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Sample records for field isolate reveals

  1. 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

  2. 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.

  3. In vitro screening of compounds against laboratory and field isolates of human hookworm reveals quantitative differences in anthelmintic susceptibility.

    PubMed

    Treger, Rebecca S; Otchere, Joseph; Keil, Martin F; Quagraine, Josephine E; Rai, Ganesha; Mott, Bryan T; Humphries, Debbie L; Wilson, Michael; Cappello, Michael; Vermeire, Jon J

    2014-01-01

    A panel of 80 compounds was screened for anthelmintic activity against a laboratory strain of Ancylostoma ceylanicum and field isolates of hookworm obtained from school children in the Kintampo North District of the Brong Ahafo Region of Ghana. Although the laboratory strain of A. ceylanicum was more susceptible to the compounds tested than the field isolates of hookworm, a twofold increase in compound concentration resulted in comparable egg hatch percent inhibition for select compounds. These data provide evidence that the efficacy of anthelmintic compounds may be species-dependent and that field and laboratory strains of hookworm differ in their sensitivities to the anthelmintics tested. These data also suggest that both compound concentration and hookworm species must be considered when screening to identify novel anthelmintic compounds.

  4. In vitro Screening of Compounds against Laboratory and Field Isolates of Human Hookworm Reveals Quantitative Differences in Anthelmintic Susceptibility

    PubMed Central

    Treger, Rebecca S.; Otchere, Joseph; Keil, Martin F.; Quagraine, Josephine E.; Rai, Ganesha; Mott, Bryan T.; Humphries, Debbie L.; Wilson, Michael; Cappello, Michael; Vermeire, Jon J.

    2014-01-01

    A panel of 80 compounds was screened for anthelmintic activity against a laboratory strain of Ancylostoma ceylanicum and field isolates of hookworm obtained from school children in the Kintampo North District of the Brong Ahafo Region of Ghana. Although the laboratory strain of A. ceylanicum was more susceptible to the compounds tested than the field isolates of hookworm, a twofold increase in compound concentration resulted in comparable egg hatch percent inhibition for select compounds. These data provide evidence that the efficacy of anthelmintic compounds may be species-dependent and that field and laboratory strains of hookworm differ in their sensitivities to the anthelmintics tested. These data also suggest that both compound concentration and hookworm species must be considered when screening to identify novel anthelmintic compounds. PMID:24297811

  5. Reproductive isolation revealed in preliminary crossbreeding experiments using field collected Triatoma dimidiata (Hemiptera: Reduviidae) from three ITS–2 defined groups

    PubMed Central

    García, Mauricio; Menes, Marianela; Dorn, Patricia L.; Monroy, Carlota; Richards, Bethany; Panzera, Francisco; Bustamante, Dulce María

    2013-01-01

    Triatoma dimidiata, a Chagas disease vector distributed in Mexico, Central America, Colombia, Venezuela, Peru and Ecuador, has been studied using genetic markers and four groups have been defined by ITS–2 sequences: 1A, 1B, 2 and 3. To gather evidence on the divergence and reproductive isolation among T. dimidiata ITS–2 groups, we carried out 15 crossbreeding experiments with field–collected sylvan and domestic T. dimidiata from Guatemala where three groups are found: 1A, 2 and 3. Reciprocal crosses between individuals from groups 1A and 2, and a cross between group 2 individuals from different habitats, produced an average 129.78±42.29 eggs with hatching success ranging from 31.6% to 90.1%. The offspring of these crosses reached the adult stage, and crosses between F1 insects produced eggs. These results suggest that there are no pre– or post– zygotic reproductive barriers between groups 1A and 2, or within group 2. Crosses between group 3 females and males from groups 1A or 2 produced on average 85.67±30.26 eggs and none of them hatched. These results support the existence of pre– zygotic barriers between T. dimidiata group 3 and groups 1A and 2. The group 3 individuals were collected in sylvatic environments in Yaxha, Peten, Guatemala. Previously, distinct chromosomal characteristics (cytotype 3) were described in individuals from this population. Based on this evidence we suggest that this population is divergent at the species level from other T. dimidiata populations. PMID:24041592

  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. Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis.

    PubMed

    Noller, Anna C; McEllistrem, M Catherine; Stine, O Colin; Morris, J Glenn; Boxrud, David J; Dixon, Bruce; Harrison, Lee H

    2003-02-01

    Escherichia coli O157:H7 is a major cause of foodborne illness in the United States. Pulsed-field gel electrophoresis (PFGE) is the molecular epidemiologic method mostly commonly used to identify food-borne outbreaks. Although PFGE is a powerful epidemiologic tool, it has disadvantages that make a DNA sequence-based approach potentially attractive. Multilocus sequence typing (MLST) analyzes the internal fragments of housekeeping genes to establish genetic relatedness between isolates. We sequenced selected portions of seven housekeeping genes and two membrane protein genes (ompA and espA) of 77 isolates that were diverse by PFGE to determine whether there was sufficient sequence variation to be useful as an epidemiologic tool. There was no DNA sequence diversity in the sequenced portions of the seven housekeeping genes and espA. For ompA, all but five isolates had sequence identical to that of the reference strains. E. coli O157:H7 has a striking lack of genetic diversity in the genes we explored, even among isolates that are clearly distinct by PFGE. Other approaches to identify improved molecular subtyping methods for E. coli 0157:H7 are needed.

  8. Analysis of the pan genome of Campylobacter jejuni isolates recovered from poultry by pulsed-field gel electrophoresis, multilocus sequence typing (MLST), and repetitive sequence polymerase chain reaction (rep-PCR) reveals different discriminatory capabilities.

    PubMed

    Wilson, Melissa K; Lane, Alison B; Law, Bibiana F; Miller, William G; Joens, Lynn A; Konkel, Michael E; White, Bryan A

    2009-11-01

    Campylobacter jejuni is one of the leading bacterial causes of food-borne illness in the USA. Molecular typing methods are often used in food safety for identifying sources of infection and pathways of transmission. Moreover, the identification of genetically related isolates (i.e., clades) may facilitate the development of intervention strategies for control and prevention of food-borne diseases. We analyzed the pan genome (i.e., core and variable genes) of 63 C. jejuni isolates recovered from chickens raised in conventional, organic, and free-range poultry flocks to gain insight into the genetic diversity of C. jejuni isolates recovered from different environments. We assessed the discriminatory power of three genotyping methods [i.e., pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and repetitive extragenic palindromic polymerase chain reaction (rep-PCR)]. The rep-PCR fingerprint was generated by determining the presence of repetitive sequences that are interspersed throughout the genome via repetitive extragenic palindromic PCR, enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and BOX element PCR (BOX-PCR) and combining the data to form a composite fingerprint. The genetic fingerprints were subjected to computer-assisted pattern analysis. Comparison of the three genotypic methods revealed that repREB-PCR showed greater discriminatory power than PFGE and MLST. ERIC-PCR and BOX-PCR yielded the highest number of PCR products and greatest reproducibility. Regardless of the genotyping method, C. jejuni isolates recovered from chickens reared in conventional, organic, and free-range environments all exhibit a high level of genotypic diversity.

  9. 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.

  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. 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.

  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.

  13. Improved CMOS field isolation using Germaniun/Boron implantation

    SciTech Connect

    Pfiester, J.R.; Alvis, J.R. )

    1988-08-01

    A novel germanium/boron implantation technique for improving the electrical field isolation for high-density CMOS circuits is demonstrated. Germanium implantation causes a reduction in dopant diffusion and segregation during field oxidation and is shown to increase the p-well field threshold voltage by as much as 40 percent with no significant degradation to junction or device performance. Selective germanium implantation with a blanket boron field implant can also improve the electrical field isolation behavior for CMOS circuits.

  14. Competitive Fitness of Phytophthora infestans Isolates Under Semiarid Field Conditions.

    PubMed

    Miller, J S; Johnson, D A

    2000-03-01

    ABSTRACT Spread of US-1 and US-8 isolates of Phytophthora infestans were observed in field plots of potato (cv. Russet Burbank) grown in Pullman, WA, in 1996 and 1997. Infected greenhouse-grown potato plants with similar lesion numbers for both strains were transplanted to field plots with four replications. Spread of the pathogen was favored by sprinkler irrigation during evening hours. Diseased leaves and stems were sampled over time to determine the spread of US-1 and US-8 isolates. In 1996, late blight developed in two of the four replications (105 and 87 total isolates recovered). From those two replications, two US-1 isolates were recovered, both from the same replication. Nine isolates from one replication and six isolates from another displayed a phenotype different from the initial isolates, as determined by compatibility type, allozyme genotype, and restriction fragment length polymorphism genotype. These putative recombinant isolates may have arisen from sexual recombination between the US-1 and US-8 isolates. The remaining isolates were of the US-8 strain. In 1997, late blight developed in all four replications (123, 122, 81, and 34 total isolates recovered). One US-1 isolate was recovered (out of 123) from one replication and three (out of 122) from another, and the remaining isolates were of the US-8 strain. Isolates with phenotypes differing from the initial isolates were not recovered in 1997. In both years, oospores were not observed in the plant tissue examined. The low number of putative recombinant isolates in 1996 and their absence in 1997 suggests that sexual reproduction between US-8 and US-1 isolates in a field setting is a rare event. The predominance of US-8 isolates recovered is a measure of the increased fitness and aggressiveness of the US-8 isolates relative to the US-1 isolate used in this study. This further substantiates the increased aggressiveness of the US-8 genotype observed on excised tissues and potted plants in previous

  15. Isolation, cloning, and pathologic analysis of Trypanosoma evansi field isolates.

    PubMed

    Mekata, Hirohisa; Konnai, Satoru; Mingala, Claro N; Abes, Nancy S; Gutierrez, Charito A; Dargantes, Alan P; Witola, William H; Inoue, Noboru; Onuma, Misao; Murata, Shiro; Ohashi, Kazuhiko

    2013-04-01

    In recent years, the emergence of highly pathogenic Trypanosoma evansi strains in the Philippines has resulted in substantial losses in livestock production. In this study, we isolated T. evansi from infected-water buffaloes in the Philippines and analyzed their virulence using mice and cattle. A total of 10 strains of T. evansi were isolated. Evaluation of the virulence of each strain using mice depicted significant differences among the strains in the prepatent period, the level of parasitemia, and the survival time of the infected animals. In mice infected with the highly pathogenic T. evansi, signs of excessive inflammation such as marked splenomegaly and increase more than 6-fold in the number of leukocytes were observed at 8 days post-infection. To study the virulence of the parasite strains in cattle (which are the common T. evansi hosts in Philippines), cattle were infected with the T. evansi isolates that showed high and low virulence in mice. The rate of parasite growth and the length of the prepatent periods were found to be similar to those observed in mice for the respective strains. The cattle infected with the highly pathogenic strain developed anemia and a marked decrease in leukocyte counts. To determine the cause of the pathological changes, we analyzed the expression levels of inflammatory cytokines and observed up-regulation of tumor necrosis factor-α in anemic infected cattle. Our findings suggest that the epidemic of T. evansi in the Philippines is characterized by T. evansi strains with varying virulences from low to very high pathogenicity in cattle.

  16. Isolated Attosecond Pulses using a Detuned Second-harmonic Field

    SciTech Connect

    Merdji, Hamed; Auguste, Thierry; Boutu, Willem; Caumes, J.-Pascal; Carre, Bertrand; Pfeifer, Thomas; Jullien, Aurelie; Neumark, Daniel M.; Leone, Stephen R.; /UC, Berkeley /LBL, Berkeley

    2007-11-07

    Calculations are presented for the generation of an isolated attosecond pulse in a multicycle two-color strong-field regime. We show that the recollision of the electron wave packet can be confined to half an optical cycle using pulses of up to 40 fs in duration. The scheme is proven to be efficient using two intense beams, one producing a strong field at {omega} and the other a strong field detuned from 2{omega}. The slight detuning {delta}{omega} of the second harmonic is used to break the symmetry of the electric field over many optical cycles and provides a coherent control for the formation of an isolated attosecond pulse.

  17. Internetwork magnetic field as revealed by two-dimensional inversions

    NASA Astrophysics Data System (ADS)

    Danilovic, S.; van Noort, M.; Rempel, M.

    2016-09-01

    Context. Properties of magnetic field in the internetwork regions are still fairly unknown because of rather weak spectropolarimetric signals. Aims: We address the matter by using the two-dimensional (2D) inversion code, which is able to retrieve the information on smallest spatial scales up to the diffraction limit, while being less susceptible to noise than most of the previous methods used. Methods: Performance of the code and the impact of various effects on the retrieved field distribution is tested first on the realistic magneto-hydrodynamic (MHD) simulations. The best inversion scenario is then applied to the real data obtained by Spectropolarimeter (SP) on board Hinode. Results: Tests on simulations show that: (1) the best choice of node position ensures a decent retrieval of all parameters; (2) the code performs well for different configurations of magnetic field; (3) slightly different noise levels or slightly different defocus included in the spatial point spread function (PSF) produces no significant effect on the results; and (4) temporal integration shifts the field distribution to a stronger, more horizontally inclined field. Conclusions: Although the contribution of the weak field is slightly overestimated owing to noise, 2D inversions are able to recover well the overall distribution of the magnetic field strength. Application of the 2D inversion code on the Hinode SP internetwork observations reveals a monotonic field strength distribution. The mean field strength at optical depth unity is ~ 130 G. At higher layers, field strength drops as the field becomes more horizontal. Regarding the distribution of the field inclination, tests show that we cannot directly retrieve it with the observations and tools at hand, however, the obtained distributions are consistent with those expected from simulations with a quasi-isotropic field inclination after accounting for observational effects.

  18. The genomic RNA1 and RNA2 sequences of the tobacco rattle virus isolates found in Polish potato fields.

    PubMed

    Yin, Zhimin; Pawełkowicz, Magdalena; Michalak, Krystyna; Chrzanowska, Mirosława; Zimnoch-Guzowska, Ewa

    2014-06-24

    Four tobacco rattle virus (TRV) isolates were identified from tobacco bait seedlings planted in soil samples from Polish potato fields. Sequence analysis of the genomic RNA1 of the isolates revealed significant similarity to the isolates Ho and AL recently found in Germany. Multiple sequence alignments of the genomic RNA2 indicated that the two isolates from northern Poland (Deb57 and Slu24) are in a cluster with the isolates PSG and PLB found in the Netherlands. The remaining two isolates, from central Poland (11r21 and Mlo7), are in a distinct group with the unique isolate SYM found in England. The RNA2 sequences of the studied isolates range from 1998 nt to 2739 nt in length, and all carry deletions of the 2b and/or 2c genes. The isolate Mlo7 has an atypical RNA2 structure, having its cp gene located in its central region. PMID:24637409

  19. Virulence of South African isolates of Haemophilus paragallinarum. Part 1: NAD-dependent field isolates.

    PubMed

    Bragg, R R

    2002-06-01

    The virulence of four South African field isolates of NAD-dependent Haemophilus paragallinarum, representing the four serovars known to occur in that country, was investigated. During this study an alternative challenge model for infectious coryza was used, in which the infectivity as well the virulence of different isolates could be evaluated. The challenge model consisted of the direct challenge, via intrasinus injection of one chicken in a row of interconnected layer cages, containing 10 chickens, which are subsequently infected by natural routes. A scoring system of the clinical signs was established in which a score is given to the ability of the isolate to produce clinical signs in the challenge birds. The mean daily disease score for the flock can be calculated and plotted on a graph to give a graphic representation of the disease profile. A mean disease score, calculated over a 20-day examination period can be calculated. Isolates can then be compared to each other, either graphically or by a comparison of the mean disease scores. It has been demonstrated using this scoring system that the South African serogroup C isolates appear to be more virulent than the South African serogroup A or B isolates. It was further established that the serovar C-3 isolate appeared to be the most virulent.

  20. 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

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

    PubMed

    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.

  2. 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.

  3. 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

  4. 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

  5. Analysis of Salmonella typhi isolates from Southeast Asia by pulsed-field gel electrophoresis.

    PubMed Central

    Thong, K L; Puthucheary, S; Yassin, R M; Sudarmono, P; Padmidewi, M; Soewandojo, E; Handojo, I; Sarasombath, S; Pang, T

    1995-01-01

    Pulsed-field gel electrophoresis (PFGE) revealed that multiple genetic variants of Salmonella typhi are simultaneously present in Southeast Asia and are associated with sporadic cases of typhoid fever and occasional outbreaks. Comparative analysis of PFGE patterns also suggested that considerable genetic diversity exists among S. typhi strains and that some PFGE patterns are shared between isolates obtained from Malaysia, Indonesia, and Thailand, implying movement of these strains within these regions of Southeast Asia, where they are endemic. PMID:7665677

  6. Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates

    PubMed Central

    Moore, Sandra; Miwanda, Berthe; Sadji, Adodo Yao; Thefenne, Hélène; Jeddi, Fakhri; Rebaudet, Stanislas; de Boeck, Hilde; Bidjada, Bawimodom; Depina, Jean-Jacques; Bompangue, Didier; Abedi, Aaron Aruna; Koivogui, Lamine; Keita, Sakoba; Garnotel, Eric; Plisnier, Pierre-Denis; Ruimy, Raymond; Thomson, Nicholas; Muyembe, Jean-Jacques; Piarroux, Renaud

    2015-01-01

    Background Since cholera appeared in Africa during the 1970s, cases have been reported on the continent every year. In Sub-Saharan Africa, cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa. Methodology/Principal Findings In this study, we applied MLVA (Multi-Locus Variable Number Tandem Repeat Analysis) typing of 337 Vibrio cholerae isolates from recent cholera epidemics in the Democratic Republic of the Congo (DRC), Zambia, Guinea and Togo. We aimed to assess the relationship between outbreaks. Applying this method, we identified 89 unique MLVA haplotypes across our isolate collection. MLVA typing revealed the short-term divergence and microevolution of these Vibrio cholerae populations to provide insight into the dynamics of cholera outbreaks in each country. Our analyses also revealed strong geographical clustering. Isolates from the African Great Lakes Region (DRC and Zambia) formed a closely related group, while West African isolates (Togo and Guinea) constituted a separate cluster. At a country-level scale our analyses revealed several distinct MLVA groups, most notably DRC 2011/2012, DRC 2009, Zambia 2012 and Guinea 2012. We also found that certain MLVA types collected in the DRC persisted in the country for several years, occasionally giving rise to expansive epidemics. Finally, we found that the six environmental isolates in our panel were unrelated to the epidemic isolates. Conclusions/Significance To effectively combat the disease, it is critical to understand the mechanisms of cholera emergence and diffusion in a region-specific manner. Overall, these findings demonstrate the relationship between distinct epidemics in West Africa and the African Great Lakes Region. This study also highlights the importance of monitoring and analyzing Vibrio cholerae isolates. PMID:26110870

  7. Genotypes and Pathogenicity of Cellulitis Isolates Reveal Traits That Modulate APEC Virulence

    PubMed Central

    Barbieri, Nicolle Lima; de Oliveira, Aline Luísa; Tejkowski, Thiago Moreira; Pavanelo, Daniel Brisotto; Rocha, Débora Assumpção; Matter, Letícia Beatriz; Callegari-Jacques, Sidia Maria; de Brito, Benito Guimarães; Horn, Fabiana

    2013-01-01

    We characterized 144 Escherichia coli isolates from severe cellulitis lesions in broiler chickens from South Brazil. Analysis of susceptibility to 15 antimicrobials revealed frequencies of resistance of less than 30% for most antimicrobials except tetracycline (70%) and sulphonamides (60%). The genotyping of 34 virulence-associated genes revealed that all the isolates harbored virulence factors related to adhesion, iron acquisition and serum resistance, which are characteristic of the avian pathogenic E. coli (APEC) pathotype. ColV plasmid-associated genes (cvi/cva, iroN, iss, iucD, sitD, traT, tsh) were especially frequent among the isolates (from 66.6% to 89.6%). According to the Clermont method of ECOR phylogenetic typing, isolates belonged to group D (47.2%), to group A (27.8%), to group B2 (17.4%) and to group B1 (7.6%); the group B2 isolates contained the highest number of virulence-associated genes. Clonal relationship analysis using the ARDRA method revealed a similarity level of 57% or higher among isolates, but no endemic clone. The virulence of the isolates was confirmed in vivo in one-day-old chicks. Most isolates (72.9%) killed all infected chicks within 7 days, and 65 isolates (38.1%) killed most of them within 24 hours. In order to analyze differences in virulence among the APEC isolates, we created a pathogenicity score by combining the times of death with the clinical symptoms noted. By looking for significant associations between the presence of virulence-associated genes and the pathogenicity score, we found that the presence of genes for invasins ibeA and gimB and for group II capsule KpsMTII increased virulence, while the presence of pic decreased virulence. The fact that ibeA, gimB and KpsMTII are characteristic of neonatal meningitis E. coli (NMEC) suggests that genes of NMEC in APEC increase virulence of strains. PMID:23977279

  8. 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

  9. Comparative Transcriptional and Genomic Analysis of Plasmodium falciparum Field Isolates

    PubMed Central

    Mackinnon, Margaret J.; Li, Jinguang; Mok, Sachel; Kortok, Moses M.; Marsh, Kevin; Preiser, Peter R.; Bozdech, Zbynek

    2009-01-01

    Mechanisms for differential regulation of gene expression may underlie much of the phenotypic variation and adaptability of malaria parasites. Here we describe transcriptional variation among culture-adapted field isolates of Plasmodium falciparum, the species responsible for most malarial disease. It was found that genes coding for parasite protein export into the red cell cytosol and onto its surface, and genes coding for sexual stage proteins involved in parasite transmission are up-regulated in field isolates compared with long-term laboratory isolates. Much of this variability was associated with the loss of small or large chromosomal segments, or other forms of gene copy number variation that are prevalent in the P. falciparum genome (copy number variants, CNVs). Expression levels of genes inside these segments were correlated to that of genes outside and adjacent to the segment boundaries, and this association declined with distance from the CNV boundary. This observation could not be explained by copy number variation in these adjacent genes. This suggests a local-acting regulatory role for CNVs in transcription of neighboring genes and helps explain the chromosomal clustering that we observed here. Transcriptional co-regulation of physical clusters of adaptive genes may provide a way for the parasite to readily adapt to its highly heterogeneous and strongly selective environment. PMID:19898609

  10. Simulations of magnetic fields in isolated disc galaxies

    NASA Astrophysics Data System (ADS)

    Pakmor, Rüdiger; Springel, Volker

    2013-06-01

    Magnetic fields are known to be dynamically important in the interstellar medium of our own Galaxy, and they are ubiquitously observed in diffuse gas in the haloes of galaxies and galaxy clusters. Yet, magnetic fields have typically been neglected in studies of the formation of galaxies, leaving their global influence on galaxy formation largely unclear. Here we extend our magnetohydrodynamics (MHD) implementation in the moving-mesh code AREPO to cosmological problems which include radiative cooling and the formation of stars. In particular, we replace our previously employed divergence cleaning approach with a Powell eight-wave scheme, which turns out to be significantly more stable, even in very dynamic environments. We verify the improved accuracy through simulations of the magneto-rotational instability in accretion discs, which reproduce the correct linear growth rate of the instability. Using this new MHD code, we simulate the formation of isolated disc galaxies similar to the Milky Way using idealized initial conditions with and without magnetic fields. We find that the magnetic field strength is quickly amplified in the initial central starburst and the differential rotation of the forming disc, eventually reaching a saturation value. At this point, the magnetic field pressure in the interstellar medium becomes comparable to the thermal pressure, and a further efficient growth of the magnetic field strength is prevented. The additional pressure component leads to a lower star formation rate at late times compared to simulations without magnetic fields, and induces changes in the spiral arm structures of the gas disc. In addition, we observe highly magnetized fountain-like outflows from the disc. These results are robust with numerical resolution and are largely independent of the initial magnetic seed field strength assumed in the initial conditions, as the amplification process is rapid and self-regulated. Our findings suggest an important influence of

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

    PubMed Central

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

    2015-01-01

    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

  12. 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.

  13. 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

  14. Genomic Analysis Reveals Novel Diversity among the 1976 Philadelphia Legionnaires’ Disease Outbreak Isolates and Additional ST36 Strains

    PubMed Central

    Mercante, Jeffrey W.; Morrison, Shatavia S.; Desai, Heta P.; Raphael, Brian H.; Winchell, Jonas M.

    2016-01-01

    Legionella pneumophila was first recognized as a cause of severe and potentially fatal pneumonia during a large-scale outbreak of Legionnaires’ disease (LD) at a Pennsylvania veterans’ convention in Philadelphia, 1976. The ensuing investigation and recovery of four clinical isolates launched the fields of Legionella epidemiology and scientific research. Only one of the original isolates, “Philadelphia-1”, has been widely distributed or extensively studied. Here we describe the whole-genome sequencing (WGS), complete assembly, and comparative analysis of all Philadelphia LD strains recovered from that investigation, along with L. pneumophila isolates sharing the Philadelphia sequence type (ST36). Analyses revealed that the 1976 outbreak was due to multiple serogroup 1 strains within the same genetic lineage, differentiated by an actively mobilized, self-replicating episome that is shared with L. pneumophila str. Paris, and two large, horizontally-transferred genomic loci, among other polymorphisms. We also found a completely unassociated ST36 strain that displayed remarkable genetic similarity to the historical Philadelphia isolates. This similar strain implies the presence of a potential clonal population, and suggests important implications may exist for considering epidemiological context when interpreting phylogenetic relationships among outbreak-associated isolates. Additional extensive archival research identified the Philadelphia isolate associated with a non-Legionnaire case of “Broad Street pneumonia”, and provided new historical and genetic insights into the 1976 epidemic. This retrospective analysis has underscored the utility of fully-assembled WGS data for Legionella outbreak investigations, highlighting the increased resolution that comes from long-read sequencing and a sequence type-matched genomic data set. PMID:27684472

  15. Life-Threatening Hypercalcemia Revealing Diffuse and Isolated Acute Sarcoid-Like Myositis

    PubMed Central

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

    2016-01-01

    Abstract 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

  16. Spore-forming thermophilic sulfate-reducing bacteria isolated from North Sea oil field waters

    SciTech Connect

    Rosnes, J.T.; Torsvik, T.; Lien, T. )

    1991-08-01

    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 (C{sub 4} through C{sub 6}) was added as a carbon source and electron donor. Representative strains were isolated and characterized. The isolates grew autotrophically on H{sub 2}-CO{sub 2} 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 78C; the spores were extremely heat resistant and survived 131C 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.

  17. Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field.

    PubMed

    Kim, Yi-Seul; Kim, Soo-Jin; Anandham, Rangasamy; Weon, Hang-Yeon; Kwon, Soon-Wo

    2013-04-01

    A bacterial isolate designated GR24-2(T) was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28-30°C, pH 7.0, and in a range of 0-1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47(T) (98.4%), R. soli DCY45(T) (98.2%), and R. ginsengisoli GR17-7(T) (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C17:1 ω9c (24.5%), iso-C16:0 (22.8%), anteiso-C15:0 (10.5%), and iso-C15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2(T) was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA-DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2(T) =KACC 12917(T) =DSM 21300(T)).

  18. Genetic analysis of paramyxovirus isolates from pacific salmon reveals two independently co-circulating lineages

    USGS Publications Warehouse

    Batts, W.N.; Falk, K.; Winton, J.R.

    2008-01-01

    Viruses with the morphological and biochemical characteristics of the family Paramyxoviridae (paramyxoviruses) have been isolated from adult salmon returning to rivers along the Pacific coast of North America since 1982. These Pacific salmon paramyxoviruses (PSPV), which have mainly been isolated from Chinook salmon Oncorhynchus tshawytscha, grow slowly in established fish cell lines and have not been associated with disease. Genetic analysis of a 505-base-pair region of the polymerase gene from 47 PsPV isolates produced 17 nucleotide sequence types that could be grouped into two major sublineages, designated A and B. The two independently co-circulating sublineages differed by 12.1-13.9% at the nucleotide level but by only 1.2% at the amino acid level. Isolates of PSPV from adult Pacific salmon returning to rivers from Alaska to California over a 25-year period showed little evidence of geographic or temporal grouping. Phylogenetic analyses revealed that these paramyxoviruses of Pacific salmon were most closely related to the Atlantic salmon paramyxovirus (ASPV) from Norway, having a maximum nucleotide diversity of 26.1 % and an amino acid diversity of 19.0%. When compared with homologous sequences of other paramyxoviruses, PSPV and ASPV were sufficiently distinct to suggest that they are not clearly members of any of the established genera in the family Paramyxoviridae. in the course of this study, a polymerase chain reaction assay was developed that can be used for confirmatory identification of PSPV. ?? Copyright by the American Fisheries Society 2008.

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

    PubMed Central

    2012-01-01

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

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

    PubMed

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

    2015-03-01

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

  1. Non-nucleolar transcription complexes of rat liver as revealed by spreading isolated nuclei.

    PubMed

    Harper, F; Puvion-Dutilleul, F

    1979-12-01

    Miller's technique was applied to isolated nuclei of rat liver. Both the usual nucleolar and non-nucleolar transcription complexes were visualized. In addition, an unusual type of putative non-ribosomal transcription unit was revealed. It was charcaterized by a high density of the lateral ribonucleoprotein (RNP) fibrils. Although these particular units exhibited a regular increase of fibril lengths, the length of the transcript-covered deoxyribonucleoprotein (DNP) fibres and the morphological aspect of the RNP fibrils distinguished them from the nucleolar 'Christmas-tree'-like figures. The linear and granular configuration of the transcripts and the absence of terminal knobs made them similar to non-nucleolar nascent RNP fibrils.

  2. 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

  3. 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 ...

  4. Multilocus sequence analysis reveals high genetic diversity in clinical isolates of Burkholderia cepacia complex from India

    PubMed Central

    Gautam, Vikas; Patil, Prashant P.; Kumar, Sunil; Midha, Samriti; Kaur, Mandeep; Kaur, Satinder; Singh, Meenu; Mali, Swapna; Shastri, Jayanthi; Arora, Anita; Ray, Pallab; Patil, Prabhu B.

    2016-01-01

    Burkholderia cepacia complex (Bcc) is a complex group of bacteria causing opportunistic infections in immunocompromised and cystic fibrosis (CF) patients. Herein, we report multilocus sequence typing and analysis of the 57 clinical isolates of Bcc collected over the period of seven years (2005–2012) from several hospitals across India. A total of 21 sequence types (ST) including two STs from cystic fibrosis patient’s isolates and twelve novel STs were identified in the population reflecting the extent of genetic diversity. Multilocus sequence analysis revealed two lineages in population, a major lineage belonging to B. cenocepacia and a minor lineage belonging to B. cepacia. Split-decomposition analysis suggests absence of interspecies recombination and intraspecies recombination contributed in generating genotypic diversity amongst isolates. Further linkage disequilibrium analysis indicates that recombination takes place at a low frequency, which is not sufficient to break down the clonal relationship. This knowledge of the genetic structure of Bcc population from a rapidly developing country will be invaluable in the epidemiology, surveillance and understanding global diversity of this group of a pathogen. PMID:27767197

  5. Global molecular phylogeography reveals persistent Arctic circumpolar isolation in a marine planktonic protist.

    PubMed

    Darling, Kate F; Kucera, Michal; Wade, Christopher M

    2007-03-20

    The high-latitude planktonic foraminifera have proved to be particularly useful model organisms for the study of global patterns of vicariance and gene flow in the oceans. Such studies demonstrate that gene flow can occur over enormous distances in the pelagic marine environment leading to cosmopolitanism but also that there are ecological and geographical barriers to gene flow producing biogeographic structure. Here, we have undertaken a comprehensive global study of genetic diversity within a marine protist species, the high-latitude planktonic foraminiferan Neogloboquadrina pachyderma. We present extensive new data sets from the North Pacific and Arctic Oceans that, in combination with our earlier data from the North Atlantic and Southern Oceans, allow us to determine the global phylogeography of this species. The new genetic data reveal a pattern of Arctic circumpolar isolation and bipolar asymmetry between the Atlantic and Pacific Oceans. We show that the ancestry of North Pacific N. pachyderma is relatively recent. It lies within the upwelling systems and subpolar waters of the Southern Hemisphere and remarkably not within the neighboring Arctic Ocean. Instead, the Arctic Ocean population forms a genetic continuum with the North Atlantic population, which became isolated from the southern populations much earlier, after the onset of Northern hemisphere glaciation. Data from the planktonic foraminiferal morphospecies Globigerina bulloides is also introduced to highlight the isolation and endemism found within the subpolar North Pacific gyre. These data provide perspective for interpretation and discussion of global gene flow and speciation patterns in the plankton.

  6. 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...

  7. Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains.

    PubMed

    Davidson, Rebecca M; Hasan, Nabeeh A; de Moura, Vinicius Calado Nogueira; Duarte, Rafael Silva; Jackson, Mary; Strong, Michael

    2013-12-01

    Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M. abscessus subsp. bolletii (MAB-B). The recently reported outbreaks of MAB-B in surgical patients in Brazil from 2004 to 2009 and in cystic fibrosis patients in the United Kingdom (UK) in 2006 to 2012 underscore the need to investigate the genetic diversity of clinical MAB strains. To this end, we sequenced the genomes of two Brazilian MAB-B epidemic isolates (CRM-0019 and CRM-0020) derived from an outbreak of skin infections in Rio de Janeiro, two unrelated MAB strains from patients with pulmonary infections in the United States (US) (NJH8 and NJH11) and one type MAB-B strain (CCUG 48898) and compared them to 25 publically available genomes of globally diverse MAB strains. Genome-wide analyses of 27,598 core genome single nucleotide polymorphisms (SNPs) revealed that the two Brazilian derived CRM strains are nearly indistinguishable from one another and are more closely related to UK outbreak isolates infecting CF patients than to strains from the US, Malaysia or France. Comparative genomic analyses of six closely related outbreak strains revealed geographic-specific large-scale insertion/deletion variation that corresponds to bacteriophage insertions and recombination hotspots. Our study integrates new genome sequence data with existing genomic information to explore the global diversity of infectious M. abscessus isolates and to compare clinically relevant outbreak strains from different continents. PMID:24055961

  8. 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

  9. Near-membrane protein dynamics revealed by evanescent field microscopy

    NASA Astrophysics Data System (ADS)

    Bezzerides, Vassilios J.; Clapham, David E.

