Athanasiadis, Antonis; Giannakopoulou, Margarita; Kariakli, Vassiliki-Eirini; Nsubuga, Rebecca N.; Karabarinde, Alex; Sandhu, Manjinder; McVean, Gil; Tyler-Smith, Chris; Tsafantakis, Emmanouil; Karaleftheri, Maria; Xue, Yali; Dedoussis, George; Zeggini, Eleftheria

    2014-01-01

    Isolated populations are emerging as a powerful study design in the search for low-frequency and rare variant associations with complex phenotypes. Here we genotype 2,296 samples from two isolated Greek populations, the Pomak villages (HELIC-Pomak) in the North of Greece and the Mylopotamos villages (HELIC-MANOLIS) in Crete. We compare their genomic characteristics to the general Greek population and establish them as genetic isolates. In the MANOLIS cohort, we observe an enrichment of missense variants among the variants that have drifted up in frequency by more than fivefold. In the Pomak cohort, we find novel associations at variants on chr11p15.4 showing large allele frequency increases (from 0.2% in the general Greek population to 4.6% in the isolate) with haematological traits, for example, with mean corpuscular volume (rs7116019, P=2.3 × 10−26). We replicate this association in a second set of Pomak samples (combined P=2.0 × 10−36). We demonstrate significant power gains in detecting medical trait associations. PMID:25373335

  15. Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13, Isolated from Vitis vinifera L. Xylem Sap

    PubMed Central

    Lai, Wan Xin; Gan, Han Ming; Hudson, André O.

    2016-01-01

    The whole-genome sequence of a new genospecies of Methylobacterium sp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server. PMID:26847900

  16. The role of magnetic fields in starburst galaxies as revealed by OH megamasers

    SciTech Connect

    McBride, James; Quataert, Eliot; Heiles, Carl; Bauermeister, Amber E-mail: eliot@astro.berkeley.edu

    2014-01-10

    We present estimates of magnetic field strengths in the interstellar media of starburst galaxies derived from measurements of Zeeman splitting associated with OH megamasers. The results for eight galaxies with Zeeman detections suggest that the magnetic energy density in the interstellar medium of starburst galaxies is comparable to their hydrostatic gas pressure, as in the Milky Way. We discuss the significant uncertainties in this conclusion, and possible measurements that could reduce these uncertainties. We also compare the Zeeman splitting derived magnetic field estimates to magnetic field strengths estimated using synchrotron fluxes and assuming that the magnetic field and cosmic rays have comparable energy densities, known as the 'minimum energy' argument. We find that the minimum energy argument systematically underestimates magnetic fields in starburst galaxies, and that the conditions that would be required to produce agreement between the minimum energy estimate and the Zeeman derived estimate of interstellar medium magnetic fields are implausible. The conclusion that magnetic fields in starburst galaxies exceed the minimum energy magnetic fields is consistent with starburst galaxies adhering to the linearity of the far-infrared-radio correlation.

  17. The ultrastructure and flexibility of thylakoid membranes in leaves and isolated chloroplasts as revealed by small-angle neutron scattering.

    PubMed

    Unnep, R; Zsiros, O; Solymosi, K; Kovács, L; Lambrev, P H; Tóth, T; Schweins, R; Posselt, D; Székely, N K; Rosta, L; Nagy, G; Garab, G

    2014-09-01

    We studied the periodicity of the multilamellar membrane system of granal chloroplasts in different isolated plant thylakoid membranes, using different suspension media, as well as on different detached leaves and isolated protoplasts-using small-angle neutron scattering. Freshly isolated thylakoid membranes suspended in isotonic or hypertonic media, containing sorbitol supplemented with cations, displayed Bragg peaks typically between 0.019 and 0.023Å(-1), corresponding to spatially and statistically averaged repeat distance values of about 275-330 Å⁻¹. Similar data obtained earlier led us in previous work to propose an origin from the periodicity of stroma thylakoid membranes. However, detached leaves, of eleven different species, infiltrated with or soaked in D2O in dim laboratory light or transpired with D2O prior to measurements, exhibited considerably smaller repeat distances, typically between 210 and 230 Å⁻¹, ruling out a stromal membrane origin. Similar values were obtained on isolated tobacco and spinach protoplasts. When NaCl was used as osmoticum, the Bragg peaks of isolated thylakoid membranes almost coincided with those in the same batch of leaves and the repeat distances were very close to the electron microscopically determined values in the grana. Although neutron scattering and electron microscopy yield somewhat different values, which is not fully understood, we can conclude that small-angle neutron scattering is a suitable technique to study the periodic organization of granal thylakoid membranes in intact leaves under physiological conditions and with a time resolution of minutes or shorter. We also show here, for the first time on leaves, that the periodicity of thylakoid membranes in situ responds dynamically to moderately strong illumination. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy. PMID:24508217

  18. Asteroseismology can reveal strong internal magnetic fields in red giant stars.

    PubMed

    Fuller, Jim; Cantiello, Matteo; Stello, Dennis; Garcia, Rafael A; Bildsten, Lars

    2015-10-23

    Internal stellar magnetic fields are inaccessible to direct observations, and little is known about their amplitude, geometry, and evolution. We demonstrate that strong magnetic fields in the cores of red giant stars can be identified with asteroseismology. The fields can manifest themselves via depressed dipole stellar oscillation modes, arising from a magnetic greenhouse effect that scatters and traps oscillation-mode energy within the core of the star. The Kepler satellite has observed a few dozen red giants with depressed dipole modes, which we interpret as stars with strongly magnetized cores. We find that field strengths larger than ~10(5) gauss may produce the observed depression, and in one case we infer a minimum core field strength of ≈10(7) gauss. PMID:26494754

  19. Isolation of marine bacteria with antimicrobial activities from cultured and field-collected soft corals.

    PubMed

    Chen, Yu-Hsin; Kuo, Jimmy; Sung, Ping-Jung; Chang, Yu-Chia; Lu, Mei-Chin; Wong, Tit-Yee; Liu, Jong-Kang; Weng, Ching-Feng; Twan, Wen-Hung; Kuo, Fu-Wen

    2012-12-01

    Bacteria associated with eight field-collected and five cultured soft corals of Briareum sp., Sinularia sp., Sarcophyton sp., Nephtheidae sp., and Lobophytum sp. were screened for their abilities in producing antimicrobial metabolites. Field-collected coral samples were collected from Nanwan Bay in southern Taiwan. Cultured corals were collected from the cultivating tank at National Museum of Marine Biology and Aquarium. A total of 1,526 and 1,138 culturable, heterotrophic bacteria were isolated from wild and cultured corals, respectively; seawater requirement and antimicrobial activity were then assessed. There is no significant difference between the ratio of seawater-requiring bacteria on the wild and cultured corals. The ratio of antibiotic-producing bacteria within the seawater-requiring bacteria did not differ between the corals. Nineteen bacterial strains that showed high antimicrobial activity were selected for 16S rDNA sequencing. Three strains could be assigned at the family level (Rhodobacteraceae). The remaining 16 strains belong to eight genera: Marinobacterium (2 strains), Pseudoalteromonas (1), Vibrio (5), Enterovibrio (1), Tateyamaria (1), Labrenzia (2), and Pseudovibrio (4). The crude extract from bacteria strains CGH2XX was found to have high cytotoxicity against the cancer cell line HL-60 (IC(50) = 0.94 μg/ml) and CCRF-CEM (IC(50) = 1.19 μg/ml). Our results demonstrate that the marine bacteria from corals have great potential in the discovery of useful medical molecules. PMID:22872580

  20. Excessive magnetic field flux density distribution from overhead isolated powerline conductors due to neutral line current.

    PubMed

    Netzer, Moshe

    2013-06-01

    Overhead isolated powerline conductors (hereinafter: "OIPLC") are the most compact form for distributing low voltage currents. From the known physics of magnetic field emission from 3-phase power lines, it is expected that excellent symmetry of the 120° shifted phase currents and where compact configuration of the 3-phase+neutral line exist, the phase current vectorial summation of the magnetic field flux density (MFFD) is expected to be extremely low. However, despite this estimation, an unexpectedly very high MFFD was found in at least three towns in Israel. This paper explains the reasons leading to high MFFD emissions from compact OIPLC and the proper technique to fix it. Analysis and measurement results had led to the failure hypothsis of neutral line poor connection design and poor grounding design of the HV-LV utility transformers. The paper elaborates on the low MFFD exposure level setup by the Israeli Environmental Protection Office which adopted a rather conservative precaution principal exposure level (2 mG averaged over 24 h). PMID:23675630

  1. Microscopic and biochemical evidence of differentially virulent field isolates of Diplocarpon rosae causing black spot disease of roses.

    PubMed

    Gachomo, Emma W; Kotchoni, Simeon O

    2010-01-01

    Black spot disease caused by Diplocarpon rosae is one of the most widespread diseases of roses that are very difficult to control due to the generative reproduction and complex genetic constitution of roses and up to now the control of black spot still requires intensive use of systemic fungicides. Here we report for the first time evidence of differentially virulent field isolates of D. rosae. Using a combination of fungal structures, disease symptoms and host cells protein expression pattern analysis we here provide direct biochemical evidence that tropical field isolates of D. rosae are more virulent and caused disease symptoms earlier than their temperate counterparts. The tropical fungal field isolates strongly induced an excessive accumulation of ROS and repressed activity of pathogenesis-related proteins such as peroxidases, chitinase and phenylalanine ammonia lyase compared to their temperate counterparts. These findings bring insights into a hidden pathogenic characteristic of tropical D. rosae field isolates compared to their temperate counterparts and open a novel dimension of parameters to be considered when controlling black spot disease of roses by fungicides in tropical versus temperate regions. Interestingly, we found that treatment of rose leaves with ROS (H2O2) prior to fungal inoculation promoted plant defense response regardless of the isolate virulence based on protein expression pattern analysis, suggesting that ROS (H2O2) can be efficiently incorporated into black spot disease management. PMID:20137960

  2. Ultrasonic propagation: a technique to reveal field induced structures in magnetic nanofluids.

    PubMed

    Parekh, Kinnari; Patel, Jaykumar; Upadhyay, R V

    2015-07-01

    The paper reports the study of magnetic field induced structures in magnetic nanofluid investigated through ultrasonic wave propagation. Modified Tarapov's theory is used to study variation in velocity anisotropy with magnetic field. The types of field induced structures depend upon the chemical structure of the carrier in which magnetic nanoparticles are dispersed. Our study indicates formation of fractals and chain respectively, in transformer oil and kerosene based fluid. This difference is explained on the basis of particle-particle interaction and particle-medium interaction. PMID:25791205

  3. Use of two SPE-GC/MS methods for field isolation and quantitation of polycyclic aromatic hydrocarbons

    SciTech Connect

    Furlong, E.T.; Koleis, J.C.; Gates, P.M.

    1995-12-31

    Increasing sensitivity and subsequently improving method-detection limits for a variety of organic contaminant compounds is an ongoing effort in environmental analytical chemistry. Several field-deployable isolation techniques have been developed for concentrating hydrophobic organic contaminants from large (> 1 liter) volumes of aqueous samples. The capacity of large-volume solid-phase extraction (LV-SPE) was used as part of a simple, efficient, field-operable technique for isolating microgram-per-liter to nanogram-per-liter quantities of polycyclic aromatic hydrocarbons (PAH) in 4- to 8-liter ground-water samples from a petroleum- contaminated aquifer near Bemidji, Minn.

  4. The adipokine chemerin amplifies electrical field-stimulated contraction in the isolated rat superior mesenteric artery.

    PubMed

    Darios, Emma S; Winner, Brittany M; Charvat, Trevor; Krasinksi, Antoni; Punna, Sreenivas; Watts, Stephanie W

    2016-08-01

    The adipokine chemerin causes arterial contraction and is implicated in blood pressure regulation, especially in obese subjects with elevated levels of circulating chemerin. Because chemerin is expressed in the perivascular adipose tissue (PVAT) that surrounds the sympathetic innervation of the blood vessel, we tested the hypothesis that chemerin (endogenous and exogenous) amplifies the sympathetic nervous system in mediating electrical field-stimulated (EFS) contraction. The superior mesenteric artery, with or without PVAT and with endothelium and sympathetic nerve intact, was mounted into isolated tissue baths and used for isometric contraction and stimulation. Immunohistochemistry validated a robust expression of chemerin in the PVAT surrounding the superior mesenteric artery. EFS (0.3-20 Hz) caused a frequency-dependent contraction in isolated arteries that was reduced by the chemerin receptor ChemR23 antagonist CCX832 alone (100 nM; with, but not without, PVAT), but not by the inactive congener CCX826 (100 nM). Exogenous chemerin-9 (1 μM)-amplified EFS-induced contraction in arteries (with and without PVAT) was blocked by CCX832 and the α-adrenergic receptor antagonist prazosin. CCX832 did not directly inhibit, nor did chemerin directly amplify, norepinephrine-induced contraction. Whole mount immunohistochemical experiments support colocalization of ChemR23 with the sympathetic nerve marker tyrosine hydroxylase in superior mesenteric PVAT and, to a lesser extent, in arteries and veins. These studies support the idea that exogenous chemerin modifies sympathetic nerve-mediated contraction through ChemR23 and that ChemR23 may be endogenously activated. This is significant because of the well-appreciated role of the sympathetic nervous system in blood pressure control. PMID:27371688

  5. Sub-inhibitory concentrations of penicillin G induce biofilm formation by field isolates of Actinobacillus pleuropneumoniae.

    PubMed

    Hathroubi, S; Fontaine-Gosselin, S-È; Tremblay, Y D N; Labrie, J; Jacques, M

    2015-09-30

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium and causative agent of porcine pleuropneumonia. This is a highly contagious disease that causes important economic losses to the swine industry worldwide. Penicillins are extensively used in swine production and these antibiotics are associated with high systemic clearance and low oral bioavailability. This may expose A. pleuropneumoniae to sub-inhibitory concentrations of penicillin G when the antibiotic is administered orally. Our goal was to evaluate the effect of sub-minimum inhibitory concentration (MIC) of penicillin G on the biofilm formation of A. pleuropneumoniae. Biofilm production of 13 field isolates from serotypes 1, 5a, 7 and 15 was tested in the presence of sub-MIC of penicillin G using a polystyrene microtiter plate assay. Using microscopy techniques and enzymatic digestion, biofilm architecture and composition were also characterized after exposure to sub-MIC of penicillin G. Sub-MIC of penicillin G significantly induced biofilm formation of nine isolates. The penicillin G-induced biofilms contained more poly-N-acetyl-D-glucosamine (PGA), extracellular DNA and proteins when compared to control biofilms grown without penicillin G. Additionally, penicillin G-induced biofilms were sensitive to DNase which was not observed with the untreated controls. Furthermore, sub-MIC of penicillin G up-regulated the expression of pgaA, which encodes a protein involved in PGA synthesis, and the genes encoding the envelope-stress sensing two-component regulatory system CpxRA. In conclusion, sub-MICs of penicillin G significantly induce biofilm formation and this is likely the result of a cell envelope stress sensed by the CpxRA system resulting in an increased production of PGA and other matrix components. PMID:26130517

  6. Bacillus depressus sp. nov., isolated from soil of a sunflower field.

    PubMed

    Wei, Xuexin; Xin, Di; Xin, Yuhua; Zhang, Hao; Wang, Tianying; Zhang, Jianli

    2016-01-01

    A Gram-stain positive, rod-shaped, endospore-forming and aerobic bacterium, designated BZ1(T), was isolated from a soil sample collected from a sunflower field in Wuyuan county, Inner Mongolia, China. On the basis of 16S rRNA gene sequence analysis, the isolate was found to be a member of the genus Bacillus and the close phylogenetic relatives to be Bacillus gottheilii WCC 4585(T), Bacillus oceanisediminis H2(T), Bacillus mesonae FJAT-13985(T) and Bacillus horneckiae DSM 23495(T) with 98.3, 98.1, 98.0 and 97.6 % sequence similarity, respectively. Strain BZ1(T) was found to grow at 6-40 °C (optimum 30-33 °C), pH 6.0-9.0 (optimum pH 7.0) and 0-5.5 % (w/v) NaCl (optimum 0.5 %). The cell wall diamino acid of the peptidoglycan of strain BZ1(T) was identified as meso-diaminopimelic acid and the predominant respiratory quinone as MK-7. The major cellular fatty acids were found to be iso-C15:0, anteiso-C15:0 and iso-C14:0, and the polar lipids to consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The novel strain was found to have a DNA G + C content 44.5 mol%. DNA-DNA hybridization with closely related strains was low. Based on phenotypic, phylogenetic and chemotaxonomic results, it is concluded that strain BZ1(T) represents a novel species within the genus Bacillus, for which we propose the name Bacillus depressus sp. nov. The type strain is BZ1(T) (= CGMCC 1.15124(T) = KCTC 33643(T)). PMID:26452774

  7. Pontibacter amylolyticus sp. nov., isolated from a deep-sea sediment hydrothermal vent field.

    PubMed

    Wu, Yue-Hong; Zhou, Peng; Jian, Shu-Ling; Liu, Zhen-Sheng; Wang, Chun-Sheng; Oren, Aharon; Xu, Xue-Wei

    2016-04-01

    A Gram-stain-negative, short rod-shaped bacterium, designated 9-2T, was isolated from a sediment sample collected from a hydrothermal vent field on the south-west Indian Ridge. It formed red colonies, produced carotenoid-like pigments and did not produce bacteriochlorophyll a. Strain 9-2T was positive for hydrolysis of DNA, gelatin and starch, but negative for hydrolysis of aesculin and Tween 60. The sole respiratory quinone was menaquinone-7 (MK-7). The main polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid and two unidentified polar lipids. The principal fatty acids (>5%) were summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B), iso-C15:0 and iso-C17:0 3-OH. The genomic DNA G+C content was 49.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 9-2T should be assigned to the genus Pontibacter. Levels of 16S rRNA gene sequence similarity between the new isolate and the type strains of Pontibacter species with validly published names were in the range 94.0-96.5%. On the basis of phenotypic and genotypic data, strain 9-2T represents a novel species of the genus Pontibacter, for which the name Pontibacter amylolyticus sp. nov. is proposed. The type strain is 9-2T (=CGMCC 1.12749T=JCM 19653T=MCCC 1K00278T). PMID:26827710

  8. Prevalence of Stx phages in environments of a pig farm and lysogenic infection of the field E. coli O157 isolates with a recombinant converting Phage.

    PubMed

    Yan, Yaxian; Shi, Yibo; Cao, Dongmei; Meng, Xiangpeng; Xia, Luming; Sun, Jianhe

    2011-02-01

    The prevalence and nature of Shiga toxin (Stx)-producing Escherichia coli (STEC) and Stx phage were investigated in 720 swine fecal samples randomly collected from a commercial breeding pig farm in China over a 1-year surveillance period. Eight STEC O157 (1.1%), 33 STEC non-O157 (4.6%), and two stx-negative O157 (0.3%) isolates were identified. Fecal filtrates were screened directly for Stx phages using E. coli K-12 derivative strains MC1061 as indicator, yielding 15 Stx1 and 57 Stx2 phages. One Stx1 and eight Stx2 phages were obtained following norfloxacin induction of the eight field STEC O157 isolates. All Stx1 phages had hexagonal heads with long tails, while Stx2 phages had three different morphologies. Notably, most of field STEC O157 isolates released more free phages and Stx toxin after induction with ciprofloxacin. Furthermore, upon infection with the recombinant phage ΦMin27(Δstx::cat), E. coli laboratory strains produced both lysogenic and lytic phage, whereas two of the eight O157 STEC isolates produced only lysogens. The lysogens from laboratory strains produced infectious particles similar to ΦMin27. Similarly, the lysogens from the STEC O157 isolates released Stx phage too, although free ΦMin27(Δstx::cat) particles were not detected. Collectively, our results reveal that breeding pig farms could be important reservoirs for Stx phages and that residual antibacterial agents may enhance the release of Stx phages and the expression of Stx. PMID:20697714

  9. Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field.

    PubMed

    Lee, Hye-Yeon; Liu, Qingmei; Kang, Myung-Suk; Kim, Soo-Ki; Lee, Soon-Youl; Im, Wan-Taek

    2016-05-01

    Two novel actinobacteria, designated strains Gsoil 097T and Gsoil 818T, isolated from soil of a ginseng field, South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. They were Gram-reaction-positive, aerobic, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Marmoricola and were related most closely to Marmicola solisilvae KIS18-7T (99.1 and 98.3 % similarity, respectively), Marmicola terrae JOS5-1T (97.9 and 97.9 %), Marmicola scoriae Sco-D01T (97.8 and 97.1 %) and Marmicola aequoreus SST-45T (97.5 and 97.0 %). The G+C content of the genomic DNA was 68.8 and 70.0 mol%, respectively. Both strains were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C17 : 1ω6c, C18 : 1ω9c, C18 : 0 10-methyl and iso-C16 : 0 as major fatty acids. These chemotaxonomic data supported the affiliation of both strains to the genus Marmoricola. However, levels of DNA-DNA relatedness between the two strains and closely related type strains of Marmoricola species were less than 30 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 097T and Gsoil 818T from other Marmoricola species with validly published names. Therefore, the two isolates represent two novel species, for which the names Marmoricola ginsengisoli sp. nov. (type strain Gsoil 097T = KACC 14267T = DSM 22772T) and Marmoricola pocheonensis sp. nov. (type strain Gsoil 818T = KACC 14275T = DSM 22773T) are proposed. PMID:26883120

  10. [Investigation of Salmonella serotype Enteritidis isolates by plasmid profile analysis and pulsed field gel electrophoresis].

    PubMed

    Us, Ebru; Erdem, Birsel; Tekeli, Alper; Gerçeker, Devran; Saran, Begüm; Bayramova, Mehseti; Sahin, Fikret

    2011-04-01

    In this study a total of 122 Salmonella serotype Enteritidis stock strains selected from the culture collection of Enterobacteriaceae Laboratory of Ankara University Faculty of Medicine, Department of Medical Microbiology, were investigated by plasmid profile analysis with the method defined by Kado and Liu and pulsed field gel electrophoresis (PFGE) according to World Health Organization protocols using SpeI and XbaI macrorestriction enzymes, for better understanding of the molecular epidemiology of S. Enteritidis. The study strains were selected from a collection of previously isolated epidemic (n= 13) and sporadic (n= 109) strains (103 stool, 16 blood and one each bile, urine and cerebrospinal fluid) obtained from 10 different cities after the year 2000. PFGE patterns were analyzed with Gene Directory software (Syngene, UK) and a similarity index was determined by using Dice coefficient and the unweighted pair group method with mathematical averaging (UPGMA). Plasmid-carrying 110 (90%) strains that harbored 1-4 plasmids with sizes ranging from 2.0 to 100 kb were separated into patterns more than 14 (p1-p14). A total of 85 (69.7%) isolates harbored the 57 kb plasmid solely or in combination with other plasmids. By PFGE, 11 distinct patterns were shown with each enzyme SpeI and XbaI. S. Enteritidis strains after digestion with macrorestriction enzyme SpeI generated 11 different PFGE patterns (A to K), whereas XbaI generated also 11 different PFGE patterns (a to k). PFGE pattern A consisted of 93 strains (76.2%) after digestion with macrorestriction enzyme SpeI, while PFGE pattern a consisted 53 (43.4%) and PFGE pattern b 42 strains (34.4%) after digestion with macrorestriction enzyme XbaI. Using two macrorestriction enzymes two PFGE cluster profiles Aa (50 strains, 40.9%) and Ab (42 strains, 34.4%) were found to be predominating among 17 different PFGE clusters. Our results confirmed the clonal nature of S. Enteritidis strains in Turkey. The use of two enzymes in

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  12. Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction

    PubMed Central

    Müller, Knut; Krause, Florian F.; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

    2014-01-01

    By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms. PMID:25501385

  13. NEAR-INFRARED-IMAGING POLARIMETRY TOWARD SERPENS SOUTH: REVEALING THE IMPORTANCE OF THE MAGNETIC FIELD

    SciTech Connect

    Sugitani, K.; Nakamura, F.; Tamura, M.; Kandori, R.; Watanabe, M.; Nishiyama, S.; Nagata, T.; Nagayama, T.; Sato, S.; Gutermuth, R. A.; Wilson, G. W.; Kawabe, R.

    2011-06-10

    The Serpens South embedded cluster, which is located in the constricted part of a long, filamentary, infrared dark cloud, is believed to be in a very early stage of cluster formation. We present results of near-infrared (JHKs) polarization observations of the filamentary cloud. Our polarization measurements of near-infrared point sources indicate a well-ordered global magnetic field that is perpendicular to the main filament, implying that the magnetic field is likely to have controlled the formation of the main filament. On the other hand, the sub-filaments, which converge on the central part of the cluster, tend to run along the magnetic field. The global magnetic field appears to be curved in the southern part of the main filament. Such morphology is consistent with the idea that the global magnetic field is distorted by gravitational contraction along the main filament toward the northern part, which contains larger mass. Applying the Chandrasekhar-Fermi method, the magnetic field strength is roughly estimated to be a few x100 {mu}G, suggesting that the filamentary cloud is close to magnetically critical.

  14. Direct isolation of myofibroblasts and fibroblasts from bleomycin-injured lungs reveals their functional similarities and differences

    PubMed Central

    2013-01-01

    Background Myofibroblasts play a crucial role in tissue repair. The functional similarities and differences between myofibroblasts and fibroblasts are not fully understood because they have not been separately isolated from a living body. The purpose of this study was to establish a method for the direct isolation of myofibroblasts and fibroblasts from injured lungs by using fluorescence-activated cell sorting and to compare their functions. Results We demonstrated that lineage-specific cell surface markers (lin), such as CD31, CD45, CD146, EpCAM (CD326), TER119, and Lyve-1 were not expressed in myofibroblasts or fibroblasts. Fibroblasts of bleomycin-injured lungs and saline-treated lungs were shown to be enriched in linneg Sca-1high, and myofibroblasts of bleomycin-injured lungs were shown to be enriched in linneg Sca-1low CD49ehigh. Results from in-vitro proliferation assays indicated in-vitro proliferation of fibroblasts but not myofibroblasts of bleomycin-injured lungs and of fibroblasts of saline-treated lungs. However, fibroblasts and myofibroblasts might have a low proliferative capacity in vivo. Analysis of genes for collagen and collagen synthesis enzymes by qRT-PCR showed that the expression levels of about half of the genes were significantly higher in fibroblasts and myofibroblasts of bleomycin-injured lungs than in fibroblasts of saline-treated lungs. By contrast, the expression levels of 8 of 11 chemokine genes of myofibroblasts were significantly lower than those of fibroblasts. Conclusions This is the first study showing a direct isolation method of myofibroblasts and fibroblasts from injured lungs. We demonstrated functional similarities and differences between myofibroblasts and fibroblasts in terms of both their proliferative capacity and the expression levels of genes for collagen, collagen synthesis enzymes, and chemokines. Thus, this direct isolation method has great potential for obtaining useful information from myofibroblasts and

  15. Role of naturally occurring genome segment reassortment in the pathogenicity of IBDV field isolates in Three-Yellow chickens.

    PubMed

    He, Xiumiao; Chen, Guo; Yang, Lin; Xuan, Jincai; Long, Han; Wei, Ping

    2016-01-01

    Reassortment among genome segments of infectious bursal disease virus (IBDV) field isolates was reported frequently worldwide, however the pathogenicity of the reassortant field IBDV is poorly understood. In this paper, a pathogenicity study on four representative IBDV field strains isolated from Southern China between 2005 and 2011 was conducted. Twenty-eight-day-old Three-Yellow chickens were divided into four groups and were inoculated intraocularly with one of the four field IBDV strains, namely NN1172, NN1005, GD10111 and JS7, respectively. The mortality and relative weight of bursa and thymus were subsequently determined in the acute phase of infection. In addition, B cells, T cells (CD4(+) and CD8(+)) and virus were quantified in the bursa of Fabricius and thymus, respectively, by flow cytometry and real-time reverse transcription-polymerase chain reaction. The results showed that isolate NN1172, of which parts of segment A and B encoding the hypervariable (v) region of viral protein (VP2) and VP1, respectively, derived from vvIBDV strains, showed the most severe pathogenicity, and caused the most severe bursal B cell depletion as well as CD4(+) and CD8(+) T cell infiltration in the bursa of Fabricius. However, the virus induced the strongest decrease in CD4(+) and CD8(+) T cells in the thymus and exhibited the most efficient viral replication in the target organs. Isolate NN1005, whose vVP2 derived from vvIBDV and VP1 from unidentified origin, exhibited relatively lower pathogenicity compared to NN1172. The other two isolates, JS7 and GD10111, of which the vVP2 derived from vvIBDV and intermediate IBDV, and VP1 from 002-73 and attenuated IBDV, respectively, showed the lowest level of virulence. Our results suggest that various IBDV field isolates with different natural segment reassortments exhibit differential pathogenicity after infection of commercial Three-Yellow chickens. PMID:27100151

  16. Neuromagnetic fields reveal cortical plasticity when learning an auditory discrimination task.

    PubMed

    Cansino, S; Williamson, S J

    1997-08-01

    Auditory evoked neuromagnetic fields of the primary and association auditory cortices were recorded while subjects learned to discriminate small differences in frequency and intensity between two consecutive tones. When discrimination was no better than chance, evoked field patterns across the scalp manifested no significant differences between correct and incorrect responses. However, when performance was correct on at least 75% of the trials, the spatial pattern of magnetic field differed significantly between correct and incorrect responses during the first 70 ms following the onset of the second tone. In this respect, the magnetic field pattern predicted when the subject would make an incorrect judgment more than 100 ms prior to indicating the judgment by a button press. One subject improved discrimination for much smaller differences between stimuli after 200 h of training. Evidence of cortical plasticity with improved discrimination is provided by an accompanying decrease of the relative magnetic field amplitude of the 100 ms response components in the primary and association auditory cortices. PMID:9295193

  17. High-field quantum calculation reveals time-dependent negative Kerr contribution.

    PubMed

    Béjot, P; Cormier, E; Hertz, E; Lavorel, B; Kasparian, J; Wolf, J-P; Faucher, O

    2013-01-25

    The exact quantum time-dependent optical response of hydrogen under strong-field near-infrared excitation is investigated and compared to the perturbative model widely used for describing the effective atomic polarization induced by intense laser fields. By solving the full 3D time-dependent Schrödinger equation, we exhibit a supplementary, quasi-instantaneous defocusing contribution missing in the weak-field model of polarization. We show that this effect is far from being negligible, in particular when closures of ionization channels occur and stems from the interaction of electrons with their parent ions. It provides an interpretation of the higher-order Kerr effect recently observed in various gases. PMID:25166165

  18. High-Field Quantum Calculation Reveals Time-Dependent Negative Kerr Contribution

    NASA Astrophysics Data System (ADS)

    Béjot, P.; Cormier, E.; Hertz, E.; Lavorel, B.; Kasparian, J.; Wolf, J.-P.; Faucher, O.

    2013-01-01

    The exact quantum time-dependent optical response of hydrogen under strong-field near-infrared excitation is investigated and compared to the perturbative model widely used for describing the effective atomic polarization induced by intense laser fields. By solving the full 3D time-dependent Schrödinger equation, we exhibit a supplementary, quasi-instantaneous defocusing contribution missing in the weak-field model of polarization. We show that this effect is far from being negligible, in particular when closures of ionization channels occur and stems from the interaction of electrons with their parent ions. It provides an interpretation of the higher-order Kerr effect recently observed in various gases.

  19. Isolation of viral haemorrhagic septicaemia virus from muskellunge, Esox masquinongy (Mitchill), in Lake St Clair, Michigan, USA reveals a new sublineage of the North American genotype

    USGS Publications Warehouse

    Elsayed, E.; Faisal, M.; Thomas, M.; Whelan, G.; Batts, W.; Winton, J.

    2006-01-01

    Viral haemorrhagic septicaemia virus (VHSV) was isolated from muskellunge, Esox masquinongy (Mitchill), caught from the NW portion of Lake St Clair, Michigan, USA in 2003. Affected fish exhibited congestion of internal organs; the inner wall of the swim bladder was thickened and contained numerous budding, fluid-filled vesicles. A virus was isolated using fish cell lines inoculated with a homogenate of kidney and spleen tissues from affected fish. Focal areas of cell rounding and granulation appeared as early as 24 h post-inoculation and expanded rapidly to destroy the entire cell sheet by 96 h. Electron microscopy revealed virions that were 170-180 nm in length by 60-70 nm in width having a bullet-shaped morphology typical of rhabdoviruses. The virus was confirmed as VHSV by reverse transcriptase-polymerase chain reaction. Sequence analysis of the entire nucleoprotein and glycoprotein genes revealed the virus was a member of the North American genotype of VHSV; however, the isolate was sufficiently distinct to be considered a separate sublineage, suggesting its origin may have been from marine species inhabiting the eastern coastal areas of the USA or Canada. ?? 2006 Blackwell Publishing Ltd.

  20. Pulsed-Field Gel Electrophoresis Genotyping of Taylorella equigenitalis Isolates Collected in the United States from 1978 to 2010▿

    PubMed Central

    Aalsburg, Alan M.; Erdman, Matthew M.

    2011-01-01

    Taylorella equigenitalis is the etiologic agent of contagious equine metritis (CEM), a venereal disease of horses. A total of 82 strains of T. equigenitalis isolated in the United States were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of genomic DNA with restriction enzyme ApaI. Twenty-eight of those strains isolated from horses in the 2009 U.S. outbreak (CEM09) were further analyzed with NotI and NaeI enzymes. When ApaI alone was used for analysis, the 82 isolates clustered into 15 different genotypes that clearly defined groups of horses with known epidemiological connections. The PFGE profiles of the CEM09 isolates were indistinguishable after digestion with ApaI, NotI, and NaeI and did not match those of isolates from previous U.S. outbreaks in 1978 and 2006 or of any other isolate from the National Veterinary Services Laboratories (NVSL) culture library. Coupled with the fact that the CEM09 isolates are epidemiologically related, these results suggest a common source for the outbreak not linked to previous occurrences of CEM in the United States. PMID:21191049

  1. Analysis of pulsed field gel electrophoresis profiles using multiple enzymes for predicting potential source reservoirs for strains of Salmonella Enteritidis and Salmonella Typhimurium isolated from humans.

    PubMed

    Son, Insook; Zheng, Jie; Keys, Christine E; Zhao, Shaohua; Meng, Jianghong; Brown, Eric W

    2013-06-01

    We reported previously on a highly discriminatory pulsed field gel electrophoresis-based (PFGE) subtyping scheme for Salmonella enterica serovar Enteritidis (SE) and Salmonella Typhimurium (ST) that relies on combined cluster analysis of up to six restriction enzymes. This approach allowed for the high-resolution separation of numerous poultry-derived SE and ST isolates into several distinct clusters that sorted along several geographical and host-linked boundaries. In this study, 101 SE and 151 ST strains isolated from poultry, swine, beef, mouse, and produce origins were combined with 62 human SE and ST isolates of unknown sources. PFGE profiles were generated across six restriction enzymes (XbaI, BlnI, SpeI, SfiI, PacI, and NotI) for human SE and ST isolates. The combined six-enzyme UPGMA trees of SE and ST revealed six separate origins of North American human SE isolates including one association with a "cosmopolitan" cluster of SEs from poultry originating in Scotland, Mexico, and China. In the case of ST, human isolates assorted readily along host lines rather than geographical partitions with the majority of human STs clustering in a larger group of STs of potential porcine origin. Such observations may underscore the ecological importance of poultry and pork reservoirs for SE and ST transmission to humans, respectively. In an examination of the relationship between enzyme diversity and congruence among enzymes, pairwise genetic diversity ranged from 6.5% to 9.7% for SE isolates and, more widely, from 17.5% to 27.4% for ST isolates. Phylogenetic congruence measures singled out XbaI, BlnI, and SfiI as most concordant for SE while XbaI and SfiI were most concordant among ST strains. Thus, these data provide the first proof of principal for concatenated PFGE, when coupled with sufficient enzyme numbers and combinations, as one effective means for predicting geographical and food source reservoirs for human isolates of these two highly prevalent Salmonella

  2. Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates.