    2004-05-01

    Evanescent Field (EF) microscopy is used to investigate the spatial and temporal dynamics of proteins in living cells. A genetically engineered ion channel fused to a fluorescent tag is expressed in cells and imaged with an objective-based EF microscope. Images are obtained from a CCD and analyzed to determine fluorescence and velocity of individual protein containing vesicles. An inverse correlation between fluorescent intensity and average motility provides a method for determination of membrane localization. Stimulation and subsequent decrease in ion channel activity is correlated with loss of protein from membrane as shown by EF microscopy and patch-clamp electrophysiology.

  10. Pulsed-field gel electrophoresis typing of Listeria monocytogenes isolated in two Finnish fish farms.

    PubMed

    Katzav, Marianne; Hyvönen, Paula; Muje, Petri; Rantala, Leila; Von Wright, Atte

    2006-06-01

    The aim of this study was to find sources of Listeria monocytogenes contamination in fish products from a fish farm. The occurrence of L. monocytogenes also was compared in two freshwater fish farms with different types of fishponds. Samples collected from chilled rainbow trout (Oncorhynchus mykiss) and the slaughterhouse environment did not contain L. monocytogenes, but Listeria innocua was found in two samples from the slaughterhouses. Ten isolates of L. monocytogenes were discovered in sediment and water samples from farming tanks and earth ponds. Further characterization by serovar revealed the same serovar (1/2a) for all the isolates. Pulsed-field gel electrophoresis was used to divide the isolates into five different pulsotypes, three of which have been identified previously in fish products on the retail market. This finding supports the assumption that the primary production, and probably the raw fish, is a source of Listeria contamination in fish products. Some of the isolates were associated with a certain type of fishpond, indicating the need for hygienic analysis of the suitability of different types of farming ponds. PMID:16786871

  11. Field isolates of Mycoplasma ovipneumoniae exhibit distinct cytopathic effects in ovine tracheal organ cultures.

    PubMed

    Niang, M; Rosenbusch, R F; DeBey, M C; Niyo, Y; Andrews, J J; Kaeberle, M L

    1998-02-01

    Ovine tracheal ring explants were infected with four different Mycoplasma ovipneumoniae and one M. arginini field isolate and their ability to induce cytopathic effects was tested by measuring ciliary activity and intracellular calmodulin release. Infected tracheal rings showed significantly decreased ciliary activity as compared to the non-infected control rings. There were, however, marked differences between isolates in the onset and severity of the effects which correlated with their ability to produce hydrogen peroxide. Infected tracheal rings released more calmodulin than the non-infected controls. The amount of calmodulin released also varied between isolates, and somewhat reflected the degree of loss of ciliary activity in the corresponding rings induced by the different isolates. Light and electron microscopic examinations of infected tracheal rings revealed disorganisation and sloughing of the epithelium, and association of mycoplasmas only with the cilia. Following repeated in vitro passages, the organisms had reduced ability to inhibit ciliary activity which correlated with decreased hydrogen peroxide production. Addition of catalase to the organ cultures delayed loss of ciliary activity. These results suggest that M. ovipneumoniae induced ciliostasis in ovine tracheal ring explants which correlated with hydrogen peroxide production. Furthermore, these M. ovipneumoniae-induced injuries to respiratory epithelial cells could contribute to the role that this organism may play in sheep respiratory disease.

  12. 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...

  13. [Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field].

    PubMed

    Lurá, M C; Di Conza, J A; González, A M; Latorre Rapela, M G; Turino, L; Ibáñez, M M; Iacona, V

    2007-01-01

    Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field. Current knowledge about epidemiology and population structure of Cercospora kikuchii is little developed and no studies regarding this subject have been reported in Argentina. The aim of this work was to select primers to study genetic variability in C. kikuchii isolated from the same soybean field using RAPD (Random Amplified Polymorphism DNA). RAPD was applied to the DNA of 5 C. kikuchii, isolated from diseased tissue of the soybean in the same field, another isolate, from a strain collection. Out of seven primers, five of them proved to be useful to study the population of C. kikuchii isolates.

  14. Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes.

    PubMed

    Chen, Yuansha; Mukherjee, Sampa; Hoffmann, Maria; Kotewicz, Michael L; Young, Shenia; Abbott, Jason; Luo, Yan; Davidson, Maureen K; Allard, Marc; McDermott, Patrick; Zhao, Shaohua

    2013-11-01

    Aminoglycoside resistance in Campylobacter has been routinely monitored in the United States in clinical isolates since 1996 and in retail meats since 2002. Gentamicin resistance first appeared in a single human isolate of Campylobacter coli in 2000 and in a single chicken meat isolate in 2007, after which it increased rapidly to account for 11.3% of human isolates and 12.5% of retail isolates in 2010. Pulsed-field gel electrophoresis analysis indicated that gentamicin-resistant C. coli isolates from retail meat were clonal. We sequenced the genomes of two strains of this clone using a next-generation sequencing technique in order to investigate the genetic basis for the resistance. The gaps of one strain were closed using optical mapping and Sanger sequencing, and this is the first completed genome of C. coli. The two genomes are highly similar to each other. A self-transmissible plasmid carrying multiple antibiotic resistance genes was revealed within both genomes, carrying genes encoding resistance to gentamicin, kanamycin, streptomycin, streptothricin, and tetracycline. Bioinformatics analysis and experimental results showed that gentamicin resistance was due to a phosphotransferase gene, aph(2")-Ig, not described previously. The phylogenetic relationship of this newly emerged clone to other Campylobacter spp. was determined by whole-genome single nucleotide polymorphisms (SNPs), which showed that it clustered with the other poultry isolates and was separated from isolates from livestock.

  15. Genome Sequence of Mycobacterium avium subspecies paratuberculosis Sheep Isolate 397 Reveals Striking Differences Among a Genetically Homogeneous Subspecies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of Mycobacterium avium subspecies paratuberculosis is remarkably homogeneous among the bovine, human and wildlife isolates. However previous work in our labs using genomic DNA hybridizations with the bovine K-10 DNA microarray has revealed substantial differences in sheep isolates. A dr...

  16. Salmonella enterica serotypes isolated from squabs reveal multidrug resistance and a distinct pathogenicity gene repertoire.

    PubMed

    Osman, K M; Marouf, S H; Mehana, O A; AlAtfeehy, N

    2014-12-01

    The consumption of squab (young unfledged pigeons) as part of the cuisine of many countries, together with the observation that squabs are vectors of zoonotic agents, may make them a public health risk. This study was designed to determine the serotypes, distribution of 11 virulence genes (invA, avrA, ssaQ, mgtC, siiD, sopB, gipA, sodC1, sopE1, spvC, bcfC) and the antimicrobial resistance profiles of salmonellae recovered from squabs. Six isolates were identified from among 45 (13.3%) squabs sampled. Three serotypes were identified according to the Kauffmann-White serotyping scheme: Salmonella Typhimurium (4/6; 66.7%), S. Braenderup (1/6; 16.7%) and S. Lomita (1/6; 16.7%). Polymerase chain reaction analyses revealed the presence of invA, sopB and bcfC in all six isolates, whereas sopE1 and gipA were absent. All six isolates were resistant to lincomycin and streptomycin, but all were susceptible to ciprofloxacin, colistin sulphate and gentamicin. Among the S. Typhimurium isolates, seven resistance profiles were identified: penicillins,aminoglycosides,fluoroquinolones, lincosamides,phenicols, tetracyclines and sulphonamides; four resistance profiles were identified in the isolates of S. Braenderup and S. Lomita: aminoglycosides, fluoroquinolones, lincosamides and polymyxin. Thus, the distribution of resistance to the antibiotics was largely dependent on serotype identity. The presence of invA, avrA, ssaQ, mgtC, siiD, sopB and bcfC was associated with resistance to chloramphenicol; invA, sopB and bcfC with resistance to streptomycin and lincosamide; and invA and sodC1 with resistance to trimethoprim-sulfamethoxazole. The identification of serotypes S. Typhimurium, S. Braenderup and S. Lomita in the squab samples has important implications because these serotypes are significant causes of food poisoning and enteric fever in humans.

  17. Revealing the Properties of the Frontier Fields Galaxies

    NASA Astrophysics Data System (ADS)

    Wise, John

    2014-10-01

    The HST campaign Frontier Fields will discover an even larger sample of galaxies at redshifts greater than 6. We propose to make observational predictions for this high-redshift population, using a suite of high-resolution cosmological simulations, that will enable the correlation between key observables and the physical properties of the first galaxies in the universe. These simulations will have finished before Cycle 22, and this proposal focuses on the analysis of the simulated galaxies. The primary goal of this proposal is to constrain the following properties: {1} star formation histories and stellar populations, {2} nebular emission and dust extinction, {3} the faint end of the luminosity function, {4} cosmic variance, and {5} galaxy morphology and structure. We will make all of the analysis data products publicly available. We will also provide a Markov Chain Monte Carlo tool to the public that will calculate the most likely galaxy properties, such as stellar mass, metallicity, and ages, given a redshift, half-light radius, and magnitudes/spectra.

  18. 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

  19. Molecular characterization of Spanish infectious bursal disease virus field isolates.

    PubMed

    Majó, N; El-Attrache, J; Banda, A; Villegas, P; Ramis, A; Pagès, A; Ikuta, N

    2002-01-01

    Nine Spanish isolates of infectious bursal disease virus (IBDV) were characterized and classified after reverse transcriptase-polymerase chain reaction of a 248-bp fragment of the VP2 gene hypervariable region and restriction fragment length polymorphism (RFLP). The restriction endonucleases (REs) used were BstNI, Sad, SspI, TaqI, DraI, and StyI. Sequencing of the amplified product and further comparison of these sequences with published sequence data from other IBDV strains were also performed. Very virulent and classic strains were identified. None of the strains identified had molecular characteristics similar to that of the American variant strains. Four very virulent strains (VG-248, 5939, 6145, and 7333) were digested by the TaqI, SspI, and StyI enzymes. The sequences of these strains were closely related to other European and Japanese very virulent IBDV (vvIBDV) strains. Strains VG-311, VG-262, and VG-208 were digested by the BstNI and Sad REs and were classified as classic strains. Strains VG-276 and VG-313 had unique RFLP patterns. VG-276 exhibited the SspI RE site, which has been reported as a characteristic of vvIBDV strains, whereas the VG-313 strain exhibited a Sad and StyI RE site indicative of the classic IBDV Edgar and 52-70 strains. However, nucleotide sequence analysis of the amplified hypervariable region strain VG-276 revealed a higher identity with the classic strains STC, 52/70, and 9109 IBDV strains, whereas strain VG-313 exhibited a higher identity with the vvIBDV strains.

  20. Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics

    PubMed Central

    Tandberg, Julia I.; Lagos, Leidy X.; Langlete, Petter; Berger, Eva; Rishovd, Anne-Lise; Roos, Norbert; Varkey, Deepa; Paulsen, Ian T.; Winther-Larsen, Hanne C.

    2016-01-01

    Membrane vesicles (MVs) are spherical particles naturally released from the membrane of Gram-negative bacteria. Bacterial MV production is associated with a range of phenotypes including biofilm formation, horizontal gene transfer, toxin delivery, modulation of host immune responses and virulence. This study reports comparative profiling of MVs from bacterial strains isolated from three widely disperse geographical areas. Mass spectrometry identified 119, 159 and 142 proteins in MVs from three different strains of Piscirickettsia salmonis isolated from salmonids in Chile (LF-89), Norway (NVI 5692) and Canada (NVI 5892), respectively. MV comparison revealed several strain-specific differences related to higher virulence capability for LF-89 MVs, both in vivo and in vitro, and stronger similarities between the NVI 5692 and NVI 5892 MV proteome. The MVs were similar in size and appearance as analyzed by electron microscopy and dynamic light scattering. The MVs from all three strains were internalized by both commercial and primary immune cell cultures, which suggest a potential role of the MVs in the bacterium’s utilization of leukocytes. When MVs were injected into an adult zebrafish infection model, an upregulation of several pro-inflammatory genes were observed in spleen and kidney, indicating a modulating effect on the immune system. The present study is the first comparative analysis of P. salmonis derived MVs, highlighting strain-specific vesicle characteristics. The results further illustrate that the MV proteome from one bacterial strain is not representative of all bacterial strains within one species. PMID:27764198

  1. The phylogenetic diversity of Spirometra erinaceieuropaei isolates from southwest China revealed by multi genes.

    PubMed

    Zhang, Xi; Wang, Han; Cui, Jing; Jiang, Peng; Lin, Mei Long; Zhang, Yun Lu; Liu, Ruo Dan; Wang, Zhong Quan

    2016-04-01

    The larval plerocercoid of Spirometra erinaceieuropaei can parasitize humans, causing a serious food borne parasitic zoonosis known as sparganosis. Sparganosis have increased in China in recent years. In this study, the prevalence of sparganum infection in wild frogs in 9 geographical areas in southwest China was firstly investigated. Of 276 caught frogs, 55 frogs were found to be infected with sparganum. Then, the population genetic structure of these sparganum isolates was explored based on four molecular markers (cytb, cox1, rrnS and 28S rDNA D1). Highly genetic diversity and the genetic differentiation among sparganum isolates from different sites were revealed in the DNA polymorphism analyses. Both the phylogenetic inference and the analysis of the median-joining network supported two clades in the southwest S. erinaceieuropaei population. However, none demographic population expansion of the southwest S. erinaceieuropaei population was observed in the neutrality test, mismatch distribution analysis and Bayesian skyline plot analysis. Finally, the phylogenetic diversity of S. erinaceieuropaei from eastern, central, southern and southwest China was analyzed, the result suggested that Chinese S. erinaceieuropaei population should be divided into two groups (Group I and Group II), and they started to divergence in the middle Pliocene.

  2. 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.

  3. 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).

  4. 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).

  5. 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

  6. Permanent-magnet Faraday isolator with the field intensity of 25 kOe

    SciTech Connect

    Mironov, E A; Snetkov, I L; Voitovich, A V; Palashov, O V

    2013-08-31

    A Faraday isolator with a single magneto-optical element is constructed and experimentally tested. It provides the isolation ratio of 30 dB at an average laser radiation power of 650 W. These parameters are obtained by increasing the field intensity in the magnetic system of the isolator and employing a low-absorption magneto-optical element. (elements of laser devices)

  7. 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

  8. Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.

    PubMed

    de la Fuente, José; Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Manrique, Marina; Tobes, Raquel; López, Vladimir; Romero, Beatriz; Domínguez, Lucas; Garrido, Joseba M; Juste, Ramón; Gortazar, Christian

    2015-06-25

    Here we report the complete genome sequences of field isolates of Mycobacterium bovis and the related mycobacterial species, Mycobacterium caprae. The genomes of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different virulence, prevalence, and host distribution phenotypes were sequenced.

  9. Modulation by applied electric fields of Purkinje and stellate cell activity in the isolated turtle cerebellum.

    PubMed Central

    Chan, C Y; Nicholson, C

    1986-01-01

    Quasi steady-state electric fields were applied across the isolated turtle cerebellum to study the relationship between applied field, neuronal morphology and the modulation of the neuronal spike firing pattern. Spiking elements were identified electrophysiologically using extracellular recording methods and by subsequent horseradish peroxidase injection, which revealed their dendritic morphology and orientation. The electric field was precisely defined by measuring the voltage gradients induced in the cerebellum by 40 s constant-current pulses. The field was constant in the vertical (dorso-ventral) axis and zero in the horizontal plane, in agreement with theory. Neurones were modulated by applying a sinusoidal field at frequencies between 0.05 and 1.0 Hz. Modulated cells exhibited an increase in firing frequency and fell into one of four classes, depending on the direction of the field that produced the modulation. Thus neurones were excited by: ventricle-directed fields (V modulation), pia-directed fields (P modulation), both of the above (V/P modulation) or showed no consistent modulation (non-modulation). Most Purkinje somata and primary dendrites (nineteen out of twenty-eight) and most Purkinje dendrites (eighteen out of thirty), were V modulated with maximum rate proportional to the peak field intensity. The dendrites of these cells were consistently oriented toward the pia. Among the stellate cells, the lower molecular layer stellates, with dendrites extending predominantly towards the pia, were mostly (nineteen out of thirty-two) V modulated. The mid-molecular layer stellates, which showed much variability in dendritic orientation, were distributed among all four of the modulation classes. The upper molecular layer stellates, with a mostly horizontal dendritic alignment, were mainly (nine out of sixteen) non-modulated. All groups of spiking elements showed a correlation between patterns of modulation by applied fields and dendritic orientation, which

  10. Increased virulence of Marek's disease virus field isolates.

    PubMed

    Witter, R L

    1997-01-01

    The continuation of an apparent evolutionary trend of Marek's disease virus (MDV) towards greater virulence may explain recent increased losses from Marek's disease (MD) in vaccinated flocks. To address this question, the virulence of 31 isolates of serotype 1 MDV obtained from layer or broiler flocks between 1987 and 1995 were characterized. Each isolate was cultured in duck embryo fibroblasts for four to six passages, and ascertained to be free from contamination with avian retroviruses, chicken anemia virus, and MDVs of other serotypes. The viruses, along with prototype viruses JM/102W and Md5, were tested for virulence by inoculation at 6 days of age into laboratory strain 15I5 x 7(1) chickens of three types: nonvaccinated, vaccinated with turkey herpesvirus (HVT) and bivalent (HVT + SB-1)-vaccinated. The results showed that three isolates did not differ from JM/102W and were classified in the virulent (vMDV) pathotype. Twenty-one isolates produced significantly higher levels of MD in HVT-vaccinated chickens than did the JM/102W control and were classified in the very virulent (vvMDV) pathotype. Seven isolates, five of which were isolated in 1994 or 1995, produced significantly higher levels of MD in bivalent-vaccinated chickens than did the Md5 (vvMDV) control. These isolates, provisionally designated as the vv+MDV pathotype, appeared to be at the high end of a virulence continuum. Several MD response parameters, including lymphoma mortality, early mortality with bursal/thymic atrophy, and frequency of visceral lymphomas or ocular lesions in nonvaccinated chickens were positively correlated with virulence. These findings support the continued evolution of MDV towards greater virulence.

  11. 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

  12. Metabolomic characterization of halophilic bacterial isolates reveals strains synthesizing rare diaminoacids under salt stress.

    PubMed

    Joghee, Nidhya Nadarajan; Jayaraman, Gurunathan

    2014-07-01

    Metabolomics-based approaches to study stress responses in bacteria have received much attention in recent years. In the present study, a metabolomic analysis of the representative halophilic bacterial isolates (Halomonas hydrothermalis VITP9, Bacillus aquimaris VITP4, Planococcus maritimus VITP21 and Virgibacillus dokdonensis VITP14) from a saltern region in India was performed using nuclear magnetic resonance spectroscopy. Chemometric analysis of (1)H NMR spectra revealed salt-dependent increase in the levels of metabolites, mainly from the aspartate and glutamate family, that are directed from the glycolytic pathway, pentose phosphate pathway and citric acid cycle. The composition of the metabolites was found to be different with respect to the species and the type of growth medium. Analysis of the two dimensional NMR data revealed accumulation of two rare diaminoacids, Nε-acetyl-α-lysine and Nδ-acetylornithine (by VITP21 and VITP4 strains respectively) apart from other well known solutes such as ectoine, proline, glutamate and glycine betaine. Metabolite profiles of strains capable of synthesizing Nε-acetyl-α-lysine and Nδ-acetylornithine suggested their biosynthesis from lysine and ornithine using aspartate and glutamate as their precursors, respectively. Further, the cells in moderate salinity (5% w/v NaCl) showed an increase in growth rate along with increase in the levels of nucleotides, whereas at higher salinity (10% w/v NaCl), the levels of aromatic and hydrophobic metabolites dropped, accompanied with a decrease in growth rate, rightly suggesting that at any salt-stress condition provided, cellular homeostasis was favored over growth. PMID:24636996

  13. 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.

  14. 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

  15. Achromobacter Species Isolated from Cystic Fibrosis Patients Reveal Distinctly Different Biofilm Morphotypes.

    PubMed

    Nielsen, Signe M; Nørskov-Lauritsen, Niels; Bjarnsholt, Thomas; Meyer, Rikke L

    2016-01-01

    Achromobacter species have attracted attention as emerging pathogens in cystic fibrosis. The clinical significance of Achromobacter infection is not yet fully elucidated; however, their intrinsic resistance to antimicrobials and ability to form biofilms renders them capable of establishing long-term chronic infections. Still, many aspects of Achromobacter biofilm formation remain uncharacterized. In this study, we characterized biofilm formation in clinical isolates of Achromobacter and investigated the effect of challenging the biofilm with antimicrobials and/or enzymes targeting the extracellular matrix. In vitro biofilm growth and subsequent visualization by confocal microscopy revealed distinctly different biofilm morphotypes: a surface-attached biofilm morphotype of small aggregates and an unattached biofilm morphotype of large suspended aggregates. Aggregates consistent with our in vitro findings were visualized in sputum samples from cystic fibrosis patients using an Achromobacter specific peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) probe, confirming the presence of Achromobacter biofilms in the CF lung. High antibiotic tolerance was associated with the biofilm phenotype, and biocidal antibiotic concentrations were up to 1000 fold higher than for planktonic cultures. Treatment with DNase or subtilisin partially dispersed the biofilm and reduced the tolerance to specific antimicrobials, paving the way for further research into using dispersal mechanisms to improve treatment strategies. PMID:27681927

  16. 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

  17. Achromobacter Species Isolated from Cystic Fibrosis Patients Reveal Distinctly Different Biofilm Morphotypes

    PubMed Central

    Nielsen, Signe M.; Nørskov-Lauritsen, Niels; Bjarnsholt, Thomas; Meyer, Rikke L.

    2016-01-01

    Achromobacter species have attracted attention as emerging pathogens in cystic fibrosis. The clinical significance of Achromobacter infection is not yet fully elucidated; however, their intrinsic resistance to antimicrobials and ability to form biofilms renders them capable of establishing long-term chronic infections. Still, many aspects of Achromobacter biofilm formation remain uncharacterized. In this study, we characterized biofilm formation in clinical isolates of Achromobacter and investigated the effect of challenging the biofilm with antimicrobials and/or enzymes targeting the extracellular matrix. In vitro biofilm growth and subsequent visualization by confocal microscopy revealed distinctly different biofilm morphotypes: a surface-attached biofilm morphotype of small aggregates and an unattached biofilm morphotype of large suspended aggregates. Aggregates consistent with our in vitro findings were visualized in sputum samples from cystic fibrosis patients using an Achromobacter specific peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) probe, confirming the presence of Achromobacter biofilms in the CF lung. High antibiotic tolerance was associated with the biofilm phenotype, and biocidal antibiotic concentrations were up to 1000 fold higher than for planktonic cultures. Treatment with DNase or subtilisin partially dispersed the biofilm and reduced the tolerance to specific antimicrobials, paving the way for further research into using dispersal mechanisms to improve treatment strategies. PMID:27681927

  18. Achromobacter Species Isolated from Cystic Fibrosis Patients Reveal Distinctly Different Biofilm Morphotypes

    PubMed Central

    Nielsen, Signe M.; Nørskov-Lauritsen, Niels; Bjarnsholt, Thomas; Meyer, Rikke L.

    2016-01-01

    Achromobacter species have attracted attention as emerging pathogens in cystic fibrosis. The clinical significance of Achromobacter infection is not yet fully elucidated; however, their intrinsic resistance to antimicrobials and ability to form biofilms renders them capable of establishing long-term chronic infections. Still, many aspects of Achromobacter biofilm formation remain uncharacterized. In this study, we characterized biofilm formation in clinical isolates of Achromobacter and investigated the effect of challenging the biofilm with antimicrobials and/or enzymes targeting the extracellular matrix. In vitro biofilm growth and subsequent visualization by confocal microscopy revealed distinctly different biofilm morphotypes: a surface-attached biofilm morphotype of small aggregates and an unattached biofilm morphotype of large suspended aggregates. Aggregates consistent with our in vitro findings were visualized in sputum samples from cystic fibrosis patients using an Achromobacter specific peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) probe, confirming the presence of Achromobacter biofilms in the CF lung. High antibiotic tolerance was associated with the biofilm phenotype, and biocidal antibiotic concentrations were up to 1000 fold higher than for planktonic cultures. Treatment with DNase or subtilisin partially dispersed the biofilm and reduced the tolerance to specific antimicrobials, paving the way for further research into using dispersal mechanisms to improve treatment strategies.

  19. 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

  20. 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.

  1. Isolation and identification of a lethal rhabdovirus from farmed rice field eels Monopterus albus.

    PubMed

    Ou, Tong; Zhu, Ruo-Lin; Chen, Zhong-Yuan; Zhang, Qi-Ya

    2013-11-01

    We provide the first description of a virus responsible for a systemic hemorrhagic disease causing high mortality in farmed rice field eels Monopterus albus in China. Typical signs exhibited by the diseased fish were extensive hemorrhages in the skin and viscera and some neurological signs, such as loss of equilibrium and disorganized swimming. Histopathological examination revealed various degrees of necrosis within the spleen and liver. Virus isolation was attempted from visceral tissues of diseased fish by inoculation on 6 fish cell lines. Typical cytopathic effects (CPE) were produced in bluegill fry (BF2) cells, so this cell line was chosen for further isolation and propagation of the virus. Electron microscopy observation showed that the negative stained viral particles had the characteristic bullet shape of rhabdoviruses and an estimated size of 60 × 120 nm. We therefore tentatively refer to this virus as Monopterus albus rhabdovirus (MoARV). Molecular characterization of MoARV, including sequence analysis of the nucleoprotein (N), phosphoprotein (P), and glycoprotein (G) genes, revealed 94.5 to 97.3% amino acid similarity to that of Siniperca chuatsi rhabdovirus. Phylogenetic analysis based on the amino acid sequences of N and G proteins indicated that MoARV should be a member of the genus Vesiculovirus. Koch's postulates were fulfilled by infecting healthy rice field eels with MoARV, which produced an acute infection. RT-PCR analysis demonstrated that MoARV RNA could be detected in both naturally and experimentally infected fish. The data suggest that MoARV was the causative pathogen of the disease.

  2. Integrative conjugative elements are widespread in field isolates of Mycoplasma species pathogenic for ruminants.

    PubMed

    Tardy, Florence; Mick, Virginie; Dordet-Frisoni, Emilie; Marenda, Marc Serge; Sirand-Pugnet, Pascal; Blanchard, Alain; Citti, Christine

    2015-03-01

    Comparative genomics have revealed massive horizontal gene transfer (HGT) between Mycoplasma species sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogen Mycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminant Mycoplasma species, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, the hominis and spiroplasma types, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance.

  3. 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

  4. Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene.

    PubMed

    Chen, Yi-Ning; Loa, Chien Chang; Ababneh, Mustafa Mohammed-Khair; Wu, Ching Ching; Lin, Tsang Long

    2015-11-01

    Turkey flocks have experienced turkey coronaviral enteritis sporadically in the United States since the 1990s. Twenty-four field isolates of turkey coronavirus (TCoV) from multiple states in the United States were recovered from 1994 to 2010 to determine the genetic relationships among them. The entire spike (S) gene of each TCoV isolate was amplified and sequenced. Pairwise comparisons were performed using the Clustal W program, revealing 90.0% to 98.4% sequence identity in the full-length S protein, 77.6% to 96.6% in the amino terminus of the S1 subunit (containing one hypervariable region in S1a), and 92.1% to 99.3% in the S2 subunit at the deduced amino acid sequence level. The conserved motifs, including two cleavage recognition sequences of the S protein, two heptad repeats, the transmembrane domain, and the Golgi retention signal were identified in all TCoV isolates. Phylogenetic analysis based on the full-length S gene was used to distinguish North American TCoV isolates from French TCoV isolates. Among the North American TCoV isolates, three distinct genetic groups with 100% bootstrap support were observed. North Carolina isolates formed group I, Texas isolates formed group II, and Minnesota isolates formed Group III. The S genes of 24 TCoV isolates from the United States remained conserved because they contained predominantly synonymous substitutions. The findings of the present study suggest endemic circulation of distinct TCoV genotypes in different geographic locations.

  5. Isolation of Candida species on media with and without added fluconazole reveals high variability in relative growth susceptibility phenotypes.

    PubMed Central

    Schoofs, A; Odds, F C; Colebunders, R; Ieven, M; Wouters, L; Goossens, H

    1997-01-01

    Mouthwashes from human immunodeficiency virus-positive individuals were sampled for yeasts by direct plating on a differential agar medium with and without added fluconazole and via enrichment broths with and without added fluconazole. The colonies of the yeasts isolated were tested for relative growth in the presence of single concentrations of itraconazole and fluconazole. Among 258 culture plates containing yeasts obtained via different isolation routes from 86 yeast-positive samples, 33 (12.7%) of the plates showed unexpectedly high colony-to-colony variation in relative growth. Intercolony variation was seen in 41 (47.7%) of the 86 isolates when relative growth data were analyzed for all colonies of an isolate tested, regardless of the medium used for isolation. The prevalence of relative growth variability with the azoles was highest for Candida glabrata (100% of 13 isolates), followed by Candida krusei (60% of 5 isolates) and Candida albicans (40% of 53 isolates), and the visual patterns of variability seen in scatter plots of the data showed species specificity. Relative growth phenotypes generally tended to be stable for each yeast colony in subcultures, whether or not the medium used for subculture contained antifungal agents. DNA fingerprinting of stable and variable C. albicans isolates showed changes in band patterns detected with the probe Ca3, suggesting that the variability may have resulted from selection of different subtypes of the yeasts during the isolation procedure. These findings suggest that the yeasts isolated from single clinical samples were often not clonal in nature. The relative growth test revealed colony variability more readily than conventional susceptibility testing. PMID:9257732

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. Molecular-genetic analysis of field isolates of Avian Leucosis Viruses in the Russian Federation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Commercial poultry farms in 14 regions of Russian Federation were monitored for avian leukosis virus (ALV) infection using virus isolation tests and serology. Results indicated the presence of two subgroups of ALV in farms located in 11 of 14 regions. Analysis of the genomes of 12 field isolates of...

  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. 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

  13. Characterization of Nontypable Haemophilus influenzae Isolates Recovered from Adult Patients with Underlying Chronic Lung Disease Reveals Genotypic and Phenotypic Traits Associated with Persistent Infection

    PubMed Central

    Garmendia, Junkal; Viadas, Cristina; Calatayud, Laura; Mell, Joshua Chang; Martí-Lliteras, Pau; Euba, Begoña; Llobet, Enrique; Gil, Carmen; Bengoechea, José Antonio; Redfield, Rosemary J.; Liñares, Josefina

    2014-01-01

    Nontypable Haemophilus influenzae (NTHi) has emerged as an important opportunistic pathogen causing infection in adults suffering obstructive lung diseases. Existing evidence associates chronic infection by NTHi to the progression of the chronic respiratory disease, but specific features of NTHi associated with persistence have not been comprehensively addressed. To provide clues about adaptive strategies adopted by NTHi during persistent infection, we compared sequential persistent isolates with newly acquired isolates in sputa from six patients with chronic obstructive lung disease. Pulse field gel electrophoresis (PFGE) identified three patients with consecutive persistent strains and three with new strains. Phenotypic characterisation included infection of respiratory epithelial cells, bacterial self-aggregation, biofilm formation and resistance to antimicrobial peptides (AMP). Persistent isolates differed from new strains in showing low epithelial adhesion and inability to form biofilms when grown under continuous-flow culture conditions in microfermenters. Self-aggregation clustered the strains by patient, not by persistence. Increasing resistance to AMPs was observed for each series of persistent isolates; this was not associated with lipooligosaccharide decoration with phosphorylcholine or with lipid A acylation. Variation was further analyzed for the series of three persistent isolates recovered from patient 1. These isolates displayed comparable growth rate, natural transformation frequency and murine pulmonary infection. Genome sequencing of these three isolates revealed sequential acquisition of single-nucleotide variants in the AMP permease sapC, the heme acquisition systems hgpB, hgpC, hup and hxuC, the 3-deoxy-D-manno-octulosonic acid kinase kdkA, the long-chain fatty acid transporter ompP1, and the phosphoribosylamine glycine ligase purD. Collectively, we frame a range of pathogenic traits and a repertoire of genetic variants in the context of

  14. MLST analysis reveals a highly conserved core genome among poultry isolates of Clostridium septicum.

    PubMed

    Neumann, Anthony P; Rehberger, Thomas G

    2009-06-01

    Clostridium septicum is a highly virulent, anaerobic bacterium capable of establishing necrotizing tissue infections and forming heat resistant endospores. Disease is primarily facilitated by secretion of numerous toxic products including a lethal pore-forming cytolysin. Spontaneously occurring clostridial myonecrosis involving C. septicum has recently reemerged as a concern for many poultry producers. However, despite its increasing prevalence, the epidemiology of infection and population structure of C. septicum remains largely unknown. In this study a multilocus sequence typing (MLST) approach was utilized to examine evolutionary relationships within a diverse collection of C. septicum isolates recovered from poultry flocks experiencing episodes of gangrenous dermatitis. The 109 isolates examined represented 42 turkey flocks and 24 different flocks of broiler chickens as well as C. septicum type strain, ATCC 12464. Isolates were recovered predominantly from gangrenous lesions although isolates from livers, gastrointestinal tracts, spleens and blood were included. The loci analyzed were csa, the major lethal toxin produced by C. septicum, and the housekeeping genes gyrA, groEL, dnaK, recA, tpi, ddl, colA and glpK. These loci were included in part because of their previous use in MLST analysis of Clostridium perfringens and Clostridium difficile. Results indicated a high level of conservation present within these housekeeping gene fragments when compared to what has been previously reported for the aforementioned clostridia. Of the 5352 bp of sequence data examined for each isolate, 99.7% (5335/5352) was absolutely conserved among the 109 isolates. Only one of the ten unique sequence types, or allelic profiles, identified among the isolates was recovered from both turkeys and broiler chickens suggesting some host species preference. Phylogenetic analyses identified two unique clusters, or clonal complexes, among these poultry isolates which may have important

  15. 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.

  16. 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

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

    PubMed

    Dudnikova, Ekaterina; Norkina, Svetlana; Vlasov, Anatoly; Slobodchuk, Anna; Lee, Lucy F; Witter, Richard L

    2007-04-01

    Although determination of the pathotype is central to the study of Marek's disease (MD) field isolates, methods are not standardized and results from different laboratories may not compare well with the original Avian Disease and Oncology Laboratory assay. This study was designed to investigate the validity of the "best fit" pathotyping assay, a simplified method recently described for testing of field isolates of MD virus (MDV). Twenty serotype 1 MDV strains were isolated from 12 breeder and commercial flocks in eight regions of the Russian Federation and were pathotyped by the best fit assay using vaccinated and non-vaccinated chickens from Schelkovo specific pathogen free breeders. Lesion responses induced by field isolates were compared with those induced by reference strains JM/102W, Md5, and 648A representing pathotypes v, vv and vv+, respectively. Based on comparison with reference strains, we determined the pathotype of eight isolates as vv+, 11 isolates as vv and one isolate as v. Lesion responses induced by the three reference strains consistently differentiated the respective pathotypes in non-vaccinated chickens and in chickens vaccinated with FC126 (serotype 3) alone or with a bivalent FC126 + 301B/1 vaccine (serotypes 3 and 2, respectively). Variation between reference strain responses in replicate trials was minimal. In some cases, calculation of the proportional distance between pairs of reference strains aided in the classification of field isolates. These results indicate that the "best fit" pathotyping assay can be conducted with local chicken strains and, in the absence of statistical analysis, provides pathotype designations that are consistent with those obtained by the Avian Disease and Oncology Laboratory method. In addition, the pathogenicity of Russian isolates appeared comparable with that of United States isolates.

  18. 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

  19. Heterogeneity among Isolates Reveals that Fitness in Low Oxygen Correlates with Aspergillus fumigatus Virulence

    PubMed Central

    Kowalski, Caitlin H.; Beattie, Sarah R.; Fuller, Kevin K.; McGurk, Elizabeth A.; Tang, Yi-Wei; Hohl, Tobias M.; Obar, Joshua J.

    2016-01-01

    ABSTRACT Previous work has shown that environmental and clinical isolates of Aspergillus fumigatus represent a diverse population that occupies a variety of niches, has extensive genetic diversity, and exhibits virulence heterogeneity in a number of animal models of invasive pulmonary aspergillosis (IPA). However, mechanisms explaining differences in virulence among A. fumigatus isolates remain enigmatic. Here, we report a significant difference in virulence of two common lab strains, CEA10 and AF293, in the murine triamcinolone immunosuppression model of IPA, in which we previously identified severe low oxygen microenvironments surrounding fungal lesions. Therefore, we hypothesize that the ability to thrive within these lesions of low oxygen promotes virulence of A. fumigatus in this model. To test this hypothesis, we performed in vitro fitness and in vivo virulence analyses in the triamcinolone murine model of IPA with 14 environmental and clinical isolates of A. fumigatus. Among these isolates, we observed a strong correlation between fitness in low oxygen in vitro and virulence. In further support of our hypothesis, experimental evolution of AF293, a strain that exhibits reduced fitness in low oxygen and reduced virulence in the triamcinolone model of IPA, results in a strain (EVOL20) that has increased hypoxia fitness and a corresponding increase in virulence. Thus, the ability to thrive in low oxygen correlates with virulence of A. fumigatus isolates in the context of steroid-mediated murine immunosuppression. PMID:27651366

  20. 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

  1. 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

  2. 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

  3. 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

  4. MRI findings of a remote and isolated vaginal metastasis revealing an adenocarcinoma of the mid-sigmoid colon.

    PubMed

    D'Arco, Felice; Pizzuti, Laura Micol; Romano, Federica; Natella, Valentina; Laccetti, Ettore; Storto, Giovanni; Maurea, Simone; Mainenti, Pier Paolo

    2014-01-01

    A remote vaginal metastasis from a colo-rectal carcinoma is extremely rare. Only few cases have been described in the literature. The radiological appearances of a vaginal metastasis from colon-rectal cancer have not been extensively investigated. We report the MRI findings with clinical and pathological correlations of a remote and isolated vaginal metastasis revealing a mid-sigmoid adenocarcinoma in a 67 years old woman.

  5. Seeing the Whole Elephant: Imaging Flow Cytometry Reveals Extensive Morphological Diversity within Blastocystis Isolates.

    PubMed

    Yason, John Anthony; Tan, Kevin Shyong Wei

    2015-01-01

    Blastocystis is a common protist isolated in humans and many animals. The parasite is a species complex composed of 19 subtypes, 9 of which have been found in humans. There are biological and molecular differences between Blastocystis subtypes although microscopy alone is unable to distinguish between these subtypes. Blastocystis isolates also display various morphological forms. Several of these forms, however, have not been properly evaluated on whether or not these play significant functions in the organism's biology. In this study, we used imaging flow cytometry to analyze morphological features of Blastocystis isolates representing 3 subtypes (ST1, ST4 and ST7). We also employed fluorescence dyes to discover new cellular features. The profiles from each of the subtypes exhibit considerable differences with the others in terms of shape, size and granularity. We confirmed that the classical vacuolar form comprises the majority in all three subtypes. We have also evaluated other morphotypes on whether these represent distinct life stages in the parasite. Irregularly-shaped cells were identified but all of them were found to be dying cells in one isolate. Granular forms were present as a continuum in both viable and non-viable populations, with non-viable forms displaying higher granularity. By analyzing the images, rare morphotypes such as multinucleated cells could be easily observed and quantified. These cells had low granularity and lower DNA content. Small structures containing nucleic acid were also identified. We discuss the possible biological implications of these unusual forms. PMID:26618361

  6. 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

  7. Global Multilocus Sequence Typing Analysis of Mycoplasma bovis Isolates Reveals Two Main Population Clusters

    PubMed Central

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

    2014-01-01

    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

  8. 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

  9. Phylogenetic Analysis of Phenotypically Characterized Cryptococcus laurentii Isolates Reveals High Frequency of Cryptic Species

    PubMed Central

    Ferreira-Paim, Kennio; Ferreira, Thatiana Bragine; Andrade-Silva, Leonardo; Mora, Delio Jose; Springer, Deborah J.; Heitman, Joseph; Fonseca, Fernanda Machado; Matos, Dulcilena; Melhem, Márcia Souza Carvalho; Silva-Vergara, Mario León

    2014-01-01

    Background Although Cryptococcus laurentii has been considered saprophytic and its taxonomy is still being described, several cases of human infections have already reported. This study aimed to evaluate molecular aspects of C. laurentii isolates from Brazil, Botswana, Canada, and the United States. Methods In this study, 100 phenotypically identified C. laurentii isolates were evaluated by sequencing the 18S nuclear ribosomal small subunit rRNA gene (18S-SSU), D1/D2 region of 28S nuclear ribosomal large subunit rRNA gene (28S-LSU), and the internal transcribed spacer (ITS) of the ribosomal region. Results BLAST searches using 550-bp, 650-bp, and 550-bp sequenced amplicons obtained from the 18S-SSU, 28S-LSU, and the ITS region led to the identification of 75 C. laurentii strains that shared 99–100% identity with C. laurentii CBS 139. A total of nine isolates shared 99% identity with both Bullera sp. VY-68 and C. laurentii RY1. One isolate shared 99% identity with Cryptococcus rajasthanensis CBS 10406, and eight isolates shared 100% identity with Cryptococcus sp. APSS 862 according to the 28S-LSU and ITS regions and designated as Cryptococcus aspenensis sp. nov. (CBS 13867). While 16 isolates shared 99% identity with Cryptococcus flavescens CBS 942 according to the 18S-SSU sequence, only six were confirmed using the 28S-LSU and ITS region sequences. The remaining 10 shared 99% identity with Cryptococcus terrestris CBS 10810, which was recently described in Brazil. Through concatenated sequence analyses, seven sequence types in C. laurentii, three in C. flavescens, one in C. terrestris, and one in the C. aspenensis sp. nov. were identified. Conclusions Sequencing permitted the characterization of 75% of the environmental C. laurentii isolates from different geographical areas and the identification of seven haplotypes of this species. Among sequenced regions, the increased variability of the ITS region in comparison to the 18S-SSU and 28S-LSU regions reinforces its

  10. 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.

  11. Genetic variability among Schistosoma japonicum isolates from the Philippines, Japan and China revealed by sequence analysis of three mitochondrial genes.

    PubMed

    Chen, Fen; Li, Juan; Sugiyama, Hiromu; Zhou, Dong-Hui; Song, Hui-Qun; Zhao, Guang-Hui; Zhu, Xing-Quan

    2015-02-01

    The present study examined sequence variability in the mitochondrial (mt) protein-coding genes cytochrome b (cytb), NADH dehydrogenase subunits 2 and 6 (nad2 and nad6) among 24 isolates of Schistosoma japonicum from different endemic regions in the Philippines, Japan and China. The complete cytb, nad2 and nad6 genes were amplified and sequenced separately from individual schistosome. Sequence variations for isolates from the Philippines were 0-0.5% for cytb, 0-0.6% for nad2, and 0-0.9% for nad6. Variation was 0-0.5%, 0.1-0.8%, 0-0.7% for corresponding genes for schistosome samples from mainland China. For worms in Japan, genetic variations were 0-0.2%, 0.1-0.2% and 0 for the three genes, respectively. Sequence variations were 0-1.0%, 0-1.8% and 0-1.1% for cytb, nad2 and nad6, respectively, among schistosome isolates from different geographical strains in the Philippines, Japan and China. Of the three countries, lowest sequence variations were found between isolates from mainland China and the Philippines and highest were detected between Japan and the Philippines in three mtDNA genes. Phylogenetic analyses based on the combined sequences of cytb, nad2 and nad6 revealed that all isolates in the Philippines clustered together sistered to samples from Yunnan and Zhejiang provinces in China, while isolates from Yamanashi in Japan were in a solitary clade. These results demonstrated the usefulness of the combined three mtDNA sequences for studying genetic diversity and population structure among S. japonicum isolates from the Philippines, China and Japan.

  12. 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.

  13. Field effect tuning of microwave Faraday rotation and isolation with large-area graphene

    NASA Astrophysics Data System (ADS)

    Skulason, Helgi S.; Sounas, Dimitrios L.; Mahvash, Farzaneh; Francoeur, Sebastien; Siaj, Mohamed; Caloz, Christophe; Szkopek, Thomas

    2015-08-01

    We have demonstrated field effect tuning of microwave frequency Faraday rotation in magnetically biased large-area graphene in a hollow circular waveguide isolator geometry. Oxidized intrinsic silicon was used as a microwave transparent back-gate for large-area graphene devices. A 26 dB modulation of isolation in the K-band was achieved with a gate voltage modulation of 10 V corresponding to a carrier density modulation of 7 × 10 11 /cm2. We have developed a simple analytical model for transmission and isolation of the structure. Field effect modulation of Faraday rotation can be extended to other two dimensional electronic systems and is anticipated to be useful for gate voltage controlled isolators, circulators, and other non-reciprocal devices.

  14. 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

  15. 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.

  16. 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

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

    PubMed

    Jiang, Yuan; Wang, Jin-Liang; 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

  18. Isolated micropenis reveals partial androgen insensitivity syndrome confirmed by molecular analysis.

    PubMed

    Bhangoo, Amrit; Paris, Francoise; Philibert, Pascal; Audran, Francoise; Ten, Svetlana; Sultan, Charles

    2010-07-01

    Partial androgen insensitivity syndrome (PAIS) is the milder variant of androgen receptor (AR) defects. The subtle effects of AR mutations present in a patient with micropenis, peno-scrotal hypospadias, infertility, clitoromegaly and posterior labial fusion. We studied the association of isolated micropenis with the genetic defects resulting in androgen resistance, that is, AR gene defects and 5-alpha reductase type 2 (SRD5A2) deficiency. We describe two cases of isolated micropenis: one in a 14-year-old boy and the other in a 3-year-old boy who was followed until he was 10 years old. There were no findings of hypospadias, cryptorchidism or gynecomastia in either of these patients. Serum gonadotrophin and androgen levels were obtained and karyotyping was done. Human chorionic gonadotropin (hCG) stimulation testing assessed the functional capacity of the testes. DNA was extracted from peripheral leukocytes, and all exons of the SRD5A2 and AR genes were amplified by polymerase chain reaction and sequenced. In both patients, baseline testosterone (T) level was low and the values were elevated after hCG testing. The sequence of the SRD5A2 gene was normal in patient 1, and a heterozygous polymorphism, V89L, was found in patient 2. Two known mutations, P390S and A870V, were identified in patients 1 and 2, respectively. Mutations in the AR gene can be associated with isolated micropenis without other features of PAIS, such as hypospadias or gynecomastia. This underlines the importance of including AR gene analysis in the evaluation of isolated micropenis with normal plasma T to ensure proper management of the patient and appropriate genetic counseling for the family.

  19. Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

    PubMed Central

    Jun, Se-Ran; Wassenaar, Trudy M.; Nookaew, Intawat; Hauser, Loren; Wanchai, Visanu; Land, Miriam; Timm, Collin M.; Lu, Tse-Yuan S.; Schadt, Christopher W.; Doktycz, Mitchel J.; Pelletier, Dale A.

    2015-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. PMID:26519390

  20. [Molecular-genetic analysis of the field isolates of avian leucosis viruses in the Russian Federation].

    PubMed

    Plotnikov, V A; Grebennikova, T V; Iuzhakov, A G; Dudnikova, E K; Norkina, S N; Zaberezhnyĭ, A D; Aliper, T I; Fadly, A M

    2012-01-01

    Results of monitoring of different subtypes of avian leukosis virus (ALV) from commercial poultry farms in 14 regions of Russian Federation were discussed. Only three regions were found to be negative. ALV was detected in other 11 regions in 46-64% cases (for different regions). The phylogenetic analysis of the genomes for the 12 field isolates of ALV was carried out in different regions of Russian Federation. The isolates belong to different subtypes of the virus and form two large groups. The genomic differences between Russian and foreign isolates within each group range from 5% to 10%.

  1. Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection

    PubMed Central

    Ye, Wenwu; Wang, Yang; Tyler, Brett M.; Wang, Yuanchao

    2016-01-01

    Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens. PMID:27746768

  2. Comparative analyses of a cystic fibrosis isolate of Bordetella bronchiseptica reveal differences in important pathogenic phenotypes.

    PubMed

    Sukumar, Neelima; Nicholson, Tracy L; Conover, Matt S; Ganguly, Tridib; Deora, Rajendar

    2014-04-01

    Bordetella bronchiseptica is a Gram-negative bacterium that infects and causes disease in a wide variety of animals. B. bronchiseptica also infects humans, thereby demonstrating zoonotic transmission. An extensive characterization of human B. bronchiseptica isolates is needed to better understand the distinct genetic and phenotypic traits associated with these zoonotic transmission events. Using whole-genome transcriptome and CGH analysis, we report that a B. bronchiseptica cystic fibrosis isolate, T44625, contains a distinct genomic content of virulence-associated genes and differentially expresses these genes compared to the sequenced model laboratory strain RB50, a rabbit isolate. The differential gene expression pattern correlated with unique phenotypes exhibited by T44625, which included lower motility, increased aggregation, hyperbiofilm formation, and an increased in vitro capacity to adhere to respiratory epithelial cells. Using a mouse intranasal infection model, we found that although defective in establishing high bacterial burdens early during the infection process, T44625 persisted efficiently in the mouse nose. By documenting the unique genomic and phenotypic attributes of T44625, this report provides a blueprint for understanding the successful zoonotic potential of B. bronchiseptica and other zoonotic bacteria.

  3. Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field.

    PubMed

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

    2013-04-01

    A Gram-stain-negative, oxidase- and catalase-positive bacterial strain that was motile by gliding and produced a pink pigment, designated DCY49(T), was isolated from soil of a ginseng field in a mountainous region of Chungbuk province, South Korea. 16S rRNA gene sequence analysis revealed that strain DCY49(T) belonged to the genus Pedobacter (93.0-96.3 % similarity). Strain DCY49(T) contained MK-7 as the predominant menaquinone. The major fatty acids were summed feature 3 (containing C16 : 1ω7c, C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0, and the main polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA of strain DCY49(T) was 40.5 mol%. Strain DCY49(T) differed from related Pedobacter species by a number of phenotypic characteristics. On the basis of data from the present polyphasic study, strain DCY49(T) is described as representing a novel species of the genus Pedobacter, for which the name Pedobacter ginsengiterrae sp. nov. is proposed. The type strain is DCY49(T) ( = KCTC 23317(T) = JCM 17338(T)).

  4. Chryseobacterium yeoncheonense sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field.

    PubMed

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

    2013-07-01

    A Gram-staining negative, aerobic, non-motile, non-flagellate, yellow-pigmented, rod-shaped bacterial strain, designated strain DCY67(T), was isolated from ginseng field in Republic of Korea. Strain DCY67(T) contained β-glucosidase activity which converts ginsenoside Rb1 to compound K. Optimum growth of DCY67(T) occurred at 30 °C and pH 6.0-6.5. Analysis of the 16S rRNA gene sequences revealed that strain DCY67(T) belonged to the family Flavobacteriaceae and was most closely related to Chryseobacterium ginsenosidimutans THG 15(T) (97.5 %). The genomic DNA G+C content was 36.1 mol%. The predominant quinones were MK-6 (90.9 %) and MK-7 (9.15 %). The major fatty acids were iso-C15:0, summed feature 3 (containing C16:1 ω7c and/or C16:1 ω6c) and iso-C17:0 3-OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY67(T) represents a novel species of the genus Chryseobacterium, for which, name Chryseobacterium yeoncheonense sp. nov. proposed the type strain is DCY67(T) (=KCTC 32090(T) = JCM 18516(T)).

  5. Genetic diversity in potato field populations of Thanatephorus cucumeris AG-3, revealed by ITS polymorphism and RAPD markers.

    PubMed

    Justesen, Annemarie Fejer; Yohalem, David; Bay, Anne; Nicolaisen, Mogens

    2003-11-01

    DNA sequence analysis of the internal transcribed spacer region 1 (ITS1) and random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability in relation to agronomic and regional factors among 60 isolates of Thanatephorus cucumeris (anamorph Rhizoctonia solani) collected from lesions on potato stems or sclerotia of potato tubers. Based on comparative sequence analysis it was shown that all isolates belonged to anastomosis group 3 subgroup Potato Type (AG-3 PT). ITS1 sequence polymorphisms were found within 45 of the 60 isolates showing that different types of the ITS-region are present in individual isolates. Cloning and sequence analysis of the ITS1 region from three selected isolates with sequence polymorphism showed that two different ITS1-types were present in each isolate. RAPD analysis identified 51 RAPD-phenotypes among the 60 investigated isolates indicating a high level of diversity within the subgroup AG-3 PT. Putative clonal isolates with identical RAPD- and ITS1-types were identified within fields, and in one case the same phenotype was found in two different fields separated by several hundred kilometers. Population subdivision analysis based on phenotypic as well as genotypic diversities showed differentiation among populations from different fields when isolates were sampled from tubers, indicating restricted gene flow among soil populations. Low differentiation was seen among field populations sampled from stems, indicating that gene flow is taking place. The population structure was not influenced by the previous crop in the rotation nor by the two cultivars 'Sava' and 'Bintje'.

  6. 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

  7. Quantitative Field Testing Heterodera glycines from Metagenomic DNA Samples Isolated Directly from Soil under Agronomic Production

    PubMed Central

    Li, Yan; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

    2014-01-01

    A quantitative PCR procedure targeting the Heterodera glycines ortholog of the Caenorhabditis elegans uncoordinated-78 gene was developed. The procedure estimated the quantity of H. glycines from metagenomic DNA samples isolated directly from field soil under agronomic production. The estimation of H. glycines quantity was determined in soil samples having other soil dwelling plant parasitic nematodes including Hoplolaimus, predatory nematodes including Mononchus, free-living nematodes and biomass. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from field soil. PMID:24587100

  8. Quantitative field testing Heterodera glycines from metagenomic DNA samples isolated directly from soil under agronomic production.

    PubMed

    Li, Yan; Lawrence, Gary W; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P

    2014-01-01

    A quantitative PCR procedure targeting the Heterodera glycines ortholog of the Caenorhabditis elegans uncoordinated-78 gene was developed. The procedure estimated the quantity of H. glycines from metagenomic DNA samples isolated directly from field soil under agronomic production. The estimation of H. glycines quantity was determined in soil samples having other soil dwelling plant parasitic nematodes including Hoplolaimus, predatory nematodes including Mononchus, free-living nematodes and biomass. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from field soil.

  9. Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism.

    PubMed

    Pinheiro, Miguel M; Ahmed, Md Atique; 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.

  10. Enhancing isolation of antenna arrays by simultaneously blocking and guiding magnetic field lines using magnetic metamaterials

    NASA Astrophysics Data System (ADS)

    Liu, Zhaotang; Wang, Jiafu; Qu, Shaobo; Zhang, Jieqiu; Ma, Hua; Xu, Zhuo; Zhang, Anxue

    2016-10-01

    In this article, we propose to enhance the isolation of antenna arrays by manipulating the near-field magnetic coupling between adjacent antennas using magnetic metamaterials (MMs). Due to the artificially designed negative or large permeability, MMs can concentrate or block the magnetic field lines where they are located, which allows us to tune the near-field magnetic coupling strengths between antennas. MMs can play a two-fold role in enhancing antenna isolation. On one hand, the magnetic fields can be blocked in gaps between adjacent antennas using MMs with negative permeability; on the other hand, the magnetic fields can be pulled towards the borders of the antenna array using MMs with large permeability. As an example, we demonstrated a four-element patch antenna array with split-ring resonators (SRR) integrated in the substrate. The measured results show that the isolation can be enhanced by more than 10 dB with the integration of SRRs, even if the gap between antennas is only about 0.082λ. This work provides an effective alternative to the design of high-isolation antenna arrays.

  11. Genomic reconnaissance of clinical isolates of emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential.

    PubMed

    Choo, Siew Woh; Wee, Wei Yee; Ngeow, Yun Fong; Mitchell, Wayne; Tan, Joon Liang; Wong, Guat Jah; Zhao, Yongbing; Xiao, Jingfa

    2014-02-11

    Mycobacterium abscessus (Ma) is an emerging human pathogen that causes both soft tissue infections and systemic disease. We present the first comparative whole-genome study of Ma strains isolated from patients of wide geographical origin. We found a high proportion of accessory strain-specific genes indicating an open, non-conservative pan-genome structure, and clear evidence of rapid phage-mediated evolution. Although we found fewer virulence factors in Ma compared to M. tuberculosis, our data indicated that Ma evolves rapidly and therefore should be monitored closely for the acquisition of more pathogenic traits. This comparative study provides a better understanding of Ma and forms the basis for future functional work on this important pathogen.

  12. 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.

  13. Molecular typing of Leptospira spp. strains isolated from field mice confirms a link to human leptospirosis.

    PubMed

    Li, S J; Wang, D M; Zhang, C C; Li, X W; Yang, H M; Tian, K C; Wei, X Y; Liu, Y; Tang, G P; Jiang, X G; Yan, J

    2013-11-01

    In recent years, human leptospirosis has been reported in Jinping and Liping counties, Guizhou province, but the leptospires have never been isolated. To track the source of infection and understand the aetiological characteristics, we performed surveillance for field mice carriage of leptospirosis in 2011. Four strains of leptospire were isolated from Apodemus agrarius. PCR confirmed the four isolates as pathogenic. Multiple-locus variable-number tandem repeat analysis (MLVA) showed that the four strains were closely related to serovar Lai strain 56601 belonging to serogroup Icterohaemorrhagiae, which is consistent with the antibody detection results from local patients. Furthermore, the diversity of leptospiral isolates from different hosts and regions was demonstrated with MLVA. Our results suggest that A. agrarius may be the main carrier of Leptospira in Jinping and Liping counties, and the serogroup Icterohaemorrhagiae serovar may be the epidemic serogroup of Leptospira. This will contribute to the control and prevention of leptospirosis in these localities. PMID:23406882

  14. Molecular typing by pulsed-field gel electrophoresis of Spanish animal and human Listeria monocytogenes isolates.

    PubMed

    Vela, A I; Fernandez-Garayzabal, J F; Vazquez, J A; Latre, M V; Blanco, M M; Moreno, M A; de La Fuente, L; Marco, J; Franco, C; Cepeda, A; Rodriguez Moure, A A; Suarez, G; Dominguez, L

    2001-12-01

    A total of 153 strains of Listeria monocytogenes isolated from different sources (72 from sheep, 12 from cattle, 18 from feedstuffs, and 51 from humans) in Spain from 1989 to 2000 were characterized by pulsed-field gel electrophoresis. The strains of L. monocytogenes displayed 55 pulsotypes. The 84 animal, 51 human, and 18 feedstuff strains displayed 31, 29, and 7 different pulsotypes, respectively, indicating a great genetic diversity among the Spanish L. monocytogenes isolates studied. L. monocytogenes isolates from clinical samples and feedstuffs consumed by the diseased animals were analyzed in 21 flocks. In most cases, clinical strains from different animals of the same flock had identical pulsotypes, confirming the existence of a listeriosis outbreak. L. monocytogenes strains with pulsotypes identical to those of clinical strains were isolated from silage, potatoes, and maize stalks. This is the first study wherein potatoes and maize stalks are epidemiologically linked with clinical listeriosis.

  15. Mechanosensory transduction of vagal and baroreceptor afferents revealed by study of isolated nodose neurons in culture.

    PubMed

    Snitsarev, Vladislav; Whiteis, Carol A; Abboud, Francois M; Chapleau, Mark W

    2002-06-28

    Changes in arterial pressure and blood volume are sensed by baroreceptor and vagal afferent nerves innervating aorta and heart with soma in nodose ganglia. The inability to measure membrane potential at the nerve terminals has limited our understanding of mechanosensory transduction. Goals of the present study were to: (1) Characterize membrane potential and action potential responses to mechanical stimulation of isolated nodose sensory neurons in culture; and (2) Determine whether the degenerin/epithelial sodium channel (DEG/ENaC) blocker amiloride selectively blocks mechanically induced depolarization without suppressing membrane excitability. Membrane potential of isolated rat nodose neurons was measured with sharp microelectrodes. Mechanical stimulation with buffer ejected from a micropipette (5, 10, 20 psi) depolarized 6 of 10 nodose neurons (60%) in an intensity-dependent manner. The depolarization evoked action potentials in 4 of the 6 neurons. Amiloride (1 microM) essentially abolished mechanically induced depolarization (15 +/- 4 mV during control vs. 1 +/- 2 mV during amiloride with 20-psi stimulation, n = 6) and action potential discharge. In contrast, amiloride did not inhibit the frequency of action potential discharge in response to depolarizing current injection (n = 6). In summary, mechanical stimulation depolarizes and triggers action potentials in a subpopulation of nodose sensory neurons in culture. The DEG/ENaC blocker amiloride at a concentration of 1 microM inhibits responses to mechanical stimulation without suppressing membrane excitability. The results support the hypothesis that DEG/ENaC subunits are components of mechanosensitive ion channels on vagal afferent and baroreceptor neurons. PMID:12144042

  16. Commonalities in Development of Pure Breeds and Population Isolates Revealed in the Genome of the Sardinian Fonni's Dog

    PubMed Central

    Dreger, Dayna L.; Davis, Brian W.; Cocco, Raffaella; Sechi, Sara; Di Cerbo, Alessandro; Parker, Heidi G.; Polli, Michele; Marelli, Stefano P.; Crepaldi, Paola; Ostrander, Elaine A.

    2016-01-01

    The island inhabitants of Sardinia have long been a focus for studies of complex human traits due to their unique ancestral background and population isolation reflecting geographic and cultural restriction. Population isolates share decreased genomic diversity, increased linkage disequilibrium, and increased inbreeding coefficients. In many regions, dogs and humans have been exposed to the same natural and artificial forces of environment, growth, and migration. Distinct dog breeds have arisen through human-driven selection of characteristics to meet an ideal standard of appearance and function. The Fonni’s Dog, an endemic dog population on Sardinia, has not been subjected to an intensive system of artificial selection, but rather has developed alongside the human population of Sardinia, influenced by geographic isolation and unregulated selection based on its environmental adaptation and aptitude for owner-desired behaviors. Through analysis of 28 dog breeds, represented with whole-genome sequences from 13 dogs and ∼170,000 genome-wide single nucleotide variants from 155 dogs, we have produced a genomic illustration of the Fonni’s Dog. Genomic patterns confirm within-breed similarity, while population and demographic analyses provide spatial identity of Fonni’s Dog to other Mediterranean breeds. Investigation of admixture and fixation indices reveals insights into the involvement of Fonni’s Dogs in breed development throughout the Mediterranean. We describe how characteristics of population isolates are reflected in dog breeds that have undergone artificial selection, and are mirrored in the Fonni’s Dog through traditional isolating factors that affect human populations. Lastly, we show that the genetic history of Fonni’s Dog parallels demographic events in local human populations. PMID:27519604

  17. 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...

  18. 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

  19. 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.

  20. 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

  1. Isolated nuclei adapt to force and reveal a mechanotransduction pathway in the nucleus.

    PubMed

    Guilluy, Christophe; Osborne, Lukas D; Van Landeghem, Laurianne; Sharek, Lisa; Superfine, Richard; Garcia-Mata, Rafael; Burridge, Keith

    2014-04-01

    Mechanical forces influence many aspects of cell behaviour. Forces are detected and transduced into biochemical signals by force-bearing molecular elements located at the cell surface, in adhesion complexes or in cytoskeletal structures. The nucleus is physically connected to the cell surface through the cytoskeleton and the linker of nucleoskeleton and cytoskeleton (LINC) complex, allowing rapid mechanical stress transmission from adhesions to the nucleus. Although it has been demonstrated that nuclei experience force, the direct effect of force on the nucleus is not known. Here we show that isolated nuclei are able to respond to force by adjusting their stiffness to resist the applied tension. Using magnetic tweezers, we found that applying force on nesprin-1 triggers nuclear stiffening that does not involve chromatin or nuclear actin, but requires an intact nuclear lamina and emerin, a protein of the inner nuclear membrane. Emerin becomes tyrosine phosphorylated in response to force and mediates the nuclear mechanical response to tension. Our results demonstrate that mechanotransduction is not restricted to cell surface receptors and adhesions but can occur in the nucleus.

  2. 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

  3. 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.

  4. In vitro sensitivity of Plasmodium falciparum field isolates to extracts from Cameroonian Annonaceae plants.

    PubMed

    Kemgne, Eugénie Aimée Madiesse; Mbacham, Wilfred Fon; Boyom, Fabrice Fekam; Zollo, Paul Henri Amvam; Tsamo, Etienne; Rosenthal, Philip J

    2012-01-01

    In a search for new plant-derived antimalarial extracts, 19 fractions were obtained from three Annonaceae species, Uvariopsis congolana (leaf, stem), Polyalthia oliveri (stem bark), and Enantia chlorantha (stem, stem bark) with yields ranging from 0.33% to 4.60%. The extracts were prepared from 500 g of each plant part, using organic solvents to afford five methanolic fractions (acetogenin rich), five water fractions, five hexane fractions, and four interface precipitates. Evaluation of the activity of fractions in vitro against field isolates of the malaria parasite Plasmodium falciparum showed that acetogenin-rich fractions and interface precipitates were the most potent, with IC(50) values ranging from 0.05 to 8.09 μg/ml. Sensitivity of parasite isolates to plant extracts varied greatly, with over 100-fold difference from isolate to isolate in some cases. The active acetogenin-rich fractions and interface precipitates were assessed in combination with chloroquine in the same conditions, and showed additive interaction in the huge majority of cases. Synergistic interactions were found in some cases with acetogenin-rich fractions. Acute toxicity of promising fractions was evaluated through oral administration in Swiss albino mice. Tested fractions appeared to be safe, with LD(50) values higher than 2 g/kg. In summary, acetogenin-rich fractions from Annonaceae species showed high potency against P. falciparum field isolates and safety by oral administration in mice, supporting their detailed investigation for antimalarial drug discovery.

  5. Whole Genome Comparison of Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity

    PubMed Central

    Dorrell, Nick; Mangan, Joseph A.; Laing, Kenneth G.; Hinds, Jason; Linton, Dennis; Al-Ghusein, Hasan; Barrell, Bart G.; Parkhill, Julian; Stoker, Neil G.; Karlyshev, Andrey V.; Butcher, Philip D.; Wren, Brendan W.