    PubMed

    Borneman, Anthony R; Zeppel, Ryan; Chambers, Paul J; Curtin, Chris D

    2014-02-01

    The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92%) of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S. cerevisiae. PMID:24550744

  3. Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates

    PubMed Central

    Borneman, Anthony R.; Zeppel, Ryan; Chambers, Paul J.; Curtin, Chris D.

    2014-01-01

    The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92%) of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S. cerevisiae. PMID:24550744

  4. Prevalence and genetic diversity of clinical Vibrio parahaemolyticus isolates from China, revealed by multilocus sequence typing scheme.

    PubMed

    Han, Dongsheng; Tang, Hui; Ren, Chuanli; Wang, Guangzhou; Zhou, Lin; Han, Chongxu

    2015-01-01

    The population structure of clinical Vibrio parahaemolyticus isolates spreading in China remains undefined. We brought 218 clinical isolates from the pubMLST database originating from different regions of China collected since the year of 1990, analyzed by multilocus sequence typing (MLST), to elucidate the prevalence and genetic diversity of V. parahaemolyticus circulating in Chinese population. The MLST scheme produced 137 sequence types (STs). These STs were clustered into six clonal complexes (CCs), six doublets, and 91 singletons, exhibiting a high level of genetic diversity. However, less diversity was displayed on the peptide level: only 46 different peptide sequence type (pST) were generated, with pST2 (44.0%, 96/218) and pST1 (15.1%, 33/218) the predominant. Further analysis confirmed all the pSTs belong to a single complex founded by pST1, pST2, pST3, and pST4. recA presented the highest degree of nucleotide diversity (0.026) and the largest number of variable sites (176) on the nucleotide level. pyrC was the most diverse locus on the peptide level, possessing the highest percentage of variable sites (9.2%, 15/163). Significant linkage disequilibrium with the alleles was detected when the Standardized Index of Association (I(S) A ) was calculated both for the entire isolates collection (0.7169, P < 0.01) and for the 137 STs (I(S) A = 0.2648, P < 0.01). In conclusion, we provide an overview of prevalence and genetic diversity of clinical V. parahaemolyticus spreading in Chinese population using MLST analysis. The results would offer genetic evidences for uncovering the microevolution relationship of V. parahaemolyticus populations. PMID:25914691

  5. Comparative Lipidomics in Clinical Isolates of Candida albicans Reveal Crosstalk between Mitochondria, Cell Wall Integrity and Azole Resistance

    PubMed Central

    Singh, Ashutosh; Yadav, Vipin; Prasad, Rajendra

    2012-01-01

    Prolonged usage of antifungal azoles which target enzymes involved in lipid biosynthesis invariably leads to the development of multi-drug resistance (MDR) in Candida albicans. We had earlier shown that membrane lipids and their fluidity are closely linked to the MDR phenomenon. In one of our recent studies involving comparative lipidomics between azole susceptible (AS) and azole resistant (AR) matched pair clinical isolates of C. albicans, we could not see consistent differences in the lipid profiles of AS and AR strains because they came from different patients and so in this study, we have used genetically related variant recovered from the same patient collected over a period of 2-years. During this time, the levels of fluconazole (FLC) resistance of the strain increased by over 200-fold. By comparing the lipid profiles of select isolates, we were able to observe gradual and statistically significant changes in several lipid classes, particularly in plasma membrane microdomain specific lipids such as mannosylinositolphosphorylceramides and ergosterol, and in a mitochondrial specific phosphoglyceride, phosphatidyl glycerol. Superimposed with these quantitative and qualitative changes in the lipid profiles, were simultaneous changes at the molecular lipid species levels which again coincided with the development of resistance to FLC. Reverse transcriptase-PCR of the key genes of the lipid metabolism validated lipidomic picture. Taken together, this study illustrates how the gradual corrective changes in Candida lipidome correspond to the development of FLC tolerance. Our study also shows a first instance of the mitochondrial membrane dysfunction and defective cell wall (CW) in clinical AR isolates of C. albicans, and provides evidence of a cross-talk between mitochondrial lipid homeostasis, CW integrity and azole tolerance. PMID:22761908

  6. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage.

    PubMed

    Benítez-Galeano, María José; Rubio, Leticia; Bertalmío, Ana; Maeso, Diego; Rivas, Fernando; Colina, Rodney

    2015-07-01

    Citrus Tristeza Virus (CTV) is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23). Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36) in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD) and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1) the genetic diversity of Uruguayan CTV isolates circulating in the country and (2) the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program. PMID:26205407

  7. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage

    PubMed Central

    Benítez-Galeano, María José; Rubio, Leticia; Bertalmío, Ana; Maeso, Diego; Rivas, Fernando; Colina, Rodney

    2015-01-01

    Citrus Tristeza Virus (CTV) is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23). Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36) in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD) and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1) the genetic diversity of Uruguayan CTV isolates circulating in the country and (2) the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program. PMID:26205407

  8. Single-pinhole diffraction of few-cycle isolated attosecond pulses with a two-color field

    NASA Astrophysics Data System (ADS)

    Shaoyi, Wang; Dan, Han; Kegong, Dong; Yuchi, Wu; Fang, Tan; Bin, Zhu; Quanping, Fan; Leifeng, Cao; Yuqiu, Gu

    2016-03-01

    The spatio-temporal characterization of an isolated attosecond pulse is investigated theoretically in a two-color field. Our results show that a few-cycle isolated attosecond pulse with the center wavelength of 16 nm can be generated effectively by adding a weak controlling field. Using the split and delay units, the isolated attosecond pulse can be split to the two same ones, and then single-pinhole diffractive patterns of the two pulses with different delays can be achieved. The diffractive patterns depend severely on the periods of the attosecond pulses, which can be helpful to obtain temporal information of the coherent sources. Project supported by the National Science Instruments Major Project of China (Grant No. 2012YQ130125), the National Natural Science Foundation of China (Grant Nos. 11405159, 11375161, and 11174259), and the Science and Technology on Plasma Physics Laboratory at CAEP (Grant No. 9140C680302130C68242).

  9. Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field.

    PubMed

    Rahalkar, Monali C; Pandit, Pranitha S; Dhakephalkar, Prashant K; Pore, Soham; Arora, Preeti; Kapse, Neelam

    2016-04-01

    Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph. PMID:26547566

  10. Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

    SciTech Connect

    Callister, S.J.; Wilkins, M.J.; Nicora, C.D.; Williams, K.H.; Banfield, J.F.; VerBerkmoes, N.C.; Hettich, R.L.; NGuessan, A.L.; Mouser, P.J.; Elifantz, H.; Smith, R.D.; Lovley, D.R.; Lipton, M.S.; Long, P.E.

    2010-07-15

    Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or “pseudo-metagenomes”, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

  11. Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles

    SciTech Connect

    Callister, Stephen J; Wilkins, Mike; Nicora, Carrie D.; Williams, Ken; Banfield, Jillian F.; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; N'Guessan, A. Lucie; Mouser, Paula J; Elifantz, Hila; Smith, Richard D.; Lovley, Derek; Lipton, Mary S; Long, Phil

    2010-01-01

    Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetateamended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or pseudo-metagenomes , for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally,ashift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

  12. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

    PubMed Central

    Schwartz, Allison R.; Potnis, Neha; Timilsina, Sujan; Wilson, Mark; Patané, José; Martins, Joaquim; Minsavage, Gerald V.; Dahlbeck, Douglas; Akhunova, Alina; Almeida, Nalvo; Vallad, Gary E.; Barak, Jeri D.; White, Frank F.; Miller, Sally A.; Ritchie, David; Goss, Erica; Bart, Rebecca S.; Setubal, João C.; Jones, Jeffrey B.; Staskawicz, Brian J.

    2015-01-01

    Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors. PMID:26089818

  13. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.

    PubMed

    Schwartz, Allison R; Potnis, Neha; Timilsina, Sujan; Wilson, Mark; Patané, José; Martins, Joaquim; Minsavage, Gerald V; Dahlbeck, Douglas; Akhunova, Alina; Almeida, Nalvo; Vallad, Gary E; Barak, Jeri D; White, Frank F; Miller, Sally A; Ritchie, David; Goss, Erica; Bart, Rebecca S; Setubal, João C; Jones, Jeffrey B; Staskawicz, Brian J

    2015-01-01

    Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors. PMID:26089818

  14. Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field.

    PubMed

    Geymonat, Estefanía; Ferrando, Lucía; Tarlera, Silvana E

    2011-11-01

    A novel methanotroph, designated strain E10(T), was isolated from a rice paddy field in Uruguay. Strain E10(T) grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30-35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2(T) (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10(T) formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14L(T), respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C(16 :0) (62.05 %). Thus, strain E10(T) (=JCM 16910(T) = DSM 23452(T)) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed. PMID:21131502

  15. Flavobacterium panacisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Jung, Sun Young; Kim, Yeon-Ju; Hoang, Van-An; Jin, Yan; Nguyen, Ngoc-Lan; Oh, Keun Huyn; Yang, Deok-Chun

    2016-09-01

    A novel bacterial strain, designated DCY70(T), was isolated from soil of a ginseng field in Republic of Korea and was characterized in order to determine its taxonomic position. The strain was Gram-reaction negative, yellow-pigmented, rod-shaped and catalase- and oxidase-positive. Based on the 16S rRNA gene sequence similarity, strain DCY70(T) was shown to belong to the genus Flavobacterium, most closely related to Flavobacterium oncorhynchi 631-08(T) (98.4 %), Flavobacterium plurextorum 1126-1H-08(T) (97.9 %), Flavobacterium chilense LM-09-Fp(T) (97.9 %) and Flavobacterium chungangense CJ(T) (97.7 %). The chemotaxonomic characteristics showed only menaquinone-6 (MK-6), iso-C15:0, iso-C15:0 3OH, iso-C17:0 3OH and summed feature 3 as major cellular fatty acids. Polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids, four unidentified polar lipids and one unidentified phospholipid. The DNA G+C content was 34.9 mol%. Based on the phylogenetic, phenotypic and genotypic data, a novel species, Flavobacterium panacisoli sp. nov., is proposed (=KCTC 32393(T) = JCM 19162(T)). PMID:27120464

  16. Field and laboratory studies reveal interacting effects of stream oxygenation and warming on aquatic ectotherms.

    PubMed

    Verberk, Wilco C E P; Durance, Isabelle; Vaughan, Ian P; Ormerod, Steve J

    2016-05-01

    Aquatic ecological responses to climatic warming are complicated by interactions between thermal effects and other environmental stressors such as organic pollution and hypoxia. Laboratory experiments have demonstrated how oxygen limitation can set heat tolerance for some aquatic ectotherms, but only at unrealistic lethal temperatures and without field data to assess whether oxygen shortages might also underlie sublethal warming effects. Here, we test whether oxygen availability affects both lethal and nonlethal impacts of warming on two widespread Eurasian mayflies, Ephemera danica, Müller 1764 and Serratella ignita (Poda 1761). Mayfly nymphs are often a dominant component of the invertebrate assemblage in streams, and play a vital role in aquatic and riparian food webs. In the laboratory, lethal impacts of warming were assessed under three oxygen conditions. In the field, effects of oxygen availability on nonlethal impacts of warming were assessed from mayfly occurrence in 42 293 UK stream samples where water temperature and biochemical oxygen demand were measured. Oxygen limitation affected both lethal and sublethal impacts of warming in each species. Hypoxia lowered lethal limits by 5.5 °C (±2.13) and 8.2 °C (±0.62) for E. danica and S. ignita respectively. Field data confirmed the importance of oxygen limitation in warmer waters; poor oxygenation drastically reduced site occupancy, and reductions were especially pronounced under warm water conditions. Consequently, poor oxygenation lowered optimal stream temperatures for both species. The broad concordance shown here between laboratory results and extensive field data suggests that oxygen limitation not only impairs survival at thermal extremes but also restricts species abundance in the field at temperatures well below upper lethal limits. Stream oxygenation could thus control the vulnerability of aquatic ectotherms to global warming. Improving water oxygenation and reducing pollution can provide

  17. The many assembly histories of massive void galaxies as revealed by integral field spectroscopy

    NASA Astrophysics Data System (ADS)

    Fraser-McKelvie, Amelia; Pimbblet, Kevin A.; Penny, Samantha J.; Brown, Michael J. I.

    2016-06-01

    We present the first detailed integral field spectroscopy study of nine central void galaxies with M⋆ > 1010 M⊙ using the Wide Field Spectrograph to determine how a range of assembly histories manifest themselves in the current day Universe. While the majority of these galaxies are evolving secularly, we find a range of morphologies, merger histories and stellar population distributions, though similarly low Hα-derived star formation rates (<1 M⊙ yr-1). Two of our nine galaxies host active galactic nuclei, and two have kinematic disruptions to their gas that are not seen in their stellar component. Most massive void galaxies are red and discy, which we attribute to a lack of major mergers. Some have disturbed morphologies and may be in the process of evolving to early-type thanks to ongoing minor mergers at present times, likely fed by tendrils leading off filaments. The diversity in our small galaxy sample, despite being of similar mass and environment means that these galaxies are still assembling at present day, with minor mergers playing an important role in their evolution. We compare our sample to a mass and magnitude-matched sample of field galaxies, using data from the Sydney-AAO Multi-object Integral field spectrograph galaxy survey. We find that despite environmental differences, galaxies of mass M⋆ > 1010 M⊙ have similarly low star formation rates (<3 M⊙ yr-1). The lack of distinction between the star formation rates of the void and field environments points to quenching of massive galaxies being a largely mass-related effect.

  18. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site

    PubMed Central

    Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; Kuehl, Jennifer V.; Price, Morgan N.; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P.

    2015-01-01

    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%. PMID:25977418

  19. Understanding the molecular mechanism of instability of the avirulence gene AVR-Pita1 in field isolates of Maganporthe oryzae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The avirulence gene AVR-Pita1 in Magnaporthe oryzae triggers a resistance response in rice plants that contain the resistance gene Pi-ta. Understanding the evolution of the AVR-Pita1 gene in field isolates should benefit the deployment of Pi-ta for the control of rice blast disease. A total of 187 f...

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

    DOE PAGESBeta

    Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; Kuehl, Jennifer V.; Price, Morgan N.; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P.; Deutschbauer, Adam

    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%.

  1. Pulsed Field Gel Electrophoresis along with Antimicrobial Resistance pattern of Salmonella serotypes isolated from broiler whole carcass rinses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pulsed field gel electrophoresis (PFGE) and antibiogram patterns have been used to evaluate the diversity within and between individual Salmonella serotypes. The objectives of the study were to evaluate the PFGE along with antimicrobial resistance patterns of Salmonella isolates originating from br...

  2. Confirming and Identifying New Loci for Rice Blast Disease Resistance using Magnaporthe oryzae Field Isolates in the US

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. Isolation of exotic Newcastle disease virus (ENDV) from field collected flies and experimental ENDV infections of three arthropod species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the 2002 Exotic Newcastle Disease (END) outbreak in California arthropods were collected from two quarantined backyard poultry premises after removal of END virus infected birds. The END virus (ENDV) isolated from field collected pools of three fly species was found to have >98% homology by ...

  4. Typing Candida albicans oral isolates from healthy brazilian schoolchildren using multilocus enzyme electrophoresis reveals two highly polymorphic taxa

    PubMed Central

    Boriollo, Marcelo Fabiano Gomes; Spolidorio, Denise Madalena Palomari; Barros, Letizia Monteiro; Bassi, Rodrigo Carlos; Garcia, José Antonio Dias; Costa, Ana Maria Duarte Dias; Rosa, Edvaldo Antonio Ribeiro; Höfling, José Francisco

    2011-01-01

    The genetic diversity of C. albicans oral isolates from 75 healthy schoolchildren from eight schools located in different geographic areas of Piracicaba city, São Paulo state, Brazil, was established using isoenzymes marker (Multilocus Enzyme Electrophoresis – MLEE) and cluster analysis. Patterns of monoclonal and polyclonal oral colonization by C. albicans within and between groups of schoolchildren were identified. However, significant divergence between the observed and the expected genotypic frequencies (Hardy-Weinberg equilibrium test) was not detected in the geographically adjacent groups, suggesting the hypothesis that populations of healthy schoolchildren do not correspond to the selection factor (differential survival) of strains. Two highly polymorphic and distantly genetically related taxa (A and B) were identified within the total population of yeasts, each contained subgroups (A1, A2, A3, A4, B1 and B2) and clusters of moderately related strains (from I to X), suggesting the existence of strains restricted or not to certain groups of geographically limited, healthy students. However, the coexistence of identical strains in healthy schoolchildren from the same school (geographically related) reinforces the hypothesis of oral transmission, where the sources of propagation could be explored. Furthermore, this could also be used in current and retrospective analyses of C. albicans isolated from immunocompetent and immunocompromised people, in order to detect commensal or potentially pathogenic yeast groups, predominantly in candidiasis, and in the development of strategies to prevent transmission or human propagation. PMID:24031720

  5. Genetic and reproductive characterisation of seasonal flowering morphs of Gentianella bohemica revealed strong reproductive isolation and possible single origin.

    PubMed

    Plenk, K; Göd, F; Kriechbaum, M; Kropf, M

    2016-01-01

    Phenotypic polymorphism represents the most obvious type of intraspecific diversity raising scientific interest in its evolution and maintenance. We studied the regional endemic Gentianella bohemica, which exhibits an early- and a late-flowering morph. Genetic variation and structuring were investigated in relation to potential pollination and mating system differences, to verify hypotheses of evolutionary integrity, origin, and reproductive isolation of both flowering morphs. We identified the rarer early-flowering morph as an independent genetic entity, being more selfing, likely stronger pollinator-limited and reproductively isolated. All analysed populations showed strong among population differentiation and low overall genetic diversity due to habitat fragmentation and reduced population sizes. These results indicate likely inbreeding, but we also found evidence for possible outbreeding depression in the late-flowering morph. Both G. bohemica morphs are characteristic of traditionally used, nutrient-poor grasslands, but they represent independent conservation units and need temporally adapted management. We, therefore, also briefly discuss our results in the general context of conservation activities in relation to intraspecific polymorphisms and strongly argue for their formal and consequent consideration. PMID:26031436

  6. Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group

    PubMed Central

    Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

    2015-01-01

    Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Malaysia and were confirmed by In-house TTS1-PCR. Isolates were subjected for multi-locus sequence typing (MLST) to explore their genotypic diversity and to investigate for possible clonal clustering of a certain sequence type. Patient’s clinical information was examined to investigate for clinical correlation among the different genotypes. In spite of small sample set, MLST results indicated predictive results; considerable genotypic diversity, predominance and novelty among B. pseudomallei collected over a single geographically-located population in Malaysia. Massive genotypic heterogeneity was observed; 8 different sequence types with predominance of sequence type 54 and discovery of two novel sequence types. However, no clear pathogenomic or organ tropism clonal relationships were predicted. PMID:26417404

  7. Biodiversity among Lactobacillus helveticus Strains Isolated from Different Natural Whey Starter Cultures as Revealed by Classification Trees

    PubMed Central

    Gatti, Monica; Trivisano, Carlo; Fabrizi, Enrico; Neviani, Erasmo; Gardini, Fausto

    2004-01-01

    Lactobacillus helveticus is a homofermentative thermophilic lactic acid bacterium used extensively for manufacturing Swiss type and aged Italian cheese. In this study, the phenotypic and genotypic diversity of strains isolated from different natural dairy starter cultures used for Grana Padano, Parmigiano Reggiano, and Provolone cheeses was investigated by a classification tree technique. A data set was used that consists of 119 L. helveticus strains, each of which was studied for its physiological characters, as well as surface protein profiles and hybridization with a species-specific DNA probe. The methodology employed in this work allowed the strains to be grouped into terminal nodes without difficult and subjective interpretation. In particular, good discrimination was obtained between L. helveticus strains isolated, respectively, from Grana Padano and from Provolone natural whey starter cultures. The method used in this work allowed identification of the main characteristics that permit discrimination of biotypes. In order to understand what kind of genes could code for phenotypes of technological relevance, evidence that specific DNA sequences are present only in particular biotypes may be of great interest. PMID:14711641

  8. Extensive Field Survey, Laboratory and Greenhouse Studies Reveal Complex Nature of Pseudomonas syringae-Associated Hazelnut Decline in Central Italy

    PubMed Central

    Lamichhane, Jay Ram; Bartoli, Claudia; Varvaro, Leonardo

    2016-01-01

    Pseudomonas avellanae (Pav) has been reported as the causal agent of bacterial decline and bacterial canker of hazelnut in Italy and Greece, respectively. Both hazelnut diseases were reported to be similar in terms of symptoms, severity and persistence. In this study, we found that both symptomatic and asymptomatic trees in the field were colonized by Pav. Multilocus Sequence Typing (MLST) analysis showed that Pav strains isolated during this study in Italy belong to the P. syringae phylogroup 1 and they are closely related to Pav strains previously isolated in Greece from hazelnut bacterial canker. On the other hand, strains isolated in earlier studies from hazelnut decline in Italy belong to both phylogroup 1 and 2 of P. syringae. Both phylogroup 1 strains of P. syringae from Greece and Italy are different than strains isolated in this study in terms of their capacity to excrete fluorescent pigments on different media. Despite the same plant genotype and cropping practices adopted, the incidence of hazelnut decline ranged from nearly 0 to 91% across our study sites. No disease developed on plants inoculated with Pav through wounding while leaf scar inoculations produced only mild disease symptoms. Based on our results and the previously reported correlation between pedo-climatic conditions and hazelnut decline, we conclude that hazelnut decline in central Italy could be incited by a combination of predisposing (adverse pedo-climatic conditions) and contributing factors (Pav). Because this is a true decline different from “bacterial canker” described in Greece, we refer to it as hazelnut decline (HD). PMID:26840951

  9. Extensive Field Survey, Laboratory and Greenhouse Studies Reveal Complex Nature of Pseudomonas syringae-Associated Hazelnut Decline in Central Italy.

    PubMed

    Lamichhane, Jay Ram; Bartoli, Claudia; Varvaro, Leonardo

    2016-01-01

    Pseudomonas avellanae (Pav) has been reported as the causal agent of bacterial decline and bacterial canker of hazelnut in Italy and Greece, respectively. Both hazelnut diseases were reported to be similar in terms of symptoms, severity and persistence. In this study, we found that both symptomatic and asymptomatic trees in the field were colonized by Pav. Multilocus Sequence Typing (MLST) analysis showed that Pav strains isolated during this study in Italy belong to the P. syringae phylogroup 1 and they are closely related to Pav strains previously isolated in Greece from hazelnut bacterial canker. On the other hand, strains isolated in earlier studies from hazelnut decline in Italy belong to both phylogroup 1 and 2 of P. syringae. Both phylogroup 1 strains of P. syringae from Greece and Italy are different than strains isolated in this study in terms of their capacity to excrete fluorescent pigments on different media. Despite the same plant genotype and cropping practices adopted, the incidence of hazelnut decline ranged from nearly 0 to 91% across our study sites. No disease developed on plants inoculated with Pav through wounding while leaf scar inoculations produced only mild disease symptoms. Based on our results and the previously reported correlation between pedo-climatic conditions and hazelnut decline, we conclude that hazelnut decline in central Italy could be incited by a combination of predisposing (adverse pedo-climatic conditions) and contributing factors (Pav). Because this is a true decline different from "bacterial canker" described in Greece, we refer to it as hazelnut decline (HD). PMID:26840951

  10. Improved protocol for isolation of Campylobacter spp. from retail broiler meat and use of pulsed field gel electrophoresis for the typing of isolates.

    PubMed

    Oyarzabal, Omar A; Williams, Aretha; Zhou, Ping; Samadpour, Mansour

    2013-10-01

    To improve the detection of Campylobacter spp. in retail broiler meat, a reference method (R subsamples) based on the enrichment of 25 g of meat in Bolton broth at 42°C under microaerobiosis was compared with an alternative method (A subsamples) consisting in the rinsing of meat samples for 30s in buffered peptone water with antimicrobials with incubation at 42°C under aerobiosis. One piece of meat (breasts, tenderloins and thighs) was rinse in experiment 1 (A1) and two pieces in experiment 2 (A2). Campylobacter spp. were isolated on agar plates and identified by PCR. Retail samples in Alabama had less prevalence (P ≤ 0.05) than samples in the state of Washington. The percentage of positive was higher (P ≤ 0.05) in A than in R subsamples and rinsing two pieces of meat yielded the highest percentage of positive subsamples. R subsamples showed variations in the prevalence by product. However, A subsamples had similar prevalence of positives among products compare to the result from reference method. More Campylobacter coli isolates were collected in A2 subsamples. Pulse field gel electrophoresis (PFGE) was used as subtyping method to study the genome similarity among the isolates from all methods. A larger diversity of isolates were detected by PFGE in A2 subsamples. Denaturing gradient gel electrophoresis analysis suggested that the initial bacterial populations of the meat samples impact the final bacterial profile after enrichment. Rinsing broiler meats was less time consuming, required less sample preparation and was more sensitive than the reference method for the isolation of naturally occurring Campylobacter spp. This new method could help with epidemiological and intervention studies to control Campylobacter spp. PMID:23545445

  11. Sensitivity of field isolates of Eimeria from two broiler complexes to anticoccidial drugs in the chicken.

    PubMed

    Chapman, H D; Hacker, A B

    1994-09-01

    The spectrum of resistance to seven currently used anticoccidial drugs in isolates of Eimeria obtained from farms two broiler complexes was examined. All isolates were resistant to monensin, salinomycin, and narasin. Lasalocid was more effective in controlling coccidiosis than the other ionophores, although most isolates were classified as resistant to the drug. The majority of isolates were sensitive or showed reduced sensitivity to robenidine, clopidol, and decoquinate. It was concluded that for drugs that have been used extensively (e.g., monensin and salinomycin), examination of isolates from one or two farms may give results applicable to the entire complex. For drugs that have been used infrequently, however (such as robenidine, clopidol, and decoquinate), examination of isolates from at least five farms would be desirable to establish the spectrum of drug sensitivity. PMID:7800639

  12. Low-Energy Structures in Strong Field Ionization Revealed by Quantum Orbits

    SciTech Connect

    Yan, Tian-Min; Popruzhenko, S. V.; Vrakking, M. J. J.; Bauer, D.

    2010-12-17

    Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schroedinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the 'strong field approximation' (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered 'low-energy structure' [C. I. Blaga et al., Nature Phys. 5, 335 (2009) and W. Quan et al., Phys. Rev. Lett. 103, 093001 (2009)].

  13. Low-energy structures in strong field ionization revealed by quantum orbits.

    PubMed

    Yan, Tian-Min; Popruzhenko, S V; Vrakking, M J J; Bauer, D

    2010-12-17

    Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schrödinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the "strong field approximation" (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered "low-energy structure" [C. I. Blaga, Nature Phys. 5, 335 (2009) and W. Quan, Phys. Rev. Lett. 103, 093001 (2009). PMID:21231586

  14. Genetically engineered maize plants reveal distinct costs and benefits of constitutive volatile emissions in the field.

    PubMed

    Robert, Christelle Aurélie Maud; Erb, Matthias; Hiltpold, Ivan; Hibbard, Bruce Elliott; Gaillard, Mickaël David Philippe; Bilat, Julia; Degenhardt, Jörg; Cambet-Petit-Jean, Xavier; Turlings, Ted Christiaan Joannes; Zwahlen, Claudia

    2013-06-01

    Genetic manipulation of plant volatile emissions is a promising tool to enhance plant defences against herbivores. However, the potential costs associated with the manipulation of specific volatile synthase genes are unknown. Therefore, we investigated the physiological and ecological effects of transforming a maize line with a terpene synthase gene in field and laboratory assays, both above- and below ground. The transformation, which resulted in the constitutive emission of (E)-β-caryophyllene and α-humulene, was found to compromise seed germination, plant growth and yield. These physiological costs provide a possible explanation for the inducibility of an (E)-β-caryophyllene-synthase gene in wild and cultivated maize. The overexpression of the terpene synthase gene did not impair plant resistance nor volatile emission. However, constitutive terpenoid emission increased plant apparency to herbivores, including adults and larvae of the above ground pest Spodoptera frugiperda, resulting in an increase in leaf damage. Although terpenoid overproducing lines were also attractive to the specialist root herbivore Diabrotica virgifera virgifera below ground, they did not suffer more root damage in the field, possibly because of the enhanced attraction of entomopathogenic nematodes. Furthermore, fewer adults of the root herbivore Diabrotica undecimpunctata howardii were found to emerge near plants that emitted (E)-β-caryophyllene and α-humulene. Yet, overall, under the given field conditions, the costs of constitutive volatile production overshadowed its benefits. This study highlights the need for a thorough assessment of the physiological and ecological consequences of genetically engineering plant signals in the field to determine the potential of this approach for sustainable pest management strategies. PMID:23425633

  15. Two thousand years of geomagnetic field direction over central Europe revealed by indirect measurements

    NASA Astrophysics Data System (ADS)

    Márton, Péter

    2010-04-01

    Supplemented by 32 new directions, the Hungarian archaeomagnetic data set now consists of 217 archaeologically dated directions ranging in age from 300 BC to 1800 AD. From this data set, reference curves of secular variation of the geomagnetic field direction were computed using hierarchical modelling and curve estimation by moving average technique. Thanks to some of the new data, the gap in the earlier reference curves around 500 AD has now been filled up. For comparison's sake, directional records of comparable length from central Europe were also processed by the same curve building method. For this purpose, all dated directional data (declination and inclination with statistics) were drawn from the GEOMAGIA50 database for France, Germany, the Ukraine and Moldavia, Bulgaria and Italy and transferred via their virtual geomagnetic poles to a reference point of their respective countries. The resulting reference curves, including those for Hungary, show more or less similar temporal behaviour to the corresponding CALS7K.2 model curves (also available from the GEOMAGIA50 database), but significant deviations from the low-order CALS7K.2 predictions are also discernible owing to the likely presence of additional higher-order complications in the regional field. Therefore, the regional field and its secular variation are suggested to be approximated by the reference rather than the predicted curves. At any other location within the study area, the direction of the regional field can be obtained by spatial interpolation from the reference curves as illustrated by isogonic and isoclinic maps shown for selected times. Local time-series of interpolated directions for other central European countries lacking reference curves might serve as master curves for magnetic dating.

  16. Crustal Fracturing Field and Presence of Fluid as Revealed by Seismic Anisotropy

    NASA Astrophysics Data System (ADS)

    Pastori, M.; Piccinini, D.; de Gori, P.; Margheriti, L.; Barchi, M. R.; di Bucci, D.

    2010-12-01

    In the last three years, we developed, tested and improved an automatic analysis code (Anisomat+) to calculate the shear wave splitting parameters, fast polarization direction (φ) and delay time (∂t). The code is a set of MatLab scripts able to retrieve crustal anisotropy parameters from three-component seismic recording of local earthquakes using horizontal component cross-correlation method. The analysis procedure consists in choosing an appropriate frequency range, that better highlights the signal containing the shear waves, and a length of time window on the seismogram centered on the S arrival (the temporal window contains at least one cycle of S wave). The code was compared to other two automatic analysis code (SPY and SHEBA) and tested on three Italian areas (Val d’Agri, Tiber Valley and L’Aquila surrounding) along the Apennine mountains. For each region we used the anisotropic parameters resulting from the automatic computation as a tool to determine the fracture field geometries connected with the active stress field. We compare the temporal variations of anisotropic parameters to the evolution of vp/vs ratio for the same seismicity. The anisotropic fast directions are used to define the active stress field (EDA model), finding a general consistence between fast direction and main stress indicators (focal mechanism and borehole break-out). The magnitude of delay time is used to define the fracture field intensity finding higher value in the volume where micro-seismicity occurs. Furthermore we studied temporal variations of anisotropic parameters and vp/vs ratio in order to explain if fluids play an important role in the earthquake generation process. The close association of anisotropic and vp/vs parameters variations and seismicity rate changes supports the hypothesis that the background seismicity is influenced by the fluctuation of pore fluid pressure in the rocks.

  17. Field measurement of beef pen manure methane and nitrous oxide reveals a surprise for inventory calculations.

    PubMed

    Redding, M R; Devereux, J; Phillips, F; Lewis, R; Naylor, T; Kearton, T; Hill, C J; Weidemann, S

    2015-05-01

    Few data exist on direct greenhouse gas emissions from pen manure at beef feedlots. However, emission inventories attempt to account for these emissions. This study used a large chamber to isolate NO and CH emissions from pen manure at two Australian commercial beef feedlots (stocking densities, 13-27 m head) and related these emissions to a range of potential emission control factors, including masses and concentrations of volatile solids, NO, total N, NH, and organic C (OC), and additional factors such as total manure mass, cattle numbers, manure pack depth and density, temperature, and moisture content. Mean measured pen NO emissions were 0.428 kg ha d (95% confidence interval [CI], 0.252-0.691) and 0.00405 kg ha d (95% CI, 0.00114-0.0110) for the northern and southern feedlots, respectively. Mean measured CH emission was 0.236 kg ha d (95% CI, 0.163-0.332) for the northern feedlot and 3.93 kg ha d (95% CI, 2.58-5.81) for the southern feedlot. Nitrous oxide emission increased with density, pH, temperature, and manure mass, whereas negative relationships were evident with moisture and OC. Strong relationships were not evident between NO emission and masses or concentrations of NO or total N in the manure. This is significant because many standard inventory calculation protocols predict NO emissions using the mass of N excreted by the animal. PMID:26024253

  18. [The effect of ionophore anticoccidial agents on coccidia isolated in field conditions 1984-1985].

    PubMed

    Bedrník, P; Jurkovic, P; Firmanová, A; Kucera, J

    1987-12-01

    Out of six isolates of coccidia of the species Eimeria tenella, obtained in the years 1984 and 1985 on farms with a stationary occurrence of coccidiosis, five were found to have reduced sensitivity or resistance to monensin. Neither were these isolates sensitive to further monovalent ionophorous anticoccidials narasin and salinomycin. The bivalent ionophorous anticoccidial lasalocid controlled five isolates completely, but for one its effectiveness was reduced. An isolate obtained on a farm with long-term absence of coccidiosis was sensitive to all anticoccidial drugs. PMID:3127981

  19. Stable Isotopic Signatures in the Isolated Brine Cyroecosystem of Lake Vida Reveal Evidence of both Abiotic and Biotic Processes

    NASA Astrophysics Data System (ADS)

    Murray, A. E.; Ostrom, N. E.; Glazer, B. T.; McKay, C.; Kenig, F.; Loeffler, F. E.; Fritsen, C. H.; Doran, P. T.