    2001-01-01

    Campylobacter jejuni is the leading cause of bacterial food-borne diarrhoeal disease throughout the world, and yet is still a poorly understood pathogen. Whole genome microarray comparisons of 11 C. jejuni strains of diverse origin identified genes in up to 30 NCTC 11168 loci ranging from 0.7 to 18.7 kb that are either absent or highly divergent in these isolates. Many of these regions are associated with the biosynthesis of surface structures including flagella, lipo-oligosaccharide, and the newly identified capsule. Other strain-variable genes of known function include those responsible for iron acquisition, DNA restriction/modification, and sialylation. In fact, at least 21% of genes in the sequenced strain appear dispensable as they are absent or highly divergent in one or more of the isolates tested, thus defining 1300 C. jejuni core genes. Such core genes contribute mainly to metabolic, biosynthetic, cellular, and regulatory processes, but many virulence determinants are also conserved. Comparison of the capsule biosynthesis locus revealed conservation of all the genes in this region in strains with the same Penner serotype as strain NCTC 11168. By contrast, between 5 and 17 NCTC 11168 genes in this region are either absent or highly divergent in strains of a different serotype from the sequenced strain, providing further evidence that the capsule accounts for Penner serotype specificity. These studies reveal extensive genetic diversity among C. jejuni strains and pave the way toward identifying correlates of pathogenicity and developing improved epidemiological tools for this problematic pathogen. PMID:11591647

  6. Strain field reconstruction in shallow trench isolation structures by CBED and LACBED

    NASA Astrophysics Data System (ADS)

    Spessot, A.; Frabboni, S.; Balboni, R.; Armigliato, A.

    2006-12-01

    Using a combination of the CBED and the LACBED techniques in the transmission electron microscopy (TEM), we have investigated the strain field in the silicon active region of a shallow trench isolation structure, underlying a TiSi 2 layer. Starting from the analysis of the deformation in a sample, thinned for TEM analysis, we have reconstructed the displacement field, simulating the split HOLZ lines visible in the experimental CBED patterns. From the comparison between the experimental LACBED patterns, taken in a suitable sample orientation to evidence the stressors distribution in the polycrystalline silicide layer, and the corresponding dynamically simulated ones, we have reproduced the strain field in the unthinned, bulk sample.

  7. A Brucella spp. Isolate from a Pac-Man Frog (Ceratophrys ornata) Reveals Characteristics Departing from Classical Brucellae

    PubMed Central

    Soler-Lloréns, Pedro F.; Quance, Chris R.; Lawhon, Sara D.; Stuber, Tod P.; Edwards, John F.; Ficht, Thomas A.; Robbe-Austerman, Suelee; O'Callaghan, David; Keriel, Anne

    2016-01-01

    Brucella are highly infectious bacterial pathogens responsible for brucellosis, a frequent worldwide zoonosis. The Brucella genus has recently expanded from 6 to 11 species, all of which were associated with mammals; The natural host range recently expanded to amphibians after some reports of atypical strains from frogs. Here we describe the first in depth phenotypic and genetic characterization of a Brucella strains isolated from a frog. Strain B13-0095 was isolated from a Pac-Man frog (Ceratophyrus ornate) at a veterinary hospital in Texas and was initially misidentified as Ochrobactrum anthropi. We found that B13-0095 belongs to a group of early-diverging brucellae that includes Brucella inopinata strain BO1 and the B. inopinata-like strain BO2, with traits that depart significantly from those of the “classical” Brucella spp. Analysis of B13-0095 genome sequence revealed several specific features that suggest that this isolate represents an intermediate between a soil associated ancestor and the host adapted “classical” species. Like strain BO2, B13-0095 does not possess the genes required to produce the perosamine based LPS found in classical Brucella, but has a set of genes that could encode a rhamnose based O-antigen. Despite this, B13-0095 has a very fast intracellular replication rate in both epithelial cells and macrophages. Finally, another major finding in this study is the bacterial motility observed for strains B13-0095, BO1, and BO2, which is remarkable for this bacterial genus. This study thus highlights several novel characteristics in strains belonging to an emerging group within the Brucella genus. Accurate identification tools for such atypical Brucella isolates and careful evaluation of their zoonotic potential, are urgently required. PMID:27734009

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

    PubMed

    Siddiqi, Muhammad Zubair; Kim, Yeon-Ju; Hoang, Van-An; Siddiqi, Muhammad Hanif; Huq, Md Amdadul; Yang, Deok-Chun

    2014-12-01

    A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81(T), and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81(T) belonged to the genus Arthrobacter. Major fatty acid was anteiso-C15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H2). The peptidoglycan type was A3α with an L-Lys-L-Ala-L-Thr-L-Ala interpeptide bridge. The DNA-DNA hybridization relatedness between strain DCY81(T) and Arthrobacter siccitolerans LMG 27359(T) (98.2 %), Arthrobacter sulfonivorans JCM 13520(T) (97.81 %), Arthrobacter scleromae DSM 17756(T) (97.59 %), Arthrobacter oxydans KCTC 3383(T) (97.3 %) was 39.1 ± 0.2, 62.2 ± 1.6, 36.8 ± 1.1 and 48.3 ± 1.6 %, respectively which show that the genotypic separation of strain DCY81(T) from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2 mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81(T) represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225(T) = JCM 19357(T)). PMID:25150449

  9. Arthrobacter ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Siddiqi, Muhammad Zubair; Kim, Yeon-Ju; Hoang, Van-An; Siddiqi, Muhammad Hanif; Huq, Md Amdadul; Yang, Deok-Chun

    2014-12-01

    A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81(T), and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81(T) belonged to the genus Arthrobacter. Major fatty acid was anteiso-C15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H2). The peptidoglycan type was A3α with an L-Lys-L-Ala-L-Thr-L-Ala interpeptide bridge. The DNA-DNA hybridization relatedness between strain DCY81(T) and Arthrobacter siccitolerans LMG 27359(T) (98.2 %), Arthrobacter sulfonivorans JCM 13520(T) (97.81 %), Arthrobacter scleromae DSM 17756(T) (97.59 %), Arthrobacter oxydans KCTC 3383(T) (97.3 %) was 39.1 ± 0.2, 62.2 ± 1.6, 36.8 ± 1.1 and 48.3 ± 1.6 %, respectively which show that the genotypic separation of strain DCY81(T) from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2 mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81(T) represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225(T) = JCM 19357(T)).

  10. 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

  11. Analysis of Group B Streptococcal Isolates from Infants and Pregnant Women in Portugal Revealing Two Lineages with Enhanced Invasiveness▿

    PubMed Central

    Martins, E. R.; Pessanha, M. A.; Ramirez, M.; Melo-Cristino, J.

    2007-01-01

    The populations of group B streptococcus (GBS) associated with vaginal carriage in pregnant women and invasive neonatal infections in Portugal were compared. GBS isolates were characterized by serotyping, pulsed-field gel electrophoresis (PFGE) profiling, and multilocus sequence typing (MLST). Serotypes III and V accounted for 44% of all colonization isolates (n = 269), whereas serotypes III and Ia amounted to 69% of all invasive isolates (n = 64). Whereas serotype Ia was associated with early-onset disease (EOD), serotype III was associated with late-onset disease (LOD). Characterization by PFGE and MLST identified very diverse populations in carriage and invasive disease. Serotype Ia was represented mainly by a single PFGE cluster defined by sequence type 23 (ST23) and the infrequent ST24. In contrast, serotype III was found in a large number of PFGE clusters and STs, but a single PFGE cluster defined by ST17 was found to be associated with invasive disease. Although serotype III was associated only with LOD, ST17 showed an enhanced capacity to cause both EOD and LOD. Our data reinforce the evidence for enhanced invasiveness of ST17 and identify a lineage expressing serotype Ia capsule and represented by ST23 and ST24 as having enhanced potential to cause EOD. PMID:17699641

  12. 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

  13. 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

    2015-10-30

    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.

  14. 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

  15. Handling and isolation in three strains of rats affect open field, exploration, hoarding and predation.

    PubMed

    Rebouças, R C; Schmidek, W R

    1997-11-01

    Male albino (Al), brown hooded (Br) and black hooded (Bl) rats were raised in social isolation or in pairs, with or without systematic handling. At 90 and 180 days of age, the animals were individually tested for activity in an open field (Of), exploratory behavior in a complex environment, food hoarding (Hd) and insect predation (Pd). Multivariate analysis of the results showed significant influences of all three factors (strain, handling and social isolation) and interactions among them. Strain affected Of, Hd and Pd, with contrastingly high performances of Br in Of, Al in Hd and Bl in Pd. Handling increased Of and exploration scores in both test series. Isolation induced higher performances in all the four behaviors in the second test series. Accentuated and stable individual differences occurred in the performances off all the behaviors. The results emphasize the subtleness and complexity of the interplay of genetic and environmental influences and stress the independence of the regulatory processes of different behaviors.

  16. 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

  17. Molecular characterization of Salmonella enterica subsp. enterica serovar choleraesuis field isolates and differentiation from homologous live vaccine strains suisaloral and SC-54.

    PubMed Central

    Weide-Botjes, M; Liebisch, B; Schwarz, S; Watts, J L

    1996-01-01

    Four independent molecular methods were used to characterize the Salmonella enterica subsp. enterica serovar choleraesuis live vaccine strains SC-54 and Suisaloral and to differentiate them from S. choleraesuis field isolates. Plasmid analysis revealed the presence of seven plasmid profiles. A virulence plasmid of 52-kbp was identified by hybridization with an spvB-spvC gene probe in each of the S. choleraesuis field isolates and in the Suisaloral vaccine strain, but not in the SC-54 vaccine strain. Ribotyping, performed with a gene probe that recognized 23S, 16S, and 5S rRNA genes, resulted in three closely related hybridization patterns. IS200 elements were not detected in the field isolates or in the two S. choleraesuis live vaccine strains. Macrorestriction analysis with the enzymes XbaI, SpeI, NotI, and SfiI differentiated the 29 S. choleraesuis strains included in this study into 10, 13, 8, and 13 different fragment patterns, respectively. While the Suisaloral vaccine strain showed a unique XbaI macrorestriction pattern, the fragment patterns of the SC-54 strain obtained with the different enzymes were shared by 2 to 18 S. choleraesuis field strains. A combination of plasmid analysis and macrorestriction analysis proved to be most suitable for the molecular typing of S. choleraesuis and the differentiation of both live vaccine strains from field isolates of this serovar. PMID:8880500

  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. 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

  20. 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

  1. 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.

  2. 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

  3. Identification and Characterization of Pathogenic Yersinia enterocolitica Isolates by PCR and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Thisted Lambertz, S.; Danielsson-Tham, M.-L.

    2005-01-01

    Approximately 550 to 600 yersiniosis patients are reported annually in Sweden. Although pigs are thought to be the main reservoir of food-borne pathogenic Yersinia enterocolitica, the role of pork meat as a vehicle for transmission to humans is still unclear. Pork meat collected from refrigerators and local shops frequented by yersiniosis patients (n = 48) were examined for the presence of pathogenic Yersinia spp. A combined culture and PCR method was used for detection, and a multiplex PCR was developed and evaluated as a tool for efficient identification of pathogenic food and patient isolates. The results obtained with the multiplex PCR were compared to phenotypic test results and confirmed by pulsed-field gel electrophoresis (PFGE). In all, 118 pork products (91 raw and 27 ready-to-eat) were collected. Pathogenic Yersinia spp. were detected by PCR in 10% (9 of 91) of the raw pork samples (loin of pork, fillet of pork, pork chop, ham, and minced meat) but in none of the ready-to-eat products. Isolates of Y. enterocolitica bioserotype 4/O:3 were recovered from six of the PCR-positive raw pork samples; all harbored the virulence plasmid. All isolates were recovered from food collected in shops and, thus, none were from the patients' home. When subjected to PFGE, the six isolates displayed four different NotI profiles. The same four NotI profiles were also present among isolates recovered from the yersiniosis patients. The application of a multiplex PCR was shown to be an efficient tool for identification of pathogenic Y. enterocolitica isolates in naturally contaminated raw pork. PMID:16000776

  4. 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

  5. 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.

  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. 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

  8. 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

  9. 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)).

  10. 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).

  11. Pulsed-field gel electrophoresis and ribotype profiles of clinical and environmental Vibrio vulnificus isolates.

    PubMed Central

    Tamplin, M L; Jackson, J K; Buchrieser, C; Murphree, R L; Portier, K M; Gangar, V; Miller, L G; Kaspar, C W

    1996-01-01

    Vibrio vulnificus belongs to the autochthonous bacterial flora of warm estuarine waters. It can cause life-threatening extraintestinal disease in persons who have underlying illness and who consume raw shellfish or contact wounds with estuarine water. Currently, very little is known about genetic diversity within this species. In this report, we describe high-level variation in restriction fragment length polymorphism profiles among 53 clinical and 78 environmental isolates, as determined by pulsed-field gel electrophoresis. In contrast, ribotype profiles showed greater similarity. When combined ribotype profiles of clinical and environmental isolates were analyzed, four predominant clusters were observed. Interestingly, a low number (16%) of clinical isolates were found in cluster C, compared with clusters A, B, and D (range, 50 to 83%). In addition, 83% of all Hawaiian isolates were located in a single cluster, indicating a possible relationship between geography and genotype. We also report that spontaneous translucent colonial morphotypes were distinct by both restriction fragment length polymorphism and biochemical profiles, compared with opaque parent strains. PMID:8837412

  12. Isolation and characterization of antagonistic fungi against potato scab pathogens from potato field soils.

    PubMed

    Tagawa, Masahiro; Tamaki, Hideyuki; Manome, Akira; Koyama, Osamu; Kamagata, Yoichi

    2010-04-01

    Potato scab is a serious plant disease caused by several Streptomyces sp., and effective control methods remain unavailable. Although antagonistic bacteria and phages against potato scab pathogens have been reported, to the best of our knowledge, there is no information about fungi that are antagonistic to the pathogens. The aim of this study was to isolate fungal antagonists, characterize their phylogenetic positions, determine their antagonistic activities against potato scab pathogens, and highlight their potential use as control agents under lower pH conditions. Fifteen fungal stains isolated from potato field soils were found to have antagonistic activity against three well-known potato scab pathogens: Streptomyces scabiei, Streptomyces acidiscabiei, and Streptomyces turgidiscabiei. These 15 fungal strains were phylogenetically classified into at least six orders and nine genera based on 18S rRNA gene sequencing analysis. These fungal isolates were related to members of the genera Penicillium, Eupenicillium, Chaetomium, Fusarium, Cladosporium, Mortierella, Kionochaeta, Pseudogymnoascus, and Lecythophora. The antagonistic activities of most of the fungal isolates were highly strengthened under the lower pH conditions, suggesting the advantage of combining their use with a traditional method such as soil acidification. This is the first report to demonstrate that phylogenetically diverse fungi show antagonistic activity against major potato scab pathogens. These fungal strains could be used as potential agents to control potato scab disease.

  13. Intraspecific variation of Rhizoctonia solani AG 3 isolates recovered from potato fields in Central Iran and South Australia.

    PubMed

    Balali, G R; Neate, S M; Kasalkheh, A M; Stodart, B J; Melanson, D L; Scott, E S

    2007-02-01

    Pectic zymogram, RFLP and PCR analyses were used to characterize Rhizoctonia solani AG 3 isolates collected from diseased potatoes in South Australia. The pectic zymogram data were compared with those obtained for isolates collected from central Iran. Analyses of bands corresponding to pectin esterase and polygalacturonase revealed three zymogram subgroups (ZG) in AG 3. In addition to the previously reported ZG7 (here renamed ZG7-1), two new zymogram subgroups, ZG7-2 and ZG7-3, were identified. Of the 446 isolates tested, 50% of the South Australian and 46% of the Iranian isolates were ZG7-1. The majority of the isolates originating from stem and root cankers were ZG7-1, whereas most of the isolates designated ZG7-2 and ZG7-3 originated from tuber-borne sclerotia. Pathogenicity tests revealed that ZG7-1 generally produced fewer sclerotia and more severe cankers of underground parts of the potato plants than the other two ZGs. Two random DNA clones, one originating from an AG 3 isolate and the other from an AG 4 isolate, were used as probes for RFLP analyses of Australian isolates. The AG 3 probe, previously identified to be specific to this group, detected a high level of genetic diversity, with 11 genotypes identified amongst 50 isolates analysed. The low-copy AG 4 probe resolved three genotypes amongst 24 isolates. For 23 isolates analysed with both markers, the combined data distinguished a total of six genotypes and similarity analysis resolved the isolates into two main groups with 50% homology. PCR, using primers for the plant intron splice junction region (R1), also revealed variation. No obvious relationship among pectic zymogram groups, RFLP and PCR genotypes was observed.

  14. [Characteristics of field isolates of Newcastle disease virus isolated in the course of outbreaks in the poultry plant in the Leningrad region in 2000].

    PubMed

    Manin, T B; Shcherbakova, L O; Bochkov, Iu A; El'nikov, V V; Pchelkina, I P; Starov, S K; Drygin, V V

    2002-01-01

    A field isolate of Newcastle disease virus (NDV) was isolated in the Russko-Vysotskaya poultry farm, Leningrad region. Within four days after infection, the isolate caused 100% mortality in 60-day-old susceptible chickens. The HA titer of the allantoic fluid samples collected after one passage in SPF-chicken embryos was 1:512, and it reacted only with the NDV specific antiserum in HI test. Intracerebral pathogenicity index and mean embryo death time were 1.97 and 49 hours, respectively. The isolate has the amino acid sequence of the protease cleavage site of the fusion protein F0 (112R-R-Q-R-R-F117), which is similar to that in the velogenic strains of NDV. Therefore, it was concluded that the virus isolated in this work was an ethiological agent of the ND outbreak in this poultry farm.

  15. The isolated head model of the plasma bullet/streamer propagation: electric field-velocity relation

    NASA Astrophysics Data System (ADS)

    Sretenović, Goran B.; Krstić, Ivan B.; Kovačević, Vesna V.; Obradović, Bratislav M.; Kuraica, Milorad M.

    2014-09-01

    A model of the isolated streamer head based on Meek's criterion of the avalanche to streamer transition is applied for description of the plasma bullet propagation in a helium/air admixture. According to the model previously proposed by Kulikovsky for streamers in air, along with the knowledge of one of three parameters: electric field, ionization integral or the width of the space charge layer, the other two parameters could be determined. Furthermore, using the streamer current or radius, it is possible to determine the electric field-streamer velocity functional dependence. Obtained results showed satisfactory agreement with both the results of the fluid model from the literature and the experimental results of plasma jet studies. Finally, for the sake of comparison, streamer velocity dependence on the electric field strength range of 10-250 kV cm-1 is determined for helium, argon and air.

  16. 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

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

    PubMed

    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 F ST 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.

  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. First clinical isolates of Cronobacter spp. (Enterobacter sakazakii) in Argentina: characterization and subtyping by pulsed-field gel electrophoresis.

    PubMed

    Asato, Valeria C; Vilches, Viviana E; Pineda, María G; Casanueva, Enrique; Cane, Alejandro; Moroni, Mirian P; Brengi, Silvina P; Pichel, Mariana G

    2013-01-01

    Cronobacter species are opportunistic pathogens associated with severe infections in neonates and immunocompromised infants. From January 2009 through September 2010, two cases of neonatal infections associated with Cronobacter malonaticus and one case associated with Cronobacter sakazakii, two of them fatal, were reported in the same hospital. These are the first clinical isolates of Cronobacter spp. in Argentina. The objective of this work was to characterize and subtype clinical isolates of Cronobacter spp. in neonate patients, as well as to establish the genetic relationship between these isolates and the foodborne isolates previously identified in the country. Pulsed-field gel electrophoresis analysis showed a genetic relationship between the C. malonaticus isolates from two patients. Different results were found when the pulsed-field gel electrophoresis patterns of clinical isolates were compared with those deposited in the National Database of Cronobacter spp.

  20. The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.

    PubMed

    Sailaja, B; Anjum, Najreen; Patil, Yogesh K; Agarwal, Surekha; Malathi, P; Krishnaveni, D; Balachandran, S M; Viraktamath, B C; Mangrauthia, Satendra K

    2013-12-01

    In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95% to east Indian isolates and 90% to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5' end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.

  1. 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.

  2. 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

  3. 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

  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. 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.

  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. 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.

  9. Phylogenetic analysis of spring virema of carp virus reveals distinct subgroups with common origins for recent isolates in North America and the UK.

    PubMed

    Miller, O; Fuller, F J; Gebreyes, W A; Lewbart, G A; Shchelkunov, I S; Shivappa, R B; Joiner, C; Woolford, G; Stone, D M; Dixon, P F; Raley, M E; Levine, J F

    2007-07-16

    Genetic relationships between 35 spring viremia of carp virus (SVCV) genogroup Ia isolates were determined based on the nucleotide sequences of the phosphoprotein (P) gene and glycoprotein (G) genes. Phylogenetic analysis based on P gene sequences revealed 2 distinct subgroups within SVCV genogroup Ia, designated SVCV Iai and Iaii, and suggests at least 2 independent introductions of the virus into the USA in 2002. Combined P- and G-sequence data support the emergence of SVCV in Illinois, USA, and in Lake Ontario, Canada, from the initial outbreak in Wisconsin, USA, and demonstrate a close genetic link to viruses isolated during routine import checks on fish brought into the UK from Asia. The data also showed a genetic link between SVCV isolations made in Missouri and Washington, USA, in 2004 and the earlier isolation made in North Carolina, USA, in 2002. However, based on the close relationship to a 2004 UK isolate, the data suggest than the Washington isolate represents a third introduction into the US from a common source, rather than a reemergence from the 2002 isolate. There was strong phylogenetic support for an Asian origin for 9 of 16 UK viruses isolated either from imported fish, or shown to have been in direct contact with fish imported from Asia. In one case, there was 100% nucleotide identity in the G-gene with a virus isolated in China.

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

    PubMed

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

    2001-09-01

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

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

    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 by transformation of field isolates (TM2, ZN19, B2 and B8) that origin...

  12. 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...

  13. 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

  14. 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.

  15. A Genome-Wide Association Study in isolated populations reveals new genes associated to common food likings.

    PubMed

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; Amin, Najaf; Sala, Cinzia; Karssen, Lennart C; Van Duijn, Cornelia; Toniolo, Daniela; Gasparini, Paolo

    2016-06-01

    Food preferences are the first factor driving food choice and thus nutrition. They involve numerous different senses such as taste and olfaction as well as various other factors such as personal experiences and hedonistic aspects. Although it is clear that several of these have a genetic basis, up to now studies have focused mostly on the effects of polymorphisms of taste receptor genes. Therefore, we have carried out one of the first large scale (4611 individuals) GWAS on food likings assessed for 20 specific food likings belonging to 4 different categories (vegetables, fatty, dairy and bitter). A two-step meta-analysis using three different isolated populations from Italy for the discovery step and two populations from The Netherlands and Central Asia for replication, revealed 15 independent genome-wide significant loci (p < 5 × 10(-8)) for 12 different foods. None of the identified genes coded for either taste or olfactory receptors suggesting that genetics impacts in determining food likings in a much broader way than simple differences in taste perception. These results represent a further step in uncovering the genes that underlie liking of common foods that in the end will greatly help understanding the genetics of human nutrition in general. PMID:27129595

  16. 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

  17. Luminescence spectroscopy of matrix-isolated atomic manganese: site size and orbital occupancy dependence of crystal field splitting.

    PubMed

    Collier, Martin A; Byrne, Owen; Murray, Ciaran; McCaffrey, John G

    2010-04-28

    Narrow linewidth emission features observed in the near-UV following y (6)P state excitation of atomic manganese isolated in the solid rare gases are assigned to b (4)D and a (4)P states. These states arise from the 3d(5)4s(2) electronic configuration, identical to that of the (6)S ground state, and the origin of the narrow linewidths. Two thermally stable sites, labeled blue and red on the basis of their position in absorption spectra, are occupied by atomic Mn in Ar and Kr while a single site is present in Xe. The red site produces a single, narrow line emission for the b (4)D state at 329 nm. In contrast, a lineshape analysis of the complex blue site b (4)D state emission between 331 and 332 nm reveals the occurrence of three zero phonon lines (ZPLs). Millisecond emission decay curves recorded for these features are found to be complex, requiring double and triple exponential fit functions. The origins of the complex decays and multiple ZPLs are shown to arise from weak crystal field splitting (CFS) of the J=7/2 spin-orbit level of the b (4)D state of atomic Mn isolated in the blue site of the solid rare gases. Fields of cubic symmetry are capable of inducing splitting for J>3/2 so atoms isolated in both single vacancy and tetravacancy sites in the fcc lattices of the solid rare gases are prone to this effect. b (4)D state emission is also produced following y (6)P excitation for Mn atoms occupying the red sites in Ar and Kr. However, Mn atoms isolated in the larger tetravacancy sites have small matrix shifts and do not exhibit any CFS. The magnitudes of the weak CF splittings are shown to depend on both the excited state electronic configurations 3d(5)4s(2) b (4)D and 3d(6)4s(1) a (4)D states and the size of the matrix site occupied by atomic Mn.

  18. 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.

  19. 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

  20. 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

  1. 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

    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

    2015-04-01

    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.

  2. 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.

  3. 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.

  4. 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

  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. Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

    PubMed Central

    Gouré, Julien; Findlay, Wendy A; Deslandes, Vincent; Bouevitch, Anne; Foote, Simon J; MacInnes, Janet I; Coulton, James W; Nash, John HE; Jacques, Mario

    2009-01-01

    Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH) were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology. PMID:19239696

  7. Genotypic diversity in Babesia bovis field isolates and vaccine strains from South Africa.

    PubMed

    Combrink, M P; Troskie, P C; Pienaar, R; Latif, A A; Mans, B J

    2014-01-31

    Genotypic diversity in Babesia bovis (cause of Asiatic redwater in cattle) vaccine strains and field isolates from South Africa were investigated using the Bv80 gene as well as microsatellites. The S11 vaccine strain possessed both A and B alleles of the Bv80 gene, as well as genotypic diversity within each allele type as defined by repeat variation resulting in different amplicon sizes. Rapid serial passage of vaccine strain from passage S10 to S24 resulted in loss of genotypic diversity that yielded a single allele A genotype with an amplicon size of 558 bp. This suggested that clonal selection occurred during rapid passaging. Extensive genotypic diversity exists in 44 field isolates characterized with both Bv80 A and B alleles, but can be readily distinguished from the S24 vaccine strain using either the Bv80 allele specific PCR assays or using multi-locus micro-satellite typing. This indicated that no recent documented clinical cases of Asiatic redwater were caused by the reversion to virulence of the current vaccine strain.

  8. 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

  9. Characterization of Fusarium isolates from asparagus fields in southwestern Ontario and influence of soil organic amendments on Fusarium crown and root rot.

    PubMed

    Borrego-Benjumea, Ana; Basallote-Ureba, María J; Melero-Vara, José M; Abbasi, Pervaiz A

    2014-04-01

    Fusarium crown and root rot (FCRR) of asparagus has a complex etiology with several soilborne Fusarium spp. as causal agents. Ninety-three Fusarium isolates, obtained from plant and soil samples collected from commercial asparagus fields in southwestern Ontario with a history of FCRR, were identified as Fusarium oxysporum (65.5%), F. proliferatum (18.3%), F. solani (6.4%), F. acuminatum (6.4%), and F. redolens (3.2%) based on morphological or cultural characteristics and polymerase chain reaction (PCR) analysis with species-specific primers. The intersimple-sequence repeat PCR analysis of the field isolates revealed considerable variability among the isolates belonging to different Fusarium spp. In the in vitro pathogenicity screening tests, 50% of the field isolates were pathogenic to asparagus, and 22% of the isolates caused the most severe symptoms on asparagus. The management of FCRR with soil organic amendments of pelleted poultry manure (PPM), olive residue compost, and fish emulsion was evaluated in a greenhouse using three asparagus cultivars of different susceptibility in soils infested with two of the pathogenic isolates (F. oxysporum Fo-1.5 and F. solani Fs-1.12). Lower FCRR symptom severity and higher plant weights were observed for most treatments on 'Jersey Giant' and 'Grande' but not on 'Mary Washington'. On all three cultivars, 1% PPM consistently reduced FCRR severity by 42 to 96% and increased plant weights by 77 to 152% compared with the Fusarium control treatment. Populations of Fusarium and total bacteria were enumerated after 1, 3, 7, and 14 days of soil amendment. In amended soils, the population of Fusarium spp. gradually decreased while the population of total culturable bacteria increased. These results indicate that soil organic amendments, especially PPM, can decrease disease severity and promote plant growth, possibly by decreasing pathogen population and enhancing bacterial activity in the soil.

  10. Quantum interference control of an isolated resonance lifetime in the weak-field limit.

    PubMed

    García-Vela, A

    2015-11-21

    Resonance states play an important role in a large variety of physical and chemical processes. Thus, controlling the resonance behavior, and particularly a key property like the resonance lifetime, opens up the possibility of controlling those resonance mediated processes. While such a resonance control is possible by applying strong-field approaches, the development of flexible weak-field control schemes that do not alter significantly the system dynamics still remains a challenge. In this work, one such control scheme within the weak-field regime is proposed for the first time in order to modify the lifetime of an isolated resonance state. The basis of the scheme suggested is quantum interference between two pathways induced by laser fields, that pump wave packet amplitude to the target resonance under control. The simulations reported here show that the scheme allows for both enhancement and quenching of the resonance survival lifetime, being particularly flexible to achieve large lifetime enhancements. Control effects on the resonance lifetime take place only while the pulse is operating. In addition, the conditions required to generate the two interfering quantum pathways are found to be rather easy to meet for general systems, which makes the experimental implementation straightforward and implies the wide applicability of the control scheme.

  11. Revealing molecular structure and dynamics through high harmonic generation driven by mid-IR fields

    NASA Astrophysics Data System (ADS)

    Marangos, Jonathan

    2010-03-01

    High harmonic generation (HHG) from molecules has recently been shown to be a promising tool for measuring instantaneous molecular structure, sub-femtosecond domain structural rearrangements in molecules and even hole dynamics initiated by laser field ionisation. To fully exploit this promise it is essential that we can; (1) systematically decouple structural and dynamic effects so that both may simultaneously be determined in the measurement, (2) can extend the method of molecular HHG imaging to a wide range of molecules. Here we demonstrate important steps towards both these objectives. Up until now HHG imaging measurements have been restricted to drive laser wavelengths close to 800nm, due to the availability of CPA titanium sapphire lasers, which dictates the use of relatively high intensities (> 2.5 x 10^14 Wcm-2) if a harmonic spectrum spanning to ˜70 eV is to be observed which is required for extracting structural data from most small molecules. By using a mid-IR laser (at 1300 nm) we show that with an intensity ˜ 1 x 10^14 W cm-2 we can observe a wide molecular harmonic spectrum spanning to ˜ 70 eV even in molecules where ionization saturation would clamp the cut-off to much lower energies if an 800nm field were used. Thus we have been able to observe evidence for two-centre interference in two new molecules, N2O and C2H2 for the first time. Moreover we can use the ability to observe a broad harmonic spectrum over a large range of intensities to reveal the subtle interplay between structural and dynamic effects in CO2 and so provide a new window into hole dynamics. [4pt] In collaboration with R. Torres, Blackett Laboratory, Imperial College London; O. Smirnova, Max-Born-Institute, Berlin; T. Siegel and L. Brugnera, Blackett Laboratory, Imperial College London; I. Procino and Jonathan G. Underwood, Department of Physics and Astronomy, University College London; C. Altucci and R. Velotta, CNSIM and Dipartimento di Scienze Fisiche, Universita di Napoli

  12. Calcium homeostasis of isolated heart muscle cells exposed to pulsed high-frequency electromagnetic fields

    SciTech Connect

    Wolke, S.; Gollnick, F.; Meyer, R.; Neibig, U.; Elsner, R.

    1996-05-01

    The intracellular calcium concentration ([Ca{sup 2+}]{sub i}) of isolated ventricular cardiac myocytes of the guinea pig was measured during the application of pulsed high-frequency electromagnetic fields. The high-frequency fields were applied in a transverse electromagnetic cell designed to allow microscopic observation of the myocytes during the presence of the high-frequency fields. The [Ca{sup 2+}]{sub i} was measured as fura-2 fluorescence by means of digital image analysis. Both the carrier frequency and the square-wave pulse-modulation pattern were varied during the experiments (carrier frequencies: 900, 1,300, and 1,800 MHz pulse modulated at 217 Hz with 14% duty cycle; pulsation pattern at 900 MHz; continuous wave, 16 Hz,and 50 Hz modulation with 50% duty cycle and 30 kHz modulation with 80% duty cycle). The mean specific absorption rate (SAR) values in the solution were within one order of magnitude of 1 mW/kg. They varied depending on the applied carrier frequency and pulse pattern. The experiments were designed in three phases: 500 s of sham exposure, followed by 500 s of field exposure, then chemical stimulation without field. The chemical stimulation (K{sup +}-depolarization) indicated the viability of the cells. The K{sup +} depolarization yielded a significant increase in [Ca{sup 2+}]{sub i}. Significant differences between sham exposure and high-frequency field exposure were not found except when a very small but statistically significant difference was detected in the case of 900 MHz/50 Hz. However, this small difference was not regarded as a relevant effect of the exposure.

  13. 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

  14. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides

    PubMed Central

    Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S.; McBee, Megan E.; Dedon, Peter C.

    2015-01-01

    A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria. PMID:25539917

  15. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

    PubMed

    Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S; McBee, Megan E; Dedon, Peter C

    2015-03-11

    A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.

  16. 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...

  17. 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 (...