    2011-12-01

    Lake Vida in the Victoria Valley of East Antarctica harbors ice-entrained brine that has been isolated from surface processes for several thousand years. The brine conditions (permanently dark, temperature of -13.4 °C, lack of oxygen, and pH of 6.2) and geochemistry are highly unusual. As an example, the brine contains excessive quantities of both reduced and oxidized nitrogen in nearly all forms, which in several cases are the highest levels found among natural ecosystems on Earth. Though this cryoecosystem appears to be relatively inhospitable, we have evidence that microbial life persists in abundance (cell levels over 107 cells per mL), is capable of protein production at in situ temperatures, and harbors a unique, but not necessarily novel, assemblage of bacterial phylotypes spanning at least eight phyla. In order to assess in situ microbial activities occurring today and in the past, and test hypotheses concerning energy generation in the brine cryoecosystem, the stable isotope signatures of nitrogen, oxygen, and hydrogen have been characterized in liquid and dissolved gas phases of the brine. The data provide evidence for both biotic and potentially abiotic formation of different fractions. The site preference of 15N-nitrous oxide (-3.64) suggests that the primary source of this dissolved gas, which is found at levels as high as 86 μM, is biologically produced by denitrification pathways. This appears to be consistent with detection of Marinobacter and Psychrobacter-related bacterial rRNA gene sequences and isolates in the brine microbial community. On the other hand, dissolved hydrogen present in the brine harbors an δH-H2 isotope signature suggesting that abiotic (potentially via serpentinization) or biotic production is equivocal based on the significant levels of fractionation observed. We postulate however, that a serpentinization production route is more favorable in this system that lies in a basin comprised of Ferrar dolerite sills and granite

  20. Isolated cholangiolitis revealed by 18F-FDG-PET/CT in a patient with fever of unknown origin.

    PubMed

    Codreanu, Ion; Zhuang, Hongming

    2011-01-01

    Cholangiolitis, inflammation of the cholangioles, is difficult to diagnose by conventional imaging modalities. We report a case of cholangiolitis revealed by fluorine-18 fluoro desoxyglucose positron emission tomography-computerized tomography ((18)F-FDG-PET/CT) after about 9 months of recurrent fevers. A 20 years old girl with a history of recurrent fevers and repeated workups at different hospitals, which didn't diagnosed the source of fever, was admitted with a recent episode of fever. An (18)F-FDG-PET/CT was requested, which demonstrated focal hypermetabolic activity in the lateral segment of the left lobe of the liver. A liver biopsy showed inflammation of small biliary ducts consistent of cholangiolitis. Enterococcus casseliflavus was found on performed cultures. This represents the first case of cholangiolitis revealed by (18)F-FDG-PET/CT imaging. PMID:21512668

  1. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota.

    PubMed

    Roach, David J; Burton, Joshua N; Lee, Choli; Stackhouse, Bethany; Butler-Wu, Susan M; Cookson, Brad T; Shendure, Jay; Salipante, Stephen J

    2015-07-01

    Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital's intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care. PMID:26230489

  2. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

    PubMed Central

    Roach, David J.; Burton, Joshua N.; Lee, Choli; Stackhouse, Bethany; Butler-Wu, Susan M.; Cookson, Brad T.

    2015-01-01

    Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital’s intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care. PMID:26230489

  3. Microdiversity of Deep-Sea Bacillales Isolated from Tyrrhenian Sea Sediments as Revealed by ARISA, 16S rRNA Gene Sequencing and BOX-PCR Fingerprinting

    PubMed Central

    Ettoumi, Besma; Guesmi, Amel; Brusetti, Lorenzo; Borin, Sara; Najjari, Afef; Boudabous, Abdellatif; Cherif, Ameur

    2013-01-01

    With respect to their terrestrial relatives, marine Bacillales have not been sufficiently investigated. In this report, the diversity of deep-sea Bacillales, isolated from seamount and non-seamount stations at 3,425 to 3,580 m depth in the Tyrrhenian Sea, was investigated using PCR fingerprinting and 16S rRNA sequence analysis. The isolate collection (n=120) was de-replicated by automated ribosomal intergenic spacer analysis (ARISA), and phylogenetic diversity was analyzed by 16S rRNA gene sequencing of representatives of each ARISA haplotype (n=37). Phylogenetic analysis of isolates showed their affiliation to six different genera of low G+C% content Gram-positive Bacillales: Bacillus, Staphylococcus, Exiguobacterium, Paenibacillus, Lysinibacillus and Terribacillus. Bacillus was the dominant genus represented by the species B. licheniformis, B. pumilus, B. subtilis, B. amyloliquefaciens and B. firmus, typically isolated from marine sediments. The most abundant species in the collection was B. licheniformis (n=85), which showed seven distinct ARISA haplotypes with haplotype H8 being the most dominant since it was identified by 63 isolates. The application of BOX-PCR fingerprinting to the B. licheniformis sub-collection allowed their separation into five distinct BOX genotypes, suggesting a high level of intraspecies diversity among marine B. licheniformis strains. This species also exhibited distinct strain distribution between seamount and non-seamount stations and was shown to be highly prevalent in non-seamount stations. This study revealed the great microdiversity of marine Bacillales and contributes to understanding the biogeographic distribution of marine bacteria in deep-sea sediments. PMID:24005887

  4. Microdiversity of deep-sea Bacillales isolated from Tyrrhenian sea sediments as revealed by ARISA, 16S rRNA gene sequencing and BOX-PCR fingerprinting.

    PubMed

    Ettoumi, Besma; Guesmi, Amel; Brusetti, Lorenzo; Borin, Sara; Najjari, Afef; Boudabous, Abdellatif; Cherif, Ameur

    2013-01-01

    With respect to their terrestrial relatives, marine Bacillales have not been sufficiently investigated. In this report, the diversity of deep-sea Bacillales, isolated from seamount and non-seamount stations at 3,425 to 3,580 m depth in the Tyrrhenian Sea, was investigated using PCR fingerprinting and 16S rRNA sequence analysis. The isolate collection (n=120) was de-replicated by automated ribosomal intergenic spacer analysis (ARISA), and phylogenetic diversity was analyzed by 16S rRNA gene sequencing of representatives of each ARISA haplotype (n=37). Phylogenetic analysis of isolates showed their affiliation to six different genera of low G+C% content Gram-positive Bacillales: Bacillus, Staphylococcus, Exiguobacterium, Paenibacillus, Lysinibacillus and Terribacillus. Bacillus was the dominant genus represented by the species B. licheniformis, B. pumilus, B. subtilis, B. amyloliquefaciens and B. firmus, typically isolated from marine sediments. The most abundant species in the collection was B. licheniformis (n=85), which showed seven distinct ARISA haplotypes with haplotype H8 being the most dominant since it was identified by 63 isolates. The application of BOX-PCR fingerprinting to the B. licheniformis sub-collection allowed their separation into five distinct BOX genotypes, suggesting a high level of intraspecies diversity among marine B. licheniformis strains. This species also exhibited distinct strain distribution between seamount and non-seamount stations and was shown to be highly prevalent in non-seamount stations. This study revealed the great microdiversity of marine Bacillales and contributes to understanding the biogeographic distribution of marine bacteria in deep-sea sediments. PMID:24005887

  5. Microsatellite-based genotyping of Candida parapsilosis sensu stricto isolates reveals dominance and persistence of a particular epidemiological clone among neonatal intensive care unit patients.

    PubMed

    Romeo, Orazio; Delfino, Demetrio; Cascio, Antonio; Lo Passo, Carla; Amorini, Maria; Romeo, Daniela; Pernice, Ida

    2013-01-01

    In this study, using multilocus microsatellite analysis, we report the genetic characterization of 27 Candida parapsilosis isolates recovered in two different periods of time (2007-2009 and 2011-2012) from infants hospitalized in the neonatal intensive care unit of a hospital in Messina, Italy. The results revealed the persistence and dominance of a particular infectious genotype among NICU patients and highlight the power of the used microsatellite markers in clarifying epidemiologic associations, detect micro-evolutionary variations and facilitating the recognition of outbreaks. PMID:23022715

  6. Near-field deformation from the El Mayor-Cucapah earthquake revealed by differential LIDAR.

    PubMed

    Oskin, Michael E; Arrowsmith, J Ramon; Hinojosa Corona, Alejandro; Elliott, Austin J; Fletcher, John M; Fielding, Eric J; Gold, Peter O; Gonzalez Garcia, J Javier; Hudnut, Ken W; Liu-Zeng, Jing; Teran, Orlando J

    2012-02-10

    Large [moment magnitude (M(w)) ≥ 7] continental earthquakes often generate complex, multifault ruptures linked by enigmatic zones of distributed deformation. Here, we report the collection and results of a high-resolution (≥nine returns per square meter) airborne light detection and ranging (LIDAR) topographic survey of the 2010 M(w) 7.2 El Mayor-Cucapah earthquake that produced a 120-kilometer-long multifault rupture through northernmost Baja California, Mexico. This differential LIDAR survey completely captures an earthquake surface rupture in a sparsely vegetated region with pre-earthquake lower-resolution (5-meter-pixel) LIDAR data. The postevent survey reveals numerous surface ruptures, including previously undocumented blind faults within thick sediments of the Colorado River delta. Differential elevation changes show distributed, kilometer-scale bending strains as large as ~10(3) microstrains in response to slip along discontinuous faults cutting crystalline bedrock of the Sierra Cucapah. PMID:22323817

  7. Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles

    SciTech Connect

    Callister, Stephen J.; Wilkins, Michael J.; Nicora, Carrie D.; Williams, Kenneth H.; Banfield, Jillian F.; VerBerkmoes, Nathan; Hettich, Robert L.; N'Guessan, A. Lucie; Mouser, Paula; Elifantz, H.; Smith, Richard D.; Lovley, Derek R.; Lipton, Mary S.; Long, Philip E.

    2010-12-01

    Stimulated by acetate-amendment field experiments conducted in 2007 and 2008, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this period, planktonic biomass was sampled at various time points and used to quantitatively evaluate proteomes, both spatially and temporally to study the dynamics of the microbial community proteome dynamics in relationship to geochemical measurements. As there were no comprehensive genome sequence data available at the time, we systematically evaluated different organisms to generate a "pseudo-metagenome" for proteomics analyses. Proteomics results supported the dominance of Geobacteraceae during biostimulation and revealed a shift from iron reduction to sulfate reduction, evidenced by changes in community membership. Because U(VI) is reduced at a lower rate during sulfate reduction, detecting this shift is important to maintaining the maximum rate of U(VI) reduction. In addition, the comparison of proteome measurements made at the end of the 2007 field experiment to the 2008 field experiment revealed a modified community structure. Importantly, the failure of a community to rebound following the cessation of biostimulation needs to be included in long-term remediation strategies.

  8. Co-transmission of the non-transmissible South African Babesia bovis S24 vaccine strain during mixed infection with a field isolate.

    PubMed

    Combrink, M P; Troskie, P C; de Klerk, D G; Pienaar, R; Latif, A A; Mans, B J

    2015-03-01

    The South African Babesia bovis live blood vaccine, originating from a field isolate attenuated by 23 serial syringe passages in splenectomized calves, has lost the ability to infect the natural vector Rhipicephalus (Boophilus) microplus. In this study, infection with mixed parasites from the vaccine strain and a field isolate, resulted in transmission of both genotype populations. Comparing the field isolate and transmitted combination indicated no significant difference in their virulence, while challenge of vaccinated cattle with these isolates showed the ability of the vaccine to protect against both. Limiting dilution of the transmitted combination, followed by infection of splenectomized cattle (n=34) yielded no single infections for the vaccine strain genotype, seven clonal lines of the field isolate and one mixture of vaccine strain and field isolate. Only one of two field isolate clonal lines selected for vector transmission study was transmitted. Showing that B. bovis isolates can contain both tick transmissible and non-transmissible subpopulations. The findings of this study also indicate the probability of vaccine co-infection transmission occurring in the field, which may result in new genotype populations of B. bovis. However, the impact of this recombination with field isolates is considered negligible since a genotypically diverse population of B. bovis is already present in South Africa. PMID:25544307

  9. Revealing the Exciton Fine Structure of PbSe Nanocrystal Quantum Dots Using Optical Spectroscopy in High Magnetic Fields

    SciTech Connect

    Schaller, Richard D.; Crooker, Scott A.; Bussian, David A.; Pietryga, Jeffrey M.; Joo, Jin; Klimov, Victor I.

    2010-08-04

    We measure the photoluminescence lifetime τ of excitons in colloidal PbSe nanocrystals (NCs) at low temperatures to 270 mK and in high magnetic fields to 15 T. For all NCs, τ increases sharply below 10 K but saturates by 500 mK. In contrast to the usual picture of well-separated “bright” and “dark” exciton states (found, e.g., in CdSe NCs), these dynamics fit remarkably well to a system having two exciton states with comparable—but small—oscillator strengths that are separated by only 300–900 μeV depending on NC size. Importantly, magnetic fields reduce τ below 10 K, consistent with field-induced mixing between the two states. Magnetic-circular dichroism studies reveal exciton g factors from 2–5, and magnetophotoluminescence shows >10% circularly polarized emission.

  10. Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence.

    PubMed

    de la Fuente, José; Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Tobes, Raquel; Manrique, Marina; López, Vladimir; Romero, Beatriz; Bezos, Javier; Dominguez, Lucas; Sevilla, Iker A; Garrido, Joseba M; Juste, Ramón; Madico, Guillermo; Jones-López, Edward; Gortazar, Christian

    2015-11-01

    Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to

  11. Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

    PubMed Central

    de la Fuente, José; Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Tobes, Raquel; Manrique, Marina; López, Vladimir; Romero, Beatriz; Bezos, Javier; Dominguez, Lucas; Sevilla, Iker A.; Garrido, Joseba M.; Juste, Ramón; Madico, Guillermo; Jones-López, Edward; Gortazar, Christian

    2015-01-01

    Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to

  12. Genomic relatedness among Actinobacillus pleuropneumoniae field strains of sterotypes 1 and 5 isolated from healthy and diseased pigs.

    PubMed Central

    Chatellier, S; Harel, J; Dugourd, D; Chevallier, B; Kobisch, M; Gottschalk, M

    1999-01-01

    Forty-four Actinobacillus pleuropneumoniae isolates recovered from both healthy and diseased pigs were characterized by random amplified polymorphic DNA analysis (RAPD), pulsed field gel electrophoresis (PFGE) and apx toxin gene typing. Nine RAPD types and 14 PFGE patterns were identified. No common RAPD or PFGE patterns were found between strains of serotype 1 and those of serotype 5. The RAPD analysis indicated that the 15 serotype 1 strains isolated from diseased pigs were assigned to 4 RAPD types, with 66% of strains characterized by the same RAPD type. By contrast, the 5 strains of serotype 1 isolated from healthy carriers were dispersed in 4 RAPD types. These data suggest that the diversity of strains isolated from healthy pigs could be higher than that of strains recovered from diseased pigs. In addition, all serotype 5 strains exhibited a unique RAPD type. Unlike RAPD, PFGE analysis allowed discrimination among isolates of serotype 1 and among those of serotype 5. All but 3 isolates showed the same apx genotype as their respective serotype reference strain. These data indicate that RAPD analysis is a valuable rapid tool for routine subtyping of strains of serotype 1. For strains of serotype 5, a combination of several typing methods, such as PFGE and apx gene typing, is needed to provide useful information on the molecular epidemiology of swine pleuropneumonia. Images Figure 1. Figure 3. PMID:10480458

  13. The Topography of Visuospatial Attention as Revealed by a Novel Visual Field Mapping Technique

    PubMed Central

    Brefczynski-Lewis, Julie A.; Datta, Ritobrato; Lewis, James W.; DeYoe, Edgar A.

    2009-01-01

    Previously, we and others have shown that attention can enhance visual processing in a spatially specific manner that is retinotopically mapped in the occipital cortex. However, it is difficult to appreciate the functional significance of the spatial pattern of cortical activation just by examining the brain maps. In this study, we visualize the neural representation of the “spotlight” of attention using a back-projection of attention-related brain activation onto a diagram of the visual field. In the two main experiments, we examine the topography of attentional activation in the occipital and parietal cortices. In retinotopic areas, attentional enhancement is strongest at the locations of the attended target, but also spreads to nearby locations and even weakly to restricted locations in the opposite visual field. The dispersion of attentional effects around an attended site increases with the eccentricity of the target in a manner that roughly corresponds to a constant area of spread within the cortex. When averaged across multiple observers, these patterns appear consistent with a gradient model of spatial attention. However, individual observers exhibit complex variations that are unique but reproducible. Overall, these results suggest that the topography of visual attention for each individual is composed of a common theme plus a personal variation that may reflect their own unique “attentional style.” PMID:18752412

  14. Metabolic properties in stroked rats revealed by relaxation-enhanced magnetic resonance spectroscopy at ultrahigh fields.

    PubMed

    Shemesh, Noam; Rosenberg, Jens T; Dumez, Jean-Nicolas; Muniz, Jose A; Grant, Samuel C; Frydman, Lucio

    2014-01-01

    (1)H magnetic resonance spectroscopy (MRS) yields site-specific signatures that directly report metabolic concentrations, biochemistry and kinetics-provided spectral sensitivity and quality are sufficient. Here, an enabling relaxation-enhanced (RE) MRS approach is demonstrated that by combining highly selective spectral excitations with operation at very high magnetic fields, delivers spectra exhibiting signal-to-noise ratios >50:1 in under 6 s for ~5 × 5 × 5 (mm)(3) voxels, with flat baselines and no interference from water. With this spectral quality, MRS was used to interrogate a number of metabolic properties in stroked rat models. Metabolic confinements imposed by randomly oriented micro-architectures were detected and found to change upon ischaemia; intensities of downfield resonances were found to be selectively altered in stroked hemispheres; and longitudinal relaxation time of lactic acid was found to increase by over 50% its control value as early as 3-h post ischaemia, paralleling the onset of cytotoxic oedema. These results demonstrate potential of (1)H MRS at ultrahigh fields. PMID:25229942

  15. Response bias reveals enhanced attention to inferior visual field in signers of American Sign Language.

    PubMed

    Dye, Matthew W G; Seymour, Jenessa L; Hauser, Peter C

    2016-04-01

    Deafness results in cross-modal plasticity, whereby visual functions are altered as a consequence of a lack of hearing. Here, we present a reanalysis of data originally reported by Dye et al. (PLoS One 4(5):e5640, 2009) with the aim of testing additional hypotheses concerning the spatial redistribution of visual attention due to deafness and the use of a visuogestural language (American Sign Language). By looking at the spatial distribution of errors made by deaf and hearing participants performing a visuospatial selective attention task, we sought to determine whether there was evidence for (1) a shift in the hemispheric lateralization of visual selective function as a result of deafness, and (2) a shift toward attending to the inferior visual field in users of a signed language. While no evidence was found for or against a shift in lateralization of visual selective attention as a result of deafness, a shift in the allocation of attention from the superior toward the inferior visual field was inferred in native signers of American Sign Language, possibly reflecting an adaptation to the perceptual demands imposed by a visuogestural language. PMID:26708522

  16. [Radio Frequency Electromagnetic Field Effect on the State of Na+/Ca2+ Exchange in the Isolated Rat Heart].

    PubMed

    Alabovsky, V V; Kudryshov, Yu B; Vinokurov, A A; Bogacheva, E V; Maslov, O V; Perov, S Yu

    2016-01-01

    It has been shown that a single exposure to 171 MHz electromagnetic field with 180 V/m electric field strength and 0.04 mW/kg specific absorption rate significantly alters the Na+/Ca2+ exchange in the isolated rat heart. It is assumed that enhancement of the Na+/Ca2+ exchange towards removing Ca2+ from the cardiomyocytes electromagnetic field exposure is a result of Ca2+ extraction from the sarcoplasmic reticulum and the increase of its intracellular level. PMID:27534068

  17. Rice-Field Drowning-Associated Pneumonia in which Pseudomonas spp., Aspergillus fumigatus, and Cunninghamella sp. Are Isolated.

    PubMed

    Yamawaki, Satoshi; Nakashima, Kei; Suzuki, Fumi; Otsuki, Ayumu; Watanabe, Junko; Takai, Motohisa; Katsurada, Masahiro; Katsurada, Naoko; Ohkuni, Yoshihiro; Misawa, Masafumi; Kaneko, Norihiro; Otsuka, Yoshihito; Aoshima, Masahiro

    2016-01-01

    We herein report the case of an 84-year-old who developed pneumonia after drowning in a rice field. Besides Aspergillus fumigatus, many pathogens previously not reported in drowning-associated pneumonia (such as Pseudomonas fluorescens, Pseudomonas putida, Nocardia niigatensis, and Cunninghamella sp.) were isolated from his sputum. He received sulbactam/ampicillin, trimethoprim/sulfamethoxazole, voriconazole, levofloxacin and liposomal amphotericin B, but died due to respiratory failure. Because the patient had drowned in a contaminated stagnant rice field and had multiple lung cavities, zygomycosis was suspected. This report provides invaluable information for the consideration of zygomycosis after an individual drowning in a rice field, even in an immunocompetent patient. PMID:27041173

  18. Resistance to anticoccidial drugs of Dutch avian Eimeria spp. field isolates originating from 1996, 1999 and 2001.

    PubMed

    Peek, H W; Landman, W J M

    2003-08-01

    Fifteen Eimeria spp. field isolates sampled on Dutch broiler farms were subjected to an Anticoccidial Sensitivity Test (AST) in a battery cage study. Four isolates dated from 1996, another four from 1999 and the last seven isolates from 2001. The selected anticoccidial drugs were monensin, narasin, salinomycin, lasalocid, nicarbazin, diclazuril, halofuginone, maduramicin and meticlorpindol/methylbenzoquate. Maduramicin and halofuginone were not included in the ASTs of 1999 and 2001, while meticlorpindol/methylbenzoquate was not tested in 1996 and 1999. Eimeria acervulina present in each of the four 1996 field isolates showed resistance for almost all products tested except maduramicin (1/4) and salinomycin (114), which appeared to be reduced sensitive. In 1999 the same species presented a similar resistance pattern for most products, although reduced sensitivity occurred for salinomycin (1/4), and sensitivity was found for diclazuril (2/4), monensin (1/4) and narasin (1/4). In the year 2001 increased sensitivity to various products was found. Higher sensitivity was found for meticlorpindol/ methylbenzoquate (7/7) and salinomycin and narasin (both 4/7), followed by nicarbazin (3/7) and monensin (2/7). Reduced sensitivity was found for monensin (3/7), lasalocid (2/7), salinomycin and narasin (1/7). E. maxima was only found in one field isolate per year. The E. maxima from 1996 was resistant to all products except narasin (sensitive) and halofuginone (reduced sensitive). In 1999 this species was reduced sensitive to narasin and lasalocid, showing resistance for the other products. The strain originating from the 2001 isolate was reduced sensitive to most products except monensin and narasin (resistant). Full sensitivity was found for meticlorpindol/ methylbenzoquate. E. tenella was present in one isolate of 1996, two of 1999 and four isolates of 2001. The AST of 1996 showed reduced sensitivity for nicarbazin, and sensitive to narasin, maduramicin and halofuginone. All

  19. Acetoanaerobium pronyense sp. nov., an anaerobic alkaliphilic bacterium isolated from a carbonate chimney of the Prony Hydrothermal Field (New Caledonia).

    PubMed

    Bes, Méline; Merrouch, Mériem; Joseph, Manon; Quéméneur, Marianne; Payri, Claude; Pelletier, Bernard; Ollivier, Bernard; Fardeau, Marie-Laure; Erauso, Gaël; Postec, Anne

    2015-08-01

    A novel anaerobic bacterial strain, ST07-YET, was isolated from a carbonate chimney of the Prony Hydrothermal Field (PHF) in New Caledonia. Cells were Gram-stain-positive, straight rods (0.7-0.8 × 3.0-5.0 μm) and motile by means of lateral flagella. Strain ST07-YET was mesophilic (optimum 35 °C), moderately alkaliphilic and halotolerant (optimum pH 8.7 and 5 g l- 1 NaCl). Elemental sulfur, sulfate, thiosulfate, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Yeast extract, peptone, tryptone, Casamino acids, crotonate, pyruvate, galactose, maltose, sucrose, ribose, trehalose and glucose were used as carbon sources. Glucose fermentation led to acetate, H2 and CO2 formation. Arginine, serine, histidine, lysine, methionine and cysteine improved growth, but the Stickland reaction was negative for the combinations of amino acids tested. The major metabolic products from yeast extract fermentation were H2, CO2, acetate, butyrate, isobutyrate, isovalerate and propionate. The predominant cellular fatty acids were C16  :  0, C16  :  1cis9, C14  :  0 and C16  :  1cis7 (>5 % of total fatty acids). The G+C content of the genomic DNA was 32.9 mol%. Phylogenetic analysis revealed that strain ST07-YET was most closely related to Clostridium sticklandii DSM 519T and Acetoanaerobium noterae NOT-3T (96.7 % and 96.8 % 16S rRNA gene sequence similarity, respectively). On the basis of phylogenetic, chemotaxonomic and physiological properties, strain ST07-YET is proposed to represent a novel species of the genus Acetoanaerobium (order Clostridiales, phylum Firmicutes) with the name Acetoanaerobium pronyense sp. nov. The type strain is ST07-YET ( = DSM 27512T = JCM 19400T). PMID:25948619

  20. Antitrypanosomal activity of aloin and its derivatives against Trypanosoma congolense field isolate

    PubMed Central

    2014-01-01

    Background There is an urgent need for the development of new, cheap, safe and highly effective drugs against African trypanosomiasis that affects both man and livestock in sub-Saharan Africa including Ethiopia. In the present study the exudate of Aloe gilbertii, an endemic Aloe species of Ethiopia, aloin, aloe-emodin and rhein were tested for their in vitro and in vivo antitrypanosomal activities against Trypanosoma congolense field isolate. Aloin was prepared from the leaf exudate of A. gilbertii by acid catalyzed hydrolysis. Aloe-emodin was obtained by oxidative hydrolysis of aloin, while rhein was subsequently derived from aloe-emodin by oxidation. In vitro trypanocidal activity tests were conducted on parasites obtained from infected mice, while mice infected with T. congolense were used to evaluate in vivo antitrypanosomal activity of the test substances. Results Results of the study showed that all the test substances arrested parasites motility at effective concentration of 4.0 mg/ml within an incubation period ranging from 15 to 40 min. Moreover, the same concentration of the test substances caused loss of infectivity of the parasites to mice during 30 days observation period. Among the tested substances, rhein showed superior activity with minimum inhibitory concentration (MIC) of 0.4 mg/ml. No adverse reactions were observed when the test substances were administered at a dose of 2000 mg/kg. Rhein at doses of 200 and 400 mg/kg, and the exudate, aloin and aloe-emodin at a dose of 400 mg/kg reduced the level of parasitaemia significantly (P < 0.05) and improved anaemia. Conclusion The results obtained in this investigation indicate that aloin and its derivatives particularly rhein have the potential to be used as a scaffold for the development of safe and cost effective antitrypanosomal drugs that can be useful in the continuing fight against African trypanosomiasis. PMID:24612613

  1. Effects of transmural field stimulation in isolated muscle strips from rabbit sphincter of Oddi and duodenum.

    PubMed

    Elbrønd, H; Tøttrup, A; Virchenko, S; Forman, A

    1994-05-01

    The purpose of the study was to compare the effect of transmural field stimulation (TMS) on isolated smooth muscle strips from rabbit sphincter of Oddi (SO), duodenal circular layer (Dc) and duodenal longitudinal layer (D1). The strips were suspended in thermostatically controlled 5-ml organ baths containing Krebs solution constantly bubbled with 5% CO2 in O2. TMS was delivered through platinum electrodes (140 V, 0.4 ms, 5 s trains, 40 Hz). The TMS responses could be divided in two main responses: (1) contraction initiated after cessation of the stimulus train, preceded by an inhibitory phase during TMS ('off'); and (2) contraction initiated during TMS ('duration'). The 'duration' response was observed in one out of 20 strips in the SO and Dc compartments, whereas 11 D1 strips (55%) showed 'duration' responses (P < 0.001). Atropine (10(-6)) converted all 'duration' responses to an 'off' response preceded by an inhibitory phase during TMS and reduced the contractile amplitudes with 40-65%. L-NNA significantly increased the number of 'duration' responses in all types of muscle, and caused a 40% increase in D1 contractile amplitude. Inhibitory responses could not be removed by atropine, propranolol and phentolamine. The results suggest that the intrinsic innervation of SO and duodenal muscle consists of a mixture of excitatory, cholinergic and inhibitory NANC pathways. The latter may utilize, wholly or partly, NO or a related compound as transmitter. A relative dominance of excitatory, cholinergic responses was present in the D1 strips, whereas inhibitory responses were dominating in the SO and Dc strips. PMID:8048339

  2. Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field.

    PubMed

    Siddiqi, Muhammad Zubair; Im, Wan-Taek

    2016-08-01

    A Gram-staining-negative, non-spore-forming, non-flagellated, rod-shaped, catalase- and oxidase-negative bacterium, designated as Gsoil 193(T), was isolated from the soil of ginseng field in Pocheon province, South Korea. 16S rRNA gene sequence analysis showed that strain Gsoil 193(T) belonged to family Xanthomonadaceae and was most closely related to Lysobacter daecheongensis KCTC 12,600(T) (96.4 %), Lysobacter panaciterrae KCTC 12601(T) (96.3 %), Lysobacter dokdonensis DSM 17958(T) (96.3 %) and Lysobacter oligotrophicus JCM 18257(T) (95.6 %). Strain Gsoil 193(T) grew at temperatures between 20 and 30 °C with an optimum of 30 °C. The pH range for growth was 5-9 pH (optimum 6-7 pH). The predominant respiratory quinone was ubiquinone Q-8 and a fatty acid profile with iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl) as the major fatty acids supported the affiliation of strain Gsoil 193(T) to the genus Lysobacter. The genomic DNA G+C content was 64.8 mol %. On the basis of the genotypic analysis, physiological and chemotaxonomic results indicate that strain Gsoil 193(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter pocheonensis sp. nov. is proposed. The type strain is Gsoil 193(T) (= DSM 18338(T) = KCTC 12624(T)). PMID:27052400

  3. Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis.

    PubMed Central

    Thong, K L; Cheong, Y M; Puthucheary, S; Koh, C L; Pang, T

    1994-01-01

    Pulsed-field gel electrophoresis (PFGE) was used to compare and analyze 158 isolates of Salmonella typhi from five well-defined outbreaks of typhoid fever in Malaysia and also isolates involved in sporadic cases of typhoid fever occurring during the same period. Digestion of chromosomal DNAs from these S. typhi isolates with the restriction endonucleases XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3') and then PFGE produced restriction endonuclease analysis (REA) patterns consisting of 11 to 24 DNA fragments ranging in size from 20 to 630 kbp. Analysis of the REA patterns generated by PFGE after digestion with XbaI and SpeI indicated that the S. typhi isolates obtained from sporadic cases of infection were much more heterogeneous (at least 13 different REA patterns were detected; Dice coefficient, between 0.73 and 1.0) than those obtained during outbreaks of typhoid fever. The clonal nature and the close genetic identities of isolates from outbreaks in Alor Setar, Penang, Kota Kinabalu, Johor Bahru, and Kota Bahru were suggested by the fact that only a limited number of REA patterns, which mostly differed by only a single band, were detected (one to four patterns; Dice coefficient, between 0.82 and 1.0), although a different pattern was associated with each of these outbreaks. Comparison of REA patterns with ribotyping for 18 S. typhi isolates involved in sporadic cases of infection showed a good correlation, in that 72% of the isolates were in the same group. There was no clear correlation of phage types with a specific REA pattern. We conclude that PFGE of s. typhi chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for comparing and differentiating S. typhi isolates for epidemiological purposes. Images PMID:7914202

  4. High-field proton magnetic resonance spectroscopy reveals metabolic effects of normal brain aging

    PubMed Central

    Harris, Janna L.; Yeh, Hung-Wen; Swerdlow, Russell H.; Choi, In-Young; Lee, Phil; Brooks, William M.

    2014-01-01

    Altered brain metabolism is likely to be an important contributor to normal cognitive decline and brain pathology in elderly individuals. To characterize the metabolic changes associated with normal brain aging, we used high-field proton magnetic resonance spectroscopy in vivo to quantify 20 neurochemicals in the hippocampus and sensorimotor cortex of young adult and aged rats. We found significant differences in the neurochemical profile of the aged brain when compared with younger adults, including lower aspartate, ascorbate, glutamate, and macromolecules, and higher glucose, myo-inositol, N-acetylaspartylglutamate, total choline, and glutamine. These neurochemical biomarkers point to specific cellular mechanisms that are altered in brain aging, such as bioenergetics, oxidative stress, inflammation, cell membrane turnover, and endogenous neuroprotection. Proton magnetic resonance spectroscopy may be a valuable translational approach for studying mechanisms of brain aging and pathology, and for investigating treatments to preserve or enhance cognitive function in aging. PMID:24559659

  5. Dark-field transmission electron microscopy of cortical bone reveals details of extrafibrillar crystals.

    PubMed

    Schwarcz, Henry P; McNally, Elizabeth A; Botton, Gianluigi A

    2014-12-01

    In a previous study we showed that most of the mineral in bone is present in the form of "mineral structures", 5-6nm-thick, elongated plates which surround and are oriented parallel to collagen fibrils. Using dark-field transmission electron microscopy, we viewed mineral structures in ion-milled sections of cortical human bone cut parallel to the collagen fibrils. Within the mineral structures we observe single crystals of apatite averaging 5.8±2.7nm in width and 28±19nm in length, their long axes oriented parallel to the fibril axis. Some appear to be composite, co-aligned crystals as thin as 2nm. From their similarity to TEM images of crystals liberated from deproteinated bone we infer that we are viewing sections through platy crystals of apatite that are assembled together to form the mineral structures. PMID:25449316

  6. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate.

    PubMed

    Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien; Cryer, Nicolai; Faivre, Nicolas; Santoni, Sylvain; Severac, Dany; Mikkelsen, Teis N; Larsen, Klaus S; Beier, Claus; Sørensen, Jesper G; Holmstrup, Martin; Ehlers, Bodil K

    2016-07-01

    Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response. PMID:27109012

  7. Remote Sensing of Desert Loess and Dune Fields Aids Revealing Proximal Loess Sources

    NASA Astrophysics Data System (ADS)

    Crouvi, O.; Gillespie, A.; Amit, R.; Enzel, Y.

    2008-12-01

    Loess is an eolian deposit composed mostly of silt-sized quartz, which serves as an important archive of Quaternary climate changes. Despite the long term support for the 'classical' glacial concept of loess formation, there have been challenges to this model focusing on the formation of silt grains in deserts, which is still controversial. The aim of this study is to trace the proximal dust sources of the Negev loess, Israel, using comprehensive remote-sensing mapping, field surveys, and laboratory analyses of hilltop, primary loess sequences. Based on field and spectral characterization of primary and secondary loess, we developed remote-sensing methodology to: 1) distinguish and classify loess types to better choose hilltop, un-reworked loess study sites; 2) map loess regionally and examine its spatial association with potential dust sources. The different loess types are spectrally distinguishable by using the difference in the magnitude of chlorophyll, ferric, Al-OH, and carbonate absorptions features that vary systematically by the relative abundance of clasts, loessial biogenic crust, and vegetation. We used band ratios and liner un-mixing techniques on ASTER and Landsat TM reflectance and thermal data to successfully map the different loess types and the regional loess distribution. We conclude that the border between the loess and the adjacent, upwind sand dunes exhibit gradual patterns of grain size, mineralogy, and spectral characteristics. These findings, together with detailed analyses of loess sequences show that the proximal dust source of the Negev loess is the adjacent sand dunes, and suggest that the silt grains were formed through eolian abrasion of sand grains. Applying the remote-sensing methodology on other desert loess (e.g. Tunisia) indicates similar pattern of gradual transition from sand dunes to loess, and suggests that this association is not unique to the Negev. Our findings imply that sand dunes are much more important proximal dust

  8. Decades of field data reveal that turtles senesce in the wild.

    PubMed

    Warner, Daniel A; Miller, David A W; Bronikowski, Anne M; Janzen, Fredric J

    2016-06-01

    Lifespan and aging rates vary considerably across taxa; thus, understanding the factors that lead to this variation is a primary goal in biology and has ramifications for understanding constraints and flexibility in human aging. Theory predicts that senescence-declining reproduction and increasing mortality with advancing age-evolves when selection against harmful mutations is weaker at old ages relative to young ages or when selection favors pleiotropic alleles with beneficial effects early in life despite late-life costs. However, in many long-lived ectotherms, selection is expected to remain strong at old ages because reproductive output typically increases with age, which may lead to the evolution of slow or even negligible senescence. We show that, contrary to current thinking, both reproduction and survival decline with adult age in the painted turtle, Chrysemys picta, based on data spanning >20 y from a wild population. Older females, despite relatively high reproductive output, produced eggs with reduced hatching success. Additionally, age-specific mark-recapture analyses revealed increasing mortality with advancing adult age. These findings of reproductive and mortality senescence challenge the contention that chelonians do not age and more generally provide evidence of reduced fitness at old ages in nonmammalian species that exhibit long chronological lifespans. PMID:27140634

  9. Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.

    PubMed

    Upadhyaya, Narayana M; Garnica, Diana P; Karaoglu, Haydar; Sperschneider, Jana; Nemri, Adnane; Xu, Bo; Mago, Rohit; Cuomo, Christina A; Rathjen, John P; Park, Robert F; Ellis, Jeffrey G; Dodds, Peter N

    2014-01-01

    The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes. PMID:25620970

  10. Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

    PubMed Central

    Upadhyaya, Narayana M.; Garnica, Diana P.; Karaoglu, Haydar; Sperschneider, Jana; Nemri, Adnane; Xu, Bo; Mago, Rohit; Cuomo, Christina A.; Rathjen, John P.; Park, Robert F.; Ellis, Jeffrey G.; Dodds, Peter N.

    2015-01-01

    The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes. PMID:25620970

  11. Screening of GNAL variants in Brazilian patients with isolated dystonia reveals a novel mutation with partial loss of function.

    PubMed

    Dos Santos, Camila Oliveira; Masuho, Ikuo; da Silva-Júnior, Francisco Pereira; Barbosa, Egberto Reis; Silva, Sonia Maria Cesar Azevedo; Borges, Vanderci; Ferraz, Henrique Ballalai; Rocha, Maria Sheila Guimarães; Limongi, João Carlos Papaterra; Martemyanov, Kirill A; de Carvalho Aguiar, Patricia

    2016-04-01

    GNAL was identified as a cause of dystonia in patients from North America, Europe and Asia. In this study, we aimed to investigate the prevalence of GNAL variants in Brazilian patients with dystonia. Ninety-one patients with isolated idiopathic dystonia, negative for THAP1 and TOR1A mutations, were screened for GNAL variants by Sanger sequencing. Functional characterization of the Gαolf protein variant was performed using the bioluminescence resonance energy transfer assay. A novel heterozygous nonsynonymous variant (p. F133L) was identified in a patient with cervical and laryngeal dystonia since the third decade of life, with no family history. This variant was not identified in healthy Brazilian controls and was not described in 63,000 exomas of the ExAC database. The F133L mutant exhibited significantly elevated levels of basal BRET and severely diminished amplitude of response elicited by dopamine, that both indicate substantial functional impairment of Gαolf in transducing receptor signals, which could be involved in dystonia pathophysiology. GNAL mutations are not a common cause of dystonia in the Brazilian population and have a lower prevalence than THAP1 and TOR1A mutations. We present a novel variant that results in partial Gαolf loss of function. PMID:26810727

  12. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

    USGS Publications Warehouse

    Wood, Dustin A.; Vandergast, A.G.; Espinal, A. Lemos; Fisher, R.N.; Holycross, A.T.

    2011-01-01

    Glacial–interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.

  13. Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D.

    PubMed

    Roberts, Evan W; Cai, Fei; Kerfeld, Cheryl A; Cannon, Gordon C; Heinhorst, Sabine

    2012-02-01

    Cyanobacteria, including members of the genus Prochlorococcus, contain icosahedral protein microcompartments known as carboxysomes that encapsulate multiple copies of the CO(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) in a thin protein shell that enhances the catalytic performance of the enzyme in part through the action of a shell-associated carbonic anhydrase. However, the exact mechanism by which compartmentation provides a catalytic advantage to the enzyme is not known. Complicating the study of cyanobacterial carboxysomes has been the inability to obtain homogeneous carboxysome preparations. This study describes the first successful purification and characterization of carboxysomes from the marine cyanobacterium Prochlorococcus marinus MED4. Because the isolated P. marinus MED4 carboxysomes were free from contaminating membrane proteins, their protein complement could be assessed. In addition to the expected shell proteins, the CsoS1D protein that is not encoded by the canonical cso gene clusters of α-cyanobacteria was found to be a low-abundance shell component. This finding and supporting comparative genomic evidence have important implications for carboxysome composition, structure, and function. Our study indicates that carboxysome composition is probably more complex than was previously assumed based on the gene complements of the classical cso gene clusters. PMID:22155772

  14. Extensive introgressive hybridization within the northern oriole group (Genus Icterus) revealed by three-species isolation with migration analysis

    PubMed Central

    Jacobsen, Frode; Omland, Kevin E

    2012-01-01

    Until recently, studies of divergence and gene flow among closely-related taxa were generally limited to pairs of sister taxa. However, organisms frequently exchange genes with other non-sister taxa. The “northern oriole” group within genus Icterus exemplifies this problem. This group involves the extensively studied hybrid zone between Baltimore oriole (Icterus galbula) and Bullock's oriole (I. bullockii), an alleged hybrid zone between I. bullockii and black-backed oriole (I. abeillei), and likely mtDNA introgression between I. galbula and I. abeillei. Here, we examine the divergence population genetics of the entire northern oriole group using a multipopulation Isolation-with-Migration (IM) model. In accordance with Haldane's rule, nuclear loci introgress extensively beyond the I. galbula–I. bullockii hybrid zone, while mtDNA does not. We found no evidence of introgression between I. bullockii and I. abeillei or between I. galbula and I. abeillei when all three species were analyzed together in a three-population model. However, traditional pairwise analysis suggested some nuclear introgression from I. abeillei into I. galbula, probably reflecting genetic contributions from I. bullockii unaccounted for in a two-population model. Thus, only by including all members of this group in the analysis was it possible to rigorously estimate the level of gene flow among these three closely related species. PMID:23145328

  15. Yeasts isolated from Algerian infants's feces revealed a burden of Candida albicans species, non-albicans Candida species and Saccharomyces cerevisiae.

    PubMed

    Seddik, Hamza Ait; Ceugniez, Alexandre; Bendali, Farida; Cudennec, Benoit; Drider, Djamel

    2016-01-01

    This study aimed at showing the yeast diversity in feces of Algerian infants, aged between 1 and 24 months, hospitalized at Bejaia hospital (northeast side of the country). Thus, 20 colonies with yeast characteristics were isolated and identified using biochemical (ID32C Api system) and molecular (sequencing of ITS1-5.8S-ITS2 region) methods. Almost all colonies isolated (19 strains) were identified as Candida spp., with predominance of Candida albicans species, and one strain was identified as Saccharomyces cerevisiae. Screening of strains with inhibitory activities unveiled the potential of Candida parapsilosis P48L1 and Candida albicans P51L1 to inhibit the growth of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923. Further studies performed with these two Candida strains revealed their susceptibility to clinically used antifungal compounds and were then characterized for their cytotoxicity and hemolytic properties. On the other hand, Saccharomyces cerevisiae P9L1 isolated as well in this study was shown to be devoid of antagonism but resulted safe and overall usable as probiotic. PMID:26404657

  16. Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil▿

    PubMed Central

    Pumphrey, Graham M.; Madsen, Eugene L.

    2008-01-01

    We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [13C]benzoic acid or [12C]benzoic acid (100 μg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring 13CO2 evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from Pseudomonas species to Burkholderia species. Isopycnic separation of heavy [13C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of Burkholderia species in the heavy fraction. Burkholderia sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [13C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species Burkholderia hospita. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate. PMID:18469130

  17. Isolation and Characterization of Mobile Genetic Elements from Microbial Assemblages Obtained from the Field Research Center Site

    SciTech Connect

    Patricia Sobecky; Cassie Hodges; Kerri Lafferty; Mike Humphreys; Melanie Raimondo; Kristin Tuttle; Tamar Barkay

    2004-03-17

    Considerable knowledge has been gained from the intensive study of a relatively limited group of bacterial plasmids. Recent efforts have begun to focus on the characterization of, at the molecular level, plasmid populations and associated mobile genetic elements (e.g., transposons, integrons) occurring in a wider range of aquatic and terrestrial habitats. Surprisingly, however, little information is available regarding the incidence and distribution of mobile genetic elements extant in contaminated subsurface environments. Such studies will provide greater knowledge on the ecology of plasmids and their contributions to the genetic plasticity (and adaptation) of naturally occurring subsurface microbial communities. We requested soil cores from the DOE NABIR Field Research Center (FRC) located on the Oak Ridge Reservation. The cores, received in February 2003, were sampled from four areas on the Oak Ridge Site: Area 1, Area 2, Area 3 (representing contaminated subsurface locales) and the background reference sites. The average core length (24 in) was subdivided into three profiles and soil pH and moisture content were determined. Uranium concentration was also determined in bulk samples. Replicate aliquots were fixed for total cell counts and for bacterial isolation. Four different isolation media were used to culture aerobic and facultative microbes from these four study areas. Colony forming units ranged from a minimum of 100 per gram soil to a maximum of 10,000 irrespective of media composition used. The vast majority of cultured subsurface isolates were gram-positive isolates and plasmid characterization was conducted per methods routinely used in the Sobecky laboratory. The percentage of plasmid incidence ranged from 10% to 60% of all isolates tested. This frequency appears to be somewhat higher than the incidence of plasmids we have observed in other habitats and we are increasing the number of isolates screened to confirm this observation. We are also

  18. Revealing backward rescattering photoelectron interference of molecules in strong infrared laser fields.

    PubMed

    Li, Min; Sun, Xufei; Xie, Xiguo; Shao, Yun; Deng, Yongkai; Wu, Chengyin; Gong, Qihuang; Liu, Yunquan

    2015-01-01

    Photoelectrons ionized from atoms and molecules in a strong laser field are either emitted directly or rescattered by the nucleus, both of which can serve as efficiently useful tools for molecular orbital imaging. We measure the photoelectron angular distributions of molecules (N2, O2 and CO2) ionized by infrared laser pulses (1320 nm, 0.2 ~ 1 × 10(14) W/cm(2)) from multiphoton to tunneling regime and observe an enhancement of interference stripes in the tunneling regime. Using a semiclassical rescattering model with implementing the interference effect, we show that the enhancement arises from the sub-laser-cycle holographic interference of the contributions of the back-rescattering and the non-rescattering electron trajectory. It is shown that the low-energy backscattering photoelectron interference patterns have encoded the structural information of the molecular initial orbitals and attosecond time-resolved dynamics of photoelectron, opening new paths in high-resolution imaging of sub-Ångström and sub-femtosecond structural dynamics in molecules. PMID:25687446

  19. Compartment shape anisotropy (CSA) revealed by double pulsed field gradient MR.

    PubMed

    Ozarslan, Evren

    2009-07-01

    The multiple scattering extensions of the pulsed field gradient (PFG) experiments can be used to characterize restriction-induced anisotropy at different length scales. In double-PFG acquisitions that involve two pairs of diffusion gradient pulses, the dependence of the MR signal attenuation on the angle between the two gradients is a signature of restriction that can be observed even at low gradient strengths. In this article, a comprehensive theoretical treatment of the double-PFG observation of restricted diffusion is presented. In the first part of the article, the problem is treated for arbitrarily shaped pores under idealized experimental conditions, comprising infinitesimally narrow gradient pulses with long separation times and long or vanishing mixing times. New insights are obtained when the treatment is applied to simple pore shapes of spheres, ellipsoids, and capped cylinders. The capped cylinder geometry is considered in the second part of the article where the solution for a double-PFG experiment with arbitrary experimental parameters is introduced. Although compartment shape anisotropy (CSA) is emphasized here, the findings of this article can be used in gleaning the volume, eccentricity, and orientation distribution function associated with ensembles of anisotropic compartments using double-PFG acquisitions with arbitrary experimental parameters. PMID:19398210

  20. Analysis of haemorrhagic septicaemia-causing isolates of Pasteurella multocida by ribotyping and field alternation gel electrophoresis (FAGE).

    PubMed

    Townsend, K M; Dawkins, H J; Papadimitriou, J M

    1997-10-16

    Ribotyping and field alternation gel electrophoresis (FAGE) were used to examine 19 Pasteurella multocida isolates, and to assess the ability of these techniques to differentiate P. multocida strains that cause haemorrhagic septicaemia (HS). Reproducible patterns were obtained from both methods, with FAGE demonstrating greater discriminatory power than ribotyping. FAGE analysis was particularly useful in distinguishing North American cultures originating from the 1922 Yellowstone National Park Buffalo 'B' strain, demonstrating the ability to detect genetic alterations induced by repeated subculture. A remarkable homogeneity was observed among Asian HS strains following ribotyping and FAGE analysis, with a clear distinction observed between virulent and avirulent HS isolates. This study has illustrated the value of genomic fingerprinting methods in distinguishing strains of similar serotype, and the capability of these methods to produce detailed characterisation of P. multocida isolates. PMID:9444075

  1. Genomic and Transcriptomic Analyses of Colistin-Resistant Clinical Isolates of Klebsiella pneumoniae Reveal Multiple Pathways of Resistance

    PubMed Central

    Wright, Meredith S.; Suzuki, Yo; Jones, Marcus B.; Marshall, Steven H.; Rudin, Susan D.; van Duin, David; Kaye, Keith; Jacobs, Michael R.

    2014-01-01

    The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae has resulted in a more frequent reliance on treatment using colistin. However, resistance to colistin (Colr) is increasingly reported from clinical settings. The genetic mechanisms that lead to Colr in K. pneumoniae are not fully characterized. Using a combination of genome sequencing and transcriptional profiling by RNA sequencing (RNA-Seq) analysis, distinct genetic mechanisms were found among nine Colr clinical isolates. Colr was related to mutations in three different genes in K. pneumoniae strains, with distinct impacts on gene expression. Upregulation of the pmrH operon encoding 4-amino-4-deoxy-l-arabinose (Ara4N) modification of lipid A was found in all Colr strains. Alteration of the mgrB gene was observed in six strains. One strain had a mutation in phoQ. Common among these seven strains was elevated expression of phoPQ and unaltered expression of pmrCAB, which is involved in phosphoethanolamine addition to lipopolysaccharide (LPS). In two strains, separate mutations were found in a previously uncharacterized histidine kinase gene that is part of a two-component regulatory system (TCRS) now designated crrAB. In these strains, expression of pmrCAB, crrAB, and an adjacent glycosyltransferase gene, but not that of phoPQ, was elevated. Complementation with the wild-type allele restored colistin susceptibility in both strains. The crrAB genes are present in most K. pneumoniae genomes, but not in Escherichia coli. Additional upregulated genes in all strains include those involved in cation transport and maintenance of membrane integrity. Because the crrAB genes are present in only some strains, Colr mechanisms may be dependent on the genetic background. PMID:25385117

  2. Isolation of Lactococcal Prolate Phage-Phage Recombinants by an Enrichment Strategy Reveals Two Novel Host Range Determinants

    PubMed Central

    Rakonjac, Jasna; O'Toole, Paul W.; Lubbers, Mark

    2005-01-01

    Virulent lactococcal prolate (or c2-like) phages are the second most common phage group that causes fermentation failure in the dairy industry. We have mapped two host range determinants in two lactococcal prolate phages, c2 and 923, for the host strains MG1363 and 112. Each phage replicates on only one of the two host strains: c2 on MG1363 and 923 on 112. Phage-phage recombinants that replicated on both strains were isolated by a new method that does not require direct selection but rather employs an enrichment protocol. After initial mixed infection of strain 112, two rotations, the first of which was carried out on strain MG1363 and the second on 112, permitted continuous amplification of double-plating recombinants while rendering one of the parent phages unamplified in each of the two rotations. Mapping of the recombination endpoints showed that the presence of the N-terminal two-thirds of the tail protein L10 of phage c2 and a 1,562-bp cosR-terminal fragment of phage 923 genome overcame blocks of infection in strains MG1363 and 112, respectively. Both infection inhibition mechanisms act at the stage of DNA entry; in strain MG1363, the infection block acts early, before phage DNA enters the cytoplasm, and in strain 112, it acts late, after most of the DNA has entered the cell but before it undergoes cos-end ligation. These are the first reported host range determinants in bacteriophage of lactic acid bacteria required for overcoming inhibition of infection at the stage of DNA entry and cos-end ligation. PMID:15838038

  3. Correlations between the Dielectric Properties and Exterior Morphology of Cells Revealed by Dielectrophoretic Field-Flow Fractionation

    PubMed Central

    Gascoyne, Peter R. C.; Shim, Sangjo; Noshari, Jamileh; Becker, Frederick F.; Stemke-Hale, Katherine

    2013-01-01

    Although dielectrophoresis (DEP) has great potential for addressing clinical cell isolation problems based on cell dielectric differences, a biological basis for predicting the DEP behavior of cells has been lacking. Here, the dielectric properties of the NCI-60 panel of tumor cell types have been measured by dielectrophoretic (DEP) field-flow fractionation, correlated with the exterior morphologies of the cells during growth, and compared with the dielectric and morphological characteristics of the subpopulations of peripheral blood. In agreement with earlier findings, cell total capacitance varied with both cell size and plasma membrane folding and the dielectric properties of the NCI-60 cell types in suspension reflected the plasma membrane area and volume of the cells at their growth sites. Therefore, the behavior of cells in DEP-based manipulations is largely determined by their exterior morphological characteristics prior to release into suspension. As a consequence, DEP is able to discriminate between cells of similar size having different morphological origins, offering a significant advantage over size-based filtering for isolating circulating tumor cells, for example. The findings provide a framework for anticipating cell dielectric behavior on the basis of structure-function relationships and suggest that DEP should be widely applicable as a surface marker-independent method for sorting cells. PMID:23172680

  4. Geographic Variation in Skull Morphology of the Large Japanese Field Mice, Apodemus speciosus (Rodentia: Muridae) Revealed by Geometric Morphometric Analysis.

    PubMed

    Shintaku, Yuta; Motokawa, Masaharu

    2016-04-01

    We analyzed geographic variation in skull morphology of the large Japanese field mouse (Apodemus speciosus) and determined changes in skull morphology that occurred during the evolutionary history of A. speciosus in relation to the estimated distribution range in the last glacial maximum (LGM). We analyzed 1,416 specimens from 78 localities using geometric morphometric techniques applied to the dorsal side of the cranium and mandible. While large variations within and among the populations in Honshu, Shikoku, and Kyushu were observed, geographic patterns were not observed. Hokkaido and peripheral island populations showed shared differentiation from the Honshu, Shikoku, and Kyushu populations with a larger skull and distinct mandible shape. In addition, these two groups also differed from each other in accumulated random shape variation. Common characteristics found in Hokkaido and peripheral island populations were considered to be the ancestral states, which were retained by geographic isolation from the main islands. Random variations in Hokkaido and the peripheral island populations were formed through stochastic processes in relation to their isolation. Characteristic morphologies widely found in the populations of Honshu, Shikoku, and Kyushu were considered to be derived states that expanded after separation from the peripheral islands. Complex geomorphology and a shift in distribution range related to climate change and altitudinal distribution are suggested to have formed the complex geographic variation in this species. PMID:27032678

  5. Life table assay of field-caught Mediterranean fruit flies, Ceratitis capitata, reveals age bias

    PubMed Central

    Kouloussis, Nikos A.; Papadopoulos, Nikos T.; Müller, Hans-Georg; Wang, Jane-Ling; Mao, Meng; Katsoyannos, Byron I.; Duyck, Pierre-François; Carey, James R.

    2012-01-01

    Though traps are used widely to sample phytophagous insects for research or management purposes, and recently in aging research, possible bias stemming from differential response of individuals of various ages to traps has never been examined. In this paper, we tested the response of Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) males and females of four ages (spanning from 1 to 40 days) to McPhail-type traps baited with a synthetic food attractant in field cages and found that the probability of trapping was significantly influenced by age. The type of food on which flies were maintained before testing (sugar or protein) also had a strong effect and interacted with age. In another experiment, we collected wild C. capitata adults of unknown age using 1–3 methods and then reared them in the laboratory until death. The survival schedules of these flies were subsequently used in a life table assay to infer their age at the time of capture. Results showed that on a single sampling date, males captured in traps baited with a food attractant were younger compared with males aspirated from fruiting host trees, or males captured in traps baited with a sex attractant. Likewise, females captured in food-baited traps were younger compared with aspirated females. In addition to providing the first evidence of age-dependent sampling bias for a phytophagous insect species, this paper also provides a novel approach to estimate the differences in the age composition of samples collected with different techniques. These findings are of utmost importance for several categories of insects, medically important groups notwithstanding. PMID:22844133

  6. Change of translational-rotational coupling in liquids revealed by field-cycling 1H NMR

    NASA Astrophysics Data System (ADS)

    Meier, R.; Schneider, E.; Rössler, E. A.

    2015-01-01

    Applying the field-cycling nuclear magnetic resonance technique, the frequency dependence of the 1H spin-lattice relaxation rate, R 1 ω = T1 - 1 ω , is measured for propylene glycol (PG) which is increasingly diluted with deuterated chloroform. A frequency range of 10 kHz-20 MHz and a broad temperature interval from 220 to about 100 K are covered. The results are compared to those of experiments, where glycerol and o-terphenyl are diluted with their deuterated counter-part. Reflecting intra- as well as intermolecular relaxation, the dispersion curves R 1 ω , x (x denotes mole fraction PG) allow to extract the rotational time constant τrot(T, x) and the self-diffusion coefficient D(T, x) in a single experiment. The Stokes-Einstein-Debye (SED) relation is tested in terms of the quantity D(T, x) τrot(T, x) which provides a measure of an effective hydrodynamic radius or equivalently of the spectral separation of the translational and the rotational relaxation contribution. In contrast to o-terphenyl, glycerol and PG show a spectral separation much larger than suggested by the SED relation. In the case of PG/chloroform mixtures, not only an acceleration of the PG dynamics is observed with increasing dilution but also the spectral separation of rotational and translational relaxation contributions continuously decreases. Finally, following a behavior similar to that of o-terphenyl already at about x = 0.6; i.e., while D(T, x) τrot(T, x) in the mixture is essentially temperature independent, it strongly increases with x signaling thus a change of translational-rotational coupling. This directly reflects the dissolution of the hydrogen-bond network and thus a change of solution structure.

  7. Analysis of Genomic Diversity among Helicobacter pylori Strains Isolated from Iranian Children by Pulsed Field Gel Electrophoresis

    PubMed Central

    Falsafi, Tahereh; Sotoudeh, Nazli; Feizabadi, Mohammad-Mehdi; Mahjoub, Fatemeh

    2014-01-01

    Objective: Presence of genomic diversity among Helicobacter pylori (H. pylori) strains have been suggested by numerous investigators. Little is known about diversity of H. pylori strains isolated from Iranian children and their association with virulence of the strains. Our purpose was to assess the degree of genomic diversity among H. pylori strains isolated from Iranian-children, on the basis of vacA genotype, cagA status of the strains, sex, age as well as the pathological status of the patients. Methods: Genomic DNA from 44 unrelated H. pylori strains isolated during 1997–2009, was examined by pulse-field gel electrophoresis (PFGE). Pathological status of the patients was performed according to the modified Sydney-system and genotype/status of vacA/cagA genes was determined by PCR. PFGE was performed using XbaI restriction-endonuclease and the field inversion-gel electrophoresis system. Findings: No significant relationship was observed between the patterns of PFGE and the cagA/vacA status/genotype. Also no relationship was observed between age, sex, and pathological status of the children and the PFGE patterns of their isolates. Similar conclusion was obtained by Total Lab software. However, more relationship was observed between the strains isolated in the close period (1997–2009, 2001–2003, 2005–2007, and 2007–2009) and more difference was observed among those obtained in the distant periods (1997 and 2009). Conclusion: H. pylori strains isolated from children in Iran are extremely diverse and this diversity is not related to their virulence characteristics. Occurrence of this extreme diversity may be related to adaptation of H. pylori strains to variable living conditions during transmission between various host individuals. PMID:26019775

  8. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... varieties of dissimilar adaptation and establishment of the stand for the production of the Certified class... varieties of dissimilar adaptation. 4 Isolation between classes of the same variety may be reduced to...

  9. 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

  10. The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment.

    PubMed

    Flórez, Ana Belén; Mayo, Baltasar

    2015-01-01

    Lactococcus garvieae is a lactic acid bacterium found in raw-milk dairy products as well as a range of aquatic and terrestrial environments. The plasmids in L. garvieae have received little attention compared to those of dairy Lactococcus lactis, in which the genes carried by these extrachromosomal elements are considered of adaptive value. The present work reports the sequencing and analysis of the plasmid complement of L. garvieae IPLA 31405, a strain isolated from a traditional, Spanish, starter-free cheese made from raw-milk. It consists of pLG9 and pLG42, of 9,124 and 42,240 nucleotides, respectively. Based on sequence and structural homology in the putative origin of replication (ori) region, pLG9 and pLG42 are predicted to replicate via a theta mechanism. Real-time, quantitative PCR showed the number of copies per chromosome equivalent of pLG9 and pLG42 to be around two and five, respectively. Sequence analysis identified eight complete open reading frames (orfs) in pLG9 and 36 in pLG42; these were organized into functional modules or cassettes containing different numbers of genes. These modules were flanked by complete or interrupted insertion sequence (IS)-like elements. Among the modules of pLG42 was a gene cluster encoding specific components of a phosphoenolpyruvate-phosphotransferase (PEP-PTS) system, including a phospho-β-galacosidase. The cluster showed a complete nucleotide identity respect to that in plasmids of L. lactis. Loss of pLG42 showed this to be involved in lactose assimilation. In the same plasmid, an operon encoding a type I restriction/modification (R/M) system was also identified. The specificity of this R/M system might be broadened by different R/M specificity subunits detected in pLG9 and in the bacterial chromosome. However, challenges of L. garvieae IPLA 31405 against L. lactis phages proved that the R/M system was not involved in phage resistance. Together, these results support the hypothesis that, as in L. lactis, pLG42

  11. The proteome of cytosolic lipid droplets isolated from differentiated Caco-2/TC7 enterocytes reveals cell-specific characteristics

    PubMed Central

    Bouchoux, Julien; Beilstein, Frauke; Pauquai, Thomas; Guerrera, I. Chiara; Chateau, Danielle; Ly, Nathalie; Alqub, Malik; Klein, Christophe; Chambaz, Jean; Rousset, Monique; Lacorte, Jean-Marc; Morel, Etienne; Demignot, Sylvie

    2011-01-01

    Background information. Intestinal absorption of alimentary lipids is a complex process ensured by enterocytes and leading to TRL [TAG (triacylglycerol)-rich lipoprotein] assembly and secretion. The accumulation of circulating intestine-derived TRL is associated with atherosclerosis, stressing the importance of the control of postprandial hypertriglyceridaemia. During the postprandial period, TAGs are also transiently stored as CLDs (cytosolic lipid droplets) in enterocytes. As a first step for determining whether CLDs could play a role in the control of enterocyte TRL secretion, we analysed the protein endowment of CLDs isolated by sucrose-gradient centrifugation from differentiated Caco-2/TC7 enterocytes, the only human model able to secrete TRL in culture and to store transiently TAGs as CLDs when supplied with lipids. Cells were analysed after a 24 h incubation with lipid micelles and thus in a state of CLD-associated TAG mobilization. Results. Among the 105 proteins identified in the CLD fraction by LC-MS/MS (liquid chromatography coupled with tandem MS), 27 were directly involved in lipid metabolism pathways potentially relevant to enterocyte-specific functions. The transient feature of CLDs was consistent with the presence of proteins necessary for fatty acid activation (acyl-CoA synthetases) and for TAG hydrolysis. In differentiated Caco-2/TC7 enterocytes, we identified for the first time LPCAT2 (lysophosphatidylcholine acyltransferase 2), involved in PC (phosphatidylcholine) synthesis, and 3BHS1 (3-β-hydroxysteroid dehydrogenase 1), involved in steroid metabolism, and confirmed their partial CLD localization by immunofluorescence. In enterocytes, LPCAT2 may provide an economical source of PC, necessary for membrane synthesis and lipoprotein assembly, from the lysoPC present in the intestinal lumen. We also identified proteins involved in lipoprotein metabolism, such as ApoA-IV (apolipoprotein A-IV), which is specifically expressed by enterocytes and has

  12. The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment

    PubMed Central

    Flórez, Ana Belén; Mayo, Baltasar

    2015-01-01

    Lactococcus garvieae is a lactic acid bacterium found in raw-milk dairy products as well as a range of aquatic and terrestrial environments. The plasmids in L. garvieae have received little attention compared to those of dairy Lactococcus lactis, in which the genes carried by these extrachromosomal elements are considered of adaptive value. The present work reports the sequencing and analysis of the plasmid complement of L. garvieae IPLA 31405, a strain isolated from a traditional, Spanish, starter-free cheese made from raw-milk. It consists of pLG9 and pLG42, of 9,124 and 42,240 nucleotides, respectively. Based on sequence and structural homology in the putative origin of replication (ori) region, pLG9 and pLG42 are predicted to replicate via a theta mechanism. Real-time, quantitative PCR showed the number of copies per chromosome equivalent of pLG9 and pLG42 to be around two and five, respectively. Sequence analysis identified eight complete open reading frames (orfs) in pLG9 and 36 in pLG42; these were organized into functional modules or cassettes containing different numbers of genes. These modules were flanked by complete or interrupted insertion sequence (IS)-like elements. Among the modules of pLG42 was a gene cluster encoding specific components of a phosphoenolpyruvate-phosphotransferase (PEP-PTS) system, including a phospho-β-galacosidase. The cluster showed a complete nucleotide identity respect to that in plasmids of L. lactis. Loss of pLG42 showed this to be involved in lactose assimilation. In the same plasmid, an operon encoding a type I restriction/modification (R/M) system was also identified. The specificity of this R/M system might be broadened by different R/M specificity subunits detected in pLG9 and in the bacterial chromosome. However, challenges of L. garvieae IPLA 31405 against L. lactis phages proved that the R/M system was not involved in phage resistance. Together, these results support the hypothesis that, as in L. lactis, pLG42

  13. Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis.

    PubMed

    Samanta, Pradipta; Sadhukhan, Sanjoy; Das, Subrata; Joshi, Alpana; Sen, Soumitra K; Basu, Asitava

    2011-10-01

    Jute (Corchorus capsularis), as a natural fibre producing plant species, ranks next to cotton only. Today, biotechnological approach has been considered as most accepted means for any genetic improvement of plant species. However, genetic control of the fibre development in jute has not yet been explored sufficiently for desired genetic improvement. One of the major impediments in exploring the genetic architecture in this crop at molecular level is the availability of good quality RNA from field-grown plant tissues mostly due to the presence of high amount of mucilage and phenolics. Development of a suitable RNA isolation method is becoming essential for deciphering developmental stage-specific gene expression pattern related to fibre formation in this crop species. A combination of modified hot borate buffer followed by isopycnic centrifugation (termed as HBIC) was adopted and found to be the best isolation method yielding sufficient quantity (~350-500 μg/gm fresh tissue) and good quality (A(260/280) ratio 1.88 to 1.91) RNA depending on the developmental stage of stem tissue from field-grown jute plant. The poly A(+) RNA purified from total RNA isolated by the present method was found amenable to efficient RT-PCR and cDNA library construction. The present development of RNA isolation was found to be appropriate for gene expression analysis related to fibre formation in this economically important jute plant in near future. PMID:21327574

  14. 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

    2014-03-01

    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. PMID:24412413

  15. Comparison of in vitro activity of danofloxacin, florfenicol, oxytetracycline, spectinomycin and tilmicosin against recent field isolates of Mycoplasma bovis.

    PubMed

    Ayling, R D; Baker, S E; Peek, M L; Simon, A J; Nicholas, R A

    2000-06-24

    The minimum inhibitory concentrations (MICS) and minimum mycoplasmacidal concentrations (MMCs) of danofloxacin, florfenicol, oxytetracycline, spectinomycin and tilmicosin against 62 recent British field isolates of Mycoplasma bovis were determined in vitro by a broth microdilution method. The isolates were most susceptible todanofloxacin with MIC90 and MMC90 values of 0.5 microg/ml and 1.0 microg/ml, respectively. They were less susceptible to florfenicol with a MIC90 of 16 microg/ml and MMC90 of 32 microg/ml. Oxytetracycline and spectinomycin had only a limited effect against the majority of isolates tested with MIC50s of 32 microg/ml and 4 microg/ml, respectively and MIC90s of 64 microg/ml and more than 128 microg/ml, respectively. Nearly 20 per cent of the isolates were highly resistant to spectinomycin, and tilmicosin was ineffective, with 92 per cent of the isolates having MIC values of 128 microg/ml or greater. There was no evidence of resistance by M bovis to danofloxacin. PMID:10909906

  16. Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem

    PubMed Central

    Van den Bogert, Bartholomeus; Boekhorst, Jos; Herrmann, Ruth; Smid, Eddy J.; Zoetendal, Erwin G.; Kleerebezem, Michiel

    2013-01-01

    The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine. PMID:24386196

  17. Generation of an extreme ultraviolet supercontinuum and isolated sub-50 as pulse in a two-colour laser field

    NASA Astrophysics Data System (ADS)

    Zhang, Gang-Tai; Liu, Xue-Shen

    2009-06-01

    We theoretically study high-order harmonic generation when a helium ion is exposed to a two-colour laser field, which is synthesized by a 5 fs/800 nm laser pulse and a 64 fs/2400 nm laser pulse. Our numerical results show that the harmonic spectrum exhibits an ultrabroad extreme ultraviolet supercontinuum when the initial state is prepared as a coherent superposition of the ground state and the first excited state. By superposing a series of properly selected harmonics, an isolated attosecond pulse with a duration of 47 as is obtained. Compared with the case of the ground state in a one-colour field, the intensity of this isolated attosecond pulse is six orders of magnitude higher. We also demonstrate these results in terms of the time-frequency analysis and the semiclassical three-step model.

  18. Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

    PubMed Central

    Kim, Eunji; Breznak, John A.; Schmidt, Thomas M.; Rodrigues, Jorge L. M.

    2012-01-01

    Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb3-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Diplosphaera colitermitum gen. nov., sp. nov., is proposed. PMID:22194293

  19. Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes.