  18. Deinococcus soli sp. nov., a gamma-radiation-resistant bacterium isolated from rice field soil.

    PubMed

    Cha, Seho; Srinivasan, Sathiyaraj; Seo, Taegun; Kim, Myung Kyum

    2014-06-01

    A Gram-negative, non-motile, short rod-shaped bacterial strain, designated N5(T), was isolated from a rice field soil in South Korea. Phylogenetic analysis based on the 16S rRNA gene sequence of the new isolate showed that strain N5(T) belongs to the genus Deinococcus, family Deinococcaceae, showing the highest sequence similarity to Deinococcus grandis KACC 11979(T) (98.4 %) and Deinococcus daejeonensis KCTC 13751(T) (97.5 %). Strain N5(T) exhibits resistance to gamma-radiation similar to that of other members of the genus Deinococcus, with a D10 value in excess of 4 kGy. Chemotaxonomic data showed that the most abundant fatty acids are C16:1ω7c (25.25 %), C15:1ω6c (19.77 %), C17:1ω6c (11.87 %), and C17:0 (9.41 %), and the major polar lipid is an unknown phosphoglycolipid. The predominant respiratory quinone is menaquinone MK-8. The DNA G+C content is 71.4 mol%. Phenotypic, phylogenetic, and chemotaxonomic data support designation of strain N5(T) as a novel species of the genus Deinococcus, for which the name Deinococcus soli sp. nov. is proposed. The type strain is N5(T) (=KCTC 33153(T) = JCM 19176(T)).

  19. 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.

  20. 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

  1. 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.

  2. 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.

  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. 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.

  5. 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.

  6. Pulsed-field gel electrophoresis for isolation of full-length phytoplasma chromosomes from plants.

    PubMed

    Marcone, Carmine

    2013-01-01

    Pulsed-field gel electrophoresis (PFGE) is a powerful technique for genomic studies of unculturable plant-pathogenic phytoplasmas, which enables separation of full-length phytoplasma chromosomes from contaminating host plant nucleic acids. The PFGE method described here involves isolation of phytoplasmal DNA from high-titer phytoplasma-infected herbaceous plants using a phytoplasma enrichment procedure, embedding of phytoplasma chromosomes in agarose blocks, and separation of entire phytoplasma chromosomes from contaminating host plant nucleic acids by electrophoresis. Full-length phytoplasma chromosomes are resolved as single, discrete bands in the gel. The identity of these bands can be confirmed by Southern blot hybridization using a ribosomal DNA fragment as a probe. The method does not utilize gamma-irradiation to linearize phytoplasma chromosomes prior to electrophoresis. PMID:22987433

  7. 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

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

    2014-06-01

    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 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 1349 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. 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.

  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. Pulsed-field gel electrophoresis patterns of Escherichia coli O157 isolates from Kansas feedlots.

    PubMed

    Sargeant, J M; Shi, X; Sanderson, M W; Renter, D G; Nagaraja, T G

    2006-01-01

    This study investigated the prevalence and distribution of Escherichia coli O157 genetic types within and among feedlots using pulsed-field gel electrophoresis to separate XbaI-digested DNA. The study population consisted of 300 pens of cattle in 30 feedlots in Kansas that were sampled (feces, water, and water sediment) within a month of being shipped for slaughter. The prevalence of E. coli O157 was 8.5% in feces, 3.1% in water, and 4.5% in water sediment samples. A total of 424 E. coli O157 isolates were characterized by pulsed-field gel electrophoresis, and 139 subtypes (100% Dice similarity with no band differences) were identified. The majority of subtypes (70/139) was identified only once, but nine were identified 10 or more times. Identical subtypes were recovered from both feces and water tanks in 10 feedlots. The majority of subtypes were identified in only one feedlot, and the number of subtypes ranged from one to 23 within a feedlot and from one to seven within a pen. There were 10 feedlots with at least 15 positive samples. In these 10 feedlots, the most common subtype accounted for 16.9-78.6% of the isolates. Common subtypes differed among feedlots. In eight of the 10 feedlots, the most common subtype was identified in multiple pens. The results support a complex ecology for E. coli O157 in feedlot operations, with factors associated with exposure and transmission likely acting at a common level for multiple feedlots, within feedlots, and within pens of cattle.

  10. Relationship between clinical manifestations and pulsed-field gel profiles of Streptococcus canis isolates from dogs and cats.

    PubMed

    Kruger, E Freya; Byrne, Barbara A; Pesavento, Patricia; Hurley, Kate F; Lindsay, Leanne L; Sykes, Jane E

    2010-11-20

    Little is known regarding the degree of genotypic relatedness between Streptococcus canis isolates from dogs and cats. The purpose of this study was to determine whether correlations existed between the genotypes of canine and feline S. canis isolates as determined using pulsed-field gel electrophoresis (PFGE) and different clinical manifestations of disease. Eighty-two isolates of S. canis were examined that had been collected from dogs and cats presenting to the University of California, Davis Veterinary Medical Teaching Hospital (VMTH) between 1998 and 2005. Associated clinical manifestations included sepsis, otitis, pyometra, skin infections, necrotizing fasciitis, respiratory disease, and urinary tract infections. In addition, 9 feline isolates from a southern California shelter that experienced an outbreak of S. canis infection manifesting as necrotizing fasciitis and death were examined. Bacterial isolates were characterized by PFGE analysis using the restriction enzyme SmaI. The relationships between banding patterns were analyzed using gel analysis software combined with visual interpretation. The feline shelter isolates of S. canis were 99% similar in bacterial PFGE profile. The remainder of samples had less than 80% similarity in PFGE banding patterns. The relatedness of the PFGE profile in the feline shelter isolates suggested a clonal origin. In the isolates from the VMTH population, there was no relationship between specific disease manifestations and PFGE profile. PFGE typing does not appear to be useful for identifying isolates associated with specific disease presentations; however may be more useful to identify outbreaks of S. canis infections or to detect clonal populations in outbreaks. PMID:20605376

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  13. 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

  14. 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

  15. Genetic diversity of Cercospora kikuchii isolates from soybean cultured in Argentina as revealed by molecular markers and cercosporin production.

    PubMed

    Lurá, María Cristina; Latorre Rapela, María Gabriela; Vaccari, María Celia; Maumary, Roxana; Soldano, Anabel; Mattio, Mónica; González, Ana María

    2011-05-01

    Leaf blight and purple seed, caused by the fungal pathogen Cercospora kikuchii (Matsumoto & Tomoyasu) M. W. Gardner are very important diseases of soybean (Glycine max L. Merr.) in Argentina. The aims of this work were: (a) to confirm and to assess the genetic variability among C. kikuchii isolates collected from different soybean growing areas in Santa Fe province using inter simple sequence repeats (ISSR) markers and sequence information from the internal transcribed spacer (ITS) region of rDNA and (b) to analyze the cercosporin production of the regional C. kikuchi isolates in order to assess whether there was any relationship between the molecular profiles and the toxin production. Isolates from different regions in Santa Fe province were studied. The sequence of the ITS regions showed high similarity (99-100%) to the GenBank sequences of C. kikuchii BRCK179 (accession number AY633838). The ISSR markers clustered all the isolates into many groups and cercosporin content was highly variable among isolates. No relationship was observed between ITS region, ISSR groups and origin or cercosporin content. The high degree of genetic variability and cercosporin production among isolates compared in this study characterizes a diverse population of C. kikuchii in the region.

  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. 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

  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.

  19. Isolation and RFLP genotyping of Toxoplasma gondii from the domestic dogs (Canis familiaris) from Grenada, West Indies revealed high genetic variability.

    PubMed

    Dubey, J P; Tiwari, K; Chikweto, A; Deallie, C; Sharma, R; Thomas, D; Choudhary, S; Ferreira, L R; Oliveira, S; Verma, S K; Kwok, O C H; Su, C

    2013-11-01

    Stray dogs are considered as sentinels in the epidemiology of Toxoplasma gondii because they are carnivores and eat a variety of foods, including garbage. In the present study, tissues and sera of 249 stray dogs (Canis familiaris) from Grenada, West Indies were examined for T. gondii infection. Sera were examined for antibodies to T. gondii by the modified agglutination test (MAT); 89 (35.7%) of 249 were seropositive with titers of 25 in seven dogs, 50 in 22 dogs, 100 in 22 dogs, 200 or higher in 38 dogs. Hearts of 76 seropositive dogs were bioassayed in mice. Viable T. gondii was isolated from 12 dogs; these isolates were designated TgDogGr1 to TgDogGr12. These isolates were further propagated in cell culture and DNA isolated from cell culture derived tachyzoites of 12 isolates was genotyped using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). The results revealed six genotypes, including ToxoDB PCR-RFLP #1, #2, #3, #7, #13 and #224, with 1, 6, 1, 2, 1 and 1 isolates, respectively. The result supports previous findings that T. gondii population genetics is highly diverse in Grenada.

  20. Complete nucleotide sequence analysis of plasmids in strains of Staphylococcus aureus clone USA300 reveals a high level of identity among isolates with closely related core genome sequences.

    PubMed

    Kennedy, Adam D; Porcella, Stephen F; Martens, Craig; Whitney, Adeline R; Braughton, Kevin R; Chen, Liang; Craig, Carly T; Tenover, Fred C; Kreiswirth, Barry N; Musser, James M; DeLeo, Frank R

    2010-12-01

    A community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain known as pulsed-field type USA300 (USA300) is epidemic in the United States. Previous comparative whole-genome sequencing studies demonstrated that there has been recent clonal emergence of a subset of USA300 isolates, which comprise the epidemic clone. Although the core genomes of these isolates are closely related, the level of diversity among USA300 plasmids was not resolved. Inasmuch as these plasmids might contribute to significant gene diversity among otherwise closely related USA300 isolates, we performed de novo sequencing of endogenous plasmids from 10 previously characterized USA300 clinical isolates obtained from different geographic locations in the United States. All isolates tested contained small (2- to 3-kb) and/or large (27- to 30-kb) plasmids. The large plasmids encoded heavy metal and/or antimicrobial resistance elements, including those that confer resistance to cadmium, bacitracin, macrolides, penicillin, kanamycin, and streptothricin, although all isolates were sensitive to minocycline, doxycycline, trimethoprim-sulfamethoxazole, vancomycin, teicoplanin, and linezolid. One of the USA300 isolates contained an archaic plasmid that encoded staphylococcal enterotoxins R, J, and P. Notably, the large plasmids (27 to 28 kb) from 8 USA300 isolates--those that comprise the epidemic USA300 clone--were virtually identical (99% identity) and similar to a large plasmid from strain USA300_TCH1516 (a previously sequenced USA300 strain from Houston, TX). These plasmids are largely divergent from the 37-kb plasmid of FPR3757, the first sequenced USA300 strain. The high level of plasmid sequence identity among the majority of closely related USA300 isolates is consistent with the recent clonal emergence hypothesis for USA300.

  1. 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).

  2. 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).

  3. Analysis of sequences from field samples reveals the presence of the recently described pepper vein yellows virus (genus Polerovirus) in six additional countries.

    PubMed

    Knierim, Dennis; Tsai, Wen-Shi; Kenyon, Lawrence

    2013-06-01

    Polerovirus infection was detected by reverse transcription polymerase chain reaction (RT-PCR) in 29 pepper plants (Capsicum spp.) and one black nightshade plant (Solanum nigrum) sample collected from fields in India, Indonesia, Mali, Philippines, Thailand and Taiwan. At least two representative samples for each country were selected to generate a general polerovirus RT-PCR product of 1.4 kb length for sequencing. Sequence analysis of the partial genome sequences revealed the presence of pepper vein yellows virus (PeVYV) in all 13 samples. A 1990 Australian herbarium sample of pepper described by serological means as infected with capsicum yellows virus (CYV) was identified by sequence analysis of a partial CP sequence as probably infected with a potato leaf roll virus (PLRV) isolate.

  4. 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

  5. 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

  6. Characterization of a New Vaccinia virus Isolate Reveals the C23L Gene as a Putative Genetic Marker for Autochthonous Group 1 Brazilian Vaccinia virus

    PubMed Central

    Oliveira, Danilo B.; Franco-Luiz, Ana P. M.; Campos, Rafael K.; Guedes, Maria I. M.; Fonseca, Flávio G.; Trindade, Giliane S.; Drumond, Betânia P.; Kroon, Erna G.; Abrahão, Jônatas S.

    2012-01-01

    Since 1999, several Vaccinia virus (VACV) isolates, the etiological agents of bovine vaccinia (BV), have been frequently isolated and characterized with various biological and molecular methods. The results from these approaches have grouped these VACV isolates into two different clusters. This dichotomy has elicited debates surrounding the origin of the Brazilian VACV and its epidemiological significance. To ascertain vital information to settle these debates, we and other research groups have made efforts to identify molecular markers to discriminate VACV from other viruses of the genus Orthopoxvirus (OPV) and other VACV-BR groups. In this way, some genes have been identified as useful markers to discriminate between the VACV-BR groups. However, new markers are needed to infer ancestry and to correlate each sample or group with its unique epidemiological and biological features. The aims of this work were to characterize a new VACV isolate (VACV DMTV-2005) molecularly and biologically using conserved and non-conserved gene analyses for phylogenetic inference and to search for new genes that would elucidate the VACV-BR dichotomy. The VACV DMTV-2005 isolate reported in this study is biologically and phylogenetically clustered with other strains of Group 1 VACV-BR, the most prevalent VACV group that was isolated during the bovine vaccinia outbreaks in Brazil. Sequence analysis of C23L, the gene that encodes for the CC-chemokine-binding protein, revealed a ten-nucleotide deletion, which is a new Group 1 Brazilian VACV genetic marker. This deletion in the C23L open reading frame produces a premature stop-codon that is shared by all Group 1 VACV-BR strains and may also reflect the VACV-BR dichotomy; the deletion can also be considered to be a putative genetic marker for non-virulent Brazilian VACV isolates and may be used for the detection and molecular characterization of new isolates. PMID:23189200

  7. Characterization of a new Vaccinia virus isolate reveals the C23L gene as a putative genetic marker for autochthonous Group 1 Brazilian Vaccinia virus.

    PubMed

    Assis, Felipe L; Almeida, Gabriel M F; Oliveira, Danilo B; Franco-Luiz, Ana P M; Campos, Rafael K; Guedes, Maria I M; Fonseca, Flávio G; Trindade, Giliane S; Drumond, Betânia P; Kroon, Erna G; Abrahão, Jônatas S

    2012-01-01

    Since 1999, several Vaccinia virus (VACV) isolates, the etiological agents of bovine vaccinia (BV), have been frequently isolated and characterized with various biological and molecular methods. The results from these approaches have grouped these VACV isolates into two different clusters. This dichotomy has elicited debates surrounding the origin of the Brazilian VACV and its epidemiological significance. To ascertain vital information to settle these debates, we and other research groups have made efforts to identify molecular markers to discriminate VACV from other viruses of the genus Orthopoxvirus (OPV) and other VACV-BR groups. In this way, some genes have been identified as useful markers to discriminate between the VACV-BR groups. However, new markers are needed to infer ancestry and to correlate each sample or group with its unique epidemiological and biological features. The aims of this work were to characterize a new VACV isolate (VACV DMTV-2005) molecularly and biologically using conserved and non-conserved gene analyses for phylogenetic inference and to search for new genes that would elucidate the VACV-BR dichotomy. The VACV DMTV-2005 isolate reported in this study is biologically and phylogenetically clustered with other strains of Group 1 VACV-BR, the most prevalent VACV group that was isolated during the bovine vaccinia outbreaks in Brazil. Sequence analysis of C23L, the gene that encodes for the CC-chemokine-binding protein, revealed a ten-nucleotide deletion, which is a new Group 1 Brazilian VACV genetic marker. This deletion in the C23L open reading frame produces a premature stop-codon that is shared by all Group 1 VACV-BR strains and may also reflect the VACV-BR dichotomy; the deletion can also be considered to be a putative genetic marker for non-virulent Brazilian VACV isolates and may be used for the detection and molecular characterization of new isolates.

  8. Multilocus sequence typing (MLST) and M13 PCR fingerprinting revealed heterogeneity amongst Cryptococcus species obtained from Italian veterinary isolates.

    PubMed

    Danesi, Patrizia; Firacative, Carolina; Cogliati, Massimo; Otranto, Domenico; Capelli, Gioia; Meyer, Wieland

    2014-09-01

    Cryptococcosis represents a fungal disease acquired from the environment with animals serving as host sentinels for human exposure. The aim of this study was to investigate the genetic characteristics of Cryptococcus isolates from veterinary sources (cats, dogs and birds) to understand their epidemiology and the genetic variability of the casual isolates. Mating-type PCR in connection with MLST analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex was used to genotype 17 C. neoformans isolates. In the absence of an MLST typing scheme Cryptococcus adeliensis, C. albidus, C. aureus, C. carnescens, C. laurentii, C. magnus and C. uniguttulatus strains were typed using M13 PCR fingerprinting. All C. neoformans isolates were MATα mating type, but hybrids possessed αADa and aADα mating and serotypes. Two C. neoformans molecular types VNI, VNIV and VNIII and VNII/VNIV hybrids were identified. Amongst the 66 non-C. neoformans strains investigated 55 M13 PCR fingerprinting types were identified. The wide variety of MLST types of C. neoformans and the occurrence of αADa and aADα hybrids in our study supports the notion of genetic recombination in the area studied. The heterogeneity of the non-C. neoformans isolates remains open to further investigations and should be taken into consideration when identifying emergent pathogens.

  9. Multilocus sequence typing (MLST) and M13 PCR fingerprinting revealed heterogeneity amongst Cryptococcus species obtained from Italian veterinary isolates.

    PubMed

    Danesi, Patrizia; Firacative, Carolina; Cogliati, Massimo; Otranto, Domenico; Capelli, Gioia; Meyer, Wieland

    2014-09-01

    Cryptococcosis represents a fungal disease acquired from the environment with animals serving as host sentinels for human exposure. The aim of this study was to investigate the genetic characteristics of Cryptococcus isolates from veterinary sources (cats, dogs and birds) to understand their epidemiology and the genetic variability of the casual isolates. Mating-type PCR in connection with MLST analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex was used to genotype 17 C. neoformans isolates. In the absence of an MLST typing scheme Cryptococcus adeliensis, C. albidus, C. aureus, C. carnescens, C. laurentii, C. magnus and C. uniguttulatus strains were typed using M13 PCR fingerprinting. All C. neoformans isolates were MATα mating type, but hybrids possessed αADa and aADα mating and serotypes. Two C. neoformans molecular types VNI, VNIV and VNIII and VNII/VNIV hybrids were identified. Amongst the 66 non-C. neoformans strains investigated 55 M13 PCR fingerprinting types were identified. The wide variety of MLST types of C. neoformans and the occurrence of αADa and aADα hybrids in our study supports the notion of genetic recombination in the area studied. The heterogeneity of the non-C. neoformans isolates remains open to further investigations and should be taken into consideration when identifying emergent pathogens. PMID:24981157

  10. 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

  11. Spectro-Polarimetric Imaging Reveals Helical Magnetic Fields in Solar Prominence Feet

    NASA Astrophysics Data System (ADS)

    Martínez González, M. J.; Manso Sainz, R.; Asensio Ramos, A.; Beck, C.; de la Cruz Rodríguez, J.; Díaz, A. J.

    2015-03-01

    Solar prominences are clouds of cool plasma levitating above the solar surface and insulated from the million-degree corona by magnetic fields. They form in regions of complex magnetic topology, characterized by non-potential fields, which can evolve abruptly, disintegrating the prominence and ejecting magnetized material into the heliosphere. However, their physics is not yet fully understood because mapping such complex magnetic configurations and their evolution is extremely challenging, and must often be guessed by proxy from photometric observations. Using state-of-the-art spectro-polarimetric data, we reconstruct the structure of the magnetic field in a prominence. We find that prominence feet harbor helical magnetic fields connecting the prominence to the solar surface below.

  12. 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

  13. 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.

  14. Taibaiella koreensis sp. nov., isolated from soil of a ginseng field.

    PubMed

    Son, Heung-Min; Kook, MooChang; Kim, Ju-Han; Yi, Tae-Hoo

    2014-03-01

    A Gram-staining-negative, strictly aerobic, motile (by gliding), non-spore-forming and rod-shaped bacterial strain, designated THG-DT86(T), was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 10-35 °C, at pH 6.5-8.5 and with 0-1.5 % (w/v) NaCl on trypticase soy agar. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-DT86(T) was shown to belong to the genus Taibaiella and was related to Taibaiella smilacinae PTJT-5(T) (95.3 %). The G+C content of the genomic DNA was 50.1 mol%. The only isoprenoid quinone detected in strain THG-DT86(T) was menaquinone-7 (MK-7) and the only polyamine was homospermidine. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 1 G and iso-C17 : 0, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophosphoglycolipid and an unidentified aminophospholipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-DT86(T) to the genus Taibaiella, and a number of biochemical tests differentiated strain THG-DT86(T) from the recognized species of the genus Taibaiella. Therefore, the novel isolate represents a novel species, for which the name Taibaiella koreensis sp. nov. is proposed, with THG-DT86(T) as the type strain ( = KACC 17171(T) = JCM 18823(T)).

  15. Epilithonimonas ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Hoang, Van-An; Kim, Yeon-Ju; Ponnuraj, Shree Priya; Nguyen, Ngoc-Lan; Hwang, Kyu-Hyon; Yang, Deok-Chun

    2015-01-01

    A novel Gram-staining-negative, rod-shaped bacterium, designated DCY78(T), was isolated from soil of a ginseng field in Yeon-cheon province (38° 04' 00″ N 126° 57' 00″ E), Republic of Korea. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY78(T) belonged to the genus Epilithonimonas and was most closely related to Epilithonimonas lactis DSM 19921(T) (98.5 % sequence similarity) and Epilithonimonas tenax DSM 16811(T) (97.8 %). Growth occurred at 10-30 °C with an optimum temperature of 28 °C. The pH range for growth was pH 5.5-8.0. The major polar lipids were found to be phosphatidylethanolamine three unidentified amino lipids and one unidentified polar lipid. The only predominant quinone was MK-6. The major polyamines were sym-homospermidine and spermidine. The major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 37.9 mol%. On the basis of the phenotypic and genotypic analysis, the isolate is classified as representative of a novel species in the genus Epilithonimonas, for which the name Epilithonimonas ginsengisoli is proposed. The type strain is DCY78(T) ( = KCTC 32174(T) = JCM 19896(T)).

  16. Hymenobacter ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

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

    2013-02-01

    A Gram-stain-negative, non-motile, red bacterium, designated DCY57(T), was isolated from soil of a ginseng field in a mountainous region of Chungnam province in South Korea. Strain DCY57(T) grew with 0-1 % (w/v) NaCl and the optimum temperature for growth was 30 °C. Strain DCY57(T) contained MK-7 as the predominant menaquinone. The polyamine was sym-homospermidine. The major fatty acids were C(16:1)ω5c, iso-C(15:0), anteiso-C(15:0) and summed feature 3 (containing C(16:1)ω7c and/or C(16:1)ω6c). The major polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids. The DNA G+C content was 58.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY57(T) was most closely related to members of the genus Hymenobacter. The isolate exhibited 91.7 % 16S rRNA gene sequence similarity with H. soli PB17(T), 94.5 % with H. flocculans A2-50A(T) and 95.8 % with H. metalli A2-91(T). On the basis of the evidence presented in this study, strain DCY57(T) represents a novel species within the genus Hymenobacter, for which the name Hymenobacter ginsengisoli sp. nov. is proposed. The type strain is DCY57(T) ( = KCTC 23674(T) = JCM 17841(T)).

  17. 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

  18. 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

  19. 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.

  20. Circular polarimetry reveals helical magnetic fields in the young stellar object HH 135-136.

    PubMed

    Chrysostomou, Antonio; Lucas, Philip W; Hough, James H

    2007-11-01

    Magnetic fields are believed to have a vital role in regulating and shaping the flow of material onto and away from protostars during their initial mass accretion phase. It is becoming increasingly accepted that bipolar outflows are generated and collimated as material is driven along magnetic field lines and centrifugally accelerated off a rotating accretion disk. However, the precise role of the magnetic field is poorly understood and evidence for its shape and structure has not been forthcoming. Here we report imaging circular polarimetry in the near-infrared and Monte Carlo modelling showing that the magnetic field along the bipolar outflow of the HH 135-136 young stellar object is helical. The field retains this shape for large distances along the outflow, so the field structure can also provide the necessary magnetic pressure for collimation of the outflow. This result lends further weight to the hypothesis--central to any theory of star formation--that the outflow is an important instrument for the removal of high-angular-momentum material from the accretion disk, thereby allowing the central protostar to increase its mass.

  1. LasR Variant Cystic Fibrosis Isolates Reveal an Adaptable Quorum-Sensing Hierarchy in Pseudomonas aeruginosa

    PubMed Central

    Feltner, John B.; Wolter, Daniel J.; Pope, Christopher E.; Groleau, Marie-Christine; Smalley, Nicole E.; Greenberg, E. Peter; Mayer-Hamblett, Nicole; Burns, Jane; Hoffman, Lucas R.

    2016-01-01

    ABSTRACT Chronic Pseudomonas aeruginosa infections cause significant morbidity in patients with cystic fibrosis (CF). Over years to decades, P. aeruginosa adapts genetically as it establishes chronic lung infections. Nonsynonymous mutations in lasR, the quorum-sensing (QS) master regulator, are common in CF. In laboratory strains of P. aeruginosa, LasR activates transcription of dozens of genes, including that for another QS regulator, RhlR. Despite the frequency with which lasR coding variants have been reported to occur in P. aeruginosa CF isolates, little is known about their consequences for QS. We sequenced lasR from 2,583 P. aeruginosa CF isolates. The lasR sequences of 580 isolates (22%) coded for polypeptides that differed from the conserved LasR polypeptides of well-studied laboratory strains. This collection included 173 unique lasR coding variants, 116 of which were either missense or nonsense mutations. We studied 31 of these variants. About one-sixth of the variant LasR proteins were functional, including 3 with nonsense mutations, and in some LasR-null isolates, genes that are LasR dependent in laboratory strains were nonetheless expressed. Furthermore, about half of the LasR-null isolates retained RhlR activity. Therefore, in some CF isolates the QS hierarchy is altered such that RhlR quorum sensing is independent of LasR regulation. Our analysis challenges the view that QS-silent P. aeruginosa is selected during the course of a chronic CF lung infection. Rather, some lasR sequence variants retain functionality, and many employ an alternate QS strategy involving RhlR. PMID:27703072

  2. Plasmodium falciparum Field Isolates from South America Use an Atypical Red Blood Cell Invasion Pathway Associated with Invasion Ligand Polymorphisms

    PubMed Central

    Lopez-Perez, Mary; Villasis, Elizabeth; Machado, Ricardo L. D.; Póvoa, Marinete M.; Vinetz, Joseph M.; Blair, Silvia; Gamboa, Dionicia; Lustigman, Sara

    2012-01-01

    Studies of Plasmodium falciparum invasion pathways in field isolates have been limited. Red blood cell (RBC) invasion is a complex process involving two invasion protein families; Erythrocyte Binding-Like (EBL) and the Reticulocyte Binding-Like (PfRh) proteins, which are polymorphic and not fully characterized in field isolates. To determine the various P. falciparum invasion pathways used by parasite isolates from South America, we studied the invasion phenotypes in three regions: Colombia, Peru and Brazil. Additionally, polymorphisms in three members of the EBL (EBA-181, EBA-175 and EBL-1) and five members of the PfRh (PfRh1, PfRh2a, PfRh2b, PfRh4, PfRh5) families were determined. We found that most P. falciparum field isolates from Colombia and Peru invade RBCs through an atypical invasion pathway phenotypically characterized as resistant to all enzyme treatments (NrTrCr). Moreover, the invasion pathways and the ligand polymorphisms differed substantially among the Colombian and Brazilian isolates while the Peruvian isolates represent an amalgam of those present in the Colombian and Brazilian field isolates. The NrTrCr invasion profile was associated with the presence of the PfRh2a pepC variant, the PfRh5 variant 1 and EBA-181 RVNKN variant. The ebl and Pfrh expression levels in a field isolate displaying the NrTrCr profile also pointed to PfRh2a, PfRh5 and EBA-181 as being possibly the major players in this invasion pathway. Notably, our studies demonstrate the uniqueness of the Peruvian P. falciparum field isolates in terms of their invasion profiles and ligand polymorphisms, and present a unique opportunity for studying the ability of P. falciparum parasites to expand their invasion repertoire after being reintroduced to human populations. The present study is directly relevant to asexual blood stage vaccine design focused on invasion pathway proteins, suggesting that regional invasion variants and global geographical variation are likely to preclude a simple

  3. 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

  4. 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.

  5. 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

  6. Molecular Typing of Fluoroquinolone-Resistant Campylobacter jejuni Isolated from Broilers in Japan Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis.

    PubMed

    Ozawa, Manao; Hiki, Mototaka; Kawanishi, Michiko; Abo, Hitoshi; Kojima, Akemi; Asai, Tetsuo; Hamamoto, Shuichi

    2016-01-01

    Fluoroquinolone-resistant Campylobacter jejuni isolates from broilers in Japan were characterized using multilocus sequence typing and pulsed-field gel electrophoresis (PFGE) in order to elucidate the genetic relationship between these strains. Forty-three of the isolates were classified into 20 sequence types and were clustered into 21 PFGE types with 70% similarity. The most dominant clonal complex (CC) was CC-21 (41.9%). Diverse PFGE patterns were observed within the same CC, but the combined analysis of PFGE type and CC revealed that the strains with the same combination were isolated from the same district or neighboring districts. On the other hand, strains with the same combination pattern were also isolated from geographically distant districts. Our results elucidate two possible reasons for the prevalence of fluoroquinolone-resistant C. jejuni among broiler farms: (1) the resistant C. jejuni is clonally disseminated within the limited area, and (2) susceptible C. jejuni acquired fluoroquinolone resistance during the use of fluoroquinolone on the farms.

  7. 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.

  8. UNNOTICED MAGNETIC FIELD OSCILLATIONS IN THE VERY QUIET SUN REVEALED BY SUNRISE/IMaX

    SciTech Connect

    Martinez Gonzalez, M. J.; Asensio Ramos, A.; Manso Sainz, R.; Khomenko, E.; MartInez Pillet, V.; Lopez Ariste, A.

    2011-04-01

    We present observational evidence for oscillations of magnetic flux density in the quiet areas of the Sun. The majority of magnetic fields on the solar surface have strengths of the order of or lower than the equipartition field (300-500 G). This results in a myriad of magnetic fields whose evolution is largely determined by the turbulent plasma motions. When granules evolve they squash the magnetic field lines together or pull them apart. Here, we report on the periodic deformation of the shapes of features in circular polarization observed at high resolution with SUNRISE. In particular, we note that the area of patches with a constant magnetic flux oscillates with time, which implies that the apparent magnetic field intensity oscillates in antiphase. The periods associated with this oscillatory pattern are compatible with the granular lifetime and change abruptly, which suggests that these oscillations might not correspond to characteristic oscillatory modes of magnetic structures, but to the forcing by granular motions. In one particular case, we find three patches around the same granule oscillating in phase, which means that the spatial coherence of these oscillations can reach 1600 km. Interestingly, the same kind of oscillatory phenomenon is also found in the upper photosphere.

  9. Unnoticed Magnetic Field Oscillations in the Very Quiet Sun Revealed by SUNRISE/IMaX

    NASA Astrophysics Data System (ADS)

    Martínez González, M. J.; Asensio Ramos, A.; Manso Sainz, R.; Khomenko, E.; Martínez Pillet, V.; Solanki, S. K.; López Ariste, A.; Schmidt, W.; Barthol, P.; Gandorfer, A.

    2011-04-01

    We present observational evidence for oscillations of magnetic flux density in the quiet areas of the Sun. The majority of magnetic fields on the solar surface have strengths of the order of or lower than the equipartition field (300-500 G). This results in a myriad of magnetic fields whose evolution is largely determined by the turbulent plasma motions. When granules evolve they squash the magnetic field lines together or pull them apart. Here, we report on the periodic deformation of the shapes of features in circular polarization observed at high resolution with SUNRISE. In particular, we note that the area of patches with a constant magnetic flux oscillates with time, which implies that the apparent magnetic field intensity oscillates in antiphase. The periods associated with this oscillatory pattern are compatible with the granular lifetime and change abruptly, which suggests that these oscillations might not correspond to characteristic oscillatory modes of magnetic structures, but to the forcing by granular motions. In one particular case, we find three patches around the same granule oscillating in phase, which means that the spatial coherence of these oscillations can reach 1600 km. Interestingly, the same kind of oscillatory phenomenon is also found in the upper photosphere.

  10. Virulence and polar tube protein genetic diversity of Nosema ceranae (Microsporidia) field isolates from Northern and Southern Europe in honeybees (Apis mellifera iberiensis).

    PubMed

    Van der Zee, Romee; Gómez-Moracho, Tamara; Pisa, Lennard; Sagastume, Soledad; García-Palencia, Pilar; Maside, Xulio; Bartolomé, Carolina; Martín-Hernández, Raquel; Higes, Mariano

    2014-08-01

    Infection of honeybees by the microsporidian Nosema ceranae is considered to be one of the factors underlying the increased colony losses and decreased honey production seen in recent years. However, these effects appear to differ in function of the climatic zone, the distinct beekeeping practices and the honeybee species employed. Here, we compared the response of Apis mellifera iberiensis worker bees to experimental infection with field isolates of N. ceranae from an Oceanic climate zone in Northern Europe (Netherlands) and from a Mediterranean region of Southern Europe (Spain). We found a notable but non-significant trend (P = 0.097) towards higher honeybee survival for bees infected with N. ceranae from the Netherlands, although no differences were found between the two isolates in terms of anatomopathological lesions in infected ventricular cells or the morphology of the mature and immature stages of the parasite. In addition, the population genetic survey of the N. ceranae PTP3 locus revealed high levels of genetic diversity within each isolate, evidence for meiotic recombination, and no signs of differentiation between the Dutch and Spanish populations. A cross-infection study is needed to further explore the differences in virulence observed between the two N. ceranae populations in field conditions.

  11. Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation.