    PubMed

    Wertz, John T; Kim, Eunji; Breznak, John A; Schmidt, Thomas M; Rodrigues, Jorge L M

    2012-03-01

    Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb(3)-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Diplosphaera colitermitum gen. nov., sp. nov., is proposed. PMID:22194293

  20. Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample.

    PubMed

    Prade, Friedrich; Fischer, Kai; Heinz, Detlef; Meyer, Pascal; Mohr, Jürgen; Pfeiffer, Franz

    2016-01-01

    Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases. PMID:27357449

  1. Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample

    NASA Astrophysics Data System (ADS)

    Prade, Friedrich; Fischer, Kai; Heinz, Detlef; Meyer, Pascal; Mohr, Jürgen; Pfeiffer, Franz

    2016-06-01

    Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases.

  2. Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample

    PubMed Central

    Prade, Friedrich; Fischer, Kai; Heinz, Detlef; Meyer, Pascal; Mohr, Jürgen; Pfeiffer, Franz

    2016-01-01

    Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases. PMID:27357449

  3. Evaluation of Lactococcus lactis Isolates from Nondairy Sources with Potential Dairy Applications Reveals Extensive Phenotype-Genotype Disparity and Implications for a Revised Species.

    PubMed

    Cavanagh, Daniel; Casey, Aidan; Altermann, Eric; Cotter, Paul D; Fitzgerald, Gerald F; McAuliffe, Olivia

    2015-06-15

    Lactococcus lactis is predominantly associated with dairy fermentations, but evidence suggests that the domesticated organism originated from a plant niche. L. lactis possesses an unusual taxonomic structure whereby strain phenotypes and genotypes often do not correlate, which in turn has led to confusion in L. lactis classification. A bank of L. lactis strains was isolated from various nondairy niches (grass, vegetables, and bovine rumen) and was further characterized on the basis of key technological traits, including growth in milk and key enzyme activities. Phenotypic analysis revealed all strains from nondairy sources to possess an L. lactis subsp. lactis phenotype (lactis phenotype); however, seven of these strains possessed an L. lactis subsp. cremoris genotype (cremoris genotype), determined by two separate PCR assays. Multilocus sequence typing (MLST) showed that strains with lactis and cremoris genotypes clustered together regardless of habitat, but it highlighted the increased diversity that exists among "wild" strains. Calculation of average nucleotide identity (ANI) and tetranucleotide frequency correlation coefficients (TETRA), using the JSpecies software tool, revealed that L. lactis subsp. cremoris and L. lactis subsp. lactis differ in ANI values by ∼14%, below the threshold set for species circumscription. Further analysis of strain TIFN3 and strains from nonindustrial backgrounds revealed TETRA values of <0.99 in addition to ANI values of <95%, implicating that these two groups are separate species. These findings suggest the requirement for a revision of L. lactis taxonomy. PMID:25841018

  4. Evaluation of Lactococcus lactis Isolates from Nondairy Sources with Potential Dairy Applications Reveals Extensive Phenotype-Genotype Disparity and Implications for a Revised Species

    PubMed Central

    Cavanagh, Daniel; Casey, Aidan; Altermann, Eric; Cotter, Paul D.; Fitzgerald, Gerald F.

    2015-01-01

    Lactococcus lactis is predominantly associated with dairy fermentations, but evidence suggests that the domesticated organism originated from a plant niche. L. lactis possesses an unusual taxonomic structure whereby strain phenotypes and genotypes often do not correlate, which in turn has led to confusion in L. lactis classification. A bank of L. lactis strains was isolated from various nondairy niches (grass, vegetables, and bovine rumen) and was further characterized on the basis of key technological traits, including growth in milk and key enzyme activities. Phenotypic analysis revealed all strains from nondairy sources to possess an L. lactis subsp. lactis phenotype (lactis phenotype); however, seven of these strains possessed an L. lactis subsp. cremoris genotype (cremoris genotype), determined by two separate PCR assays. Multilocus sequence typing (MLST) showed that strains with lactis and cremoris genotypes clustered together regardless of habitat, but it highlighted the increased diversity that exists among “wild” strains. Calculation of average nucleotide identity (ANI) and tetranucleotide frequency correlation coefficients (TETRA), using the JSpecies software tool, revealed that L. lactis subsp. cremoris and L. lactis subsp. lactis differ in ANI values by ∼14%, below the threshold set for species circumscription. Further analysis of strain TIFN3 and strains from nonindustrial backgrounds revealed TETRA values of <0.99 in addition to ANI values of <95%, implicating that these two groups are separate species. These findings suggest the requirement for a revision of L. lactis taxonomy. PMID:25841018

  5. Central European Dobrava Hantavirus Isolate from a Striped Field Mouse (Apodemus agrarius)

    PubMed Central

    Klempa, Boris; Stanko, Michal; Labuda, Milan; Ulrich, Rainer; Meisel, Helga; Krüger, Detlev H.

    2005-01-01

    Dobrava virus (DOBV) is a hantavirus that causes hemorrhagic fever with renal syndrome (HFRS) in Europe. It is hosted by at least two rodent species, Apodemus flavicollis and A. agrarius. According to their natural hosts they form the distinct genetic lineages DOBV-Af and DOBV-Aa, respectively. We have now established a DOBV isolate named Slovakia (SK/Aa) from an A. agrarius animal captured in Slovakia. The complete S and M and partial L segment nucleotide sequences of the new isolate were determined. Phylogenetic analyses showed that the SK/Aa isolate clustered together with the other DOBV-Aa sequences amplified from A. agrarius before and can be taken as the representative of this genetic lineage. SK/Aa, in comparison with a DOBV-Af isolate, was used for serotyping neutralizing antibodies of HFRS patients in Central Europe. Most patients' sera exhibited a higher endpoint titer when probed with our new isolate, suggesting that DOBV-Aa strains are responsible for most of the DOBV-caused HFRS cases in this region. PMID:15956394

  6. Extension of the high-order harmonics and an isolated sub-100 as pulse generation in a two-colour laser field

    NASA Astrophysics Data System (ADS)

    Zhai, Zhen; Liu, Xue-shen

    2008-06-01

    We theoretically investigate the high-order harmonic generation (HHG) when a helium ion model is irradiated by a two-colour laser field, which is synthesized by a 5 fs pulse at 800 nm and a 10 fs pulse at 394 nm. The harmonic spectrum reveals a double-plateau structure and an extreme ultraviolet supercontinuum spectrum in the lower second plateau can be superposed to produce attosecond pulses. By increasing the intensity of 10 fs pulse at 394 nm, the cutoff of the second plateau is extended effectively and the harmonics in the second plateau become in phase. Consequently, an isolated 63 as pulse is observed. These results can be explained in terms of the time-frequency characteristics of attosecond pulses and a semiclassic three-step model.

  7. Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.

    PubMed

    Auburn, Sarah; Marfurt, Jutta; Maslen, Gareth; Campino, Susana; Ruano Rubio, Valentin; Manske, Magnus; Machunter, Barbara; Kenangalem, Enny; Noviyanti, Rintis; Trianty, Leily; Sebayang, Boni; Wirjanata, Grennady; Sriprawat, Kanlaya; Alcock, Daniel; Macinnis, Bronwyn; Miotto, Olivo; Clark, Taane G; Russell, Bruce; Anstey, Nicholas M; Nosten, François; Kwiatkowski, Dominic P; Price, Ric N

    2013-01-01

    Whole genome sequencing (WGS) of Plasmodium vivax is problematic due to the reliance on clinical isolates which are generally low in parasitaemia and sample volume. Furthermore, clinical isolates contain a significant contaminating background of host DNA which confounds efforts to map short read sequence of the target P. vivax DNA. Here, we discuss a methodology to significantly improve the success of P. vivax WGS on natural (non-adapted) patient isolates. Using 37 patient isolates from Indonesia, Thailand, and travellers, we assessed the application of CF11-based white blood cell filtration alone and in combination with short term ex vivo schizont maturation. Although CF11 filtration reduced human DNA contamination in 8 Indonesian isolates tested, additional short-term culture increased the P. vivax DNA yield from a median of 0.15 to 6.2 ng µl(-1) packed red blood cells (pRBCs) (p = 0.001) and reduced the human DNA percentage from a median of 33.9% to 6.22% (p = 0.008). Furthermore, post-CF11 and culture samples from Thailand gave a median P. vivax DNA yield of 2.34 ng µl(-1) pRBCs, and 2.65% human DNA. In 22 P. vivax patient isolates prepared with the 2-step method, we demonstrate high depth (median 654X coverage) and breadth (≥89%) of coverage on the Illumina GAII and HiSeq platforms. In contrast to the A+T-rich P. falciparum genome, negligible bias was observed in coverage depth between coding and non-coding regions of the P. vivax genome. This uniform coverage will greatly facilitate the detection of SNPs and copy number variants across the genome, enabling unbiased exploration of the natural diversity in P. vivax populations. PMID:23308154

  8. Deep sequencing revealed genome-wide single-nucleotide polymorphism and plasmid content of Erwinia amylovora strains isolated in Middle Atlas, Morocco.

    PubMed

    Hannou, Najat; Mondy, Samuel; Planamente, Sara; Moumni, Mohieddine; Llop, Pablo; López, María; Manceau, Charles; Barny, Marie-Anne; Faure, Denis

    2013-10-01

    Erwinia amylovora causes economic losses that affect pear and apple production in Morocco. Here, we report comparative genomics of four Moroccan E. amylovora strains with the European strain CFBP1430 and North-American strain ATCC49946. Analysis of single nucleotide polymorphisms (SNPs) revealed genetic homogeneity of Moroccan's strains and their proximity to the European strain CFBP1430. Moreover, the collected sequences allowed the assembly of a 65 kpb plasmid, which is highly similar to the plasmid pEI70 harbored by several European E. amylovora isolates. This plasmid was found in 33% of the 40 E. amylovora strains collected from several host plants in 2009 and 2010 in Morocco. PMID:23770248

  9. 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

  10. 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

  11. Characterization of a Multiresistant Mosaic Plasmid from a Fish Farm Sediment Exiguobacterium sp. Isolate Reveals Aggregation of Functional Clinic-Associated Antibiotic Resistance Genes

    PubMed Central

    Yang, Jing; Wang, Chao; Wu, Jinyu; Liu, Li; Zhang, Gang

    2014-01-01

    The genus Exiguobacterium can adapt readily to, and survive in, diverse environments. Our study demonstrated that Exiguobacterium sp. strain S3-2, isolated from marine sediment, is resistant to five antibiotics. The plasmid pMC1 in this strain carries seven putative resistance genes. We functionally characterized these resistance genes in Escherichia coli, and genes encoding dihydrofolate reductase and macrolide phosphotransferase were considered novel resistance genes based on their low similarities to known resistance genes. The plasmid G+C content distribution was highly heterogeneous. Only the G+C content of one block, which shared significant similarity with a plasmid from Exiguobacterium arabatum, fit well with the mean G+C content of the host. The remainder of the plasmid was composed of mobile elements with a markedly lower G+C ratio than the host. Interestingly, five mobile elements located on pMC1 showed significant similarities to sequences found in pathogens. Our data provided an example of the link between resistance genes in strains from the environment and the clinic and revealed the aggregation of antibiotic resistance genes in bacteria isolated from fish farms. PMID:24362420

  12. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu(2+) Treatment.

    PubMed

    Quan, Meifang; Xie, Junyan; Liu, Xuemei; Li, Yang; Rang, Jie; Zhang, Tong; Zhou, Fengjuan; Xia, Liqiu; Hu, Shengbiao; Sun, Yunjun; Ding, Xuezhi

    2016-01-01

    Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu(2+.) Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain. PMID:27303381

  13. Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu2+ Treatment

    PubMed Central

    Quan, Meifang; Xie, Junyan; Liu, Xuemei; Li, Yang; Rang, Jie; Zhang, Tong; Zhou, Fengjuan; Xia, Liqiu; Hu, Shengbiao; Sun, Yunjun; Ding, Xuezhi

    2016-01-01

    Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu2+. Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain. PMID:27303381

  14. Sequence and phylogenetic analysis of virulent Newcastle disease virus isolates from Pakistan during 2009–2013 reveals circulation of new sub genotype

    SciTech Connect

    Siddique, Naila; Naeem, Khalid; Abbas, Muhammad Athar; Ali Malik, Akbar; Rashid, Farooq; Rafique, Saba; Ghafar, Abdul; Rehman, Abdul

    2013-09-15

    Despite observing the standard bio-security measures at commercial poultry farms and extensive use of Newcastle disease vaccines, a new genotype VII-f of Newcastle disease virus (NDV) got introduced in Pakistan during 2011. In this regard 300 ND outbreaks recorded so far have resulted into huge losses of approximately USD 200 million during 2011–2013. A total of 33 NDV isolates recovered during 2009–2013 throughout Pakistan were characterized biologically and phylogenetically. The phylogenetic analysis revealed a new velogenic sub genotype VII-f circulating in commercial and domestic poultry along with the earlier reported sub genotype VII-b. Partial sequencing of Fusion gene revealed two types of cleavage site motifs; lentogenic {sup 112}GRQGRL{sup 117} and velogenic {sup 112}RRQKRF{sup 117} along with some point mutations indicative of genetic diversity. We report here a new sub genotype of virulent NDV circulating in commercial and backyard poultry in Pakistan and provide evidence for the possible genetic diversity which may be causing new NDV out breaks. - Highlights: • The first report of isolation of new genotype VII-f of virulent Newcastle disease virus (NDV) in Pakistan. • We report the partial Fusion gene sequences of new genotype VII-f of virulent NDV from Pakistan. • We report the phylogenetic relationship of new NDV strains with reported NDV strains. • Provide outbreak history of new virulent NDV strain in commercial and backyard poultry in Pakistan. • We provide possible evidence for the role of backyard poultry in NDV outbreaks.

  15. RELAXATION OF MAGNETIC FIELD RELATIVE TO PLASMA DENSITY REVEALED FROM MICROWAVE ZEBRA PATTERNS ASSOCIATED WITH SOLAR FLARES

    SciTech Connect

    Yu Sijie; Yan Yihua; Tan Baolin E-mail: yyh@nao.cas.cn

    2012-12-20

    It is generally considered that the emission of microwave zebra pattern (ZP) structures requires high density and high temperature, which is similar to the situation of the flaring region where primary energy is released. Therefore, a parameter analysis of ZPs may reveal the physical conditions of the flaring source region. This work investigates the variations of 74 microwave ZP structures observed by the Chinese Solar Broadband Radio Spectrometer (SBRS/Huairou) at 2.6-3.8 GHz in nine solar flares, and we find that the ratio between the plasma density scale height L{sub N} and the magnetic field scale height L{sub B} in emission sources displays a tendency to decrease during the flaring processes. The ratio L{sub N} /L{sub B} is about 3-5 before the maximum of flares. It decreases to about 2 after the maximum. The detailed analysis of three typical X-class flares implies that the variation of L{sub N} /L{sub B} during the flaring process is most likely due to topological changes of the magnetic field in the flaring source region, and the stepwise decrease of L{sub N} /L{sub B} possibly reflects the magnetic field relaxation relative to the plasma density when the flaring energy is released. This result may also constrain solar flare modeling to some extent.

  16. Möbius-strip-like columnar functional connections are revealed in somato-sensory receptive field centroids

    PubMed Central

    Wright, James Joseph; Bourke, Paul David; Favorov, Oleg Vyachesslavovich

    2014-01-01

    Receptive fields of neurons in the forelimb region of areas 3b and 1 of primary somatosensory cortex, in cats and monkeys, were mapped using extracellular recordings obtained sequentially from nearly radial penetrations. Locations of the field centroids indicated the presence of a functional system in which cortical homotypic representations of the limb surfaces are entwined in three-dimensional Möbius-strip-like patterns of synaptic connections. Boundaries of somatosensory receptive field in nested groups irregularly overlie the centroid order, and are interpreted as arising from the superposition of learned connections upon the embryonic order. Since the theory of embryonic synaptic self-organization used to model these results was devised and earlier used to explain findings in primary visual cortex, the present findings suggest the theory may be of general application throughout cortex and may reveal a modular functional synaptic system, which, only in some parts of the cortex, and in some species, is manifest as anatomical ordering into columns. PMID:25400552

  17. Draft Genome Sequence of the Field Isolate Brucella melitensis Strain Bm IND1 from India

    PubMed Central

    Rao, Sashi Bhushan; Gupta, Vivek K.; Kumar, Mukesh; Hegde, Nagendra R.; Splitter, Gary A.; Reddanna, Pallu

    2014-01-01

    Brucella spp. are facultative intracellular bacterial pathogens causing the zoonotic disease brucellosis. Here, we report the draft genome sequence of the Brucella melitensis strain from India designated Bm IND1, isolated from stomach contents of an aborted goat fetus. PMID:24874680

  18. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.

    PubMed

    de Souza, Rocheli; Sant'Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  19. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields

    PubMed Central

    de Souza, Rocheli; Sant’Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  20. Optimization of an antibiotic sensitivity assay for Mycoplasma hyosynoviae and susceptibility profiles of field isolates from 1997 to 2011.

    PubMed

    Schultz, K K; Strait, E L; Erickson, B Z; Levy, N

    2012-07-01

    Mycoplasma hyosynoviae is a common agent responsible for polyarthritis leading to decreased production in swine herds worldwide. Antimicrobial agents are used to combat infections; however breakpoints for M. hyosynoviae have not yet been established. A number of methods have previously been utilized to analyze minimum inhibitory concentrations (MICs) for antibiotics against M. hyosynoviae; however these techniques as currently described are not easily standardized between laboratories. A dry microbroth dilution method was conducted to compare the minimum inhibitory concentrations (MICs) for 18 antibiotics, representative of different classes, against 24 recent isolates (23 field isolates and the type strain) of M. hyosynoviae. The MICs were determined using standard, commercially available 96-well Sensititre(®) plates containing various freeze-dried antibiotics at a range of concentrations appropriate to their potency. Clindamycin (CLI), a lincosamide antibiotic, showed the highest activity and most consistent inhibition for all isolates with an MIC(50) of ≤ 0.12 μg/ml. Tiamulin (TIA), a pleuromutilin derivative, exhibited an MIC(50) of ≤ 0.25 μg/ml. The isolates had similar levels of susceptibility to the quinolones, enrofloxacin (ENRO) and danofloxacin (DANO), exhibiting an MIC(50) of 0.25 μg/ml and 0.5 μg/ml, respectively. For the macrolides, the MIC(50) for tylosin (TYLT) and tilmicosin (TIL) was ≤ 0.25 μg/ml and ≤ 2 μg/ml respectively, but was ≤ 16 μg/ml for tulathromycin (TUL). For the aminoglycosides, the MIC(50) for gentamicin (GEN) was ≤ 0.5 μg/ml, while spectinomycin (SPE) and neomycin (NEO) had an MIC(50) of ≤ 4 μg/ml. The tetracyclines, oxytetracycline (OXY) and chlortetracycline (CTET) both had an MIC(50) of ≤ 2 μg/ml. Florfenicol (FFN) exhibited a MIC(50) of ≤ 1 μg/ml. All isolates were resistant to penicillin (PEN), ampicillin (AMP), ceftiofur (TIO), trimethoprim/sulfamethoxazole (SXT), and sulphadimethoxine (SDM) at all

  1. Frequencies of virulence genes and pulse field gel electrophoresis fingerprints in Escherichia coli isolates from canine pyometra.

    PubMed

    Maluta, Renato P; Borges, Clarissa A; Beraldo, Lívia G; Cardozo, Marita V; Voorwald, Fabiana A; Santana, André M; Rigobelo, Everlon C; Toniollo, Gilson H; Avila, Fernando A

    2014-11-01

    Escherichia coli is the most common bacterial agent isolated from canine pyometra. The frequencies of 24 virulence genes and pulsed field gel electrophoresis (PFGE) profiles were determined for 23 E. coli isolates from cases of canine pyometra in Brazil. The frequencies of virulence genes were 91.3% fimH, 91.3% irp-2, 82.6% fyuA, 56.5% iroN, 47.8% traT, 39.1% usp, 34.8% sfaD/E, 34.8% tsh, 30.4% papC, 30.4% hlyA, 26.1% papGIII, 26.1% cnf-1, 21.7% papE/F, 21.7% iss, 17.4% iutA, 17.4% ompT, 17.4% cvaC, 17.4% hlyF, 17.4% iucD, 13.0% iucC, 13.0% astA, 4.3% papGII, 0% afaB/C and 0% papGI. The high frequency of yersiniabactin (fyuA and irp2) and salmochelin (iroN) genes suggests that iron uptake systems might be important in the pathogenesis of canine pyometra. PFGE profiles of 19 isolates were heterogeneous, confirming that E. coli isolates from canine pyometra are unlikely to be epidemic clones. PMID:25201253

  2. Efficacy of commercial canarypox vaccine for protecting Hawai'i 'Amakihi from field isolates of Avipoxvirus

    USGS Publications Warehouse

    Atkinson, Carter T.; Wiegand, Kimberly C.; Triglia, Dennis; Jarvi, Susan I.

    2010-01-01

    At least three variants of avian pox virus are present in Hawai‘i - Fowlpox from domestic poultry and a group of genetically distinct viruses that cluster within two clades (Pox Variant 1 and Pox Variant 2) that are most similar to Canarypox based on DNA sequence of the virus 4b core protein gene. We tested whether Hawai‘i ‘Amakihi can be protected from wild virus isolates with an attenuated live Canarypox vaccine that is closely related to isolates that cluster within clade 1 (Pox Variant 1) based on sequence of the attenuated Canarypox virus 4b core protein. Thirty-one (31) Hawai`i ‘Amakihi (Hemignathus virens) with no prior physical evidence of pox infection were collected on Mauna Kea from xeric, high elevation habitats with low pox prevalence and randomly divided into two groups. One group of 16 was vaccinated with Poximmune C® while the other group received a sham vaccination with virus diluent. Four of 15 (27%) vaccinated birds developed potentially life-threatening disseminated lesions or lesions of unusually long duration, while one bird never developed a vaccine-associated lesion or "take". After vaccine-associated lesions healed, vaccinated birds were randomly divided into three groups of five and challenged with either a wild isolate of Fowlpox, a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 1 (Pox Variant 1) or a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 2 (Pox Variant 2). Similarly, three random groups of five unvaccinated ‘Amakihi were challenged with the same virus isolates. Vaccinated and unvaccinated ‘Amakihi challenged with Fowlpox had transient infections with no clinical signs of infection. Mortality in vaccinated ‘Amakihi that were challenged with Pox Variant 1 and Pox Variant 2 ranged from 0% (0/5) for Pox Variant 1 to 60% (3/5) for Pox Variant 2. Mortality in unvaccinated ‘Amakihi ranged from 40% (2/5) for Pox Variant 1 to 100% (5/5) for Pox Variant 2. While the vaccine provided some

  3. POPULATION SYNTHESIS OF YOUNG ISOLATED NEUTRON STARS: THE EFFECT OF FALLBACK DISK ACCRETION AND MAGNETIC FIELD EVOLUTION

    SciTech Connect

    Fu, Lei; Li, Xiang-Dong

    2013-10-01

    The spin evolution of isolated neutron stars (NSs) is dominated by their magnetic fields. The measured braking indices of young NSs show that the spin-down mechanism due to magnetic dipole radiation with constant magnetic fields is inadequate. Assuming that the NS magnetic field is buried by supernova fallback matter and re-emerges after accretion stops, we carry out a Monte Carlo simulation of the evolution of young NSs, and show that most of the pulsars have braking indices ranging from –1 to 3. The results are compatible with the observational data of NSs associated with supernova remnants. They also suggest that the initial spin periods of NSs might occupy a relatively wide range.

  4. Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars ▿ †

    PubMed Central

    Triplett, L. R.; Hamilton, J. P.; Buell, C. R.; Tisserat, N. A.; Verdier, V.; Zink, F.; Leach, J. E.

    2011-01-01

    The species Xanthomonas oryzae is comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. Although X. oryzae is not considered endemic in the United States, an X. oryzae-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterized X. oryzae pathovars. In the current study, a draft genome sequence from two U.S. Xanthomonas strains revealed that the U.S. strains form a novel clade within the X. oryzae species, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools. PMID:21515727

  5. Whole-Genome Sequencing Reveals Laboratory Salmonella Typhimurium Strain 14028s as a Likely Source of Outbreak Isolates from 2009-2010

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Next-generation sequencing (NGS) of bacterial isolates has emerged as valuable tool for tracking of an outbreak source. Between 2009 and 2011, clinical isolates of Salmonella Typhimurium sharing the JPXX01.0014 (XbaI) PFGE type were isolated across the U.S. The initial isolates were asso...

  6. Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype.

    PubMed

    Brown, Tyler S; Jacob, Christopher G; Silva, Joana C; Takala-Harrison, Shannon; Djimdé, Abdoulaye; Dondorp, Arjen M; Fukuda, Mark; Noedl, Harald; Nyunt, Myaing Myaing; Kyaw, Myat Phone; Mayxay, Mayfong; Hien, Tran Tinh; Plowe, Christopher V; Cummings, Michael P

    2015-03-01

    Multiple transcontinental waves of drug resistance in Plasmodium falciparum have originated in Southeast Asia before spreading westward, first into the rest of Asia and then to sub-Saharan Africa. In vitro studies have suggested that hypermutator P. falciparum parasites may exist in Southeast Asia and that an increased rate of acquisition of new mutations in these parasites may explain the repeated emergence of drug resistance in Southeast Asia. This study is the first to test the hypermutator hypothesis using field isolates. Using genome-wide SNP data from human P. falciparum infections in Southeast Asia and West Africa and a test for relative rate differences we found no evidence of increased relative substitution rates in P. falciparum isolates from Southeast Asia. Instead, we found significantly increased substitution rates in Mali and Bangladesh populations relative to those in populations from Southeast Asia. Additionally we found no association between increased relative substitution rates and parasite clearance following treatment with artemisinin derivatives. PMID:25514047

  7. Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype

    PubMed Central

    Brown, Tyler S.; Jacob, Christopher G.; Silva, Joana C.; Takala-Harrison, Shannon; Djimdé, Abdoulaye; Dondorp, Arjen M.; Fukuda, Mark; Noedl, Harald; Nyunt, Myaing Myaing; Kyaw, Myat Phone; Mayxay, Mayfong; Hien, Tran Tinh; Plowe, Christopher V.; Cummings, Michael P.

    2015-01-01

    Multiple transcontinental waves of drug resistance in Plasmodium falciparum have originated in Southeast Asia before spreading westward, first into the rest of Asia and then to sub-Saharan Africa. In vitro studies have suggested that hypermutator P. falciparum parasites may exist in Southeast Asia and that an increased rate of acquisition of new mutations in these parasites may explain the repeated emergence of drug resistance in Southeast Asia. This study is the first to test the hypermutator hypothesis using field isolates. Using genome-wide SNP data from human P. falciparum infections in Southeast Asia and West Africa and a test for relative rate differences we found no evidence of increased relative substitution rates in P. falciparum isolates from Southeast Asia. Instead, we found significantly increased substitution rates in Mali and Bangladesh populations relative to those in populations from Southeast Asia. Additionally we found no association between increased relative substitution rates and parasite clearance following treatment with artemisinin derivatives. PMID:25514047

  8. MAGNETIC FIELD IN THE ISOLATED MASSIVE DENSE CLUMP IRAS 20126+4104

    SciTech Connect

    Shinnaga, Hiroko; Phillips, Thomas G.; Novak, Giles; Vaillancourt, John E.; Machida, Masahiro N.; Kataoka, Akimasa; Tomisaka, Kohji; Davidson, Jacqueline; Houde, Martin; Dowell, C. Darren; Leeuw, Lerothodi

    2012-05-10

    We measured polarized dust emission at 350 {mu}m toward the high-mass star-forming massive dense clump IRAS 20126+4104 using the SHARC II Polarimeter, SHARP, at the Caltech Submillimeter Observatory. Most of the observed magnetic field vectors agree well with magnetic field vectors obtained from a numerical simulation for the case when the global magnetic field lines are inclined with respect to the rotation axis of the dense clump. The results of the numerical simulation show that rotation plays an important role on the evolution of the massive dense clump and its magnetic field. The direction of the cold CO 1-0 bipolar outflow is parallel to the observed magnetic field within the dense clump as well as the global magnetic field, as inferred from optical polarimetry data, indicating that the magnetic field also plays a critical role in an early stage of massive star formation. The large-scale Keplerian disk of the massive (proto)star rotates in an almost opposite sense to the clump's envelope. The observed magnetic field morphology and the counterrotating feature of the massive dense clump system provide hints to constrain the role of magnetic fields in the process of high-mass star formation.

  9. Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

    PubMed Central

    Bass, David; Moureau, Gregory; Tang, Shuoya; McAlister, Erica; Culverwell, C. Lorna; Glücksman, Edvard; Wang, Hui; Brown, T. David K.; Gould, Ernest A.; Harbach, Ralph E.; de Lamballerie, Xavier; Firth, Andrew E.

    2013-01-01

    We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected. PMID:24260463

  10. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates.

    PubMed

    Gascuel, Quentin; Bordat, Amandine; Sallet, Erika; Pouilly, Nicolas; Carrere, Sébastien; Roux, Fabrice; Vincourt, Patrick; Godiard, Laurence

    2016-01-01

    The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved. PMID:26845339

  11. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates

    PubMed Central

    Gascuel, Quentin; Bordat, Amandine; Sallet, Erika; Pouilly, Nicolas; Carrere, Sébastien; Roux, Fabrice

    2016-01-01

    The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved. PMID:26845339

  12. Molecular epidemiology of Legionella pneumophila environmental isolates representing nine different serogroups determined by automated ribotyping and pulsed-field gel electrophoresis.

    PubMed Central

    Boccia, S.; Stenico, A.; Amore, R.; Moroder, L.; Orsini, M.; Romano-Spica, V.; Ricciardi, G.

    2005-01-01

    The purposes of the study were (i) to describe the abundance and epidemiology of Legionellaceae in the man-made environment in a northern Italian area, (ii) to assess the concordance between pulsed-field gel electrophoresis (PFGE) and automated ribotyping (AR) techniques for genotyping L. pneumophila and (iii) to investigate the correlation between serogrouping and genotyping data. Water was sampled from reservoirs in 12 buildings across an area of 80-km radius. Despite the water temperature always being maintained above 55 degrees C, all of the buildings sampled were contaminated with Legionellaceae on at least one occasion and 63 L. pneumophila isolates representing nine different serogroups were collected. The two DNA methods revealed a high degree of genetic heterogeneity, even though identical L. pneumophila clones were recovered at different sites. The AR technique provided a fairly reliable approximation of PFGE results (73% concordance), however there was poor correlation between serogrouping and genotyping data as identical DNA fingerprints were shared by isolates of different serogroups. PMID:16274507

  13. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    PubMed

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity. PMID:27346642

  14. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability.

    PubMed

    Henneberger, Ruth; Chiri, Eleonora; Bodelier, Paul E L; Frenzel, Peter; Lüke, Claudia; Schroth, Martin H

    2015-05-01

    Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body. PMID:25186436

  15. Characterization of western European field isolates and vaccine strains of avian infectious laryngotracheitis virus by restriction fragment length polymorphism and sequence analysis.

    PubMed

    Neff, C; Sudler, C; Hoop, R K

    2008-06-01

    Infectious laryngotracheitis is a dramatic disease of the upper respiratory tract in poultry caused by a herpesvirus. In this study we investigated the characteristics of western European field isolates of infectious laryngotracheitis virus (ILTV) to gain more information on their diversity. The examined 104 isolates, collected from acute outbreaks during the last 35 years, originated from eight different countries: Switzerland (48), Germany (21), Sweden (14), the United Kingdom (9), Italy (5), Belgium (4), Austria (2), and Norway (1). Two vaccines, a chicken embryo origin product and a tissue culture origin product, were included in the survey. Polymerase chain reaction (PCR) was performed to amplify a 2.1-kb DNA fragment of ILTV using primers generated for the thymidine kinase (TK) gene. After digestion of the resulting PCR products by restriction endonuclease HaeIII, restriction fragment length polymorphism analysis was carried out. PCR amplicons of three field isolates and both vaccine strains were selected for sequencing. Here 98 field isolates showed the same cleavage pattern and were identical to both vaccine strains (clone 1). They differed from five Swiss isolates with identical cleavage pattern (clone 2) and one Swedish isolate (clone 3). The present study demonstrated that at least three clones of ILTV have been circulating in western Europe during the last 35 years. The 104 isolates analyzed showed a high genetic similarity regarding the TK gene, and a large majority of the field isolates (98/104) were genetically related to the vaccine strains. PMID:18646457

  16. Preferential flow pathways revealed by field based stable isotope analysis of CO2 by mid-infrared laser spectroscopy

    NASA Astrophysics Data System (ADS)

    van Geldern, Robert; Nowak, Martin; Zimmer, Martin; Szizybalski, Alexandra; Myrttinen, Anssi; Barth, Johannes A. C.; Jost, Hj

    2016-04-01

    A newly developed and commercially available isotope ratio laser spectrometer for CO2 analyses has been tested during a 10-day field monitoring campaign at the Ketzin pilot site for CO2 storage in northern Germany. The laser instrument is based on tunable laser direct absorption in the mid-infrared. The instrument recorded a continuous 10-day carbon stable isotope data set with 30 minutes resolution directly on-site in a field-based laboratory container during a tracer experiment. To test the instruments performance and accuracy the monitoring campaign was accompanied by daily CO2 sampling for laboratory analyses with isotope ratio mass spectrometry (IRMS). The carbon stable isotope ratios measured by conventional IRMS technique and by the new mid-infrared laser spectrometer agree remarkably well within 2σ analytical precision (<0.3 ‰). This proves the capability of the new mid-infrared direct absorption technique to measure high precision and accurate real-time table isotope data directly in the field. The injected CO2 tracer had a distinct δ13C value that was largely different from the reservoir background value. The laser spectroscopy data revealed a prior to this study unknown, intensive dynamic with fast changing δ13C values. The arrival pattern of the tracer suggest that the observed fluctuations were probably caused by migration along separate and distinct preferential flow paths between injection well and observation well. The new technique might contribute to a better tracing of the migration of the underground CO2 plume and help to ensure the long-term integrity of the reservoir.

  17. Comparative study on the in vitro replication and genomic variability of Argentinean field isolates of bovine herpesvirus type 4 (BoHV-4).

    PubMed

    Verna, A E; Pérez, S E; Manrique, J M; Leunda, M R; Odeón, A C; Jones, L R

    2016-06-01

    Bovine herpesvirus 4 (BoHV-4) is a gammaherpesvirus, belonging to the Rhadinovirus genus, which is increasingly associated with various problems of the reproductive tract of cattle. In Argentina, analysis of BoHV-4 strains isolated from cervico-vaginal mucus of aborted cows revealed a high genetic divergence among strains, which could be classified in three different groups: Genotype 1 comprises Movar-like strains (European prototype), Genotype 2 includes DN599-like strains (American prototype) and Genotype 3 corresponds to a novel genotype group. Understanding the replication behavior in cell cultures and the molecular characteristics of this pathogen of cattle is critical for the rational design of in vitro experiments. The aim of this work was to quantitatively evaluate the replication properties of different Argentinean BoHV-4 strains and to characterize their phylogenetic relationships. Significant differences were evident among the virus titers of the different BoHV-4 isolates in vitro. The most conserved gene was the major capsid protein (ORF25). The glycoprotein B (gB), glycoprotein H (gH), and thymidine kinsase (TK) genes displayed both synonymous and non-synonymous substitutions, with the highest diversity observed for gB, which displayed amino acid substitutions in 24 out of the 178 positions examined. Strains 09/759, 12/512, and 07/568 presented a deletion encompassing amino acid position 27 to 35, whereas strains 07/435 and 09/227 had a deletion from position 28 to 35. Two strains, 07/435 and 09/227, also displayed the highest divergence compared to the other strains analyzed. This study provides information about the in vitro replication and behavior of nine field isolates of BoHV-4. These findings are relevant since available information on the in vitro growth characteristics of BoHV-4 strains is scarce. The results from this study may also be useful for establishing comparisons with other related viruses. PMID:26995219

  18. Bias field free tunability of microwave properties based on geometrically controlled isolated permalloy nanomagnets

    NASA Astrophysics Data System (ADS)

    Haldar, Arabinda; Adeyeye, Adekunle Olusola

    2016-04-01

    We have investigated the static and dynamic properties of two lithographically patterned bi-stable nanomagnets. Different ground magnetic states were realized using a simple in-plane field initialization technique. These states were directly imaged with magnetic force microscopy. Using the broadband ferromagnetic spectroscopy, we show that different magnetic ground states are associated with distinct microwave absorption spectra due to the variation of the internal magnetic field leading to large shift between the absorption spectra. Our experimental observations are in good agreement with micromagnetic simulations which also indicate the possibility of sub-ns switching between magnetic states using a rectangular pulse field.

  19. Generation of short and intense isolated Attosecond pulses by field-controlled excited states

    NASA Astrophysics Data System (ADS)

    Jooya, Hossein Z.; Li, Peng-Cheng; Liao, Sheng-Lun; Chu, Shih-I.

    2014-05-01

    A new mechanism for the coherent control of the generation of an isolated and ultrashort attosecond laser pulse with enhanced intensity is reported. Frequency and time delay of a weak high harmonics, added to a two color laser, are optimized to produce a 45 attosecond pulse with intensity of more than 70 times bigger than the original one. Resonance excitation and subsequent ionization are analyzed, along with electron trajectory investigation from wavelet time-frequency profile to explain the mechanism of the observed augmentation in this high-harmonic generation. This work is partially supported by DOE.

  20. Characterization of Nivalenol-Producing Fusarium culmorum Isolates Obtained from the Air at a Rice Paddy Field in Korea.

    PubMed

    Kim, Da-Woon; Kim, Gi-Yong; Kim, Hee-Kyoung; Kim, Jueun; Jeon, Sun Jeong; Lee, Chul Won; Lee, Hyang Burm; Yun, Sung-Hwan

    2016-06-01

    Together with the Fusarium graminearum species complex, F. culmorum is a major member of the causal agents of Fusarium head blight on cereals such as wheat, barley and corn. It causes significant yield and quality losses and results in the contamination of grain with mycotoxins that are harmful to humans and animals. In Korea, F. culmorum is listed as a quarantine fungal species since it has yet to be found in the country. In this paper, we report that two isolates (J1 and J2) of F. culmorum were collected from the air at a rice paddy field in Korea. Species identification was confirmed by phylogenetic analysis using multi-locus sequence data derived from five genes encoding translation elongation factor, histone H3, phosphate permease, a reductase, and an ammonia ligase and by morphological comparison with reference strains. Both diagnostic PCR and chemical analysis confirmed that these F. culmorum isolates had the capacity to produce nivalenol, the trichothecene mycotoxin, in rice substrate. In addition, both isolates were pathogenic on wheat heads and corn stalks. This is the first report on the occurrence of F. culmorum in Korea. PMID:27298593

  1. Characterization of Nivalenol-Producing Fusarium culmorum Isolates Obtained from the Air at a Rice Paddy Field in Korea

    PubMed Central

    Kim, Da-Woon; Kim, Gi-Yong; Kim, Hee-Kyoung; Kim, Jueun; Jeon, Sun Jeong; Lee, Chul Won; Lee, Hyang Burm; Yun, Sung-Hwan

    2016-01-01

    Together with the Fusarium graminearum species complex, F. culmorum is a major member of the causal agents of Fusarium head blight on cereals such as wheat, barley and corn. It causes significant yield and quality losses and results in the contamination of grain with mycotoxins that are harmful to humans and animals. In Korea, F. culmorum is listed as a quarantine fungal species since it has yet to be found in the country. In this paper, we report that two isolates (J1 and J2) of F. culmorum were collected from the air at a rice paddy field in Korea. Species identification was confirmed by phylogenetic analysis using multi-locus sequence data derived from five genes encoding translation elongation factor, histone H3, phosphate permease, a reductase, and an ammonia ligase and by morphological comparison with reference strains. Both diagnostic PCR and chemical analysis confirmed that these F. culmorum isolates had the capacity to produce nivalenol, the trichothecene mycotoxin, in rice substrate. In addition, both isolates were pathogenic on wheat heads and corn stalks. This is the first report on the occurrence of F. culmorum in Korea. PMID:27298593

  2. Changes in cell death of peripheral blood lymphocytes isolated from children with acute lymphoblastic leukemia upon stimulation with 7 Hz, 30 mT pulsed electromagnetic field.

    PubMed

    Kaszuba-Zwoińska, Jolanta; Ćwiklińska, Magdalena; Balwierz, Walentyna; Chorobik, Paulina; Nowak, Bernadeta; Wójcik-Piotrowicz, Karolina; Ziomber, Agata; Malina-Novak, Kinga; Zaraska, Wiesław; Thor, Piotr J

    2015-03-01

    Pulsed electromagnetic field (PEMF) influenced the viability of proliferating in vitro peripheral blood mononuclear cells (PBMCs) isolated from Crohn's disease patients as well as acute myeloblastic leukemia (AML) patients by induction of cell death, but did not cause any vital changes in cells from healthy donors. Experiments with lymphoid U937 and monocytic MonoMac6 cell lines have shown a protective effect of PEMF on the death process in cells treated with death inducers. The aim of the current study was to investigate the influence of PEMF on native proliferating leukocytes originating from newly diagnosed acute lymphoblastic leukemia (ALL) patients. The effects of exposure to PEMF were studied in PBMCs from 20 children with ALL. PBMCs were stimulated with three doses of PEMF (7 Hz, 30 mT) for 4 h each with 24 h intervals. After the last stimulation, the cells were double stained with annexin V and propidium iodide dye to estimate viability by flow cytometric analysis. The results indicated an increase of annexin V positive as well as double stained annexin V and propidium iodide positive cells after exposure to threefold PEMF stimulation. A low-frequency pulsed electromagnetic field induces cell death in native proliferating cells isolated from ALL patients. The increased vulnerability of proliferating PBMCs to PEMF-induced interactions may be potentially applied in the therapy of ALL. The analysis of expression of apoptosis-related genes revealed changes in mRNA of some genes engaged in the intrinsic apoptotic pathway belonging to the Bcl-2 family and the pathway with apoptosis-inducing factor (AIF) abundance upon PEMF stimulation of PBMCs. PMID:26204398

  3. Efficacy of maduramicin against ionophore-tolerant field isolates of coccidia in broilers.

    PubMed

    McDougald, L R; Wang, G T; Kantor, S; Schenkel, R; Quarles, C

    1987-01-01

    Maduramicin ammonium was given at 2.5-8 ppm in the feed to broilers experimentally infected with coccidia recently isolated from broiler farms where ionophores had been used for several years. Infection pressure varied from mild to severe in five trials: mortality in unmedicated controls ranged from 0 to 59%, intestinal lesion scores were high, and weight gain was depressed by the infections. The cultures of Eimeria were partly resistant to ionophores: birds medicated with monensin at 100-121 ppm had only modest reductions in lesion scores and incomplete protection against weight loss or mortality. Control of infections by maduramicin was significant at 4 ppm but best at 5-7 ppm. Maduramicin was more effective than monensin or narasin, but about the same as salinomycin, in reducing lesions and mortality and in protecting performance. Maduramicin was well tolerated within the dose range of 5-7 ppm. PMID:3619823

  4. In vitro antibiotic susceptibility of field isolates of Mycoplasma synoviae in Argentina.

    PubMed

    Cerdá, R O; Giacoboni, G I; Xavier, J A; Sansalone, P L; Landoni, M F

    2002-01-01

    Minimum inhibitory concentrations (MICs) were determined in vitro for 7 antibiotics (aivlosin, enrofloxacine, tylosin, tiamulin, kitasamycin, chlortetracycline, and oxytetracycline) against eight recent local Argentinean isolates and two standard strains of Mycoplasma synoviae. Aivlosin (3-acetyl-4"-isovaleryl tylosin tartrate), tylosin, and tiamulin showed the lowest MICs with MIC90s of 0.006, 0.012, and 0.05 microg/ml, respectively. Except one strain that showed resistant values to chlortetracycline (> or = 12.5 microg/ml), all the analyzed strains were susceptible in different degrees to all the antibiotics tested. In this study, the improved activity of the tylosin-derived drug, aivlosin, was confirmed because it showed, in most strains, MIC values half those for tylosin. PMID:11922338

  5. Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001.

    PubMed

    Wang, Xiangru; Wei, Liuya; Wang, Bin; Zhang, Ruixuan; Liu, Canying; Bi, Dingren; Chen, Huanchun; Tan, Chen

    2016-01-01

    Avian pathogenic Escherichia coli is an important etiological agent of avian colibacillosis, which manifests as respiratory, hematogenous, meningitic, and enteric infections in poultry. It is also a potential zoonotic threat to human health. The diverse genomes of APEC strains largely hinder disease prevention and control measures. In the current study, pyrosequencing was used to analyze and characterize APEC strain ACN001 (= CCTCC 2015182(T) = DSMZ 29979(T)), which was isolated from the liver of a diseased chicken in China in 2010. Strain ACN001 belongs to extraintestinal pathogenic E. coli phylogenetic group B1, and was highly virulent in chicken and mouse models. Whole genome analysis showed that it consists of six different plasmids along with a circular chromosome of 4,936,576 bp, comprising 4,794 protein-coding genes, 108 RNA genes, and 51 pseudogenes, with an average G + C content of 50.56 %. As well as 237 coding sequences, we identified 39 insertion sequences, 12 predicated genomic islands, 8 prophage-related sequences, and 2 clustered regularly interspaced short palindromic repeats regions on the chromosome, suggesting the possible occurrence of horizontal gene transfer in this strain. In addition, most of the virulence and antibiotic resistance genes were located on the plasmids, which would assist in the distribution of pathogenicity and multidrug resistance elements among E. coli populations. Together, the information provided here on APEC isolate ACN001 will assist in future study of APEC strains, and aid in the development of control measures. PMID:26823959

  6. Multiple superhyperfine fields in a {DyFe2Dy} coordination cluster revealed using bulk susceptibility and (57)Fe Mössbauer studies.

    PubMed

    Peng, Yan; Mereacre, Valeriu; Anson, Christopher E; Powell, Annie K

    2016-08-01

    A [DyFeDy(μ3-OH)2(pmide)2(p-Me-PhCO2)6] coordination cluster, where pmideH2 = N-(2-pyridylmethyl)iminodiethanol, has been synthesized and the magnetic properties studied. The dc magnetic measurements reveal dominant antiferromagnetic interactions between the metal centres. The ac measurements reveal zero-field quantum tunnelling of the magnetisation (QTM) which can be understood, but not adequately modelled, in terms of at least three relaxation processes when appropriate static (dc) fields are applied. To investigate this further, (57)Fe Mössbauer spectroscopy was used and well-resolved nuclear hyperfine structures could be observed, showing that on the Mössbauer time scale, without applied field or else with very small applied fields, the iron nuclei experience three or more superhyperfine fields arising from the slow magnetisation reversal of the strongly polarized fields of the Dy(III) ions. PMID:27424877

  7. From Isolation to Collaboration: Rethinking the Preservice Field Experience from a Community Perspective

    ERIC Educational Resources Information Center

    Bower, Laura A.; Klecka, Cari L.; Silva, Susan

    2010-01-01

    In this article, we report the action research that shaped the development of the Growing Career Educators project, a teacher-designed field experience for preservice teachers within a high school in the fifth-largest school district in the country. The research consisted of two cycles of action research, both of which focused on whether a…

  8. Partial sequencing of recent Portuguese myxoma virus field isolates exhibits a high degree of genetic stability.

    PubMed

    Muller, A; Silva, E; Abrantes, J; Esteves, P J; Ferreira, P G; Carvalheira, J C; Nowotny, N; Thompson, G

    2010-01-01

    To study genetic changes underlying myxoma virus evolution in its new host, the European rabbit (Oryctolagus cuniculus), we sequenced selected genomic regions of nine recent virulent field strains and a live attenuated vaccine strain ("MAV", Germany). DNA was extracted from cell culture passaged myxoma virus. A total of 4863 bp (approximately 3% of the genome) of 10 regions spanning 12 genes of the myxoma viruses was sequenced and compared to the original virulent strain "Lausanne" and its attenuated field derivative strain "6918". The field strains displayed a maximum of three (strains C43, C95) and a minimum of one (strains CD01, CD05) nucleotide substitutions. These were distributed through all analysed coding regions, except gene M022L (major envelope protein), where all strains were identical to "Lausanne" and "6918". Two new single nucleotide insertions were observed in some of the field strains: within the intergenic region M014L/M015L and within gene M009L, where it leads to a frameshift. These insertions were located after homopolymeric regions. The vaccine strain displayed 37 nucleotide substitutions, predominantly (95%) located in genes M022L and M036L. Interestingly, regions M009L and M014L/M015L of the vaccine were not amplified successfully, suggesting major genomic changes that could account for its attenuated phenotype. Our results support a high degree of genetic stability of myxoma virus over the past five decades. None of the analysed genome regions by its own seems sufficient for the genetic characterisation of field strains. PMID:19709821

  9. Time Series Measurements of Diffuse Hydrothermal Flow at the ASHES Vent Field Reveal Tidally Modulated Heat and Volume Flux

    NASA Astrophysics Data System (ADS)

    Mittelstaedt, E. L.; Fornari, D. J.; Crone, T. J.

    2015-12-01

    Existing time-series measurements of temperature and velocity of diffuse hydrothermal fluids exhibit variability over a range of periods from seconds to days. Frequency analysis of these measurements reveals differences between studies and field locations including nearly white spectra, as well as spectra with peaks at tidal and inertial periods. Based upon these results, previous authors have suggested several processes that may control diffuse flow rates, including tidally induced currents and 'tidal pumping', and have also suggested that there are no systematic controls. To further investigate the processes that control variability in diffuse flow, we use data from a new, deep-sea camera and temperature measurement system, the Diffuse Effluent Measurement System (DEMS), deployed during the July, 2014 cruise of the R/V Atlantis. The DEMS was deployed with DSV Alvin above a fracture network at the Phoenix vent within the ASHES vent field (Axial Seamount, 1541 mbsl). The system collected 20 seconds of imagery at 20 Hz and 24 seconds of temperature measurements at 1 Hz each hour over the period between July 22 and August 2nd. Velocities of the upwelling fluids were calculated using Diffuse Fluid Velocimetry (DFV; Mittelstaedt et al., 2010). DFV is a cross correlation technique that tracks moving index of refraction anomalies (i.e., hot parcels of fluid) through time. Over the ~12 day deployment, median flow rates ranged from 0.5 cm/s to 6 cm/s and mean fluid temperature anomalies from 0°C up to ~6.5°C, yielding an average heat flux density of 0.23 MW/m2. Spectral analysis of both the measured temperatures and calculated velocities yield a peak in normalized power at the semi-diurnal lunar period (M2, 12.4hrs), but no other spectral peaks above the 95% confidence level. Here, we present these results and discuss their implications for the tidal current and tidal pressure models of diffuse flow variability at the ASHES vent field.

  10. Analysing one isolated single walled carbon nanotube in the near-field domain with selective nanovolume Raman spectroscopy.

    PubMed

    Atalay, Han; Lefrant, Serge

    2004-09-01

    In this paper, we describe a new method to the selective nanovolume analysing of one isolated single walled carbon nanotube (SWNT). This concept is based on actually available imaging micro-spectrometry systems for working in near-field domain combined with a stigmatic solid immersion lens. This combination of different analytical methods, and modified and configured equipment entitles us to expand the functionality toward a three-dimensional (3D) nanovolume Raman mapping and photoluminescence intensity with a possible discrimination in polarization, as well as photoluminescence decaytime constant mapping with their unique combination. Subsequently, selective spectra can be acquired from the same location on the samples. By spectrally selecting a SWNT, we registered the spatial distribution of the emitted photons in x, y, z vectors to determine the position of a SWNT in the near-field domain. For the SWNTs that are localized with an accuracy better than 18 nm in the x, y and <1 nm in the z directions, we demonstrate an analytical sensitivity close to a single nanotube with unity throughput. This near-field capability is applied to resolve local variations unambiguously in the Raman spectrum along one single SWNT. Finally, in this paper, we report what we believe to be the first evidence of Raman mapping and 3D real optical imaging of carbon nanotubes with near-field resolution. PMID:15570957

  11. Cholinergic neurons and terminal fields revealed by immunohistochemistry for the vesicular acetylcholine transporter. II. The peripheral nervous system.

    PubMed

    Schäfer, M K; Eiden, L E; Weihe, E

    1998-05-01

    immunoreactivity was particularly useful for identification of parasympathetic intrinsic ganglia, and their terminal fields, in heart, uterus, and other peripheral organs receiving parasympathetic innervation. Extensive vesicular acetylcholine transporter-positive terminal fields were apparent in both atrial and ventricular tissues of the heart targeting cardiomyocytes as well as cardiac microvessels. Pericardiac brown adipose tissue was also supplied by vesicular acetylcholine transporter-positive varicose fibres. The enteric ganglia of the myenteric and submucous plexus, their synaptic junctions with circular and longitudinal smooth muscle, and terminal fields of the lamina propria of the stomach and intestine and of the local microvasculature were intensely vesicular acetylcholine transporter positive. Vesicular acetylcholine transporter-positive innervation was delivered to the exocrine and endocrine pancreas originating from vesicular acetylcholine transporter-positive intrapancreatic ganglia. Vesicular acetylcholine transporter immunoreactivity in urogenital organs revealed the patterns of terminal cholinergic fields arising from the sacral parasympathetic innervation of these structures. Components of the cholinergic nervous system in the periphery whose existence has been controversial have been confirmed, and the existence of new components of the cholinergic nervous system has been documented, with vesicular acetylcholine transporter immunohistochemistry. Visualization of vesicular acetylcholine transporter will allow documentation of changes in synaptic patency during development, in disease, and during changes in neurotransmission accompanying injury and dystrophy, in the peripheral nervous system. PMID:9539210

  12. Genotypic variations in field isolates of Theileria species infecting giraffes (Giraffa camelopardalis tippelskirchi and Giraffa camelopardalis reticulata) in Kenya.

    PubMed

    Githaka, Naftaly; Konnai, Satoru; Skilton, Robert; Kariuki, Edward; Kanduma, Esther; Murata, Shiro; Ohashi, Kazuhiko

    2013-10-01

    Recently, mortalities among giraffes, attributed to infection with unique species of piroplasms were reported in South Africa. Although haemoparasites are known to occur in giraffes of Kenya, the prevalence, genetic diversity and pathogenicity of these parasites have not been investigated. In this study, blood samples from 13 giraffes in Kenya were investigated microscopically and genomic DNA extracted. PCR amplicons of the hyper-variable region 4 (V4) of Theileria spp. small subunit ribosomal RNA (18S rRNA) gene were hybridized to a panel of genus- and species-specific oligonucleotide probes by reverse line blot (RLB). Two newly designed oligonucleotide probes specific for previously identified Theileria spp. of giraffes found single infections in eight of the specimens and mixed infections in the remaining five samples. Partial 18S rRNA genes were successfully amplified from 9 samples and the PCR amplicons were cloned. A total of 28 plasmid clones representing the Kenyan isolates were analyzed in the present study and compared with those of closely-related organisms retrieved from GenBank. In agreement with RLB results, the nucleotide sequence alignment indicated the presence of mixed infections in the giraffes. In addition, sequence alignment with the obtained 18S rRNA gene sequences revealed extensive microheterogeneities within and between isolates, characterized by indels in the V4 regions and point mutations outside this region. Phylogeny with 18S rRNA gene sequences from the detected parasites and those of related organisms places Theileria of giraffes into two major groups, within which are numerous clades that include the isolates reported in South Africa. Collectively, these data suggest the existence of at least two distinct Theileria species among giraffes, and extensive genetic diversity within the two parasite groups. PMID:23792245

  13. WIPP (Waste Isolation Pilot Plant) horizon free field fluid transport characteristics

    SciTech Connect

    Peterson, E.W.; Lagus, P.L.; Lie, K.

    1987-12-01

    This report describes the first attempt to measure the free field brine transport characteristics of the host rock. The data, which have been used to estimate the brine permeability, also suggest free field pore pressure values. One borehole was located in a competent predominantly halite bed with the test region positioned approximately nine meters from the rib. A second borehole intersected Marker Bed 139, which is a one meter thick fractured predominantly anhydrite layer. For this second borehole, the test region was positioned approximately 12 meters from the invert/rib intersection. A description of the tests provided in Section 2. Data obtained during these tests are described in Section 3. Analysis of these data and the associated uncertainties inherent in the data interpretation are presented in Section 4. Test results are given in Section 5. Conclusions are provided in Section 6. 13 refs., 65 figs.

  14. The vital activity of organisms in infralow frequency magnetic fields. 5. Isolated blood cells

    SciTech Connect

    Khizhenkov, P.K.; Zinkovich, I.I.; Bilobrov, V.M.

    1995-07-01

    Results are presented of experimental investigations of the effect of alternating magnetic fields H of various amplitudes, shapes, and frequencies on the osmotic resistance of erythrocytes (ORE), the phagocytic activity of leukocytes (PAL), the malonic dialdehyde accumulation (MDA), and the albumen escape to the incubative medium. The specificity and intraspecific variability of the ORE and PAL characteristics are also shown. Under the effect of H the albumen escape was noted to decrease while the MDA concentration became larger.

  15. Hypnocyclicus thermotrophus gen. nov., sp. nov. isolated from a microbial mat in a hydrothermal vent field.

    PubMed

    Roalkvam, Irene; Bredy, Florian; Baumberger, Tamara; Pedersen, Rolf-B; Steen, Ida Helene

    2015-12-01

    The bacterial strain, IR-2T, was isolated from a microbial mat sampled near a hydrothermal vent in the Greenland Sea. Phylogenetic analysis, based on the 16S rRNA gene, showed that the closest relatives of IR-2T were Ilyobacter tartaricus, Ilyobacter insuetus, Propionigenium modestum and Fusobacterium varium (91 % 16S rRNA gene sequence similarity). The cells of the novel strain were Gram-stain-negative and pleomorphic; changing from long motile rods to non-motile ring structures during the growth cycle. Growth occurred at 20-55 °C (optimally at 48 °C), with 1-6 % (w/v) NaCl (optimally with 2 %), and at pH 5.3-8.0 (optimally at pH 6.0-8.0). The strain had obligate fermentative growth on various sugars and yeast extract. The DNA G+C content of strain IR-2T was 25.7 mol%. The cell sugars comprised mainly ribose, mannose and glucose, while the main polar lipids were glycolipids, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. The fatty acid content of strain IR-2 was dominated by saturated and unsaturated iso-branched or anteiso-branched forms. Strain IR-2 represents a novel genus and species, for which the name Hypnocyclicus thermotrophus gen. nov., sp. nov. is proposed. The type strain is IR-2T ( = DSM 100055 = JCM 30901). PMID:26373292

  16. Discovery of a candidate old, isolated neutron star in the field of a galactic cirrus cloud

    NASA Technical Reports Server (NTRS)

    Stocke, John T.; Wang, Q. Daniel; Perlman, Eric S.; Donahue, Megan E.; Schachter, Jonathan F.

    1995-01-01

    New x-ray optical, and radio observations of the bright, unidentified x-ray source MS 0317.7-6647 are presented suggesting that this source is a likely compact stellar remnant. As part of the Einstein Extended Medium Sensivity Survey, this source was discovered serendipitously in the Einstein Imaging Proportional Counter pointing towards the nearby (4.5 Mpc) spiral galaxy NGC 1313. The very high x-ray to optical flux ratio, pointlike ROSAT HRI detection, and extremely soft component in the x-ray spectrum of MS 0317.7-6647 eliminate all the usual classes of optical counterparts to faint x-ray sources except for a very massive x-ray binary (and black hole candidate) in NGC 1313, a nearby, companionless pulsar similar to Geminga, or a very nearby ( approximately 100 pc) isolated, old neutron star slowly accreting interstellar matter onto its magnetic poles. The presence of an IR cirrus cloud which shadows the approximately 0.25 keV x-ray background in this direction supports the latter possibilty.

  17. Field and laboratory testing of seal materials proposed for the Waste Isolation Pilot Plant

    SciTech Connect

    Knowles, M.K.; Howard, C.L.

    1996-02-05

    The Small Scale Seal Performance Tests (SSSPT) were a series of in situ tests designed to evaluate the feasibility of various materials for sealing purposes. Testing was initiated in 1985 and concluded in 1995. Materials selected for the SSSPT included salt-saturated concrete, a 50%/50% mixture of crushed salt and bentonite, bentonite, and crushed salt. This paper presents a summary of the SSSPT field program, results of the in situ testing, and a discussion of post-testing laboratory studies of salt-saturated concrete. Results of the SSSPT support the use of salt-saturated concrete, compacted bentonite clay, and compacted crushed salt as sealing materials for the WIPP.

  18. Micro-digitate Silica Structures on Earth and Mars: Potential Biosignatures Revealed in the Geyser Field of El Tatio, Chile

    NASA Astrophysics Data System (ADS)

    Ruff, S. W.; Farmer, J. D.

    2015-12-01

    Opaline silica outcrops and soil identified by the Spirit rover adjacent to "Home Plate" in Gusev crater are associated with a suite of geologic features that demonstrates that they are the products of a volcanic hydrothermal system, the first such example verified on Mars [1]. Fumarolic acid-sulfate leaching of basaltic precursor materials was suggested as the origin of the opaline silica, based largely on geochemical arguments. A more complete analysis by Ruff et al. [2] included stratigraphic and textural observations of the outcrops to advance the hypothesis of a hot spring and/or geyser-related origin under alkaline-neutral conditions; acid-sulfate leaching appears much less tenable. But the nodular expression of many of the outcrops and sub-cm-scale "digitate protrusions" they contain remained enigmatic, precluding a complete explanation for the silica. Now, new observations of silica deposits produced in small discharge channels from hot springs and geysers in a high elevation geothermal field known as El Tatio in the Atacama Desert of northern Chile reveal remarkably similar features, including infrared spectral characteristics and what we describe here as micro-digitate silica structures. We hypothesize that these structures at El Tatio arise through microbial mediation of silica precipitation, i.e., that they are microstromatolites and that they provide favorable environments for the capture and preservation of microbial biosignatures. Similar features have been identified among hot spring silica deposits in Yellowstone National Park, the Taupo Volcanic Zone of New Zealand, and Iceland [e.g., 3; 4; 5]. Our ongoing field and lab studies are intended provide a robust assessment of the biogenicity of the micro-digitate silica structures and other aspects of El Tatio silica sinter deposits and test their viability as direct analogs to similar features found among the Home Plate silica deposits on Mars. [1] Squyres, S. W., et al. (2008), Science, 320, 1063

  19. Icelandic basaltic geothermal field: A natural analog for nuclear waste isolation in basalt

    SciTech Connect

    Ulmer, G.C.; Grandstaff, D.E. . Dept. of Geology)

    1984-11-21

    Analog studies of Icelandic geothermal fields have shown that the design of nuclear waste repositories in basalt can benefit by comparison to the data base already available from the development of these geothermal fields. A high degree of similarity exists between these two systems: their petrology, groundwater geochemistry, mineral solubilities, hydrologic parameters, temperature ranges, water-rock redox equilibria, hydrothermal pH values, and secondary mineralogies all show considerable overlap in the range of values. The experimentally-simulated hydrothermal studies of the basaltic nuclear waste repository rocks have, at this time, produced a data base that receives a strong confirmation from the Icelandic analog. Furthermore, the Icelandic analog should eventually be employed to extrapolate into higher and lower temperatures, into longer time-base chemical comparisons, and into more realistic mineral deposition studies, than have been possible in the laboratory evaluations of the nuclear waste repository designs. This eventual use of the Icelandic analog will require cooperative work with the Icelandic Geological Survey. 46 refs., 4 figs., 2 tabs.

  20. Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections.

    PubMed

    Vuataz, Laurent; Sartori, Michel; Gattolliat, Jean-Luc; Monaghan, Michael T

    2013-03-01

    The biodiversity and endemism of Madagascar are among the most extraordinary and endangered in the world. This includes the island's freshwater biodiversity, although detailed knowledge of the diversity, endemism, and biogeographic origin of freshwater invertebrates is lacking. The aquatic immature stages of mayflies (Ephemeroptera) are widely used as bio-indicators and form an important component of Malagasy freshwater biodiversity. Many species are thought to be microendemics, restricted to single river basins in forested areas, making them particularly sensitive to habitat reduction and degradation. The Heptageniidae are a globally diverse family of mayflies (>500 species) but remain practically unknown in Madagascar except for two species described in 1996. The standard approach to understanding their diversity, endemism, and origin would require extensive field sampling on several continents and years of taxonomic work followed by phylogenetic analysis. Here we circumvent this using museum collections and freshly collected individuals in a combined approach of DNA taxonomy and phylogeny. The coalescent-based GMYC analysis of DNA barcode data (mitochondrial COI) revealed 14 putative species on Madagascar, 70% of which were microendemics. A phylogenetic analysis that included African and Asian species and data from two mitochondrial and four nuclear loci indicated the Malagasy Heptageniidae are monophyletic and sister to African species. The genus Compsoneuria is shown to be paraphyletic and the genus Notonurus is reinstalled for African and Malagasy species previously placed in Compsoneuria. A molecular clock excluded a Gondwanan vicariance origin and instead favoured a more recent overseas colonization of Madagascar. The observed monophyly and high microendemism highlight their conservation importance and suggest the DNA-based approach can rapidly provide information on the diversity, endemism, and origin of freshwater biodiversity. Our results underline the

  1. Molecular typing of Iranian field isolates Mycoplasma synoviae and their differentiation from the live commercial vaccine strain MS-H using vlhA gene.

    PubMed

    Bayatzadeh, Mohammad Ali; Pourbakhsh, Seyed Ali; Ashtari, Abass; Abtin, Ali Reza; Abdoshah, Mohammad

    2014-01-01

    1. The single-copy domain of the N-terminal region of the vlhA gene of Mycoplasma synoviae was sequenced, analysed and verified and used to type Iranian field isolates of M. synoviae and the MS-H live vaccine strain. In addition, a restriction fragment length polymorphism (RFLP) method was developed to differentiate between field isolates of Iranian and MS-H vaccine strains. 2. All sequences were analysed and aligned; the percentage similarity of the DNA was calculated and dendrograms were constructed. Based on single nucleotide polymorphism (SNP) that existed in all field isolates in Iran, the PCR-RFLP method allowed the differentiation of all M. synoviae field isolates from the vaccine strain. 3. Using phylogenetic analysis, the isolates were assigned to 8 unique genotypes and, within each group, DNA had a high level of similarity. 4. DNA sequence analysis and PCR-RFLP of the amplicon based on percent similarity and evolutionary relationship appeared to be useful tools for strain differentiation whether M. synoviae clinical isolates from infected chickens were derived from the vaccine strain or wild-type strains. 5. This study confirms the potential value of strain typing for epidemiological purposes and suggests that phylogenetic studies are essential to understand the true relationships between strains. PMID:24405029

  2. Fungicide efflux and the MgMFS1 transporter contribute to the multidrug resistance phenotype in Zymoseptoria tritici field isolates.

    PubMed

    Omrane, Selim; Sghyer, Hind; Audéon, Colette; Lanen, Catherine; Duplaix, Clémentine; Walker, Anne-Sophie; Fillinger, Sabine

    2015-08-01

    Septoria leaf blotch is mainly controlled by fungicides. Zymoseptoria tritici, which is responsible for this disease, displays strong adaptive capacity to fungicide challenge. It developed resistance to most fungicides due to target site modifications. Recently, isolated strains showed cross-resistance to fungicides with unrelated modes of action, suggesting a resistance mechanism known as multidrug resistance (MDR). We show enhanced prochloraz efflux, sensitive to the modulators amitryptiline and chlorpromazine, for two Z. tritici strains, displaying an MDR phenotype in addition to the genotypes CYP51(I381V Y461H) or CYP51(I381V ΔY459/) (G460) , respectively, hereafter named MDR6 and MDR7. Efflux was also inhibited by verapamil in the MDR7 strain. RNA sequencing lead to the identification of several transporter genes overexpressed in both MDR strains. The expression of the MgMFS1 gene was the strongest and constitutively high in MDR field strains. Its inactivation in the MDR6 strain abolished resistance to fungicides with different modes of action supporting its involvement in MDR in Z. tritici. A 519 bp insert in the MgMFS1 promoter was detected in half of the tested MDR field strains, but absent from sensitive field strains, suggesting that the insert is correlated with the observed MDR phenotype. Besides MgMfs1, other transporters and mutations may be involved in MDR in Z. tritici. PMID:25627815

  3. Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar

    PubMed Central

    2014-01-01

    Background Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased. Results Our aim was to search for genetic footprints of Myanmar’s geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards. Conclusion Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia. PMID:24467713

  4. Common ancestry and novel genetic traits of Francisella novicida-like isolates from North America and Australia as revealed by comparative genomic analyses.

    PubMed

    Siddaramappa, Shivakumara; Challacombe, Jean F; Petersen, Jeannine M; Pillai, Segaran; Hogg, Geoff; Kuske, Cheryl R

    2011-08-01

    Francisella novicida is a close relative of Francisella tularensis, the causative agent of tularemia. The genomes of F. novicida-like clinical isolates 3523 (Australian strain) and Fx1 (Texas strain) were sequenced and compared to F. novicida strain U112 and F. tularensis strain Schu S4. The strain 3523 chromosome is 1,945,310 bp and contains 1,854 protein-coding genes. The strain Fx1 chromosome is 1,913,619 bp and contains 1,819 protein-coding genes. NUCmer analyses revealed that the genomes of strains Fx1 and U112 are mostly colinear, whereas the genome of strain 3523 has gaps, translocations, and/or inversions compared to genomes of strains Fx1 and U112. Using the genome sequence data and comparative analyses with other members of the genus Francisella, several strain-specific genes that encode putative proteins involved in RTX toxin production, polysaccharide biosynthesis/modification, thiamine biosynthesis, glucuronate utilization, and polyamine biosynthesis were identified. The RTX toxin synthesis and secretion operon of strain 3523 contains four open reading frames (ORFs) and was named rtxCABD. Based on the alignment of conserved sequences upstream of operons involved in thiamine biosynthesis from various bacteria, a putative THI box was identified in strain 3523. The glucuronate catabolism loci of strains 3523 and Fx1 contain a cluster of nine ORFs oriented in the same direction that appear to constitute an operon. Strains U112 and Schu S4 appeared to have lost the loci for RTX toxin production, thiamine biosynthesis, and glucuronate utilization as a consequence of host adaptation and reductive evolution. In conclusion, comparative analyses provided insights into the common ancestry and novel genetic traits of these strains. PMID:21666011

  5. Molecular detection of field isolates of Turkey Eimeria by polymerase chain reaction amplification of the cytochrome c oxidase I gene.