    PubMed

    Papadopulos, Alexander S T; Kaye, Maria; Devaux, Céline; Hipperson, Helen; Lighten, Jackie; Dunning, Luke T; Hutton, Ian; Baker, William J; Butlin, Roger K; Savolainen, Vincent

    2014-08-01

    It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.

  12. 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

  13. Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

    PubMed Central

    Papadopulos, Alexander S. T.; Kaye, Maria; Devaux, Céline; Hipperson, Helen; Lighten, Jackie; Dunning, Luke T.; Hutton, Ian; Baker, William J.; Butlin, Roger K.; Savolainen, Vincent

    2014-01-01

    It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry. PMID:24958917

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

    PubMed

    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

    2014-11-06

    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.

  15. Determination of discriminating dose and evaluation of amitraz resistance status in different field isolates of Rhipicephalus (Boophilus) microplus in India.

    PubMed

    Kumar, Sachin; Sharma, Anil Kumar; Ray, D D; Ghosh, Srikant

    2014-07-01

    Field tick isolates of Rhipicephalus (Boophilus) microplus were collected from eleven districts located in the northern and eastern states of India to access the resistance status to "Amitraz". Adult immersion test was optimized using laboratory reared acaricide susceptible IVRI-I line and minimum effective concentration was determined as 487.7 ppm with 95 % confidence interval of 455.8-521.8. The discriminating concentration was determined as 975.4 ppm and was tested on female ticks collected by two stage stratified sampling from organized dairy farms and villages. Based on three variables, viz.,mortality, egg masses and reproductive index, the resistance level was categorized.Resistance to amitraz was detected at level I in 3 isolates (RF = 1.56-5.0), at level II in 6 isolates (RF = 9.3-23.3) and at level III in 1 isolate (RF = 27.3) whereas one isolate was found susceptible. The highest resistance was found in the SKR isolate (RF = 27.3) and minimal resistance was detected in the N-24P isolate (RF = 1.56). These experimental data will help in designing tick control strategy which is suffering from acaricide failure and to overcome development of resistance in ticks. PMID:24659517

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Comprehensive Analysis of an Isolation Area Obtained by Local Oxidation of Silicon Without Field Implant

    NASA Astrophysics Data System (ADS)

    Fay, Jean-Luc; Beluch, Jean; Allirand, Laurence; Brosset, Dominique; Despax, Bernard; Bafleur, Marise; Sarrabayrouse, Gerard

    1999-09-01

    Isolation area, obtained by local oxidation of silicon (LOCOS) without field implant, naturally shows a high sensitivity of the leakage current to fixed charges in metal oxide semiconductor (MOS) parasitic transistors. It has been shown that during the deposition of the nitride capacitor insulator-layer, fixed charges are generated in the underlying plasma-deposited oxides. The behavior of the P-channel MOS (PMOS) parasitic transistor can be well accounted for by considering fixed charge creation in the thick part of the gate insulator. In the case of the N-channel MOS (NMOS) transistor, the leakage current is controlled by the bird's beak region where a high interface state density exists. The NMOS behavior has been explained taking into account the charge creation as well as a decrease in interface state density during nitride deposition. A new “recipe” for the nitride deposition based on a very low thermal budget has been established. Finally, a high threshold voltage and a reasonably low leakage current have been achieved for both the NMOS and PMOS parasitic transistors.

  3. 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)).

  4. Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing bacteria isolated from soil of ginseng field.

    PubMed

    Huq, Md Amdadul; Kim, Yeon-Ju; Hoang, Van-An; Siddiqi, Muhammad Zubair; Yang, Deok-Chun

    2015-04-01

    A novel bacterial strain DCY89(T) was isolated from soil sample of ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, spore-forming and motile with flagella. The strain was aerobic, esculin and starch positive, catalase- and oxidase-negative, optimum growth temperature, and pH were 25-30 °C and 6.0-7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY89(T) was shown to belong to the genus Paenibacillus and the closest phylogenetic relatives were Paenibacillus cellulosilyticus KACC 14175(T) (98.2%), Paenibacillus kobensis KACC 15273(T) (98.1%), Paenibacillus xylaniclasticus KCTC 13719(T) (96.9%), and Paenibacillus curdlanolyticus KCTC 3759(T) (96.64%). The DNA G+C content was 52.5 mol%, and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15:0, iso-C16:0, and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY89(T) represented a novel species within the genus Paenibacillus, for which we propose the name Paenibacillus ginsengiterrae. The type strain is DCY89(T) (JCM 19887(T) = KCTC 33430(T)).

  5. Biodegradation of buprofezin by Rhodococcus sp. strain YL-1 isolated from rice field soil.

    PubMed

    Li, Chao; Zhang, Ji; Wu, Zhi-Guo; Cao, Li; Yan, Xin; Li, Shun-Peng

    2012-03-14

    A buprofezin-degrading bacterium, YL-1, was isolated from rice field soil. YL-1 was identified as Rhodococcus sp. on the basis of the comparative analysis of 16S rDNA sequences. The strain could use buprofezin as the sole source of carbon and nitrogen for growth and was able to degrade 92.4% of 50 mg L(-1) buprofezin within 48 h in liquid culture. During the degradation of buprofezin, four possible metabolites, 2-tert-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one, N-tert-butyl-thioformimidic acid formylaminomethyl ester, 2-isothiocyanato-2-methyl-propane, and 2-isothiocyanato-propane, were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The catechol 2,3-dioxygenase activity was strongly induced during the degradation of buprofezin. A novel microbial biodegradation pathway for buprofezin was proposed on the basis of these metabolites. The inoculation of soils treated with buprofezin with strain YL-1 resulted in a higher degradation rate than that observed in noninoculated soils, indicating that strain YL-1 has the potential to be used in the bioremediation of buprofezin-contaminated environments.

  6. Fabrication and investigation on field-dependent properties of natural rubber based magneto-rheological elastomer isolator

    NASA Astrophysics Data System (ADS)

    Ain Abd Wahab, Nurul; Amri Mazlan, Saiful; Ubaidillah; Kamaruddin, Shamsul; Intan Nik Ismail, Nik; Choi, Seung-Bok; Haziq Rostam Sharif, Amirul

    2016-10-01

    This study presents a laminated magnetorheological elastomer (MRE) isolator which applies to vibration control in practice. The proposed isolator is fabricated with multilayer MRE sheets associated with the natural rubber (NR) as a matrix, and steel plates. The fabricated MRE isolator is then magnetically analysed to achieve high magnetic field intensity which can produce high damping force required for effective vibration control. Subsequently, the NR-based MRE specimen is tested to identify the field-dependent rheological properties such as storage modulus with 60 weight percentage of carbonyl iron particles. It is shown from this test that the MR effect of MRE specimen is quantified to reach up to 120% at 0.8 T. Following the design stage, the electromagnetic simulation using the finite element method magnetic (FEMM) software is carried out for analysing the magnetic flux distribution in the laminated MRE isolator. The laminated MRE isolator is then examined to a series of compression for static and dynamic test under various applied currents using the dynamic fatigue machine and biaxial dynamic testing machine. It is shown that the static compression force is increased by 14.5% under strong magnetic field compared to its off-state. Meanwhile, the dynamic compression test results show that the force increase of the laminated MRE isolator is up to 16% and 7% for low and high frequency respectively. From the results presented in this work, it is demonstrated that the full-scale concept of the MRE isolator can be one of the potential candidates for vibration control applications by tunability of the dynamic stiffness.

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

    DOE PAGES

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

  9. Revealing molecular structure and dynamics through high-order harmonic generation driven by mid-IR fields

    SciTech Connect

    Torres, R.; Siegel, T.; Brugnera, L.; Ivanov, M. Yu.; Marangos, J. P.; Procino, I.; Underwood, Jonathan G.; Altucci, C.; Velotta, R.; Springate, E.; Froud, C.; Turcu, I. C. E.; Patchkovskii, S.; Smirnova, O.

    2010-05-15

    High-order harmonic generation (HHG) from molecules produces spectra that are modulated by interferences that encode both the static structure and the electron dynamics initiated by interaction with the laser field. Using a midinfrared (mid-IR) laser at 1300 nm, we are able to study the region of the harmonic spectrum containing such interferences in CO{sub 2} over a wide range of intensities. This allows for isolation and characterization of interference minima arising due to subcycle electronic dynamics triggered by the laser field, which had previously been identified but not systematically separated. Our experimental and theoretical results demonstrate important steps toward combining attosecond temporal and angstrom-scale spatial resolution in molecular HHG imaging.

  10. 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)].

  11. 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.

  12. Proteomic analysis of hyperadhesive Candida glabrata clinical isolates reveals a core wall proteome and differential incorporation of adhesins.

    PubMed

    Gómez-Molero, Emilia; de Boer, Albert D; Dekker, Henk L; Moreno-Martínez, Ana; Kraneveld, Eef A; Ichsan; Chauhan, Neeraj; Weig, Michael; de Soet, Johannes J; de Koster, Chris G; Bader, Oliver; de Groot, Piet W J

    2015-12-01

    Attachment to human host tissues or abiotic medical devices is a key step in the development of infections by Candida glabrata. The genome of this pathogenic yeast codes for a large number of adhesins, but proteomic work using reference strains has shown incorporation of only few adhesins in the cell wall. By making inventories of the wall proteomes of hyperadhesive clinical isolates and reference strain CBS138 using mass spectrometry, we describe the cell wall proteome of C. glabrata and tested the hypothesis that hyperadhesive isolates display differential incorporation of adhesins. Two clinical strains (PEU382 and PEU427) were selected, which both were hyperadhesive to polystyrene and showed high surface hydrophobicity. Cell wall proteome analysis under biofilm-forming conditions identified a core proteome of about 20 proteins present in all C. glabrata strains. In addition, 12 adhesin-like wall proteins were identified in the hyperadherent strains, including six novel adhesins (Awp8-13) of which only Awp12 was also present in CBS138. We conclude that the hyperadhesive capacity of these two clinical C. glabrata isolates is correlated with increased and differential incorporation of cell wall adhesins. Future studies should elucidate the role of the identified proteins in the establishment of C. glabrata infections. PMID:26546455

  13. 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

  14. 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

  15. Equinoctial Activity Over Titan Dune Fields Revealed by Cassini/vims

    NASA Astrophysics Data System (ADS)

    Rodriguez, S.; Le Mouelic, S.; Barnes, J. W.; Hirtzig, M.; Rannou, P.; Sotin, C.; Brown, R. H.; Bow, J.; Vixie, G.; Cornet, T.; Bourgeois, O.; Narteau, C.; Courrech Du Pont, S.; Le Gall, A.; Reffet, E.; Griffith, C. A.; Jaumann, R.; Stephan, K.; Buratti, B. J.; Clark, R. N.; Baines, K. H.; Nicholson, P. D.; Coustenis, A.

    2012-12-01

    Titan, the largest satellite of Saturn, is the only satellite in the solar system with a dense atmosphere. The close and continuous observations of Titan by the Cassini spacecraft, in orbit around Saturn since July 2004, bring us evidences that Titan troposphere and low stratosphere experience an exotic, but complete meteorological cycle similar to the Earth hydrological cycle, with hydrocarbons evaporation, condensation in clouds, and rainfall. Cassini monitoring campaigns also demonstrate that Titan's cloud coverage and climate vary with latitude. Titan's tropics, with globally weak meteorological activity and widespread dune fields, seem to be slightly more arid than the poles, where extensive and numerous liquid reservoirs and sustained cloud activity have been discovered. Only a few tropo-spheric clouds have been observed at Titan's tropics during the southern summer. As equinox was approaching (in August 2009), they occurred more frequently and appeared to grow in strength and size. We present here the observation of intense brightening at Titan's tropics, very close to the equinox. These detections were conducted with the Visual and Infrared Mapping Spectrometer (VIMS) onboard Cassini. We will discuss the VIMS images of the three individual events detected so far, observed during the Titan's flybys T56 (22 May 2009), T65 (13 January 2010) and T70 (21 June 2010). T56, T65 and T70 observations show an intense and transient brighten-ing of large regions very close to the equator, right over the extensive dune fields of Senkyo, Belet and Shangri-La. They all appear spectrally and morphologically different from all transient surface features or atmospheric phenomena previously reported. Indeed, these events share in particular a strong brightening at wavelengths greater than 2 μm (especially at 5 μm), making them spectrally distinct from the small tropical clouds observed before the equinox and the large storms observed near the equator in September and October

  16. Analysis of Complete Nucleotide Sequences of Angolan Hepatitis B Virus Isolates Reveals the Existence of a Separate Lineage within Genotype E

    PubMed Central

    Lago, Barbara V.; Mello, Francisco C.; Ribas, Flavia S.; Valente, Fatima; Soares, Caroline C.; Niel, Christian; Gomes, Selma A.

    2014-01-01

    Hepatitis B virus genotype E (HBV/E) is highly prevalent in Western Africa. In this work, 30 HBV/E isolates from HBsAg positive Angolans (staff and visitors of a private hospital in Luanda) were genetically characterized: 16 of them were completely sequenced and the pre-S/S sequences of the remaining 14 were determined. A high proportion (12/30, 40%) of subjects tested positive for both HBsAg and anti-HBs markers. Deduced amino acid sequences revealed the existence of specific substitutions and deletions in the B- and T-cell epitopes of the surface antigen (pre-S1- and pre-S2 regions) of the virus isolates derived from 8/12 individuals with concurrent HBsAg/anti-HBs. Phylogenetic analysis performed with 231 HBV/E full-length sequences, including 16 from this study, showed that all isolates from Angola, Namibia and the Democratic Republic of Congo (n = 28) clustered in a separate lineage, divergent from the HBV/E isolates from nine other African countries, namely Cameroon, Central African Republic, Côte d'Ivoire, Ghana, Guinea, Madagascar, Niger, Nigeria and Sudan, with a Bayesian posterior probability of 1. Five specific mutations, namely small S protein T57I, polymerase Q177H, G245W and M612L, and X protein V30L, were observed in 79-96% of the isolates of the separate lineage, compared to a frequency of 0–12% among the other HBV/E African isolates. PMID:24632784

  17. 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

  18. Incidence of Plasmids in Marine Vibrio spp. Isolated from an Oil Field in the Northwestern Gulf of Mexico

    PubMed Central

    Hada, Howard S.; Sizemore, Ronald K.

    1981-01-01

    Presumptive marine Vibrio spp. were collected from an operational oil field and control site located in the northwestern Gulf of Mexico. Of 440 isolates analyzed for the presence of extrachromosomal deoxyribonucleic acid elements or plasmids by using the cleared lysate and agarose gel techniques, 31% showed distinct plasmid bands on agarose gels. A majority of the plasmids detected were estimated to have molecular masses of 10 × 106 or less. Multiple plasmids were observed in approximately half of the plasmid-containing strains. A number of isolates contained plasmids with similar banding and mobility patterns. The oil field area had noticeably more plasmid-containing strains (35 versus 23% in the control site) and a greater number of plasmids per plasmid-containing strain (an average of 2.5 plasmids, versus 1.5 in the control site). Oil field discharges might have resulted in increased plasmid incidence and diversity. Images PMID:16345685

  19. The Attentional Field Revealed by Single-Voxel Modeling of fMRI Time Courses

    PubMed Central

    DeYoe, Edgar A.

    2015-01-01

    The spatial topography of visual attention is a distinguishing and critical feature of many theoretical models of visuospatial attention. Previous fMRI-based measurements of the topography of attention have typically been too crude to adequately test the predictions of different competing models. This study demonstrates a new technique to make detailed measurements of the topography of visuospatial attention from single-voxel, fMRI time courses. Briefly, this technique involves first estimating a voxel's population receptive field (pRF) and then “drifting” attention through the pRF such that the modulation of the voxel's fMRI time course reflects the spatial topography of attention. The topography of the attentional field (AF) is then estimated using a time-course modeling procedure. Notably, we are able to make these measurements in many visual areas including smaller, higher order areas, thus enabling a more comprehensive comparison of attentional mechanisms throughout the full hierarchy of human visual cortex. Using this technique, we show that the AF scales with eccentricity and varies across visual areas. We also show that voxels in multiple visual areas exhibit suppressive attentional effects that are well modeled by an AF having an enhancing Gaussian center with a suppressive surround. These findings provide extensive, quantitative neurophysiological data for use in modeling the psychological effects of visuospatial attention. PMID:25810532

  20. 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

  1. [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

  2. 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.

  3. 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

  4. Isolation and Characterization of Noncytopathic Pestivirus Mutants Reveals a Role for Nonstructural Protein NS4B in Viral Cytopathogenicity

    PubMed Central

    Qu, Lin; McMullan, Laura K.; Rice, Charles M.

    2001-01-01

    Isolates of bovine viral diarrhea virus (BVDV), the prototype pestivirus, are divided into cytopathic (cp) and noncytopathic (ncp) biotypes according to their effect on cultured cells. The cp viruses also differ from ncp viruses by the production of viral nonstructural protein NS3. However, the mechanism by which cp viruses induce cytopathic effect in cell culture remains unknown. Here we used a genetic approach to isolate ncp variants that arose from a cp virus at low frequency. A bicistronic BVDV (cp strain NADL) was created that expressed puromycin acetyltransferase as a dominant selectable marker. This bicistronic virus exhibited slightly slower growth kinetics and smaller plaques than NADL but remained cp. A number of independent ncp variants were isolated by puromycin selection. Remarkably, these ncp variants produced NS3 and viral RNA at levels comparable to those of the cp parent. Sequence analyses uncovered no change in NS3, but for all ncp variants a Y2441C substitution at residue 15 of NS4B was found. Introduction of the Y2441C substitution into the NADL or bicistronic cp viruses reconstituted the ncp phenotype. Y2441 is highly conserved among pestiviruses and is located in a region of NS4B predicted to be on the cytosolic side of the endoplasmic reticulum membrane. Other engineered substitutions for Y2441 also affected viral cytopathogenicity and viability, with Y2441V being cp, Y2441A being ncp, and Y2441D rendering the virus unable to replicate. The ncp substitutions for Y2441 resulted in slightly increased levels of NS2-3 relative to NS3. We also showed that NS3, NS4B, and NS5A could be chemically cross-linked in NADL-infected cells, indicating that they are associated as components of a multiprotein complex. Although the mechanism remains to be elucidated, these results demonstrate that mutations in NS4B can attenuate BVDV cytopathogenicity despite NS3 production. PMID:11602707

  5. 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

  6. 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

  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. 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

    2015-07-22

    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.

  9. 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

  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

    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

  12. 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

  13. Sphingomonas kyeonggiense sp. nov., isolated from soil of a ginseng field.

    PubMed

    Son, Heung-Min; Kook, Moochang; Tran, Hanh T H; Kim, Ki-Young; Park, Sang-Yong; Kim, Ju-Han; Yi, Tae-Hoo

    2014-04-01

    A Gram-staining negative bacterium, THG-DT81(T), which was isolated from soil of a ginseng field, was investigated using a polyphasic taxonomic approach. Cells were oxidase- and catalase-positive, aerobic, rod-shaped and motile with one polar flagellum. Strain THG-DT81(T) grew optimally at pH 7.0 and in the absence of NaCl on trypticase soy agar. Its optimum growth temperature was 25-28 °C. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain THG-DT81(T) belongs to the family Sphingomonadaceae and was related to Sphingomonas pituitosa EDIV(T) (98.0 % similarity), S. leidyi ATCC 15260(T) (97.8 %), S. trueperi LMG 2142(T) (97.1 %), S. azotifigens NBRC 15497(T) (97.1 %), S. koreensis JSS26 (T) (97.1 %) and S. dokdonensis DS-4(T) (97.0 %). Strain THG-DT81(T) contained Q-10 as the predominant ubiquinone and C18:1 ω7c and C16:0 as the major fatty acids. The G+C content of the genomic DNA was determined to be 66.8 mol %. The major component in the polyamine pattern was identified as sym-homospermidine. The major polar lipids detected in strain THG-DT81(T) were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The DNA-DNA relatedness values of the strain THG-DT81(T) and its closest phylogenetically neighbors were below 21 %. The phenotypic characteristics and genotypic data demonstrated the affiliation of strain THG-DT81(T) to the genus Sphingomonas. On the basis of the polyphasic taxonomic data presented, strain THG-DT81(T) is described as a novel species of genus Sphingomonas, for which the name Sphingomonas kyeonggiense sp. nov. is proposed. The type strain is THG-DT81(T) (= KACC 17173(T) = JCM 18825(T)).

  14. Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil.

    PubMed

    Kitamura, Koji; Fujita, Takashi; Akada, Shinji; Tonouchi, Akio

    2011-06-01

    A pure culture of an obligately anaerobic, hydrogenotrophic, methanogenic archaeon, designated strain 169(T), which grows with hydrogen and carbon dioxide as the sole energy and carbon sources, was isolated from an anaerobic propionate-oxidizing enrichment culture originally obtained as an inoculant from rice-field soil in Japan. Cells of strain 169(T) were non-motile, Gram-reaction-variable and rod-shaped or slightly curved rods with rounded ends (1.6-5.0 × 0.35-0.5 µm). Strain 169(T) had fimbriae at both ends of the cell (up to ~10 per cell) but did not possess flagella. Ultrathin sections showed a single-layered, electron-dense cell wall about 6 nm thick, which is typical of Gram-positive bacteria. Growth was observed at 15 °C-45 °C (optimum 40 °C), at pH  6.5-9.6 (optimum pH 7.5-8.5) and in 0-70 g NaCl l(-1) (0-1.2 M) (optimum 5 g NaCl l(-1); 0.086 M). Strain 169(T) utilized only hydrogen and carbon dioxide as energy and carbon sources. The DNA G+C content was 39.3 mol%. The results of 16S rRNA gene sequence analysis indicated that strain 169(T) was most closely related to Methanobacterium subterraneum DSM 11074(T) (96.8 % sequence similarity) and Methanobacterium formicicum DSM 1535(T) (96.4 %). On the basis of its morphological, physiological and phylogenetic characteristics, strain 169(T) ( = DSM 22026(T) = JCM 15797(T)) represents a novel species of the genus Methanobacterium, for which the name Methanobacterium kanagiense sp. nov. is proposed. PMID:20639228

  15. 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)).

  16. Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Kim, Yeon-Ju; Kim, Sang-Rae; Nguyen, Ngoc-Lan; Yang, Deok-Chun

    2013-11-01

    A novel bacterial strain, designated DCY54(T), was isolated from a field cultivated with ginseng in Yongin, Republic of Korea. Cells were Gram-reaction-negative, yellow-pigmented, rod-shaped, non-spore-forming, and strictly aerobic. They were motile by gliding and produced flexirubin-type pigments. Growth occurred optimally at 25-30 °C, at pH 5.0-7.0 and in the presence of 0-1 % NaCl. The 16S rRNA sequence analysis demonstrated that strain DCY54(T) was most closely related to Flavobacterium defluvii EMB117(T) (96.9 %). The only isoprenoid quinone of strain DCY 54(T) was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major cellular fatty acids (>15 %) were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 33.3 mol%. Phylogenetic inference and phenotypic data supported affiliation of strain DCY54(T) to the genus Flavobacterium. Several physiological and biochemical tests differentiated strain DCY54(T) from the species of the genus Flavobacterium with validly published names. On the basis of data from a polyphasic study, strain DCY54(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY54(T) ( = KCTC 23318(T) = JCM 17336(T)).

  17. Bacillus ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Min, Jin Woo; Liang, Zhi-qi; Yang, Deok-Chun

    2013-03-01

    A novel bacterial strain DCY53(T) was isolated from a soil sample from a ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, endospore-forming and motile with flagella. The strain was aerobic, catalase- and oxidase-positive, optimum growth temperature and pH were 30-37 °C and 6.0-7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY53(T) was shown to belong to the genus Bacillus and the closest phylogenetic relatives were Bacillus pocheonensis KCTC 13943(T) (98.3 %), Bacillus bataviensis LMG 21833(T) (98.0 %), Bacillus soli LMG 21838(T) (97.9 %), Bacillus drentensis LMG 21831(T) (97.8 %), Bacillus niacini DSM 2923(T) (97.8 %), Bacillus novalis LMG 21837(T) (97.7 %), Bacillus vireti LMG 21834(T) (97.6 %) and Bacillus fumarioli LMG 17489(T) (97.3 %). The DNA G+C content was 43.6 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The DNA-DNA relatedness with closest relatives was below 55 %. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY53(T) represented a novel species within the genus Bacillus, for which we propose the name Bacillus ginsengisoli. The type strain is DCY53(T) ( = KCTC 13945(T) = JCM 17335(T)).

  18. Humibacter ginsengiterrae sp. nov., and Humibacter ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Kim, Eul-Kon; Hoang, Van-An; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Sukweenadhi, Johan; Kang, Jong-Pyo; Yang, Deok-Chun

    2015-08-01

    Two novel Gram-staining-positive bacteria, designated DCY60T and DCY90T, were isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence comparisons showed the two novel strains were closely related to members of the genus Humibacter with greatest similarity to Humibacter antri KCTC 33009T (98.8 and 98.4% for DCY60T and DCY90T, respectively). The predominant menaquinones present were MK-11 and MK-12. The major fatty acids were anteiso-C17 : 0 and summed feature 8 containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C contents of strains DCY60T and DCY90T were 62.8 and 66.8 mol%, respectively. The peptidoglycan of both strains contained the amino acids ornithine, 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. The cell-wall sugars of strain DCY60T comprised glucose, galactose, rhamnose and xylose, while strain DCY90T contained glucose, galactose, rhamnose and ribose. The major polar lipids of both strains were phosphatidylglycerol, an unidentified glycolipid, and an unknown phospholipid. On the basis of the phenotypic analysis strains DCY60T and DCY90T represent novel species of the genus Humibacter, for which names Humibacter ginsengiterrae sp. nov. (type strain DCY60T = KCTC 33520T = JCM 30079T) and Humibacter ginsengisoli sp. nov. (type strain DCY90T = KCTC 33521T = JCM 30080T) are proposed.

  19. One-day pulsed-field gel electrophoresis protocol for rapid determination of emetic Bacillus cereus isolates.

    PubMed

    Kaminska, Paulina S; Fiedoruk, Krzysztof; Jankowska, Dominika; Mahillon, Jacques; Nowosad, Karol; Drewicka, Ewa; Zambrzycka, Monika; Swiecicka, Izabela

    2015-04-01

    Bacillus cereus, the Gram-positive and spore-forming ubiquitous bacterium, may cause emesis as the result of food intoxication with cereulide, a heat-stable emetic toxin. Rapid determination of cereulide-positive B. cereus isolates is of highest importance due to consequences of this intoxication for human health and life. Here we present a 1-day pulsed-field gel electrophoresis for emetic B. cereus isolates, which allows rapid and efficient determination of their genomic relatedness and helps determining the source of intoxication in case of outbreaks caused by these bacilli.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil.

    PubMed

    Pumphrey, Graham M; Madsen, Eugene L

    2008-07-01

    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 [(13)C]benzoic acid or [(12)C]benzoic acid (100 microg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring (13)CO(2) 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 [(13)C]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 [(13)C]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.

  8. Field Flumes to Floodplains: Revealing the Influence of Flow Dynamics in Structuring Aquatic Ecosystems

    NASA Astrophysics Data System (ADS)

    Harvey, J. W.

    2011-12-01

    Decades of research has demonstrated the role of flood pulses in energy flow and nutrient cycling in large rivers. However, the study of hydroecology in small to medium size channels has often focused on static processes occurring during steady channel baseflow. Yet storm dynamics and their ecological effects are key issues for land managers responding to accelerating land use change in urban and agricultural areas, grazing lands, and in forested watersheds. As a means to understand the role of variable flows, researchers are increasingly moving towards study designs that explicitly address natural or experimentally altered flows in streams, or manipulation of flow in controlled "stair step" of experimental discharges in smaller field flumes. Studies often focus on both dissolved and fine particulate materials, their redistribution by stormflow, and physical effects of bedform migration and expansion and contraction of surface-water storage and hyporheic zones. In this framework investigators are seeking not only to identify the factors causing "hot spots" of biogeochemical transformation in streams, but also the "hot moments" related to flow variation and its interactions with geomorphic, sediment, and solute dynamics. Examples illustrating these advancements come from studies of flash floods from urban areas and their effects of solute and sediment dynamics in a 2nd order stream, nitrogen cycling and floodplain dynamics in a 5th order river, and longer term co-evolution of pulsed flow hydraulics, geomorphic form, and sediment and nutrient retention in two contrasting river and wetland corridors in the southwestern U.S. and southern Florida.

  9. Compartment Shape Anisotropy (CSA) Revealed by Double Pulsed Field Gradient MR

    PubMed Central

    Özarslan, Evren

    2009-01-01

    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

  10. Dark field optical imaging reveals vascular changes in an inducible hamster cheek pouch model during carcinogenesis

    PubMed Central

    Hu, Fangyao; Morhard, Robert; Murphy, Helen A.; Zhu, Caigang; Ramanujam, Nimmi

    2016-01-01

    In this study, we propose a low-cost cross-polarized dark field microscopy system for in vivo vascular imaging to detect head and neck cancer. A simple-to-use Gabor-filter-based image processing technique was developed to objectively and automatically quantify several important vascular features, including tortuosity, length, diameter and area fraction, from vascular images. Simulations were performed to evaluate the accuracies of vessel segmentation and feature extraction for our algorithm. Sensitivity and specificity for vessel segmentation of the Gabor masks both remained above 80% at all contrast levels when compared to gold-standard masks. Errors for vascular feature extraction were under 5%. Moreover, vascular contrast and vessel diameter were identified to be the two primary factors which affected the segmentation accuracies. After our algorithm was validated, we monitored the blood vessels in an inducible hamster cheek pouch carcinogen model over 17 weeks and quantified vascular features during carcinogenesis. A significant increase in vascular tortuosity and a significant decrease in vessel length were observed during carcinogenesis. PMID:27699096

  11. Dark field optical imaging reveals vascular changes in an inducible hamster cheek pouch model during carcinogenesis

    PubMed Central

    Hu, Fangyao; Morhard, Robert; Murphy, Helen A.; Zhu, Caigang; Ramanujam, Nimmi

    2016-01-01

    In this study, we propose a low-cost cross-polarized dark field microscopy system for in vivo vascular imaging to detect head and neck cancer. A simple-to-use Gabor-filter-based image processing technique was developed to objectively and automatically quantify several important vascular features, including tortuosity, length, diameter and area fraction, from vascular images. Simulations were performed to evaluate the accuracies of vessel segmentation and feature extraction for our algorithm. Sensitivity and specificity for vessel segmentation of the Gabor masks both remained above 80% at all contrast levels when compared to gold-standard masks. Errors for vascular feature extraction were under 5%. Moreover, vascular contrast and vessel diameter were identified to be the two primary factors which affected the segmentation accuracies. After our algorithm was validated, we monitored the blood vessels in an inducible hamster cheek pouch carcinogen model over 17 weeks and quantified vascular features during carcinogenesis. A significant increase in vascular tortuosity and a significant decrease in vessel length were observed during carcinogenesis.

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

    PubMed Central

    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 × 1014 W/cm2) 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

  13. 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

  14. 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

  15. The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components.

    PubMed

    Aeberhard, Lukas; Banhart, Sebastian; Fischer, Martina; Jehmlich, Nico; Rose, Laura; Koch, Sophia; Laue, Michael; Renard, Bernhard Y; Schmidt, Frank; Heuer, Dagmar

    2015-06-01

    Chlamydia trachomatis is an important human pathogen that replicates inside the infected host cell in a unique vacuole, the inclusion. The formation of this intracellular bacterial niche is essential for productive Chlamydia infections. Despite its importance for Chlamydia biology, a holistic view on the protein composition of the inclusion, including its membrane, is currently missing. Here we describe the host cell-derived proteome of isolated C. trachomatis inclusions by quantitative proteomics. Computational analysis indicated that the inclusion is a complex intracellular trafficking platform that interacts with host cells' antero- and retrograde trafficking pathways. Furthermore, the inclusion is highly enriched for sorting nexins of the SNX-BAR retromer, a complex essential for retrograde trafficking. Functional studies showed that in particular, SNX5 controls the C. trachomatis infection and that retrograde trafficking is essential for infectious progeny formation. In summary, these findings suggest that C. trachomatis hijacks retrograde pathways for effective infection.

  16. Hepatitis C Virus Heteroduplex Tracking Assay for Genotype Determination Reveals Diverging Genotype 2 Isolates in Italian Hemodialysis Patients

    PubMed Central

    Calvo, Pier Luigi; Kansopon, Joe; Sra, Kuldip; Quan, Stella; DiNello, Robert; Guaschino, Roberto; Calabrese, Giovanni; Danielle, Franca; Brunetto, Mauizia Rossana; Bonino, Ferruccio; Massaro, Anna Lucia; Polito, Alan; Houghton, Michael; Weiner, Amy J.