    PubMed

    Rathinam, T; Gadde, U; Chapman, H D

    2015-07-01

    Oocysts of Eimeria spp. were isolated from litter samples obtained from 30 commercial turkey farms. Genomic DNA was extracted from clean oocysts, and polymerase chain amplification of the species-specific cytochrome c oxidase subunit I (COI) gene was performed for five species of turkey Eimeria. The species tested were Eimeria adenoeides, Eimeria meleagrimitis, Eimeria meleagridis, Eimeria dispersa, and Eimeria gallopavonis. All DNA samples were positive for E. meleagrimitis, nine were positive for E. adenoeides, two were positive for E. dispersa, and none for E. meleagridis and E. gallopavonis. E. meleagrimitis occurred as a single species in 21 (70 %) of the farms while 9 (30 %) farms had a mixed species with E. meleagrimitis and E. adenoeides and 2 (7 %) were triple positive with E. meleagrimitis, E. adenoeides, and E. dispersa. This is the first account of the field prevalence of turkey Eimeria species using molecular methods. PMID:26017345

  6. Biodegradation of diesel oil by an Arabian Sea sediment culture isolated from the vicinity of an oil field.

    PubMed

    Mukherji, Suparna; Jagadevan, Sheeja; Mohapatra, Gita; Vijay, Avinash

    2004-12-01

    Laboratory scale batch studies were performed to test the diesel oil biodegradation ability of ES1 cultures isolated from Arabian Sea sediments obtained from the vicinity of an oil field. This culture could utilize diesel as the sole source of carbon and energy. Under aerobic conditions, 39% loss of diesel oil was observed over 8 days where 80% of the loss was due to aliphatic constituents. Under anoxic nitrate reducing conditions the rate and extent of degradation was significantly lower, i.e., 18% over 50 days. Salt acclimatized cultures could tolerate salinities up to 3.5% and demonstrated optimal performance at a salinity of 0.5%. The optimum N/P ratio for these cultures was found to be in the range of 2:1-5:1. Addition of two trace elemental substance formulations exhibited a significant inhibitory effect on culture growth. This culture has good potential for decontamination of oil-contaminated marine and subsurface environments. PMID:15288270

  7. Correlation between convection electric fields in the nightside magnetosphere and several wave and particle phenomena during two isolated substorms.

    NASA Technical Reports Server (NTRS)

    Carpenter, D. L.; Fraser-Smith, A. C.; Unwin, R. S.; Hones, E. W., Jr.; Heacock, R. R.

    1971-01-01

    Correlation of several magnetoionospheric wave and particle phenomena previously linked observationally to magnetospheric substorms and inferred to involve convection electric fields with whistler measurements of convection activity during two relatively isolated substorms. The events occurred at about 0600 UT on July 15, 1965, and about 0500 UT on Oct. 13, 1965. The correlated phenomena include cross-L inward plasma drifts near midnight within the plasmaphere, diffuse auroral radar echoes observed near the dusk meridian, IPDP micropulsations (intervals of pulsations of diminishing period) in the premidnight sector, apparent contractions and expansions of the plasma sheet at about 20 earth radii in the magnetotail, and Pc 1/Pi 1 micropulsation events near or before midnight. Two new vlf phenomena occurred during the October 13 event - a noise band within the plasmasphere associated with a convecting whistler path, and ?hisslers,' falling-tone auroral-hiss forms repeated at intervals of about 2 sec.

  8. Biosynthesis of compatible solutes in rhizobial strains isolated from Phaseolus vulgaris nodules in Tunisian fields

    PubMed Central

    2010-01-01

    Background Associated with appropriate crop and soil management, inoculation of legumes with microbial biofertilizers can improve food legume yield and soil fertility and reduce pollution by inorganic fertilizers. Rhizospheric bacteria are subjected to osmotic stress imposed by drought and/or NaCl, two abiotic constraints frequently found in semi-arid lands. Osmostress response in bacteria involves the accumulation of small organic compounds called compatible solutes. Whereas most studies on rhizobial osmoadaptation have focussed on the model species Sinorhizobium meliloti, little is known on the osmoadaptive mechanisms used by native rhizobia, which are good sources of inoculants. In this work, we investigated the synthesis and accumulations of compatible solutes by four rhizobial strains isolated from root nodules of Phaseolus vulgaris in Tunisia, as well as by the reference strain Rhizobium tropici CIAT 899T. Results The most NaCl-tolerant strain was A. tumefaciens 10c2, followed (in decreasing order) by R. tropici CIAT 899, R. leguminosarum bv. phaseoli 31c3, R. etli 12a3 and R. gallicum bv. phaseoli 8a3. 13C- and 1H-NMR analyses showed that all Rhizobium strains synthesized trehalose whereas A. tumefaciens 10c2 synthesized mannosucrose. Glutamate synthesis was also observed in R. tropici CIAT 899, R. leguminosarum bv. phaseoli 31c3 and A. tumefaciens 10c2. When added as a carbon source, mannitol was also accumulated by all strains. Accumulation of trehalose in R. tropici CIAT 899 and of mannosucrose in A. tumefaciens 10c2 was osmoregulated, suggesting their involvement in osmotolerance. The phylogenetic analysis of the otsA gene, encoding the trehalose-6-phosphate synthase, suggested the existence of lateral transfer events. In vivo 13C labeling experiments together with genomic analysis led us to propose the uptake and conversion pathways of different carbon sources into trehalose. Collaterally, the β-1,2-cyclic glucan from R. tropici CIAT 899 was co

  9. Oxygen Implant Isolation of n-GaN Field-Effect Transistor Structures

    SciTech Connect

    Dang, G.; Cao, X.A.; Ren, F.; Pearton, S.J.; Han, J.; Baca, A.G.; Shul, R.J.

    1999-07-20

    Multiple-energy (30-325 keV) O{sup +} implantation into GaN field-effect transistor structures (n {approximately} 10{sup 18} cm{sup {minus}3}, 3000 {angstrom} thick) can produce as-implanted sheet resistances of 4 x 10{sup 12} {Omega}/{open_square}, provided care is taken to ensure compensation of the region up to the projected range of the lowest energy implant. The sheet resistance remains above 10{sup 7} {Omega}/{open_square} to annealing temperatures of {approximately} 650 C and displays an activation energy of 0.29 eV. No diffusion of the implanted oxygen was observed for anneals up to 800 C.

  10. Hidden local symmetry of Eu{sup 3+} in xenotime-like crystals revealed by high magnetic fields

    SciTech Connect

    Han, Yibo; Ma, Zongwei; Zhang, Junpei; Wang, Junfeng; Du, Guihuan; Xia, Zhengcai; Han, Junbo Li, Liang; Yu, Xuefeng

    2015-02-07

    The excellent optical properties of europium-doped crystals in visible and near infrared wavelength regions enable them to have broad applications in optoelectronics, laser crystals and sensing devices. The local site crystal fields can affect the intensities and peak positions of the photo-emission lines strongly, but they are usually difficult to be clarified due to magnetically degenerate 4f electronic levels coupling with the crystal fields. Here, we provide an effective way to explore the hidden local symmetry of the Eu{sup 3+} sites in different hosts by taking photoluminescence measurements under pulsed high magnetic fields up to 46 T. The zero-field photoluminescence peaks split further at high magnetic fields when the Zeeman splitting energy is comparable to or larger than that of the crystal field induced zero-field splitting. In particular, a magnetic field induced crossover of the local crystal fields has been observed in the GdVO{sub 4}:Eu{sup 3+} crystal, which resulted from the alignment of Gd{sup 3+} magnetic moment in high magnetic fields; and a hexagonally symmetric local crystal fields was observed in the YPO{sub 4} nanocrystals at the Eu{sup 3+} sites characterized by the special axial and rhombic crystal field terms. These distinct Zeeman splitting behaviors uncover the crystal fields-related local symmetry of luminescent Eu{sup 3+} centers in different hosts or magnetic environments, which are significant for their applications in optics and optoelectronics.

  11. Sabin Vaccine Reversion in the Field: a Comprehensive Analysis of Sabin-Like Poliovirus Isolates in Nigeria

    PubMed Central

    Chang, Stewart; Iber, Jane; Zhao, Kun; Adeniji, Johnson A.; Bukbuk, David; Baba, Marycelin; Behrend, Matthew; Burns, Cara C.; Oberste, M. Steven

    2015-01-01

    ABSTRACT To assess the dynamics of genetic reversion of live poliovirus vaccine in humans, we studied molecular evolution in Sabin-like poliovirus isolates from Nigerian acute flaccid paralysis cases obtained from routine surveillance. We employed a novel modeling approach to infer substitution and recombination rates from whole-genome sequences and information about poliovirus infection dynamics and the individual vaccination history. We confirmed observations from a recent vaccine trial that VP1 substitution rates are increased for Sabin-like isolates relative to the rate for the wild type due to increased nonsynonymous substitution rates. We also inferred substitution rates for attenuating nucleotides and confirmed that reversion can occur in days to weeks after vaccination. We combine our observations for Sabin-like virus evolution with the molecular clock for VP1 of circulating wild-type strains to infer that the mean time from the initiating vaccine dose to the earliest detection of circulating vaccine-derived poliovirus (cVDPV) is 300 days for Sabin-like virus type 1, 210 days for Sabin-like virus type 2, and 390 days for Sabin-like virus type 3. Phylogenetic relationships indicated transient local transmission of Sabin-like virus type 3 and, possibly, Sabin-like virus type 1 during periods of low wild polio incidence. Comparison of Sabin-like virus recombinants with known Nigerian vaccine-derived poliovirus recombinants shows that while recombination with non-Sabin enteroviruses is associated with cVDPV, the recombination rates are similar for Sabin isolate-Sabin isolate and Sabin isolate–non-Sabin enterovirus recombination after accounting for the time from dosing to the time of detection. Our study provides a comprehensive picture of the evolutionary dynamics of the oral polio vaccine in the field. IMPORTANCE The global polio eradication effort has completed its 26th year. Despite success in eliminating wild poliovirus from most of the world, polio

  12. GENOTYPING STUDIES OF TOXOPLASMA GONDII ISOLATES FROM AFRICA REVEALED THAT THE ARCHYTYPAL CLONAL LINEAGES PREDOMINATE AS IN NORTH AMERICA AND EUROPE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Until recently, Toxoplasma gondii was considered to be clonal with very little genetic variability. Recent studies indicate that T. gondii isolates from Brazil are genetically and biologically different from T. gondii isolates from USA and Europe. However, little is known of the genetics of T. gondi...

  13. Formation of electrical field accompanying temperature jump in isolated spinach chloroplasts.

    PubMed

    Shimizu, M; Nishimura, M

    1977-03-11

    Temperature-jump-induced absorbance changes of spinach chloroplasts in the dark were studied. After the temperature rise, a fast absorbance decrease and a succeeding slow absorbance increase were observed at the wavelength of 515 nm. The spectrum of the fast phase had positive maxima (increase in absorbance) at 430, 470 and 673 nm and a negative maxima (decrease in absorbance) at 525 nm. Permeant ions, tetraphenylboron-, tetraphenylarsonium+, and tetraphenylphosphonium+, decreased the extent of the fast absorbance change and increased the rate of slow recovery. Additions of inorganic potassium salts had a similar effect. Valinomycin, added in the presence of potassium ion, also increased the rate of slow recovery. These ions and ionophore had a parallel effect also on the recovery of flash-induced 515-nm absorbance change in chloroplasts. Electroneutral nigerericin did not affect the temperature-jump-induced absorbanc change. These results suggest the formation of electrical field across the thylakoid membrane in the dark accompanying the temperature rise. A possible involvement of the movement of water molecules (thermo-osmosis) in the observed absorbance changes is also discussed. PMID:849433

  14. Differential Association of Plasmodium falciparum Na+/H+ Exchanger Polymorphism and Quinine Responses in Field- and Culture-Adapted Isolates of Plasmodium falciparum ▿ †

    PubMed Central

    Pelleau, Stéphane; Bertaux, Lionel; Briolant, Sébastien; Ferdig, Michael T.; Sinou, Véronique; Pradines, Bruno; Parzy, Daniel; Jambou, Ronan

    2011-01-01

    Plasmodium falciparum isolates with decreased susceptibility to quinine are increasingly being found in malaria patients. Mechanisms involved in this resistance are not yet understood. Several studies claim that alongside mutations in the Pfcrt and Pfmdr1 genes, the Pfnhe-1 Na+/H+ exchanger polymorphism plays a role in decreasing susceptibility. However, conflicting results on the link between the Pfnhe-1 gene and quinine resistance arise from field- and culture-adapted isolates. We tested the association between Pfnhe-1, Pfcrt, and Pfmdr1 polymorphisms in field- and culture-adapted isolates from various countries with their in vitro susceptibility to quinine. Field isolates presented a higher diversity of the Pfnhe-1 microsatellite sequence than culture-adapted isolates. In culture-adapted isolates but not in field isolates, mutations in the Pfcrt and Pfmdr1 genes, as well as a higher number of DNNND repeats in the Pfnhe-1 gene, were associated with a higher 50% inhibitory concentration (IC50) of quinine. Furthermore, most of the culture-adapted isolates with more than one DNNND repeat in the Pfnhe-1 gene also harbored mutated Pfcrt and Pfmdr1 genes with an apparent cumulative effect on quinine susceptibility. This study supports the involvement of the Pfnhe-1 gene in the modulation of the in vitro quinine response when associated with mutated Pfcrt and Pfmdr1 genes. Culture adaptation could be responsible for selection of specific haplotypes of these three genes. Methods used for drug testing might thus influence the association between Pfnhe-1 polymorphism and quinine susceptibility. However, we do not exclude the possibility that in particular settings, Pfnhe-1 polymorphism can be used as a molecular marker for surveillance of quinine resistance. PMID:21947391

  15. Complete Genome Sequence of a Field Isolate of Classical Swine Fever Virus Belonging to Subgenotype 2.1b from Hunan Province, China.

    PubMed

    Shao, Weixing; Liu, Shuang; Wu, Faxing; Zhang, Zhi; Dong, Yaqin; Li, Xiaocheng

    2015-01-01

    We report the complete genome sequence of a field isolate of classical swine fever virus (CSFV), Hunan 23/2013, belonging to the predominant subgenotype 2.1b. This strain was originally isolated from diseased pigs in Hunan Province, China. This report will help in understanding the molecular diversity of CSFV stains circulating in China and in selecting and developing a suitable vaccine candidate for CSF control. PMID:26205876

  16. A survey of Tomato and Potato fields in Florida reveals unique genotypes of Phytophthora infestans between 2005 and 2007

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Late blight, caused by Phytophthora infestans, affects tomatoes and potatoes in Florida during the winter-spring crop season. During the 2005 season, late blight epidemics were severe and chemical control was largely ineffective. Isolates from 2005 2007 were characterized based on growth on three me...

  17. Phylogenetic analysis based on the PKS gene involved in fusaric acid biosynthesis production reveals close relationship between US race 1 lineage isolates & Australian biotype isolates of Fusarium Oxysporum f. sp. Vasinfectum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Isolates of Fusarium oxysporum f. sp. vasinfectum, the causal agent of fusarium wilt of cotton, vary significantly in their virulence. Isolates have been further subcategorized into pathogenic races based on their differential interaction with host genotypes. Phylogenetic analysis based on three n...

  18. Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor.

    PubMed

    Chen, Kuan-I; Pan, Chien-Yuan; Li, Keng-Hui; Huang, Ying-Chih; Lu, Chia-Wei; Tang, Chuan-Yi; Su, Ya-Wen; Tseng, Ling-Wei; Tseng, Kun-Chang; Lin, Chi-Yun; Chen, Chii-Dong; Lin, Shih-Shun; Chen, Yit-Tsong

    2015-01-01

    Many transcribed RNAs are non-coding RNAs, including microRNAs (miRNAs), which bind to complementary sequences on messenger RNAs to regulate the translation efficacy. Therefore, identifying the miRNAs expressed in cells/organisms aids in understanding genetic control in cells/organisms. In this report, we determined the binding of oligonucleotides to a receptor-modified silicon nanowire field-effect transistor (SiNW-FET) by monitoring the changes in conductance of the SiNW-FET. We first modified a SiNW-FET with a DNA probe to directly and selectively detect the complementary miRNA in cell lysates. This SiNW-FET device has 7-fold higher sensitivity than reverse transcription-quantitative polymerase chain reaction in detecting the corresponding miRNA. Next, we anchored viral p19 proteins, which bind the double-strand small RNAs (ds-sRNAs), on the SiNW-FET. By perfusing the device with synthesized ds-sRNAs of different pairing statuses, the dissociation constants revealed that the nucleotides at the 3'-overhangs and pairings at the terminus are important for the interactions. After perfusing the total RNA mixture extracted from Nicotiana benthamiana across the device, this device could enrich the ds-sRNAs for sequence analysis. Finally, this bionanoelectronic SiNW-FET, which is able to isolate and identify the interacting protein-RNA, adds an additional tool in genomic technology for the future study of direct biomolecular interactions. PMID:26616332

  19. Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor

    NASA Astrophysics Data System (ADS)

    Chen, Kuan-I.; Pan, Chien-Yuan; Li, Keng-Hui; Huang, Ying-Chih; Lu, Chia-Wei; Tang, Chuan-Yi; Su, Ya-Wen; Tseng, Ling-Wei; Tseng, Kun-Chang; Lin, Chi-Yun; Chen, Chii-Dong; Lin, Shih-Shun; Chen, Yit-Tsong

    2015-11-01

    Many transcribed RNAs are non-coding RNAs, including microRNAs (miRNAs), which bind to complementary sequences on messenger RNAs to regulate the translation efficacy. Therefore, identifying the miRNAs expressed in cells/organisms aids in understanding genetic control in cells/organisms. In this report, we determined the binding of oligonucleotides to a receptor-modified silicon nanowire field-effect transistor (SiNW-FET) by monitoring the changes in conductance of the SiNW-FET. We first modified a SiNW-FET with a DNA probe to directly and selectively detect the complementary miRNA in cell lysates. This SiNW-FET device has 7-fold higher sensitivity than reverse transcription-quantitative polymerase chain reaction in detecting the corresponding miRNA. Next, we anchored viral p19 proteins, which bind the double-strand small RNAs (ds-sRNAs), on the SiNW-FET. By perfusing the device with synthesized ds-sRNAs of different pairing statuses, the dissociation constants revealed that the nucleotides at the 3‧-overhangs and pairings at the terminus are important for the interactions. After perfusing the total RNA mixture extracted from Nicotiana benthamiana across the device, this device could enrich the ds-sRNAs for sequence analysis. Finally, this bionanoelectronic SiNW-FET, which is able to isolate and identify the interacting protein-RNA, adds an additional tool in genomic technology for the future study of direct biomolecular interactions.

  20. The rph1 gene is a common contributor to the evolution of phosphine resistance in independent field isolates of Rhyzopertha dominica.

    PubMed

    Mau, Yosep S; Collins, Patrick J; Daglish, Gregory J; Nayak, Manoj K; Pavic, Hervoika; Ebert, Paul R

    2012-01-01

    Phosphine is the only economically viable fumigant for routine control of insect pests of stored food products, but its continued use is now threatened by the world-wide emergence of high-level resistance in key pest species. Phosphine has a unique mode of action relative to well-characterised contact pesticides. Similarly, the selective pressures that lead to resistance against field sprays differ dramatically from those encountered during fumigation. The consequences of these differences have not been investigated adequately. We determine the genetic basis of phosphine resistance in Rhyzopertha dominica strains collected from New South Wales and South Australia and compare this with resistance in a previously characterised strain from Queensland. The resistance levels range from 225 and 100 times the baseline response of a sensitive reference strain. Moreover, molecular and phenotypic data indicate that high-level resistance was derived independently in each of the three widely separated geographical regions. Despite the independent origins, resistance was due to two interacting genes in each instance. Furthermore, complementation analysis reveals that all three strains contain an incompletely recessive resistance allele of the autosomal rph1 resistance gene. This is particularly noteworthy as a resistance allele at rph1 was previously proposed to be a necessary first step in the evolution of high-level resistance. Despite the capacity of phosphine to disrupt a wide range of enzymes and biological processes, it is remarkable that the initial step in the selection of resistance is so similar in isolated outbreaks. PMID:22363668

  1. Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols.

    PubMed

    Croes, Sarah; Weyens, Nele; Colpaert, Jan; Vangronsveld, Jaco

    2015-07-01

    Plant-associated bacteria are intensively investigated concerning their characteristics for plant growth promotion, biocontrol mechanisms and enhanced phytoremediation efficiency. To obtain endophytes, different sampling and isolation protocols are used although their representativeness is not always clearly demonstrated. The objective of this study was to acquire representative pictures of the cultivable bacterial root, stem and leaf communities for all Brassica napus L. individuals growing on the same field. For each plant organ, genotypic identifications of the endophytic communities were performed using three replicates. Root replicates were composed of three total root systems, whereas stem and leaf replicates needed to consist of six independent plant parts in order to be representative. Greater variations between replicates were found when considering phenotypic characteristics. Correspondence analysis revealed reliable phenotypic results for roots and even shoots, but less reliable ones for leaves. Additionally, realistic Shannon-Wiener biodiversity indices were calculated for all three organs and showed similar Evenness factors. Furthermore, it was striking that all replicates and thus the whole plant contained Pseudomonas and Bacillus strains although aboveground and belowground plant tissues differed in most dominant bacterial genera and characteristics. PMID:25367683

  2. Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus.

    PubMed

    Servín-Garcidueñas, Luis E; Rogel, Marco A; Ormeño-Orrillo, Ernesto; Zayas-Del Moral, Alejandra; Sánchez, Federico; Martínez-Romero, Esperanza

    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

  3. 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

  4. Complete genome sequence of nine isolates of canna yellow streak virus reveals its relationship to the sugarcane mosaic virus (SCMV) subgroup of potyviruses.

    PubMed

    Chauhan, Ravendra P; Rajakaruna, Punsasi; Verchot, Jeanmarie

    2015-03-01

    Complete genome sequences were obtained from nine isolates of canna yellow streak virus (CaYSV). CaYSV belongs to the sugarcane mosaic virus (SCMV) subgroup of potyviruses with johnsongrass mosaic virus (JGMV) as its closest relative. Multiple sequence alignments showed a pattern of amino acid substitutions in the CP sequences, which enabled us to relate these isolates to South East Asian or European isolates. Biological characterization of CaYSV identified Nicotiana benthamiana, Chenopodium quinoa and Phaseolus vulgaris as experimental hosts. Given the popularity and global trade of cannas, a clear picture of the genetic diversity of CaYSV is critical to disease management. PMID:25567205

  5. Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

    SciTech Connect

    Rockel, Beate; Schmaler, Tilo; Huang, Xiaohua; Dubiel, Wolfgang

    2014-07-25

    Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts

  6. Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin.

    PubMed

    Douillard, François P; Kant, Ravi; Ritari, Jarmo; Paulin, Lars; Palva, Airi; de Vos, Willem M

    2013-09-01

    The members of the Lactobacillus genus are widely used in the food and feed industry and show a remarkable ecological adaptability. Several Lactobacillus strains have been marketed as probiotics as they possess health-promoting properties for the host. In the present study, we used two complementary next-generation sequencing technologies to deduce the genome sequences of two Lactobacillus casei strains LcA and LcY, which were isolated from the products Actimel and Yakult, commercialized as probiotics. The LcA and LcY draft genomes have, respectively, an estimated size of 3067 and 3082 Mb and a G+C content of 46.3%. Both strains are close to identical to each other and differ by no more than minor chromosomal re-arrangements, substitutions, insertions and deletions, as evident from the verified presence of one insertion-deletion (InDel) and only 29 single-nucleotide polymorphisms (SNPs). In terms of coding capacity, LcA and LcY are predicted to encode a comparable exoproteome, indicating that LcA and LcY are likely to establish similar interactions with human intestinal cells. Moreover, both L. casei LcA and LcY harboured a 59.6 kb plasmid that shared high similarities with plasmids found in other L. casei strains, such as W56 and BD-II. Further analysis revealed that the L. casei plasmids constitute a good evolution marker within the L. casei species. The plasmids of the LcA and LcY strains are almost identical, as testified by the presence of only three verified SNPs, and share a 3.5 kb region encoding a remnant of a lactose PTS system that is absent from the plasmids of W56 and BD-II but conserved in another smaller L. casei plasmid (pLC2W). Our observations imply that the results obtained in animal and human experiments performed with the Actimel and Yakult strains can be compared with each other as these strains share a very recent common ancestor. PMID:23815335

  7. Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin

    PubMed Central

    Douillard, François P; Kant, Ravi; Ritari, Jarmo; Paulin, Lars; Palva, Airi; Vos, Willem M

    2013-01-01

    Summary The members of the Lactobacillus genus are widely used in the food and feed industry and show a remarkable ecological adaptability. Several Lactobacillus strains have been marketed as probiotics as they possess health-promoting properties for the host. In the present study, we used two complementary next-generation sequencing technologies to deduce the genome sequences of two Lactobacillus casei strains LcA and LcY, which were isolated from the products Actimel and Yakult, commercialized as probiotics. The LcA and LcY draft genomes have, respectively, an estimated size of 3067 and 3082 Mb and a G+C content of 46.3%. Both strains are close to identical to each other and differ by no more than minor chromosomal re-arrangements, substitutions, insertions and deletions, as evident from the verified presence of one insertion-deletion (InDel) and only 29 single-nucleotide polymorphisms (SNPs). In terms of coding capacity, LcA and LcY are predicted to encode a comparable exoproteome, indicating that LcA and LcY are likely to establish similar interactions with human intestinal cells. Moreover, both L. casei LcA and LcY harboured a 59.6 kb plasmid that shared high similarities with plasmids found in other L. casei strains, such as W56 and BD-II. Further analysis revealed that the L. casei plasmids constitute a good evolution marker within the L. casei species. The plasmids of the LcA and LcY strains are almost identical, as testified by the presence of only three verified SNPs, and share a 3.5 kb region encoding a remnant of a lactose PTS system that is absent from the plasmids of W56 and BD-II but conserved in another smaller L. casei plasmid (pLC2W). Our observations imply that the results obtained in animal and human experiments performed with the Actimel and Yakult strains can be compared with each other as these strains share a very recent common ancestor. Funding Information The present work was supported by the Center of Excellence in

  8. Molecular Analysis of Isoniazid-Resistant Mycobacterium tuberculosis Isolates from England and Wales Reveals the Phylogenetic Significance of the ahpC −46A Polymorphism

    PubMed Central

    Baker, L. V.; Brown, T. J.; Maxwell, O.; Gibson, A. L.; Fang, Z.; Yates, M. D.; Drobniewski, F. A.

    2005-01-01

    The present study investigated the prevalence and diagnostic potential of the most commonly reported mutations associated with isoniazid resistance, katG 315Thr, katG 315Asn, inhA −15T, inhA −8A, and the oxyR-ahpC intergenic region, in a population sample of 202 isoniazid-resistant Mycobacterium tuberculosis isolates and 176 randomly selected fully sensitive isolates from England and Wales identified by using a directed oligonucleotide array and limited DNA sequencing. The strains were recovered from patients originating from 29 countries; 41 isolates were multidrug resistant. Mutations affecting katG 315, the inhA promoter, and the oxyR-ahpC intergenic region were found in 62.7, 21.9, and 30% of 169 genotypically distinct isoniazid-resistant isolates, respectively, whereas they were found in 0, 0, and 8% of susceptible strains, respectively. The frequency of mutation at each locus was unrelated to the resistance profile or previous antituberculous drug therapy. The commonest mutation in the oxyR-ahpC intergenic region, ahpC −46A, was present in 23.7% of isoniazid-resistant isolates and 7.5% of susceptible isolates. This proved to be a phylogenetic marker for a subgroup of M. tuberculosis strains originating on the Indian subcontinent, which shared IS6110-based restriction fragment length polymorphism and spoligotype features with the Delhi strain and Central Asian strain CAS1; and this marker is strongly associated with isoniazid resistance and the katG 315Thr mutation. In total, 82.8% of unrelated isoniazid-resistant isolates could be identified by analysis of just two loci: katG 315 and the inhA promoter. Analysis of the oxyR-ahpC intergenic region, although phylogenetically interesting, does not contribute significantly to further identification of isoniazid-resistant isolates. PMID:15793126

  9. MAGNETIC FIELDS IN LARGE-DIAMETER H II REGIONS REVEALED BY THE FARADAY ROTATION OF COMPACT EXTRAGALACTIC RADIO SOURCES

    SciTech Connect

    Harvey-Smith, L.; Madsen, G. J.; Gaensler, B. M.

    2011-08-01

    We present a study of the line-of-sight magnetic fields in five large-diameter Galactic H II regions. Using the Faraday rotation of background polarized radio sources, as well as dust-corrected H{alpha} surface brightness as a probe of electron density, we estimated the strength and orientation of the magnetic field along 93 individual sight lines through the H II regions. Each of the H II regions displayed a coherent magnetic field. The magnetic field strength (line-of-sight component) in the regions ranges from 2 to 6 {mu}G, which is similar to the typical magnetic field strength in the diffuse interstellar medium. We investigated the relationship between magnetic field strength and electron density in the five H II regions. The slope of magnetic field versus density in the low-density regime (0.8 cm{sup -3} < n{sub e} <30 cm{sup -3}) is very slightly above zero. We also calculated the ratio of thermal to magnetic pressure, {beta}{sub th}, for each data point, which fell in the range 1.01 < {beta}{sub th} < 25. Finally, we studied the orientation of the magnetic field in the solar neighborhood (d < 1.1 kpc) using our data from five H II regions along with existing measurements of the line-of-sight magnetic field strength from polarized pulsars whose distances have been determined from their annual parallax. We identify a net direction for the magnetic field in the solar neighborhood, but find no evidence for a preferred vertical direction of the magnetic field above or below the Galactic plane.

  10. A Novel Population of Fusarium fujikuroi Isolated from Southeastern U.S. Winegrapes Reveals the Need to Re-Evaluate the Species' Fumonisin Production.

    PubMed

    Bolton, Stephanie L; Brannen, Phillip M; Glenn, Anthony E

    2016-01-01

    Mycotoxins pose a challenge to a safe food supply worldwide, and their threat is expected to worsen with our changing climate. The need for diligence is exemplified by the discovery of fumonisin B2 in wine, which joins ochratoxin A as a mycotoxin of concern in the grape-wine chain. To elucidate the mycotoxin risk in southeastern American wine, grape samples were collected from vineyards during harvest in 2013 and potentially mycotoxigenic fungi (Fusarium and Aspergillus) were isolated from the samples. Numerous Fusarium isolates were recovered and identified to the species level by comparison of translation elongation factor 1-α gene sequences to verified strains. Fusarium fujikuroi was the most abundant species recovered (239 isolates), followed by F. proliferatum (52), F. incarnatum-equiseti (14), F. oxysporum (7), F. concentricum (1), and F. solani (1). In vitro assays quantified fumonisin production for representative isolates via liquid chromatography-tandem mass spectrometry. Surprisingly, nearly all F. fujikuroi isolates produced fumonisins B1, B2, and B3 at levels comparable to both the F. proliferatum isolates and the positive control, Fusarium verticillioides. Such capacity for fumonisin production refutes the generally accepted notion that F. fujikuroi produces undetectable or low levels of fumonisins and provides evidence to reconsider this species as a mycotoxigenic threat to economically significant crops. PMID:27589800

  11. Analysis of HCV-6 isolates among Asian-born immigrants in North America reveals their high genetic diversity and a new subtype.

    PubMed

    Lu, Ling; Wu, Tao; Xiong, Lu; Li, Chunhua; Nguyen, Mindie H; Murphy, Donald G

    2016-05-01

    We characterized full-length genomes for 15 HCV-6 isolates, all from Asian immigrants living in North America. Among these isolates, nine were novel variants showing >15% nucleotide differences from their nearest relatives, representing lineages distinct from known subtypes. The other six were classified into subtypes 6c, 6h, 6q, 6r, and 6s. The partial sequences were also determined for five additional HCV-6 isolates, three from the US and two from Canada. The latter two were assigned to new subtype 6xf as they were found to classify with two other isolates for which we recently reported their full-length genomes. We further analyzed partial Core-E1 sequences of 100 HCV-6 isolates sampled in North America, seven from the US and 93 from Canada and all from Asian immigrants except for four from Caucasians. These 100 isolates belonged to 20 assigned subtypes and 16 unclassified lineages showing great genetic diversity and enhanced significance to public health. PMID:26896932

  12. Experimental and numerical investigation of the unsteady flow field and tone generation in an isolated centrifugal fan impeller

    NASA Astrophysics Data System (ADS)

    Wolfram, Daniel; Carolus, Thomas H.

    2010-10-01

    In spite of a low circumferential Mach number the sound of isolated centrifugal fan impellers is sometimes dominated by distinctive tones at blade passing frequency (BPF) and integer multiples. This paper reports on an experimental and numerical investigation intended to unveil the tone generating mechanism. The sound spectra from three impellers operating at a large range of speed were measured and decomposed into Strouhal and Helmholtz number dependent functions. This led to the preliminary conclusion that the BPF related tones are exclusively flow-induced. Based on hot-wire and blade pressure fluctuation measurements and a subsequent correlation analysis, coherent flow structures different from those associated with the principal azimuthal flow pattern due to the blades were detected. Eventually a numerical three-dimensional unsteady flow simulation revealed an inlet vortex. It takes on a helical form, with the vortex core slowly varying its position with respect to the impeller center. As the blades cut through that quasi-stationary helical vortex they encounter blade force fluctuations, producing the BPF tones. Slow spin of the vortex core and slow variation of vortex strength were identified as the reasons for amplitude modulation of the BPF tone.

  13. Magnetism and the atmosphere of Mars --- How polarimetric microwave observations may reveal magnetic properties of the southern crustal field

    NASA Astrophysics Data System (ADS)

    Larsson, R.; Ramstad, R.; Mendrok, J.; Buehler, S. A.; Kasai, Y.

    2013-12-01

    The southern crustal magnetic field of Mars has been mapped by satellite-borne magnetometers at 400 and 100 km above the surface. Between these heights, the magnetic field strength increases from around 100 nT to about 1000 nT in peak strength. The strong increase in field strength over a short distance indicates a surface source much stronger. Predictions by models put the surface magnetism at around 15,000 to 20,000 nT at its strongest. The close surface field strength has not been measured directly as no landers with magnetometers have reached the southern crust. Even if a landing was to take place and the near surface field could be mapped directly, a magnetometer will only gauge the magnetism locally so a moving platform is required to determine the overall field. A better map of the magnetic field of Mars would help support a multitude of efforts. The atmospheric escape rate, and therefore the evolution of atmospheric constituents, is coupled to the fields because it forces ionized particles to accelerate. The long-term evolution the crust can be better understood from the remaining magnetic field --- when and how did the global field disappear, and what was the cause? Answers to both questions strongly depend on the field today. In spirit of exploration, it has been suggested that the crustal fields can act as a protective dome for potential explorers; protecting the visitors against some of the charged cosmic particles that could otherwise be harmful to them. Our work suggests that a highly resolving spectropolarimeter in the microwave region observing an oxygen line on-board a satellite looking at the limb of Mars should be able to detect the magnetic field due to the polarized propagation caused by the Zeeman effect. The magnetic field of Mars is weak so the observation would not be of fully split lines. Instead, each perturbed line will contribute to a common polarized residual around the Doppler width of the central line. We present simulations from the

  14. Comparison of molecular and biological characteristics of a modified live porcine reproductive and respiratory syndrome virus (PRRSV) vaccine (ingelvac PRRS MLV), the parent strain of the vaccine (ATCC VR2332), ATCC VR2385, and two recent field isolates of PRRSV.

    PubMed

    Opriessnig, T; Halbur, P G; Yoon, K-J; Pogranichniy, R M; Harmon, K M; Evans, R; Key, K F; Pallares, F J; Thomas, P; Meng, X J

    2002-12-01

    The objectives of this study were to compare the molecular and biological characteristics of recent porcine reproductive and respiratory syndrome virus (PRRSV) field isolates to those of a modified live virus (MLV) PRRS vaccine and its parent strain. One hundred seventeen, 4-week-old pigs were randomly assigned to six groups. Group 1 (n = 20) served as sham-inoculated negative controls, group 2 (n = 19) was inoculated with Ingelvac PRRS MLV vaccine, group 3 (n = 20) was inoculated with the parent strain of the vaccine (ATCC VR2332), group 4 (n = 19) was inoculated with vaccine-like PRRSV field isolate 98-38803, group 5 (n = 19) was inoculated with PRRSV field isolate 98-37120, and group 6 (n = 20) was inoculated with known high-virulence PRRSV isolate ATCC VR2385. The levels of severity of gross lung lesions (0 to 100%) among the groups were significantly different at both 10 (P < 0.0001) and 28 days postinoculation (p.i.) (P = 0.002). At 10 days p.i., VR2332 (26.5% +/- 4.64%) and VR2385 (36.4% +/- 6.51%) induced gross lesions of significantly greater severity than 98-38803 (0.0% +/- 0.0%), 98-37120 (0.8% +/- 0.42%), Ingelvac PRRS MLV (0.9% +/- 0.46%), and negative controls (2.3% +/- 1.26%). At 28 days p.i., 98-37120 (17.2% +/- 6.51%) induced gross lesions of significantly greater severity than any of the other viruses. Analyses of the microscopic-interstitial-pneumonia-lesion scores (0 to 6) revealed that VR2332 (2.9 +/- 0.23) and VR2385 (3.1 +/- 0.35) induced significantly more severe lesions at 10 days p.i. At 28 days p.i., VR2385 (2.5 +/- 0.27), VR2332 (2.3 +/- 0.21), 98-38803 (2.6 +/- 0.29), and 98-37120 (3.0 +/- 0.41) induced significantly more severe lesions than Ingelvac PRRS MLV (0.7 +/- 0.17) and controls (0.7 +/- 0.15). The molecular analyses and biological characterizations suggest that the vaccine-like isolate 98-38803 (99.5% amino acid homology based on the ORF5 gene) induces microscopic pneumonia lesions similar in type to, but different in severity

  15. Genomic Analysis Reveals Multi-Drug Resistance Clusters in Group B Streptococcus CC17 Hypervirulent Isolates Causing Neonatal Invasive Disease in Southern Mainland China.

    PubMed

    Campisi, Edmondo; Rosini, Roberto; Ji, Wenjing; Guidotti, Silvia; Rojas-López, Maricarmen; Geng, Guozhu; Deng, Qiulian; Zhong, Huamin; Wang, Weidong; Liu, Haiying; Nan, Cassandra; Margarit, Immaculada; Rinaudo, C D

    2016-01-01

    Neonatal invasive disease caused by group B Streptococcus (GBS) represents a significant public health care concern globally. However, data related to disease burden, serotype distribution, and molecular epidemiology in China and other Asian countries are very few and specifically relative to confined regions. The aim of this study was to investigate the genetic characteristics of GBS isolates recovered from neonates with invasive disease during 2013-2014 at Guangzhou and Changsha hospitals in southern mainland China. We assessed the capsular polysaccharide type, pilus islands (PIs) distribution and hvgA gene presence in a panel of 26 neonatal clinical isolates, of which 8 were recovered from Early Onset Disease and 18 from Late Onset Disease (LOD). Among 26 isolates examined, five serotypes were identified. Type III was the most represented (15 cases), particularly among LOD strains (n = 11), followed by types Ib (n = 5), V (n = 3), Ia (n = 2) and II (n = 1). We performed whole-genome sequencing analysis and antimicrobial susceptibility testing on the 14 serotype III isolates belonging to the hypervirulent Clonal Complex 17 (serotype III-CC17). The presence of PI-2b alone was associated with 13 out of 14 serotype III-CC17 strains. Genome analysis led us to identify two multi-drug resistance gene clusters harbored in two new versions of integrative and conjugative elements (ICEs), carrying five or eight antibiotic resistance genes, respectively. These ICEs replaced the 16 kb-locus that normally contains the PI-1 operon. All isolates harboring the identified ICEs showed multiple resistances to aminoglycoside, macrolide, and tetracycline antibiotic classes. In conclusion, we report the first whole-genome sequence analysis of 14 GBS serotype III-CC17 strains isolated in China, representing the most prevalent lineage causing neonatal invasive disease. The acquisition of newly identified ICEs conferring multiple antibiotic resistance could in part explain the spread of

  16. Genomic Analysis Reveals Multi-Drug Resistance Clusters in Group B Streptococcus CC17 Hypervirulent Isolates Causing Neonatal Invasive Disease in Southern Mainland China

    PubMed Central

    Campisi, Edmondo; Rosini, Roberto; Ji, Wenjing; Guidotti, Silvia; Rojas-López, Maricarmen; Geng, Guozhu; Deng, Qiulian; Zhong, Huamin; Wang, Weidong; Liu, Haiying; Nan, Cassandra; Margarit, Immaculada; Rinaudo, C. D.

    2016-01-01

    Neonatal invasive disease caused by group B Streptococcus (GBS) represents a significant public health care concern globally. However, data related to disease burden, serotype distribution, and molecular epidemiology in China and other Asian countries are very few and specifically relative to confined regions. The aim of this study was to investigate the genetic characteristics of GBS isolates recovered from neonates with invasive disease during 2013–2014 at Guangzhou and Changsha hospitals in southern mainland China. We assessed the capsular polysaccharide type, pilus islands (PIs) distribution and hvgA gene presence in a panel of 26 neonatal clinical isolates, of which 8 were recovered from Early Onset Disease and 18 from Late Onset Disease (LOD). Among 26 isolates examined, five serotypes were identified. Type III was the most represented (15 cases), particularly among LOD strains (n = 11), followed by types Ib (n = 5), V (n = 3), Ia (n = 2) and II (n = 1). We performed whole-genome sequencing analysis and antimicrobial susceptibility testing on the 14 serotype III isolates belonging to the hypervirulent Clonal Complex 17 (serotype III-CC17). The presence of PI-2b alone was associated with 13 out of 14 serotype III-CC17 strains. Genome analysis led us to identify two multi-drug resistance gene clusters harbored in two new versions of integrative and conjugative elements (ICEs), carrying five or eight antibiotic resistance genes, respectively. These ICEs replaced the 16 kb-locus that normally contains the PI-1 operon. All isolates harboring the identified ICEs showed multiple resistances to aminoglycoside, macrolide, and tetracycline antibiotic classes. In conclusion, we report the first whole-genome sequence analysis of 14 GBS serotype III-CC17 strains isolated in China, representing the most prevalent lineage causing neonatal invasive disease. The acquisition of newly identified ICEs conferring multiple antibiotic resistance could in part explain the spread

  17. 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

  18. Epidemiological Analysis of Salmonella enteritidis Isolates from Humans and Broiler Chickens in Thailand by Phage Typing and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Boonmar, Sumalee; Bangtrakulnonth, Aroon; Pornrunangwong, Srirat; Terajima, Jun; Watanabe, Haruo; Kaneko, Ken-Ichi; Ogawa, Masuo

    1998-01-01

    To determine the phage types (PT) of Salmonella enteritidis found in Thailand and to clarify the potential for human infection by S. enteritidis in broiler chicken meat, human and poultry isolates taken from Thailand between 1990 and 1997 were phage typed and analyzed by pulsed-field gel electrophoresis (PFGE). Ten different PT were found among the 302 isolates phage typed, with PT 4 being the most frequent in human (73.9%) and poultry (76.2%) isolates, followed by PT 1 (8.0%), 8 (3.6%), and 7a (2.2%) in human isolates and by PT 7a (4.9%), 1 (3.7%), and 12 (2.4%) in poultry isolates. Of the 53 isolates analyzed by PFGE, 45 showed an indistinguishable pattern (pattern A) by BlnI-digested PFGE and the other 8 isolates showed a very similar pattern that differed by only a few bands. These results indicate the spread of a genetically identical clone of S. enteritidis in humans and poultry in Thailand. PMID:9542918

  19. Structural characterization of amphiphilic siderophores produced by a soda lake isolate, Halomonas sp. SL01, reveals cysteine-, phenylalanine- and proline-containing head groups.

    PubMed

    Figueroa, Luis O'mar Serrano; Schwarz, Benjamin; Richards, Abigail M

    2015-11-01

    Soap Lake, located in Washington State, is a naturally occurring saline and alkaline lake. Several organisms inhabiting this lake have been identified as producers of siderophores that are unique in structure. Bacterial isolates, enriched from Soap Lake sediment and water samples, were screened for siderophore production using both the chrome azurol S (CAS) agar plate and liquid methods. Bacterial isolate Halomonas sp. SL01 was found to produce relatively high concentrations of siderophores in liquid medium (up to 40 µM). Siderophores from the isolate were separated from the culture supernatant using solid phase extraction and purified by high-performance liquid chromatography (HPLC). Siderophore structure was determined using LC/MS/MS (liquid chromatography/mass spectrometry/mass spectrometry) and fatty acid methyl ester (FAME) GC. Two distinct new families of amphiphilic siderophores were produced by isolate SL01. All siderophores ranged in size from 989 to 1096 atomic mass units and consisted of a conserved peptidic head group (per family), which coordinates iron, coupled to fatty acid moieties. The fatty acyl moieties were C10-C14 in length and some with hydroxyl substitutions at the third α position. These siderophores resembled amphiphilic aquachelin siderophores produced by Halomonas aquamarina strain DS40M3, a marine bacterium as well as siderophores from isolate Halomonas sp. SL28 that was found to produce amphiphilic siderophores. Bacteria thriving under saline and alkaline conditions are capable of producing unique siderophores resembling those produced by microbes inhabiting marine environments. PMID:26439615

  20. Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys.

    PubMed

    Rougemont, Q; Gaigher, A; Lasne, E; Côte, J; Coke, M; Besnard, A-L; Launey, S; Evanno, G

    2015-12-01

    Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here, we used a combination of mating trials, experimental crosses and population genetic analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (Lampetra planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size-assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically based divergent selection may explain these variable levels of divergence among sympatric population pairs, but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress towards speciation. PMID:26348652

  1. Anticoccidial efficacy of semduramicin. 2. Evaluation against field isolates including comparisons with salinomycin, maduramicin, and monensin in battery tests.

    PubMed

    Logan, N B; McKenzie, M E; Conway, D P; Chappel, L R; Hammet, N C

    1993-11-01

    The efficacy of semduramicin (AVIAX), a novel polyether ionophore, was profiled in a series of 57 battery tests conducted in the United States and the United Kingdom. The studies employed mixed and monospecific infections of Eimeria acervulina, Eimeria mivati/Eimeria mitis, Eimeria brunetti, Eimeria maxima, Eimeria necatrix, and Eimeria tenella derived from North American and European field isolates. Ten-day-old broiler cockerels in pens of 8 to 10 birds were continuously medicated in feed beginning 24 h before challenge in tests of 6 to 8 days' duration. At the use level of 25 ppm, semduramicin effectively controlled mortality, lesions, and weight gain depression that occurred in unmedicated, infected controls for all species. In comparison with 60 ppm salinomycin, semduramicin significantly (P < .05) improved weight gain against E. brunetti and E. tenella, lesion control against E. brunetti and E. maxima, and the control of coccidiosis mortality against E. tenella. Salinomycin was superior (P < .05) to all treatments in maintenance of weight gain and control of lesions for E. acervulina. Maduramicin at 5 ppm was inferior (P < .05) to semduramicin in control of E. acervulina and E. maxima lesions, but was superior (P < .05) to all treatments in maintenance of weight gain and control of lesions in E. tenella infections. The data indicate that semduramicin at 25 ppm is well tolerated in broilers and possesses broad spectrum anticoccidial activity. PMID:8265495

  2. Low Frequency Electromagnetic Field Conditioning Protects against I/R Injury and Contractile Dysfunction in the Isolated Rat Heart

    PubMed Central

    Bialy, Dariusz; Wawrzynska, Magdalena; Bil-Lula, Iwona; Krzywonos-Zawadzka, Anna; Wozniak, Mieczyslaw; Cadete, Virgilio J. J.

    2015-01-01

    Low frequency electromagnetic field (LF-EMF) decreases the formation of reactive oxygen species, which are key mediators of ischemia/reperfusion (I/R) injury. Therefore, we hypothesized that the LF-EMF protects contractility of hearts subjected to I/R injury. Isolated rat hearts were subjected to 20 min of global no-flow ischemia, followed by 30 min reperfusion, in the presence or absence of LF-EMF. Coronary flow, heart rate, left ventricular developed pressure (LVDP), and rate pressure product (RPP) were determined for evaluation of heart mechanical function. The activity of cardiac matrix metalloproteinase-2 (MMP-2) and the contents of coronary effluent troponin I (TnI) and interleukin-6 (IL-6) were measured as markers of heart injury. LF-EMF prevented decreased RPP in I/R hearts, while having no effect on coronary flow. In addition, hearts subjected to I/R exhibited significantly increased LVDP when subjected to LF-EMF. Although TnI and IL-6 levels were increased in I/R hearts, their levels returned to baseline aerobic levels in I/R hearts subjected to LF-EMF. The reduced activity of MMP-2 in I/R hearts was reversed in hearts subjected to LF-EMF. The data presented here indicate that acute exposure to LF-EMF protects mechanical function of I/R hearts and reduces I/R injury. PMID:25961016

  3. Molecular characterization of Italian Candida parapsilosis isolates reveals the cryptic presence of the newly described species Candida orthopsilosis in blood cultures from newborns.

    PubMed

    Romeo, Orazio; Delfino, Demetrio; Costanzo, Barbara; Cascio, Antonio; Criseo, Giuseppe

    2012-03-01

    The authors report the molecular characterization of Candida parapsilosis isolates recovered from the blood and venous central catheter tips of patients admitted to different care units of the Polyclinic Hospital, University of Messina, Italy. Among 97 presumed C. parapsilosis isolates examined, 94 were identified as C. parapsilosis sensu stricto and the remaining 3 isolates were found to belong to the cryptic species Candida orthopsilosis which was recovered only from blood cultures of neonates (<30 days old) born prematurely. No C. metapsilosis was found in this study. This study emphasizes the role of C. parapsilosis as an important nosocomial pathogen, and it also describes, for the first time, the occurrence of C. orthopsilosis in newborns. PMID:22244186

  4. Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

    PubMed Central

    Ahmed, Sanaa A.; Awosika, Joy; Baldwin, Carson; Bishop-Lilly, Kimberly A.; Biswas, Biswajit; Broomall, Stacey; Chain, Patrick S. G.; Chertkov, Olga; Chokoshvili, Otar; Coyne, Susan; Davenport, Karen; Detter, J. Chris; Dorman, William; Erkkila, Tracy H.; Folster, Jason P.; Frey, Kenneth G.; George, Matroner; Gleasner, Cheryl; Henry, Matthew; Hill, Karen K.; Hubbard, Kyle; Insalaco, Joseph; Johnson, Shannon; Kitzmiller, Aaron; Krepps, Michael; Lo, Chien-Chi; Luu, Truong; McNew, Lauren A.; Minogue, Timothy; Munk, Christine A.; Osborne, Brian; Patel, Mohit; Reitenga, Krista G.; Rosenzweig, C. Nicole; Shea, April; Shen, Xiaohong; Strockbine, Nancy; Tarr, Cheryl; Teshima, Hazuki; van Gieson, Eric; Verratti, Kathleen; Wolcott, Mark; Xie, Gary

    2012-01-01

    In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the outbreak and a collection of historical E. coli O104:H4 isolates using draft genome assemblies. We present the complete, closed genome sequences of an isolate from the 2011 outbreak (2011C–3493) and two isolates from cases of bloody diarrhea that occurred in the Republic of Georgia in 2009 (2009EL–2050 and 2009EL–2071). Comparative genome analysis indicates that, while the Georgian strains are the nearest neighbors to the 2011 outbreak isolates sequenced to date, structural and nucleotide-level differences are evident in the Stx2 phage genomes, the mer/tet antibiotic resistance island, and in the prophage and plasmid profiles of the strains, including a previously undescribed plasmid with homology to the pMT virulence plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that 2009EL–2071 possessed higher resistance to polymyxin and membrane-disrupting agents. Finally, we show evidence by electron microscopy of the presence of a common phage morphotype among the European and Georgian strains and a second phage morphotype among the Georgian strains. The presence of at least two stx2 phage genotypes in host genetic backgrounds that may derive from a recent common ancestor of the 2011 outbreak isolates indicates that the emergence of stx2 phage-containing E. coli O104:H4 strains probably occurred more than once, or that the current outbreak isolates may be the result of a recent transfer of a new stx2 phage element into a pre-existing stx2-positive genetic background. PMID:23133618

  5. Draft Genome Sequence of Rhodococcus rhodochrous Strain KG-21, a Soil Isolate from Oil Fields of Krishna-Godavari Basin, India

    PubMed Central

    Dawar, Chhavi

    2015-01-01

    Here, we present the 6.1-Mb draft genome sequence of Rhodococcus rhodochrous strain KG-21, a soil isolate from the oil fields of Krishna-Godavari Basin in Andhra Pradesh, India. This genomic resource may help in the identification of the gene(s) involved in hydrocarbon degradation and their possible deployment for bioremediation. PMID:26472842

  6. ESR in zero field of the photoinduced triplet state in isolated reaction centers of rhodopseudomonas sphaeroides R-26 detected by the singlet ground-state absorbance

    NASA Astrophysics Data System (ADS)

    Den Blanken, H. J.; Van Der Zwet, G. P.; Hoff, A. J.

    1982-01-01

    We have measured zero-field resonance transitions of the triplet state of the primary donor monitoring the transmittance at 890 nm at 1.2 K in isolated reaction centers of Rhodopseudomonas sphaeroides R-26. The transitions correspond to a decrease in transmittance, confirming the energy transfer model for the transitions detected via the antenna fluorescence in whole cells.

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

    SciTech Connect

    Ray, Jayashree; Waters, R. Jordan; Skerker, Jeffrey M.; Kuehl, Jennifer V.; Price, Morgan N.; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P.; Deutschbauer, Adam

    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%.

  8. Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields

    PubMed Central

    Brito, Patrícia H.; Serrano, Mónica

    2015-01-01

    Here, we report two genome sequences of endospore-forming bacteria isolated from the rice fields of Comporta, Portugal, identified as Bacillus aryabhattai C765 and Bacillus aerophilus C772. Both species were previously identified in air samples from the upper atmosphere, but our findings suggest their presence in a wider range of environmental niches. PMID:25858824

  9. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field

    PubMed Central

    Bao, Zhihua; Shinoda, Ryo

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  10. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field.

    PubMed

    Bao, Zhihua; Shinoda, Ryo; Minamisawa, Kiwamu

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  11. Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)

    PubMed Central

    Poltaraus, Andrey B.; Sokolova, Diyana S.; Grouzdev, Denis S.; Ivanov, Timophey M.; Malakho, Sophia G.; Korshunova, Alena V.; Rozanov, Aleksey S.; Tourova, Tatiyana P.

    2016-01-01

    The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus. PMID:27284131

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Draft Genome Sequence of Pseudomonas sp. Strain 2-92, a Biological Control Strain Isolated from a Field Plot Under Long-Term Mineral Fertilization

    PubMed Central

    Adam, Zaky; Chen, Qing; Lewis, Christopher T.; Lévesque, C. André; Xu, Renlin

    2014-01-01

    Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term mineral fertilization, strongly inhibits the growth of Fusarium graminearum, Rhizoctonia solani, and Gaeumannomyces graminis. Here, we report the draft genome sequence of Pseudomonas sp. strain 2-92. PMID:24407636

  14. High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism

    PubMed Central

    Assumpção, Monica B; Moreira, Fabiano C; Hamoy, Igor G; Magalhães, Leandro; Vidal, Amanda; Pereira, Adenilson; Burbano, Rommel; Khayat, André; Silva, Artur; Santos, Sidney; Demachki, Samia; Ribeiro-dos-Santos, Ândrea; Assumpção, Paulo

    2015-01-01

    Field effect in cancer, also called “field cancerization”, attempts to explain the development of multiple primary tumors and locally recurrent cancer. The concept of field effect in cancer has been reinforced, since molecular alterations were found in tumor-adjacent tissues with normal histopatho-logical appearances. With the aim of investigating field effects in gastric cancer (GC), we conducted a high-throughput sequencing of the miRnome of four GC samples and their respective tumor-adjacent tissues and compared them with the miRnome of a gastric antrum sample from patients without GC, assuming that tumor-adjacent tissues could not be considered as normal tissues. The global number of miRNAs and read counts was highest in tumor samples, followed by tumor-adjacent and normal samples. Analyzing the miRNA expression profile of tumor-adjacent miRNA, hsa-miR-3131, hsa-miR-664, hsa-miR-483, and hsa-miR-150 were significantly downregulated compared with the antrum without tumor tissue (P-value < 0.01; fold-change <5). Additionally, hsa-miR-3131, hsa-miR-664, and hsa-miR-150 were downregulated (P-value < 0.001) in all paired samples of tumor and tumor-adjacent tissues, compared with antrum without tumor mucosa. The field effect was clearly demonstrated in gastric carcinogenesis by an epigenetics-based approach, and potential biomarkers of the GC field effect were identified. The elevated expression of miRNAs in adjacent tissues and tumors tissues may indicate that a cascade of events takes place during gastric carcinogenesis, reinforcing the notion of field effects. This phenomenon seems to be linked to DNA methylation patterns in cancer and suggests the involvement of an epigenetic network mechanism. PMID:26244015

  15. High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism.

    PubMed

    Assumpção, Monica B; Moreira, Fabiano C; Hamoy, Igor G; Magalhães, Leandro; Vidal, Amanda; Pereira, Adenilson; Burbano, Rommel; Khayat, André; Silva, Artur; Santos, Sidney; Demachki, Samia; Ribeiro-Dos-Santos, Ândrea; Assumpção, Paulo

    2015-01-01

    Field effect in cancer, also called "field cancerization", attempts to explain the development of multiple primary tumors and locally recurrent cancer. The concept of field effect in cancer has been reinforced, since molecular alterations were found in tumor-adjacent tissues with normal histopatho-logical appearances. With the aim of investigating field effects in gastric cancer (GC), we conducted a high-throughput sequencing of the miRnome of four GC samples and their respective tumor-adjacent tissues and compared them with the miRnome of a gastric antrum sample from patients without GC, assuming that tumor-adjacent tissues could not be considered as normal tissues. The global number of miRNAs and read counts was highest in tumor samples, followed by tumor-adjacent and normal samples. Analyzing the miRNA expression profile of tumor-adjacent miRNA, hsa-miR-3131, hsa-miR-664, hsa-miR-483, and hsa-miR-150 were significantly downregulated compared with the antrum without tumor tissue (P-value < 0.01; fold-change <5). Additionally, hsa-miR-3131, hsa-miR-664, and hsa-miR-150 were downregulated (P-value < 0.001) in all paired samples of tumor and tumor-adjacent tissues, compared with antrum without tumor mucosa. The field effect was clearly demonstrated in gastric carcinogenesis by an epigenetics-based approach, and potential biomarkers of the GC field effect were identified. The elevated expression of miRNAs in adjacent tissues and tumors tissues may indicate that a cascade of events takes place during gastric carcinogenesis, reinforcing the notion of field effects. This phenomenon seems to be linked to DNA methylation patterns in cancer and suggests the involvement of an epigenetic network mechanism. PMID:26244015

  16. Whole-Genome Sequencing of a Campylobacter jejuni Strain Isolated from Retail Chicken Meat Reveals the Presence of a Megaplasmid with Mu-Like Prophage and Multidrug Resistance Genes

    PubMed Central

    Marasini, Daya

    2016-01-01

    Genome sequencing of Campylobacter jejuni strain T1-21 isolated from retail chicken meat revealed the presence of a chromosome of 1,565,978 bp and a megaplasmid of 82,732 bp that contains Mu-like prophage and multidrug resistance genes. This is the first reported sequence of a Campylobacter megaplasmid >55 kb. PMID:27231378

  17. Whole-Genome Sequencing of a Campylobacter jejuni Strain Isolated from Retail Chicken Meat Reveals the Presence of a Megaplasmid with Mu-Like Prophage and Multidrug Resistance Genes.

    PubMed

    Marasini, Daya; Fakhr, Mohamed K

    2016-01-01

    Genome sequencing of Campylobacter jejuni strain T1-21 isolated from retail chicken meat revealed the presence of a chromosome of 1,565,978 bp and a megaplasmid of 82,732 bp that contains Mu-like prophage and multidrug resistance genes. This is the first reported sequence of a Campylobacter megaplasmid >55 kb. PMID:27231378

  18. 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. PMID:23577627

  19. Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation.

    PubMed

    Cleary, David W; Devine, Vanessa T; Jefferies, Johanna M C; Webb, Jeremy S; Bentley, Stephen D; Gladstone, Rebecca A; Faust, Saul N; Clarke, Stuart C

    2016-01-01

    Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom's childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin--antitoxin systems, were also observed. PMID:27016484

  20. Draft Genome Sequence of Hymenobacter sp. Strain IS2118, Isolated from a Freshwater Lake in Schirmacher Oasis, Antarctica, Reveals Diverse Genes for Adaptation to Cold Ecosystems.

    PubMed

    Koo, Hyunmin; Ptacek, Travis; Crowley, Michael; Swain, Ashit K; Osborne, John D; Bej, Asim K; Andersen, Dale T

    2014-01-01

    Hymenobacter sp. IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica, produces extracellular polymeric substance (EPS) and manifests tolerance to cold, UV radiation (UVR), and oxidative stress. We report the 5.26-Mb draft genome of strain IS2118, which will help us to understand its adaptation and survival mechanisms in Antarctic extreme ecosystems. PMID:25103756

  1. Draft Genome Sequence of Hymenobacter sp. Strain IS2118, Isolated from a Freshwater Lake in Schirmacher Oasis, Antarctica, Reveals Diverse Genes for Adaptation to Cold Ecosystems

    PubMed Central

    Ptacek, Travis; Crowley, Michael; Swain, Ashit K.; Osborne, John D.; Bej, Asim K.; Andersen, Dale T.

    2014-01-01

    Hymenobacter sp. IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica, produces extracellular polymeric substance (EPS) and manifests tolerance to cold, UV radiation (UVR), and oxidative stress. We report the 5.26-Mb draft genome of strain IS2118, which will help us to understand its adaptation and survival mechanisms in Antarctic extreme ecosystems. PMID:25103756

  2. Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment.

    PubMed

    Goedhals, D; Bester, P A; Paweska, J T; Swanepoel, R; Burt, F J

    2014-09-01

    Crimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown. PMID:24786748

  3. Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation

    PubMed Central

    Cleary, David W.; Devine, Vanessa T.; Jefferies, Johanna M.C.; Webb, Jeremy S.; Bentley, Stephen D.; Gladstone, Rebecca A.; Faust, Saul N.; Clarke, Stuart C.

    2016-01-01

    Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom’s childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin-–antitoxin systems, were also observed. PMID:27016484

  4. Regulation of mammary stem cell population with dietary intake of soy protein isolate reveals novel mechanisms for diet-mediated control of mammary tumorigenesis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breast cancer risk is highly modified by environmental factors including diet. Previously, we showed that dietary intake of soy protein isolate (SPI) decreased mammary tumor incidence and increased mammary tumor latency in rats relative to those fed a control casein (CAS) diet, when exposed to the c...

  5. Variable Nucleotide Tandem-Repeat Analysis Revealing a Unique Group of Leptospira interrogans Serovar Pomona Isolates Associated with California Sea Lions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leptospira interrogans serovar Pomona is commonly isolated from a variety of wildlife and domesticated livestock. It is difficult to assess whether disease outbreaks with serovar Pomona in given animal populations are due to endemic infections or accidental exposure. Unlike many leptospiral serovars...

  6. Newcastle disease virus isolates from US waterfowl reveal novel genomic subgroups with diverse and evolving genetics and the potential for spillover into US live bird markets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Distribution of genetic groups (genogroups) of Newcastle disease virus (NDV) isolated during 1986 to 2005 in the U.S. from 209 waterfowl and shorebirds (W&S) and 17 live bird market (LBM) samples was investigated. Waterfowl and shorebirds viruses were distinct from vaccine viruses and from the viru...

  7. Phenotypic and genotypic characterization of Brucella strains isolated from autochthonous livestock reveals the dominance of B. abortus biovar 3a in Nigeria.

    PubMed

    Bertu, Wilson J; Ducrotoy, Marie J; Muñoz, Pilar M; Mick, Virginie; Zúñiga-Ripa, Amaia; Bryssinckx, Ward; Kwaga, Jacob K P; Kabir, Junaid; Welburn, Susan C; Moriyón, Ignacio; Ocholi, Reuben A

    2015-10-22

    Brucellosis is a worldwide widespread zoonosis caused by bacteria of the genus Brucella. Control of this disease in a given area requires an understanding of the Brucella species circulating in livestock and humans. However, because of the difficulties intrinsic to Brucella isolation and typing, such data are scarce for resource-poor areas. The paucity of bacteriological data and the consequent imperfect epidemiological picture are particularly critical for Sahelian and Sub-Sahara African countries. Here, we report on the characterization of 34 isolates collected between 1976 and 2012 from cattle, sheep and horses in Nigeria. All isolates were identified as Brucella abortus by Bruce-ladder PCR and assigned to biovar 3 by conventional typing. Further analysis by enhanced AMOS-ERY PCR showed that all of them belonged to the 3a sub-biovar, and MLVA analysis grouped them in a cluster clearly distinct from that formed by European B. abortus biovar 3b strains. Nevertheless, MLVA detected heterogeneity within the Nigerian biovar 3a strains. The close genetic profiles of the isolates from cattle, sheep and horses, suggest that, at least in some parts of Nigeria, biovar 3a circulates among animal species that are not the preferential hosts of B. abortus. Consistent with previous genetic analyses of 7 strains from Ivory Cost, Gambia and Togo, the analysis of these 34 Nigerian strains supports the hypothesis that the B. abortus biovar 3a lineage is dominant in West African countries. PMID:26315770

  8. Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage

    PubMed Central

    Biggs, Patrick J.; Fearnhead, Paul; Hotter, Grant; Mohan, Vathsala; Collins-Emerson, Julie; Kwan, Errol; Besser, Thomas E.; Cookson, Adrian; Carter, Philip E.; French, Nigel P.

    2011-01-01

    Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in 1.659 Mb (H22082) and 1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of 2 kb. This includes a 12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates. PMID:22096527

  9. Deep resequencing of Trichinella spiralis reveals previously un-described single nucleotide polymorphisms and intra-isolate variation within the mitochondrial genome.

    PubMed

    Webb, Kristen M; Rosenthal, Benjamin M

    2010-03-01

    The phylogeny and historical dispersal of Trichinella spp. have been studied, in part, by sequencing portions of the mitochondrial genome. Such studies rely on two untested beliefs: that variation in a portion is representative of the entire mitochondrial genome, and that each isolate is characterized by only one mitochondrial haplotype. We have used next generation DNA sequencing technology to obtain the complete mitochondrial genome sequence from a second isolate of T. spiralis. By aligning it to the only previously sequenced genome, we sought to establish whether the exceptionally deep sequencing coverage provided by such an approach could detect regions of the genome which had been misassembled, or nucleotide positions which may vary within an isolate. The new data broadly confirm the gene order and sequence assembly for protein-coding regions. However, in the repetitive non-coding region, alignment to the previously published genome sequence proved difficult. Such discrepancies may represent true biological variation, but may rather result from methodological or algorithmic sources. Within the 13,902bp protein-coding region, 7 polymorphisms were identified. Six of these polymorphisms occurred within protein-coding genes and three alter an amino acid sequence, one occurred in a tRNA-Ile sequence, and four were found to vary within our isolate. Thus, comparing only two isolates of T. spiralis has enabled the discovery of previously unrecognized variation within the species. Characterizing diversity within and among the mitochondrial genomes of additional species of Trichinella would undoubtedly yield further insights into the diversification history of the genus. Our study affirms that next generation DNA sequencing technology can reliably characterize a complete mitochondrial genome. PMID:20083232

  10. Molecular characterization of enterohemorrhagic Escherichia coli hemolysin gene (EHEC-hlyA)-harboring isolates from cattle reveals a diverse origin and hybrid diarrheagenic strains.

    PubMed

    Askari Badouei, Mahdi; Morabito, Stefano; Najafifar, Arash; Mazandarani, Emad

    2016-04-01

    In the present study we investigated the occurrence of Escherichia coli strains harboring the gene encoding enterohemorrhagic E. coli hemolysin (EHEC-HlyA) in cattle and the association of this gene with various diarrheagenic E. coli (DEC) pathotypes. First, the bovine E. coli isolates were screened for EHEC-hlyA gene by PCR, and then they were characterized for the phylogenetic groups and the presence of the major virulence genes of different DEC pathotypes. In total, 25 virulence gene profiles were observed in 54 EHEC-hlyA+ isolates that reflect a considerable heterogeneity. The EHEC-hlyA+ strains were mostly associated with EHEC (72%), while only 7.4% were enteropathogenic E. coli (EPEC). We also showed the presence of estA gene of enterotoxigenic E. coli (ETEC) in 6 isolates (11.1%). Interestingly, two of the estA+ strains showed hybrid pathotypes with one carrying eae/estA (EPEC/ETEC), and the other one stx2/astA/estA (EHEC/ETEC). None of the isolates were related to enteroaggregative E. coli (EAggEC), enteroinvasive E. coli (EIEC), and necrotoxigenic E. coli (NTEC). The EHEC-plasmid encoded genes occurred in seven different combinations with EHEC-hlyA/saa/subA/espP being the most prevalent (46.3%). All stx-/eae+ strains carried O island 57 (OI-57) molecular marker(s) that may indicate these to be the progenitors of EHEC or strains losing stx. The most prevalent phylogroup was B1 (61.1%), but the most heterogeneous strains including the hybrid strains belonged to A phylogroup. Overall, our results indicate that cattle EHEC-hlyA encoding E. coli isolates consist of diverse diarrheagenic strains with the possible existence of hybrid pathotypes. Future studies are required to clarify the evolutionary aspects and clinical significance of these strains in humans and domestic animals. PMID:26855346

  11. Small RNA deep sequencing revealed that mixed infection of known and unknown viruses were common in field collected vegetable samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In an effort to characterize the causal agents for plant diseases in field collected samples using the small RNA deep sequencing technology, numerous known or novel viruses and viroids were identified. In many cases, a mixed infection with multiple pathogen species was common. Such situation compl...

  12. Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates.

    PubMed

    Cooke, Fiona J; Wain, John; Fookes, Maria; Ivens, Alasdair; Thomson, Nicholas; Brown, Dere