    1998-01-01

    A heteroduplex tracking assay (HTA) was developed for genetic analyses of the hepatitis C virus (HCV) using single-stranded probes from the core (C)/E1 region. Nucleotide sequencing of reverse transcriptase (RT)-PCR products from 15 Italian dialysis patients confirmed the specificity and accuracy of the HTA genotyping method, which identified 5 of 15 (33.3%) 1b, 7 of 15 (46.7%) 3a, and 3 of 15 (20%) type 2 infections. The genotypes of an additional 12 HCV antibody-positive blood donors from different geographical locations were also in agreement with the genotypes determined by the Inno-LiPA HCV II kit (Innogenetics) and/or restriction fragment length polymorphism (RFLP). Isolates which had between 35 to 40% nucleotide divergence from control subtype 1a, 1b, 2a, 2b, or 3a standards could be typed. Surprisingly, HTA detected one 1b-2 coinfection which was missed by DNA sequencing. Three samples that were designated non-2a or 2b type 2 by HTA were found to be type 2a by both RFLP and direct nucleotide sequencing of the 5′ untranslated region. The genetic distance between patient type 2 and control 2a, 2b, and 2c isolates indicated that a new subtype was present in the population being studied. Serotyping (RIBA serotyping strip immunoblot assay kit) of 23 dialysis patients showed that the genotype could be determined in 6 of 8 (75%) C/E1 RT-PCR-negative and 15 of 23 (65.2%) RT-PCR-positive samples, indicating that the two tests complement each other. PMID:9431953

  17. Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance

    PubMed Central

    van Hal, Sebastiaan J.; Ip, Camilla L. C.; Ansari, M. Azim; Wilson, Daniel J.; Espedido, Bjorn A.; Jensen, Slade O.; Bowden, Rory

    2016-01-01

    Enterococcus faecium, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E. faecium population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of E. faecium nosocomial infections and establishing routes of transmission. Several forms of the Tn1549-like element–vanB gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of in situ evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible E. faecium with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant E. faecium patient transmission events, underlining the need for careful consideration before modifying current E. faecium infection control strategies. PMID:27713836

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

    PubMed

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

    2002-09-01

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

  19. 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.

  20. 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

  1. 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

  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

    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

  3. 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

  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. 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.

  6. 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.

  7. 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.

  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. 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.

  11. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment.

    PubMed Central

    Liesack, W; Stackebrandt, E

    1992-01-01

    A molecular ecological study was performed on an Australian soil sample to unravel a substantial portion of the bacterial diversity. A large fragment of the 16S rRNA gene was amplified, using DNA isolated by lysing the microorganisms directly within the soil matrix, and a clone library was generated. Comparative sequence analysis of 30 clones and dot blot hybridization of 83 additional clones with defined oligonucleotide probes revealed the presence of three major groups of prokaryotes of the domain Bacteria. The first one comprises 57 clones that indicate relatives of nitrogen-fixing bacteria of the alpha-2 subclass of the class Proteobacteria; the second group of 7 clones originates from members of the order Planctomycetales that, however, reveal no close relationship to any of the described Planctomycetales species; 22 clones of the third group are indicative of members of a novel main line of descent, sharing a common ancestry with members of planctomycetes and chlamydiae. Images PMID:1629164

  12. 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.

  13. 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

  14. Diversity of pulsed-field gel electrophoresis patterns of cereulide-producing isolates of Bacillus cereus and Bacillus weihenstephanensis.

    PubMed

    Castiaux, Virginie; N'guessan, Elise; Swiecicka, Izabela; Delbrassinne, Laurence; Dierick, Katelijne; Mahillon, Jacques

    2014-04-01

    Bacillus cereus is an important foodborne pathogen causing diarrhoea, emesis and in, rare cases, lethal poisonings. The emetic syndrome is caused by cereulide, a heat-stable toxin. Originally considered as a rather homogenous group, the emetic strains have since been shown to display some diversity, including the existence of two clusters of mesophilic B. cereus and psychrotolerant B. weihenstephanensis. Using pulsed-field gel electrophoresis (PFGE) analysis, this research aimed to better understand the diversity and spatio-temporal occurrence of emetic strains originating from environmental or food niches vs. those isolated from foodborne cases. The diversity was evaluated using a set of 52 B. cereus and B. weihenstephanensis strains isolated between 2000 and 2011 in ten countries. PFGE analysis could discriminate 17 distinct profiles (pulsotypes). The most striking observations were as follows: (1) more than one emetic pulsotype can be observed in a single outbreak; (2) the number of distinct isolates involved in emetic intoxications is limited, and these potentially clonal strains frequently occurred in successive and independent food poisoning cases; (3) isolates from different countries displayed identical profiles; and (4) the cereulide-producing psychrotolerant B. weihenstephanensis were, so far, only isolated from environmental niches.

  15. Methanocella conradii sp. nov., a Thermophilic, Obligate Hydrogenotrophic Methanogen, Isolated from Chinese Rice Field Soil

    PubMed Central

    Lü, Zhe; Lu, Yahai

    2012-01-01

    Background Methanocellales contributes significantly to anthropogenic methane emissions that cause global warming, but few pure cultures for Methanocellales are available to permit subsequent laboratory studies (physiology, biochemistry, etc.). Methodology/Principal Findings By combining anaerobic culture and molecular techniques, a novel thermophilic methanogen, strain HZ254T was isolated from a Chinese rice field soil located in Hangzhou, China. The phylogenetic analyses of both the 16S rRNA gene and mcrA gene (encoding the α subunit of methyl-coenzyme M reductase) confirmed its affiliation with Methanocellales, and Methanocella paludicola SANAET was the most closely related species. Cells were non-motile rods, albeit with a flagellum, 1.4–2.8 µm long and by 0.2–0.3 µm in width. They grew at 37–60°C (optimally at 55°C) and salinity of 0–5 g NaCl l−1 (optimally at 0–1 g NaCl l−1). The pH range for growth was 6.4–7.2 (optimum 6.8). Under the optimum growth condition, the doubling time was 6.5–7.8 h, which is the shortest ever observed in Methanocellales. Strain HZ254T utilized H2/CO2 but not formate for growth and methane production. The DNA G+C content of this organism was 52.7 mol%. The sequence identities of 16S rRNA gene and mcrA gene between strain HZ254T and SANAET were 95.0 and 87.5% respectively, and the genome based Average Nucleotide Identity value between them was 74.8%. These two strains differed in phenotypic features with regard to substrate utilization, possession of a flagellum, doubling time (under optimal conditions), NaCl and temperature ranges. Taking account of the phenotypic and phylogenetic characteristics, we propose strain HZ254T as a representative of a novel species, Methanocella conradii sp. nov. The type strain is HZ254T ( = CGMCC 1.5162T = JCM 17849T = DSM 24694T). Conclusions/Significance Strain HZ254T could potentially serve as an excellent laboratory model for studying Methanocellales due to its

  16. Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field.

    PubMed

    Son, Heung-Min; Kook, Moochang; Park, Sang-Yong; Mavlonov, Gafurjon T; Yi, Tae-Hoo

    2013-12-01

    A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107(T) was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107(T) was found to occur at 4-37 °C (optimum, 20-30 °C), at pH 5.5-10 (optimum, pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5(T) (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107(T) was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C15:0 (26.3 %), iso-C17:0 3OH (12.6 %) and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107(T) has β-glucosidase activity to convert ginsenosides Rb1 and Rd into Gyp17 and F2. DNA-DNA hybridization with F. denitrificans ED5(T) was 52 %. Strain THG-107(T) could be distinguished from F. denitrificans ED5(T) and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107(T) is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107(T) = KACC 16219(T) = LMG 26575(T)).

  17. Nocardioides panaciterrulae sp. nov., isolated from soil of a ginseng field, with ginsenoside converting activity.

    PubMed

    Kim, Jin-Kwang; Liu, Qing-Mei; Park, Hye-Yoon; Kang, Myung-Suk; Kim, Sun-Chang; Im, Wan-Taek; Yoon, Min-Ho

    2013-06-01

    A Gram-positive, coccoid to rod-shaped, non-spore-forming bacterium, designated Gsoil 958(T), was isolated from soil of a ginseng field located in Pocheon province in South Korea. This bacterium was characterized in order to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 958(T) was observed to grow well at 25-30 °C and at pH 7.0 on R2A and nutrient agar without NaCl supplementation. Strain Gsoil 958(T) was determined to have β-glucosidase activity and the ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to F2 via gypenoside XVII and Rd. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 958(T) was shown to belong to the family Nocardioidaceae and related most closely to Nocardioides koreensis MSL-09(T) (97.6 % 16S rRNA gene sequence similarity), Nocardioides aquiterrae GW-9(T) (97.0 %), and Nocardioides sediminis MSL-01(T) (97.0 %). The sequence similarities with other validly named species within the genus Nocardioides were less than 96.8 %. Strain Gsoil 958(T) was characterized chemotaxonomically as having LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone, and iso-C16:0, iso-C16:1 H, iso-C14:0, iso-C15:0 were identified as the major fatty acids. The G + C content of genomic DNA was determined to be 70.8 mol %. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 958(T) to the genus Nocardioides. The results of both physiological and biochemical tests allowed for differentiation of strain Gsoil 958(T) from the recognized Nocardioides species. Therefore, strain Gsoil 958(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides panaciterrulae sp. nov. is proposed, with the type strain Gsoil 958(T) (KACC 14271(T) = KCTC 19471(T) = DSM 21350(T)).

  18. 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

  19. 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

  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. Evidence for high genetic diversity of NAD1 and COX1 mitochondrial haplotypes among triclabendazole resistant and susceptible populations and field isolates of Fasciola hepatica (liver fluke) in Australia.

    PubMed

    Elliott, T; Muller, A; Brockwell, Y; Murphy, N; Grillo, V; Toet, H M; Anderson, G; Sangster, N; Spithill, T W

    2014-02-24

    In recent years, the global incidence of Fasciola hepatica (liver fluke) infections exhibiting resistance to triclabendazole (TCBZ) has increased, resulting in increased economic losses for livestock producers and threatening future control. The development of TCBZ resistance and the worldwide discovery of F. hepatica population diversity has emphasized the need to further understand the genetic structure of drug susceptible and resistant Fasciola populations within Australia. In this study, the genetic diversity of liver flukes was estimated by sequencing mitochondrial DNA (mtDNA) encoding the NAD1 (530 bp) and COX1 (420 bp) genes of 208 liver flukes (F. hepatica) collected from three populations: field isolates obtained from abattoirs from New South Wales (NSW) and Victoria (Vic); three TCBZ-resistant fluke populations from NSW and Victoria; and the well-established TCBZ-susceptible Sunny Corner laboratory isolate. Overall nucleotide diversity for all flukes analysed of 0.00516 and 0.00336 was estimated for the NAD1 and COX1 genes respectively. Eighteen distinct haplotypes were established for the NAD1 gene and six haplotypes for the COX1 gene, resulting in haplotype diversity levels of 0.832 and 0.482, respectively. One field isolate showed a similar low level of haplotype diversity as seen in the Sunny Corner laboratory isolate. Analysis of TCBZ-resistant infrapopulations from 3 individual cattle grazing one property revealed considerable sequence parasite diversity between cattle. Analysis of parasite TCBZ-resistant infrapopulations from sheep and cattle revealed haplotypes unique to each host, but no significant difference between parasite populations. Fst analysis of fluke populations revealed little differentiation between the resistant and field populations. This study has revealed a high level of diversity in field and drug resistant flukes in South-Eastern Australia.

  3. Microsatellite markers isolated in olive ( Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars.

    PubMed

    Cipriani, G.; Marrazzo, M. T.; Marconi, R.; Cimato, A.; Testolin, R.

    2002-02-01

    We have isolated and sequenced 52 microsatellites or simple sequence repeats (SSRs) from nearly 60 positive clones obtained from two 'Frantoio' olive genomic libraries enriched in (AC/GT) and (AG/CT) repeats, respectively. The repeat-containing fragments obtained from genomic DNA restricted with Tsp509I were separated using a biotinylated probe bound to streptavidin-coated paramagnetic beads. Fragments were then cloned into lambda ZAPII vector and sequenced. Thirty of the 36 primer pairs which gave correct re-amplification in the source genome were used to assay the polymorphism of 12 olive cultivars, namely four well-known cultivars ('Coratina', 'Frantoio', 'Leccino', 'Pendolino') and eight ancient cultivars grown locally near Lake Garda ('Casaliva', 'Favarol', 'Fort', 'Grignan', 'Less', 'Raza', 'Rossanel', 'Trep'). The local cultivars were each re- presented by two to four long-lived individuals. The analysis was carried out using (33)P-labelled primers and 6% polyacrylamide sequencing gels. All except two microsatellites showed polymorphism, the number of alleles varying from 1 to 5. The average genetic diversity ( H) was 0.55. The power of discrimination ( PD) was 0.60. All cultivars, including the local ones, were easily separated from each other. Variations in the SSR pattern were observed among individual plants of the same cultivar in four out of the eight local cultivars analysed. Several primer pairs (17%) amplified more than one locus.

  4. Phylogeography of the Tropical Planktonic Foraminifera Lineage Globigerinella Reveals Isolation Inconsistent with Passive Dispersal by Ocean Currents

    PubMed Central

    Weiner, Agnes K. M.; Weinkauf, Manuel F. G.; Kurasawa, Atsushi; Darling, Kate F.; Kucera, Michal; Grimm, Guido W.

    2014-01-01

    Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale. Our data confirm the existence of multiple, well isolated genetic lineages. An analysis of their abundance and distribution indicates that our sampling is likely to approximate the actual total diversity. Unexpectedly, we observe an uneven allocation of cryptic diversity among the phylogenetic lineages. We show that this pattern is neither an artifact of sampling intensity nor a function of lineage age. Instead, we argue that it reflects an ongoing speciation process in one of the three major lineages. Surprisingly, four of the six genetic types in the hyperdiverse lineage are biogeographically restricted to the Indopacific. Their mutual co-occurrence and their hierarchical phylogenetic structure provide no evidence for an origin through sudden habitat fragmentation and their limitation to the Indopacific challenges the view of a global gene flow within the warm-water provinces. This phenomenon shows that passive dispersal is not sufficient to describe the distribution of plankton diversity. Rather, these organisms show differentiated distribution patterns shaped by species interactions and reflecting phylogenetic contingency with unique histories of diversification rates. PMID:24663038

  5. Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes.

    PubMed

    Dinesh, Balachandra; Lau, Nyok-Sean; Furusawa, Go; Kim, Seok-Won; Taylor, Todd D; Foong, Swee Yeok; Shu-Chien, Alexander Chong

    2016-02-01

    To date, the genus Mangrovimonas consists of only one species, Mangrovimonas yunxiaonensis strain LY01 that is known to have algicidal effects against harmful algal blooms (HABs) of Alexandrium tamarense. In this study, the whole genome sequence of three Mangrovimonas-like strains, TPBH4(T)(=LMG 28913(T),=JCM 30882(T)), ST2L12(T)(=LMG 28914(T),=JCM 30880(T)) and ST2L15(T)(=LMG 28915(T),=JCM 30881(T)) isolated from estuarine mangrove sediments in Perak, Malaysia were described. The sequenced genomes had a range of assembly size ranging from 3.56 Mb to 4.15 Mb which are significantly larger than that of M. yunxiaonensis LY01 (2.67 Mb). Xylan, xylose, L-arabinan and L-arabinose utilization genes were found in the genome sequences of the three Mangrovimonas-like strains described in this study. In contrast, these carbohydrate metabolism genes were not found in the genome sequence of LY01. In addition, TPBH4(T) and ST2L12(T) show capability to degrade xylan using qualitative plate assay method. PMID:26795059

  6. 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.

  7. 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

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

    PubMed

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

    2013-11-01

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

  9. Phylogenetic Analysis of H6 Influenza Viruses Isolated from Rosy-Billed Pochards (Netta peposaca) in Argentina Reveals the Presence of Different HA Gene Clusters ▿

    PubMed Central

    Rimondi, Agustina; Xu, Kemin; Craig, Maria Isabel; Shao, Hongxia; Ferreyra, Hebe; Rago, Maria Virginia; Romano, Marcelo; Uhart, Marcela; Sutton, Troy; Ferrero, Andrea; Perez, Daniel R.; Pereda, Ariel

    2011-01-01

    Until recently, influenza A viruses from wild waterfowl in South America were rarely isolated and/or characterized. To explore the ecology of influenza A viruses in this region, a long-term surveillance program was established in 2006 for resident and migratory water birds in Argentina. We report the characterization of 5 avian influenza viruses of the H6 hemagglutinin (HA) subtype isolated from rosy-billed pochards (Netta peposaca). Three of these viruses were paired to an N2 NA subtype, while the other two were of the N8 subtype. Genetic and phylogenetic analyses of the internal gene segments revealed a close relationship with influenza viruses from South America, forming a unique clade and supporting the notion of independent evolution from influenza A viruses in other latitudes. The presence of NS alleles A and B was also identified. The HA and NA genes formed unique clades separate from North American and Eurasian viruses, with the exception of the HA gene of one isolate, which was more closely related to the North American lineage, suggesting possible interactions between viruses of North American and South American lineages. Animal studies suggested that these Argentine H6 viruses could replicate and transmit inefficiently in chickens, indicating limited adaptation to poultry. Our results highlight the importance of continued influenza virus surveillance in wild birds of South America, especially considering the unique evolution of these viruses. PMID:21976652

  10. 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.

  11. Phylogeny of Trypanosoma ( Megatrypanum ) theileri and related trypanosomes reveals lineages of isolates associated with artiodactyl hosts diverging on SSU and ITS ribosomal sequences.

    PubMed

    Rodrigues, A C; Paiva, F; Campaner, M; Stevens, J R; Noyes, H A; Teixeira, M M G

    2006-02-01

    SSU ribosomal sequences of trypanosomes from Brazilian cattle and water buffalo were used to infer phylogenetic relationships between non-pathogenic T. theileri and allied species parasitic in artiodactyls. T. theileri trypanosomes from distinct geographical regions in Brazil and from other countries were tightly clustered into the 'clade T. theileri' distant from the 'T. brucei clade' of pathogenic parasites of artiodactyls, and also distinct from trypanosomes of other mammals. The existence of this monophyletic assemblage (T. theileri clade) composed only by isolates from artiodactyl species justifies the continued recognition of the subgenus T. (Megatrypanum) with T. theileri as its type species. Phylogenies based on SSU and ITS1 ribosomal sequences produced the same branching pattern with isolates from different mammalian hosts clustered in 5 lineages: A, related to water buffalo; B, C and D, to cattle; E, to fallow deer. The pattern of host specificity allied to some congruence between host and parasite phylogenies suggested association of these trypanosomes with their respective hosts. Segregation of cattle isolates into three lineages revealed an overall geographical structure. Moreover, positioning of trypanosomes infecting tabanids in the T. theileri clade is consistent with the role of these flies as important vectors of these trypanosomes.

  12. Population Structure Analysis of Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates from Brazil Reveals Predominance of Clonal Complexes 1, 15, and 79.

    PubMed

    Camargo, Carlos Henrique; Tiba, Monique Ribeiro; Saes, Marta Regina; Vasconcellos, Francielli Mahnic de; Santos, Luis Fernando Dos; Romero, Eliete Caló; Garcia, Doroti de Oliveira

    2016-04-01

    The population structure of 71 carbapenem-resistantAcinetobacter baumanniiclinical isolates from several hospitals in Brazil was investigated by ApaI pulsed-field gel electrophoresis,blaOXA-51-like subtyping, and multilocus sequence typing (Institute Pasteur scheme). In addition to the predominance of strains carryingblaOXA-23, we detected the presence ofblaOXA-72andblaOXA-231 We observed a predominance of clonal complex 1 (CC1), CC15, and CC79 and representative strains of the worldwide-disseminated international clone I.

  13. Population Structure Analysis of Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates from Brazil Reveals Predominance of Clonal Complexes 1, 15, and 79

    PubMed Central

    Tiba, Monique Ribeiro; Saes, Marta Regina; de Vasconcellos, Francielli Mahnic; dos Santos, Luis Fernando; Romero, Eliete Caló; Garcia, Doroti de Oliveira

    2016-01-01

    The population structure of 71 carbapenem-resistant Acinetobacter baumannii clinical isolates from several hospitals in Brazil was investigated by ApaI pulsed-field gel electrophoresis, blaOXA-51-like subtyping, and multilocus sequence typing (Institute Pasteur scheme). In addition to the predominance of strains carrying blaOXA-23, we detected the presence of blaOXA-72 and blaOXA-231. We observed a predominance of clonal complex 1 (CC1), CC15, and CC79 and representative strains of the worldwide-disseminated international clone I. PMID:26833161

  14. Reducing contralateral SI activity reveals hindlimb receptive fields in the SI forelimb-stump representation of neonatally amputated rats.

    PubMed

    Pluto, Charles P; Chiaia, Nicolas L; Rhoades, Robert W; Lane, Richard D

    2005-09-01

    In adult rats that sustained forelimb amputation on the day of birth, >30% of multiunit recording sites in the forelimb-stump representation of primary somatosensory cortex (SI) also respond to cutaneous hindlimb stimulation when cortical GABA(A+B) receptors are blocked (GRB). This study examined whether hindlimb receptive fields could also be revealed in forelimb-stump sites by reducing one known source of excitatory input to SI GABAergic neurons, the contralateral SI cortex. Corpus callosum projection neurons connect homotopic SI regions, making excitatory contacts onto pyramidal cells and interneurons. Thus in addition to providing monosynaptic excitation in SI, callosal fibers can produce disynaptic inhibition through excitatory synapses with inhibitory interneurons. Based on the latter of these connections, we hypothesized that inactivating the contralateral (intact) SI forelimb region would "unmask" normally suppressed hindlimb responses by reducing the activity of SI GABAergic neurons. The SI forelimb-stump representation was first mapped under normal conditions and then during GRB to identify stump/hindlimb responsive sites. After GRB had dissipated, the contralateral (intact) SI forelimb region was mapped and reversibly inactivated with injections of 4% lidocaine, and selected forelimb-stump sites were retested. Contralateral SI inactivation revealed hindlimb responses in approximately 60% of sites that were stump/hindlimb responsive during GRB. These findings indicate that activity in the contralateral SI contributes to the suppression of reorganized hindlimb receptive fields in neonatally amputated rats.

  15. 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

  16. Polyphasic study of Zymomonas mobilis strains revealing the existence of a novel subspecies Z. mobilis subsp. francensis subsp. nov., isolated from French cider.

    PubMed

    Coton, Monika; Laplace, Jean-Marie; Auffray, Yanick; Coton, Emmanuel

    2006-01-01

    Zymomonas mobilis strains recently isolated from French 'framboisé' ciders were compared with collection strains of the two defined subspecies, Z. mobilis subsp. mobilis and Z. mobilis subsp. pomaceae, using a polyphasic approach. Six strains isolated from six different regions of France were compared with three strains of Z. mobilis subsp. mobilis, including the type strain LMG 404T, and four strains of Z. mobilis subsp. pomaceae, including the type strain LMG 448T, using phenotypic and genotypic methods. For phenotypic characterization, both physiological tests and SDS-PAGE protein profiles revealed significant differences between the two known subspecies and the French isolates; three distinct groups were observed. These findings were further confirmed by random amplified polymorphic DNA and repetitive extragenic palindromic-PCR genotyping methods in which the French isolates were clearly distinguished from the other two subspecies. Sequence analysis of a fragment ranging from 604 to 617 nucleotides corresponding to the 16S-23S rRNA gene intergenic spacer region (ISR), a 592 nucleotide HSP60 gene fragment and a 1044 nucleotide gyrB gene fragment confirmed the presence of three distinct groups. The French strains exhibited almost 94 % similarity to the ISR, 90 % to HSP60 and 86 % to gyrB sequences of the three collection strains of Z. mobilis subsp. mobilis and 87, 84 and 80 % sequence similarity, respectively, was observed with the four Z. mobilis subsp. pomaceae strains. Based on both the phenotypic and genotypic results, the French strains are proposed to represent a novel subspecies, Zymomonas mobilis subsp. francensis subsp. nov. Strain AN0101T (= LMG 22974T = CIP 108684T) was designated as the type strain. PMID:16403876

  17. 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.

  18. Characterization of CbCyp51 from field isolates of Cercospora beticola.

    PubMed

    Bolton, Melvin D; Birla, Keshav; Rivera-Varas, Viviana; Rudolph, Kurt D; Secor, Gary A

    2012-03-01

    The hemibiotrophic fungus Cercospora beticola causes leaf spot of sugar beet. Leaf spot control measures include the application of sterol demethylation inhibitor (DMI) fungicides. However, reduced sensitivity to DMIs has been reported recently in the Red River Valley sugar beet-growing region of North Dakota and Minnesota. Here, we report the cloning and molecular characterization of CbCyp51, which encodes the DMI target enzyme sterol P450 14α-demethylase in C. beticola. CbCyp51 is a 1,632-bp intron-free gene with obvious homology to other fungal Cyp51 genes and is present as a single copy in the C. beticola genome. Five nucleotide haplotypes were identified which encoded three amino acid sequences. Protein variant 1 composed 79% of the sequenced isolates, followed by protein variant 2 that composed 18% of the sequences and a single isolate representative of protein variant 3. Because resistance to DMIs can be related to polymorphism in promoter or coding sequences, sequence diversity was assessed by sequencing >2,440 nucleotides encompassing CbCyp51 coding and flanking regions from isolates with varying EC(50) values (effective concentration to reduce growth by 50%) to DMI fungicides. However, no mutations or haplotypes were associated with DMI resistance or sensitivity. No evidence for alternative splicing or differential methylation of CbCyp51 was found that might explain reduced sensitivity to DMIs. However, CbCyp51 was overexpressed in isolates with high EC(50) values compared with isolates with low EC(50) values. After exposure to tetraconazole, isolates with high EC(50) values responded with further induction of CbCyp51, with a positive correlation of CbCyp51 expression and tetraconazole concentration up to 2.5 μg ml(-1). PMID:22085297

  19. 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

  20. 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

  1. 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

  2. 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

  3. Pulsed-field gel electrophoresis analysis of Bordetella pertussis isolates circulating in Europe from 1998 to 2009.

    PubMed

    Advani, Abdolreza; Hallander, Hans O; Dalby, Tine; Krogfelt, Karen Angeliki; Guiso, Nicole; Njamkepo, Elisabeth; von Könnig, Carl Heinz Wirsing; Riffelmann, Marion; Mooi, Frits R; Sandven, Per; Lutynska, Anna; Fry, Norman K; Mertsola, Jussi; He, Qiushui

    2013-02-01

    Between 1998 and 2009, Bordetella pertussis clinical isolates were collected during three periods, i.e., 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), and 2007 to 2009 (n = 140), from nine countries with distinct vaccination programs, i.e., Denmark, Finland, France, Germany, The Netherlands, Norway, Poland, Sweden, and the United Kingdom. Pulsed-field gel electrophoresis (PFGE) analysis was performed according to standardized recommendations for epidemiological typing of B. pertussis. There were 81 different PFGE profiles, five of which (BpSR3, BpSR5, BpSR10, BpSR11, and BpSR12) were observed in 61% of the 396 isolates and shown to be predominant in almost all countries. The major profile, BpSR11, showed a decreasing trend from 25% to 30% in 1998 to 2005 to 13% in 2007 to 2009, and there were increases in BpSR3 and BpSR10 from 0% and 8% to 21% and 22%, respectively. One difference between these profiles is that BpSR11 contains isolates harboring the fim3-2 allele and BpSR3 and BpSR10 contain isolates harboring the fim3-1 allele. The total proportion of the five predominant profiles increased from 44% in 1998 to 2001 to 63% in 2004 to 2005 to 70% in 2007 to 2009. In conclusion, common PFGE profiles were identified in B. pertussis populations circulating in European countries with different vaccination programs and different vaccine coverages. These prevalent isolates contain the novel pertussis toxin promoter ptxP3 allele. However, there is evidence for diversifying selection between ptxP3 strains characterized by distinct PFGE profiles. This work shows that, even within a relatively short time span of 10 years, successful isolates which spread through Europe and cause large shifts in B. pertussis populations may emerge.

  4. Typing of Listeria monocytogenes isolates originating from the food processing industry with automated ribotyping and pulsed-field gel electrophoresis.

    PubMed

    Aarnisalo, Kaarina; Autio, Tiina; Sjöberg, Anna-Maija; Lundén, Janne; Korkeala, Hannu; Suihko, Maija-Liisa

    2003-02-01

    A total of 486 Listeria monocytogenes isolates originating from 17 Finnish food processing plants (representing meat, poultry, fish, and dairy production) were collected and typed by automated ribotyping using EcoRI as the restriction enzyme. The isolates were divided into 16 different ribotypes (RTs). Some of these isolates (121), representing all EcoRI types and 16 food plants, were subjected to ribotyping with the PvuII enzyme, to pulsed-field gel electrophoresis (PFGE) typing with AscI and SmaI restriction enzymes, and to serotyping with O-antigen antisera. Nineteen ribotypes were generated with PvuII, 42 macrorestriction patterns were generated with AscI and 24 with SmaI, and three serotypes were generated with antisera. When the results were combined, the overall number of RTs was 23, and that of the PFGE types was 46. Thus, the overall discrimination power of PFGE was higher (discrimination index [DI] 0.966) than that of ribotyping (DI 0.906). The most common serotype (90.1% of the isolates) was 1/2, and isolates of serotype 4 (3.3%) were rare. There was no connection between food sectors and RTs or PFGE types, but PFGE indicated the single plants (78.3% of the types) better than ribotyping (56.5%). On the basis of its automation and on the availability of identification databases, automated ribotyping had some advantages over PFGE. Overall, automated ribotyping can be considered a practical and rapid tool when Listeria contamination is suspected and when screening a large number of isolates is necessary, e.g., when tracing contamination sources. However, in cases of outbreaks, the identical patterns must be confirmed by PFGE, which is a more discriminatory method.

  5. Three species of Borrelia burgdorferi sensu lato (B. burgdorferi sensu stricto, B afzelii, and B. garinii) identified from cerebrospinal fluid isolates by pulsed-field gel electrophoresis and PCR.

    PubMed Central

    Busch, U; Hizo-Teufel, C; Boehmer, R; Fingerle, V; Nitschko, H; Wilske, B; Preac-Mursic, V

    1996-01-01

    A total of 36 European Borrelia burgdorferi sensu lato cerebrospinal fluid isolates (mainly from southern Germany) were analyzed by pulsed-field gel electrophoresis (PFGE) for large restriction fragment pattern (LRFP) and linear plasmid profiles. Analyzing this large panel of isolates, we detected all three species of B. burgdorferi sensu lato pathogenic for humans in cerebrospinal fluid from patients with Lyme neuroborreliosis by PFGE typing after MluI digestion: 21 B. garinii (58%), 10 B. afzelii (28%), and 4 B. burgdorferi sensu stricto (11%) strains as well as 1 isolate with bands characteristic of both B. afzelii and B. garinii. Species classification by PFGE typing was confirmed by 16S rRNA-specific PCR. Eighteen isolates (11 B. garinii, 6 B. afzelii, and 1 B. burgdorferi sensu stricto isolate) were further characterized by LRFP with four different restriction enzymes (ApaI, KspI, SmaI, and XhoI). All B. afzelii isolates showed identical patterns for each restriction enzyme group. Considerable heterogeneity was demonstrated within the B. garinii group. Subsequent analysis of plasmid profiles revealed only marginal differences for B. afzelii strains but different patterns for B. garinii isolates. In one B. afzelii strain we found a linear plasmid of about 110 kbp not described before. LRFP analysis by PFGE is a suitable tool for the molecular characterization of B. burgdorferi sensu lato strains and allows determination not only of the species but also of the subtypes within B. garinii. PMID:8727878

  6. Laboratory and field evaluation of Korean entomopathogenic nematode isolates against the oriental beetle Exomala orientalis (Coleoptera: Scarabaeidae).

    PubMed

    Lee, Dong Woon; Choo, Ho Yul; Kaya, Harry K; Lee, Sang Myeong; Smitley, David R; Shin, Hong Kyun; Park, Chung Gyoo

    2002-10-01

    The oriental beetle Exomala (Anomala) orientalis (Waterhouse) is an important pest of turfgrass in Korean golf courses, and although a few chemical insecticides are registered for insect pest control, they are not very effective against scarab larvae. There is also a growing concern in Korea about the run-off of insecticides into sensitive habitats and the potential for groundwater contamination. A safe and environmentally sound alternative is needed to conventional insecticides. We therefore evaluated six Korean entomopathogenic nematode isolates: S. carpocapsae Pocheon, S. glaseri Dongrae, S. glaseri Mungyeong, S. longicaudum Gongju, S. longicaudum Nonsan, and Heterorhabditis sp. Gyeongsan for their potential as bioinsecticides for control of E. orientalis. In addition, we evaluated a reduced chemical insecticide approach that combined chlorpyrifos-methyl with nematodes. In laboratory tests Heterorhabditis sp. Gyeongsan was the most efficacious, causing 100% mortality of the second and 38% of the third instars. All other nematode isolates caused 50-80% mortality of the second and 15-30% of the third instars. E. orientalis pupae were highly susceptible to all the Korean entomopathogenic nematode isolates except S. carpocapsae. In artificially infested field plots, all Korean nematode isolates cause 50-70% mortality of the third instar. A combination of a one-half rate of Heterorhabditis sp. and a one-half rate chlorpyrifos-methyl was synergistic, causing 91% mortality compared with 69% for the full rate of Heterorhabditis sp. or 22% for the full rate of chlorpyrifos-methyl. In a second field trial, a natural infestation of preoverwintering third instar was treated. In this trial a one-half rate of S. longicaudum Nonsan plus a one-half rate of chlorpyrifos-methyl caused 96.8% mortality, much more than a full rate of S. longicaudum Nonsan (45.9% mortality) or a full rate of chlorpyrifos-methyl (28.7% mortality). The interactions of Heterorhabditis sp. and S

  7. 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

  8. Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.

    PubMed

    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.

  9. Isolated neurosarcoidosis revealed by diabetes insipidus, visual loss and diplopia in a child patient: a diagnostic problem.

    PubMed

    Jomaa, Rached; Sfar, Mohamed Habib; Mhenni, Samia Younes; Jenzri, Saleh; Jerbi, Saida; Zantour, Baha; Messoud, Riad

    2009-01-01

    We report a case of 15-yr-old child that was presented with headache, polyuria, polydipsia, recent ocular motor and abducens nerve palsies and rapid visual loss. He had a long history of progressive symmetric muscular weakness predominant in the lower limb girdle. Water deprivation revealed central diabetes insipidus. Hormonal explorations demonstrated preserved pituitary function with mild hyperprolactinemia at 21.5 ng/ml (N: 2.6 to 13.1 ng/ml). Magnetic resonance imaging showed an extensive isosignal T1 and hyposignal T2 enhanced lesion infiltrating the pituitary gland, optic-chiasmal hypothalamic region, cavernous sinus, cerebrum tent and sphenoid and temporal meningeal spaces. The serum level of angiotensin converting enzyme and cerebrospinal fluid analysis were normal. No other systemic localisation was identified. Muscle biopsy objectified dystrophic changes. Genetic study identified a delT 521 mutation characteristic of Limb-girdle muscular dystrophy type 2C. Corticotherapy rapidly ameliorated the neurological symptoms. This patient was diagnosed as having neurosarcoidosis. Neurosarcoidosis is rarely reported in childhood. We discuss the problems related to diagnosis in such a situation below. PMID:24790380

  10. Historical divergence of mechanical isolation agents in the ground beetle Carabus arrowianus as revealed by phylogeographical analyses.

    PubMed

    Nagata, Nobuaki; Kubota, Kohei; Takami, Yasuoki; Sota, Teiji

    2009-04-01

    In the carabid genus Carabus subgenus Ohomopterus, diverged body size and genital morphology serve as mechanical reproductive barriers. To elucidate the diverging process of body and genital sizes in Carabus arrowianus, which exhibits marked morphological diversity among geographical populations and may represent an early stage of speciation, we analysed a mitochondrial gene sequence for 1051 individuals from 63 populations and male morphology for 359 individuals from 47 populations. Two discrete morphological groups segregated by geographical barriers were distinguished, one of which possessed smaller bodies and shorter genitalia (S group) than the other (L group), which exhibited larger bodies and exaggerated genitalia. Genetic divergence between the two groups was significant but not large. Phylogeographical and population genetic analyses indicated that the L group was derived from the S group, and a coalescent simulation revealed that the two groups diverged during the latest middle Pleistocene (0.13 million years ago), with a much larger effective population size in the L group than the S group. Because the body size divergence could not be explained by adaptation to climatic conditions and genital morphology is considered to be subject to sexual selection, we postulated that a population division and colonization in favourable habitats caused by the Pleistocene climatic and geographical change might facilitate natural and sexual selection for enlarged body and genital sizes in the L group. PMID:19368646

  11. 11beta-Hydroxysteroid dehydrogenase 1 inhibiting constituents from Eriobotrya japonica revealed by bioactivity-guided isolation and computational approaches.

    PubMed

    Rollinger, Judith M; Kratschmar, Denise V; Schuster, Daniela; Pfisterer, Petra H; Gumy, Christel; Aubry, Evelyne M; Brandstötter, Sarah; Stuppner, Hermann; Wolber, Gerhard; Odermatt, Alex

    2010-02-15

    The inhibition of 11beta-hydroxysteroid dehydrogenase 1 (11beta-HSD1), which catalyzes the conversion of inactive 11-ketoglucocorticoids to active 11beta-hydroxyglucocorticoids, emerged as promising strategy to treat symptoms of the metabolic syndrome, including obesity and type 2 diabetes. In this study the leaves of the anti-diabetic medicinal plant loquat (Eriobotrya japonica) were phytochemically investigated following hints from a pharmacophore-based virtual screening and a bioactivity-guided approach. Determination of the 11beta-HSD1 and 11beta-HSD2 inhibitory activities in cell lysates revealed triterpenes from the ursane type as selective, low micro-molar inhibitors of 11beta-HSD1, that is, corosolic acid (1), 3-epicorosolic acid methyl ester (4), 2-alpha hydroxy-3-oxo urs-12-en-28-oic acid (6), tormentic acid methyl ester (8), and ursolic acid (9). Importantly, a mixture of loquat constituents with moderate activities displayed a pronounced additive effect. By means of molecular modeling studies and the identification of the 11beta-HSD1-inhibiting 11-keto-ursolic acid (17) and 3-acetyl-11-keto-ursolic acid (18) a structure-activity relationship was deduced for this group of pentacyclic triterpenes. The mechanism of action elucidated in the present work together with the previously determined pharmacological activities provides these natural products with an astonishing multi-targeted anti-diabetic profile.

  12. 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

  13. 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.

  14. Genetic diversity of Mycoplasma gallisepticum field isolates using partial sequencing of the pvpA gene fragment in Russia.

    PubMed

    Sprygin, A V; Andreychuk, D B; Elatkin, N P; Zinyakov, N G; Kolosov, S N; Mudrak, N S; Irza, V N; Drygin, V V; Borisov, A V; Perevozchikova, N A

    2010-06-01

    The genetic diversity of the pvpA gene of Mycoplasma gallisepticum (MG) samples originating from commercial chickens was investigated. In the present study, we evaluated the genetic variability of 26 field samples of MG detected in commercial chickens and turkeys from 18 regions of Russia and compared them to the reference strains of MG available in GenBank. Genetic variability was evaluated by partial nucleotide sequencing of the pvpA gene, which encodes a putative cytadhesin protein. Comparisons with MG strains and isolates from the United States, Australia, China, and Iran using sequence analysis of PCR products showed that Russian MG field samples clustered more closely to each other than to the international reference MG strains. The MG pvpA sequences were found to be highly variable with a discrimination index of 0.975 for Russian field samples. No apparent cluster was found using the criteria of year or location of detection. DNA sequence polymorphism and size variation in the pvpA gene were shown among the Russian MG field samples and could be used for MG typing. These findings might help better understand the relationship among MG isolates from Russia and other countries.

  15. 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

  16. 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

  17. Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.

    PubMed

    Son, Heung-Min; Yang, Jung-Eun; Park, Yongjin; Han, Chang-Kyun; Kim, Song-Gun; Kook, Moochang; Yi, Tae-Hoo

    2013-10-01

    A bacterial strain THG-B283(T), which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283(T) grew optimally at around pH 7.0, at 25-28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283(T) belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224(T) (98.2 %), S. aquatilis JSS7(T) (98.1 %), S. insulae DS-28(T) (97.6 %), S. mali IFO 15500(T) (97.1 %) and S. pruni IFO 15498(T) (97.0 %). Strain THG-B283(T) contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283(T) to the genus Sphingomonas. DNA-DNA relatedness between strain THG-B283(T) and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283(T) represents a novel species of genus Sphingomonas, for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283(T) ( = KACC 16224(T) = LMG 26582(T)).

  18. Epidemiological analysis of Salmonella enterica Enteritidis isolates in Japan by phage-typing and pulsed-field gel electrophoresis.

    PubMed Central

    Terajima, J.; Nakamura, A.; Watanabe, H.

    1998-01-01

    Salmonella enterica serotype Enteritidis isolates of phage types (PTs) PT1, PT4, PT13a and PT22 derived from sporadic cases and outbreaks of food poisoning in Japan during 1994 and 1995 were analysed by pulsed-field gel electrophoresis (PFGE). While PT1 strains from 5 different outbreaks showed 14 PFGE patterns, 5 PFGE patterns were observed among PT4 isolates from 5 different outbreaks and 6 independent isolates from imported chicken. Interestingly, 8 out of 9 PT4 strains associated with foreign travel to Southeast Asia were indistinguishable in PFGE pattern from 5 independent isolates of imported chicken from England. Although both PT13a and PT22 were first reported in Japan in 1994, PT22 showed various PFGE patterns compared to PT13a which had the same pattern within an outbreak, unlike PT1. These results could indicate that multiple clonal lines of PT1 and PT22 had already spread while relatively fewer clonal lines of PT4 and PT13a might exist in Japan. PMID:9692599

  19. 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

  20. 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

  1. 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.

  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. 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.

  4. Pulsed Field Gel Electrophoresis types of Candida albicans isolates from an intensive care unit in a Tunisian hospital.

    PubMed

    Khadraoui, Nadia; Kallel, Kalthoum; Bouchami, Ons; Bouchakoua, Myriam; Kaouech, Amira; Belhadj, Slah; Ben Lakhal, Slah; Ben Hassen, Assia; Chaker, Emna

    2011-01-01

    Candida albicans is the most important cause of fungal infections in intensive care units. The aim of this work was to compare the profiles of C. albicans in order to specify their genetic polymorphism and to determine the origin of these infections. Thirty-five C. albicans strains were collected from different clinical samples of 12 patients and three health-workers in an intensive care unit (ICU) in Rabta hospital of Tunisia, between August 2007 and April 2008. After digestion with BssHII, the isolates were typed by pulsed field gel electrophoresis (PFGE). The PFGE profiles were analyzed using a visual method, which showed three PFGE types (A, B and C) and the dendrogram generated three clusters (clusters I to III). An average similarity coefficient of 0.83, suggests that isolates are related.

  5. Comparative sequence analysis of the reovirus S4 genes from 13 serotype 1 and serotype 3 field isolates.

    PubMed Central

    Kedl, R; Schmechel, S; Schiff, L

    1995-01-01

    The reovirus sigma 3 protein is a major outer capsid protein that may function to regulate translation within infected cells. To facilitate the understanding of sigma 3 structure and functions and the evolution of mammalian reoviruses, we sequenced cDNA copies of the S4 genes from 10 serotype 3 and 3 serotype 1 reovirus field isolates and compared these sequences with sequences of prototypic strains of the three reovirus serotypes. We found that the sigma 3 proteins are highly conserved: the two longest conserved regions contain motifs proposed to function in binding zinc and double-stranded RNA. We used the 16 viral isolates to investigate the hypothesis that structural interactions between sigma 3 and the cell attachment protein, sigma 1, constrain their evolution and to identify a determinant within sigma 3 that is in close proximity to the sigma 1 hemagglutination site. PMID:7527088

  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.

  7. 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

  8. 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

  9. Field method for isolation of trichostrongyle larvae from vegetation of natural pastures of Arctic ruminants.

    PubMed

    Raundrup, K; Clemmensen, S; Forchhammer, M C; Kapel, C M O

    2003-04-01

    The extent to which wild ruminant populations are exposed to infective helminth larvae on their natural pastures is relatively undetermined. In the present study, a modified method for sampling of herbage and isolation of trichostrongyle infective third-stage larvae from natural pastures was used successfully in a muskox habitat in low-Arctic Greenland. The method, a revision of the Macro-Baermann method, is particularly aimed at fieldwork under primitive conditions.

  10. Field method for isolation of trichostrongyle larvae from vegetation of natural pastures of Arctic ruminants.

    PubMed

    Raundrup, K; Clemmensen, S; Forchhammer, M C; Kapel, C M O

    2003-04-01

    The extent to which wild ruminant populations are exposed to infective helminth larvae on their natural pastures is relatively undetermined. In the present study, a modified method for sampling of herbage and isolation of trichostrongyle infective third-stage larvae from natural pastures was used successfully in a muskox habitat in low-Arctic Greenland. The method, a revision of the Macro-Baermann method, is particularly aimed at fieldwork under primitive conditions. PMID:12760673

  11. Site-specific distribution and competitive ability of indigenous bean-nodulating rhizobia isolated from organic fields in Minnesota.

    PubMed

    Wongphatcharachai, Manoosak; Wang, Ping; Staley, Christopher; Chun, Chan Lan; Ferguson, John A; Moncada, Kristine M; Sheaffer, Craig C; Sadowsky, Michael J

    2015-11-20

    Organic dry bean production systems have received increasing interest in many regions of the US, including Minnesota. Thus, improving biological N2 fixation would be highly beneficial for organic crop production. To date, only limited work has been done to select efficient N2-fixing rhizobia for organic dry bean production. In this study, soil samples from 25 organic fields in Minnesota, with a previous cropping history of dry beans, soybeans or both, were collected during May to July 2012. Genetic diversity of indigenous dry bean-rhizobia (511 isolates) was determined by using horizontal, fluorophore-enhanced, repetitive, extragenic, and palindromic-PCR (HFERP) DNA fingerprinting and isolates were classified as belonging to 58 different genotypes. The more abundant rhizobia isolated from bean nodules comprised 35.6% of the population. None of the isolates were identical to commonly-used commercial strains used in the U.S., including Rhizobium tropici CIAT899. Seventeen predominant genotypes were shown to represent two main species, Rhizobium leguminosarum bv. phaseoli (67.1%) and Rhizobium etli (30.2%). One of the indigenous strains, orgK9, displayed efficient N2-fixation and competitive ability relative to the commercial strains tested. The lack of large numbers of indigenous dry bean-rhizobia at most study sites will be useful to avoid competition problems between inoculant strains and indigenous rhizobia. This will allow inoculation with highly effective N2-fixing rhizobia, thus resulting in improved crop productivity. Our results highlight the existence of site-specific rhizobial genotypes in different organic fields and identify strains that may prove useful as novel inoculants for organic dry bean production systems.

  12. Perceptual suppression revealed by adaptive multi-scale entropy analysis of local field potential in monkey visual cortex.

    PubMed

    Hu, Meng; Liang, Hualou

    2013-04-01

    Generalized flash suppression (GFS), in which a salient visual stimulus can be rendered invisible despite continuous retinal input, provides a rare opportunity to directly study the neural mechanism of visual perception. Previous work based on linear methods, such as spectral analysis, on local field potential (LFP) during GFS has shown that the LFP power at distinctive frequency bands are differentially modulated by perceptual suppression. Yet, the linear method alone may be insufficient for the full assessment of neural dynamic due to the fundamentally nonlinear nature of neural signals. In this study, we set forth to analyze the LFP data collected from multiple visual areas in V1, V2 and V4 of macaque monkeys while performing the GFS task using a nonlinear method - adaptive multi-scale entropy (AME) - to reveal the neural dynamic of perceptual suppression. In addition, we propose a new cross-entropy measure at multiple scales, namely adaptive multi-scale cross-entropy (AMCE), to assess the nonlinear functional connectivity between two cortical areas. We show that: (1) multi-scale entropy exhibits percept-related changes in all three areas, with higher entropy observed during perceptual suppression; (2) the magnitude of the perception-related entropy changes increases systematically over successive hierarchical stages (i.e. from lower areas V1 to V2, up to higher area V4); and (3) cross-entropy between any two cortical areas reveals higher degree of asynchrony or dissimilarity during perceptual suppression, indicating a decreased functional connectivity between cortical areas. These results, taken together, suggest that perceptual suppression is related to a reduced functional connectivity and increased uncertainty of neural responses, and the modulation of perceptual suppression is more effective at higher visual cortical areas. AME is demonstrated to be a useful technique in revealing the underlying dynamic of nonlinear/nonstationary neural signal.

  13. 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

  14. 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

  15. 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

  16. Isolation of Legionella species from Noyu (unattended natural hot springs in mountains and fields) samples in Japan.

    PubMed

    Furuhata, Katsunori; Edagawa, Akiko; Ishizaki, Naoto; Fukuyama, Masafumi

    2013-01-01

    In order to understand the habitation conditions of the bacteria of the genus Legionella in Noyu (unattended natural hot springs in mountains and fields) in Japan, isolation of Legionella spp. was attempted in the Noyu samples from 11 prefectures nationwide between May and September 2012, and the following results were obtained. Overall, Legionella spp. was isolated from 16 of 43 samples (37.2%). The species was isolated from the Hokkaido region to the Chugoku region but not from the Shikoku region to the Kyushu region. The number of bacteria detected was usually small, less than 5.0 × 10(1) CFU/100 ml, as found in 11 samples (68.8%), while counts of 10(2) or more to 10(3) or less CFU/100 ml were found in two samples (12.5%). Legionella pneumophila was the most commonly found strain, with 19 strains (90.5%) found, and was the dominant species. Regarding the serogrouping, four strains (21.1%) fell under group 1, the most common grouping, followed by three strains (15.8%) in group 3, two strains (10.5%) in group 5, etc. Moreover, the detected bacterial strains other than L. pneumophila included two strains (9.5%) of L. londiniensis. The temperature of the Noyu from which Legionella spp. was isolated was between 33.1°C and 41.5°C with a pH ranging from 5.2 to 8.1. The present report is the first report to clarify the habitation conditions of strains of Legionella spp. isolated from Noyu in Japan.

  17. Long-term isolation and recent range expansion from glacial refugia revealed for the endemic springtail Gomphiocephalus hodgsoni from Victoria Land, Antarctica.

    PubMed

    Stevens, Mark I; Hogg, Ian D

    2003-09-01

    We examined the phylogeography of the endemic Antarctic collembolan Gomphiocephalus hodgsoni using allozymes and mitochondrial DNA (mtDNA; COI) to determine if potentially limited dispersal and long-term habitat fragmentation have promoted regional genetic differentiation. Allozyme analyses showed that differentiation among 21 populations within the Ross Dependency was high (FST = 0.55) with two main groups each representing a distinct geographical region: (1) Ross Island and Beaufort Island; and (2) all continental sites. Ross Island populations showed low levels of differentiation (FST = 0.05) and no correlation with geographical distance, suggesting their derivation from a single glacial refuge. By contrast, continental regions revealed moderate levels of differentiation (FST = 0.27) and a strong correlation with geographical distance, indicating a much older history with several refugia likely. Two sympatric allozyme genotypes were found at three continental sites from Taylor Valley and were congruent with two mtDNA haplotypes, implying nonrandom breeding groups. Although haplotype sharing between one Ross Island site (Cape Bird) and one continental site (Granite Harbour) was identified, the clades showed mostly fragmented allopatric distributions. The extensive Pleistocene glaciations, in conjunction with limited dispersal opportunities, appear to have promoted isolation and divergence among the fragmented habitats. Furthermore, the McMurdo Sound appears to be an effective isolating barrier to dispersal. However, we suggest that the unaided dispersal capacity of G. hodgsoni is unlikely to account for the limited mixing of haplotypes across the McMurdo Sound and recent human- or bird-mediated dispersal is highly probable.

  18. 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

  19. 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

  20. Phylogenetic analysis of Pomacea canaliculata isolates collected from rice fields in different origins of China by combined mitochondrial 12S and 16S genes.

    PubMed

    Li, Xiao-Yan; Bian, Qing-Qing; Zhao, Guang-Hui

    2015-02-01

    To study the genetic relationships of Pomacea canaliculata collected from rice fields in China, the mitochondrial (mt) 12S and 16S of 9 P. canaliculata isolates from 5 southern provinces in China were sequenced and analyzed. The intra-specific sequence variations of P. canaliculata were 0-1.1% for 12S and 0--0.6% for 16S, while the inter-specific variations among common Pomacea species in mt 12S and 16S were 3.0-11.7% and 2.3-10.1%, respectively. Phylogenetic analysis based on combined sequences of mt 12S and 16S revealed complex genetic structure of P. canaliculata in China. Two phylogenetic groups of P. canaliculata were indicated in China with one group sistered to P. canaliculata isolates from USA, and two groups were even found in the same province. The phylogenetic relationships of Pomacea spp. also could be effectively inferred by combined sequences of mt 12S and 16S. These findings provided basic information for further study of population genetics and diffusion pattern of P. canaliculata in China as well as in the world. PMID:23876192

  1. Phylogenetic analysis of Pomacea canaliculata isolates collected from rice fields in different origins of China by combined mitochondrial 12S and 16S genes.

    PubMed

    Li, Xiao-Yan; Bian, Qing-Qing; Zhao, Guang-Hui

    2015-02-01

    To study the genetic relationships of Pomacea canaliculata collected from rice fields in China, the mitochondrial (mt) 12S and 16S of 9 P. canaliculata isolates from 5 southern provinces in China were sequenced and analyzed. The intra-specific sequence variations of P. canaliculata were 0-1.1% for 12S and 0--0.6% for 16S, while the inter-specific variations among common Pomacea species in mt 12S and 16S were 3.0-11.7% and 2.3-10.1%, respectively. Phylogenetic analysis based on combined sequences of mt 12S and 16S revealed complex genetic structure of P. canaliculata in China. Two phylogenetic groups of P. canaliculata were indicated in China with one group sistered to P. canaliculata isolates from USA, and two groups were even found in the same province. The phylogenetic relationships of Pomacea spp. also could be effectively inferred by combined sequences of mt 12S and 16S. These findings provided basic information for further study of population genetics and diffusion pattern of P. canaliculata in China as well as in the world.

  2. Difference Between Dormant Conduction Sites Revealed by Adenosine Triphosphate Provocation and Unipolar Pace-Capture Sites Along the Ablation Line After Pulmonary Vein Isolation.

    PubMed

    Kogawa, Rikitake; Okumura, Yasuo; Watanabe, Ichiro; Sonoda, Kazumasa; Sasaki, Naoko; Takahashi, Keiko; Iso, Kazuki; Nagashima, Koichi; Ohkubo, Kimie; Nakai, Toshiko; Kunimoto, Satoshi; Hirayama, Atsushi

    2016-01-01

    Dormant pulmonary vein (PV) conduction revealed by adenosine/adenosine triphosphate (ATP) provocation test and exit block to the left atrium by pacing from the PV side of the ablation line ("pace and ablate" method) are used to ensure durable pulmonary vein isolation (PVI). However, the mechanistic relation between ATP-provoked PV reconnection and the unexcitable gap along the ablation line is unclear.Forty-five patients with atrial fibrillation (AF) (paroxysmal: 31 patients, persistent: 14 patients; age: 61.1 ± 9.7 years) underwent extensive encircling PVI (EEPVI, 179 PVs). After completion of EEPVI, an ATP provocation test (30 mg, bolus injection) and unipolar pacing (output, 10 mA; pulse width, 2 ms) were performed along the previous EEPVI ablation line to identify excitable gaps. Dormant conduction was revealed in 29 (34 sites) of 179 PVs (16.2%) after EEP-VI (22/45 patients). Pace capture was revealed in 59 (89 sites) of 179 PVs (33.0%) after EEPVI (39/45 patients), and overlapping sites, ie, sites showing both dormant conduction and pace capture, were observed in 22 of 179 (12.3%) PVs (17/45 patients).Some of the ATP-provoked dormant PV reconnection sites were identical to the sites with excitable gaps revealed by pace capture, but most of the PV sites were differently distributed, suggesting that the main underling mechanism differs between these two forms of reconnection. These findings also suggest that performance of the ATP provocation test followed by the "pace and ablate" method can reduce the occurrence of chronic PV reconnections.

  3. 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.

  4. 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.

  5. Landau-like theory for universality of critical exponents in quasistationary states of isolated mean-field systems

    NASA Astrophysics Data System (ADS)

    Ogawa, Shun; Yamaguchi, Yoshiyuki Y.

    2015-06-01

    An external force dynamically drives an isolated mean-field Hamiltonian system to a long-lasting quasistationary state, whose lifetime increases with population of the system. For second order phase transitions in quasistationary states, two nonclassical critical exponents have been reported individually by using a linear and a nonlinear response theories in a toy model. We provide a simple way to compute the critical exponents all at once, which is an analog of the Landau theory. The present theory extends the universality class of the nonclassical exponents to spatially periodic one-dimensional systems and shows that the exponents satisfy a classical scaling relation inevitably by using a key scaling of momentum.

  6. 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

  7. In vitro inhibition of field isolates of feline calicivirus with short interfering RNAs (siRNAs).

    PubMed

    McDonagh, Phillip; Sheehy, Paul A; Fawcett, Anne; Norris, Jacqueline M

    2015-05-15

    Feline calicivirus (FCV) is a common infection of domestic cats. Most infections are mild and self-limiting; however more severe disease manifestations, such as FCV-associated virulent systemic disease, may be associated with significant morbidity and mortality. There is currently a lack of effective antiviral treatments for these disease manifestations. In this study, a panel of eight siRNAs were designed to target four conserved regions of the FCV genome. siRNAs were screened for in vitro antiviral efficacy against the reference strain FCV F9 by determination of extracellular virus titres and morphological assessment of protection from cytopathic effect. Three of the siRNA (FCV3.7, FCV4.1, and FCV4.2) demonstrated a marked antiviral effect with a greater than 99% reduction in extracellular viral titre. Titration of these effective siRNAs demonstrated a clear concentration-response relationship, with IC50 values of approximately 1 nM, and combination treatment with multiple siRNAs demonstrated additive or synergistic effects. To assess the potential usefulness of the compounds in a clinical setting, siRNAs were screened against a panel of six recent Australian FCV isolates from cats with FCV-related disease. The siRNAs shown to be effective against the reference strain FCV F9 were active against the majority of the isolates tested, although some variability was noted. Taken together these data suggest potential therapeutic application of antiviral RNAi for treating FCV-associated disease in cats.

  8. Comparison of Botrytis cinerea populations isolated from two open-field cultivated host plants.

    PubMed

    Asadollahi, Mojtaba; Fekete, Erzsébet; Karaffa, Levente; Flipphi, Michel; Árnyasi, Mariann; Esmaeili, Mahdi; Váczy, Kálmán Zoltán; Sándor, Erzsébet

    2013-07-19

    The necrotrophic fungus Botrytis cinerea is reported to infect more than 220 host plants worldwide. In phylogenetical-taxonomical terms, the pathogen is considered a complex of two cryptic species, group I and group II. We sampled populations of B. cinerea on sympatric strawberry and raspberry cultivars in the North-East of Hungary for three years during flowering and the harvest period. Four hundred and ninety group II B. cinerea isolates were analyzed for the current study. Three different data sets were generated: (i) PCR-RFLP patterns of the ADP-ATP translocase and nitrate reductase genes, (ii) MSB1 minisatellite sequence data, and (iii) the fragment sizes of five microsatellite loci. The structures of the different populations were similar as indicated by Nei's gene diversity and haplotype diversity. The F statistics (Fst, Gst), and the gene flow indicated ongoing differentiation within sympatric populations. The population genetic parameters were influenced by polymorphisms within the three data sets as assessed using Bayesian algorithms. Data Mining analysis pointed towards the five microsatellite loci as the most defining markers to study differentiation in the 490 isolates. The results suggest the occurrence of host-specific, sympatric divergence of generalist phytoparasites in perennial hosts. PMID:23353014

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. Flavobacterium panaciterrae sp. nov., a β-glucosidase producing bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field.

    PubMed

    Jin, Yan; Kim, Yeon-Ju; Hoang, Van-An; Young Jung, Sun; Nguyen, Ngoc-Lan; Woo Min, Jin; Wang, Chao; Yang, Deok-Chun

    2014-01-01

    The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DCY69(T) is JX233806. A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile strain, designated strain DCY69(T), was isolated from the soil of a ginseng field in the Republic of Korea. Colonies of strain DCY69(T) were circular, 0.5-1.5 mm diameter, yellow, and convex on an R2A agar plate after 2 days. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DCY69(T) belonged to the genus Flavobacterium with 90.5-98.3% gene sequence similarity. The major predominant quinone was MK-6. The major cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and unidentified polar lipids (L1, L2). The genomic DNA G+C content of strain DCY69(T) was 35.0mol%. The strain DCY69(T) transformed ginsenoside Rb1 into Rd and F2. Based on the polyphasic taxonomic data, strain DCY69(T) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium panaciterrae sp. nov. is proposed. The type strain is DCY69(T)(= KCTC 32392(T) = JCM 19161(T)), isolated from the soil of a ginseng field in the Republic of Korea.

  14. Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character

    PubMed Central

    Fisher, Marilyn; Hirsch, Nicolas; Cox, Amanda; Reeder, Rollin; Carruthers, Samantha; Hall, Amanda; Stemple, Derek L.; Grainger, Robert M.

    2014-01-01

    SUMMARY The retinal anterior homeobox (rax) gene encodes a transcription factor necessary for vertebrate eye development. rax transcription is initiated at the end of gastrulation in Xenopus, and is a key part of the regulatory network specifying anterior neural plate and retina. We describe here a Xenopus tropicalis rax mutant, the first mutant analyzed in detail from a reverse genetic screen. As in other vertebrates, this nonsense mutation results in eyeless animals, and is lethal peri-metamorphosis. Tissue normally fated to form retina in these mutants instead forms tissue with characteristics of diencephalon and telencephalon. This implies that a key role of rax, in addition to defining the eye field, is in preventing alternative forebrain identities. Our data highlight that brain and retina regions are not determined by the mid-gastrula stage but are by the neural plate stage. An RNA-Seq analysis and in situ hybridization assays for early gene expression in the mutant revealed that several key eye field transcription factors (e.g. pax6, lhx2 and six6) are not dependent on rax activity through neurulation. However, these analyses identified other genes either up- or down-regulated in mutant presumptive retinal tissue. Two neural patterning genes of particular interest that appear up-regulated in the rax mutant RNA-seq analysis are hesx1 and fezf2. These genes were not previously known to be regulated by rax. The normal function of rax is to partially repress their expression by an indirect mechanism in the presumptive retina region in wildtype embryos, thus accounting for the apparent up-regulation in the rax mutant. Knock-down experiments using antisense morpholino oligonucleotides directed against hesx1 and fezf2 show that failure to repress these two genes contributes to transformation of presumptive retinal tissue into non-retinal forebrain identities in the rax mutant. PMID:25224223

  15. Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character.

    PubMed

    Fish, Margaret B; Nakayama, Takuya; Fisher, Marilyn; Hirsch, Nicolas; Cox, Amanda; Reeder, Rollin; Carruthers, Samantha; Hall, Amanda; Stemple, Derek L; Grainger, Robert M

    2014-11-15

    The retinal anterior homeobox (rax) gene encodes a transcription factor necessary for vertebrate eye development. rax transcription is initiated at the end of gastrulation in Xenopus, and is a key part of the regulatory network specifying anterior neural plate and retina. We describe here a Xenopus tropicalis rax mutant, the first mutant analyzed in detail from a reverse genetic screen. As in other vertebrates, this nonsense mutation results in eyeless animals, and is lethal peri-metamorphosis. Tissue normally fated to form retina in these mutants instead forms tissue with characteristics of diencephalon and telencephalon. This implies that a key role of rax, in addition to defining the eye field, is in preventing alternative forebrain identities. Our data highlight that brain and retina regions are not determined by the mid-gastrula stage but are by the neural plate stage. An RNA-Seq analysis and in situ hybridization assays for early gene expression in the mutant revealed that several key eye field transcription factors (e.g. pax6, lhx2 and six6) are not dependent on rax activity through neurulation. However, these analyses identified other genes either up- or down-regulated in mutant presumptive retinal tissue. Two neural patterning genes of particular interest that appear up-regulated in the rax mutant RNA-seq analysis are hesx1 and fezf2. These genes were not previously known to be regulated by rax. The normal function of rax is to partially repress their expression by an indirect mechanism in the presumptive retina region in wildtype embryos, thus accounting for the apparent up-regulation in the rax mutant. Knock-down experiments using antisense morpholino oligonucleotides directed against hesx1 and fezf2 show that failure to repress these two genes contributes to transformation of presumptive retinal tissue into non-retinal forebrain identities in the rax mutant.

  16. 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

  17. 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.

  18. 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…

  19. Revealing the consequences and errors of substance arising from the inverse confusion between the crystal (ligand) field quantities and the zero-field splitting ones

    NASA Astrophysics Data System (ADS)

    Rudowicz, Czesław; Karbowiak, Mirosław

    2015-01-01

    Survey of recent literature has revealed a doubly-worrying tendency concerning the treatment of the two distinct types of Hamiltonians, namely, the physical crystal field (CF), or equivalently ligand field (LF), Hamiltonians and the zero-field splitting (ZFS) Hamiltonians, which appear in the effective spin Hamiltonians (SH). The nature and properties of the CF (LF) Hamiltonians have been mixed up in various ways with those of the ZFS Hamiltonians. Such cases have been identified in a rapidly growing number of studies of the transition-ion based systems using electron magnetic resonance (EMR), optical spectroscopy, and magnetic measurements. These findings have far ranging implications since these Hamiltonians are cornerstones for interpretation of magnetic and spectroscopic properties of the single transition ions in various crystals or molecules as well as the exchange coupled systems (ECS) of transition ions, e.g. single molecule magnets (SMM) or single ion magnets (SIM). The seriousness of the consequences of such conceptual problems and related terminological confusions has reached a level that goes far beyond simple semantic issues or misleading keyword classifications of papers in journals and scientific databases. The prevailing confusion, denoted as the CF=ZFS confusion, pertains to the cases of labeling the true ZFS quantities as purportedly the CF (LF) quantities. Here we consider the inverse confusion between the CF (LF) quantities and the SH (ZFS) ones, denoted the ZFS=CF confusion, which consists in referring to the parameters (or Hamiltonians), which are the true CF (LF) quantities, as purportedly the ZFS (or SH) quantities. Specific cases of the ZFS=CF confusion identified in recent textbooks, reviews and papers, especially SMM- and SIM-related ones, are surveyed and the pertinent misconceptions are clarified. The serious consequences of the terminological confusions include misinterpretation of data from a wide range of experimental techniques and

  20. 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.

  1. 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.

  2. Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.

    PubMed

    Song, Wei; Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Cai, Wei; Jacobs, Donald J

    2013-01-01

    We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface.

  3. Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.

    PubMed

    Song, Wei; Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Cai, Wei; Jacobs, Donald J

    2013-01-01

    We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface. PMID:23833681

  4. 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.

  5. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... contaminating source. The figures in the “Field” column indicate the minimum number of plants or heads in which one plant or head of another variety is permitted. The figure in the “Seed” column indicate the... Hybrid (Chemically assisted) 57 0 52 53 330(59 100.59m) 54 1,000 0.2 Bean: Field and garden 7 1 23 0...

  6. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... contaminating source. The figures in the “Field” column indicate the minimum number of plants or heads in which one plant or head of another variety is permitted. The figure in the “Seed” column indicate the... Hybrid (Chemically assisted) 57 0 52,53 330(59 100.59m) 54 1,000 0.2 Bean: Field and garden 7 1 23 0...

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

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... contaminating source. The figures in the “Field” column indicate the minimum number of plants or heads in which one plant or head of another variety is permitted. The figure in the “Seed” column indicate the... Hybrid (Chemically assisted) 57 0 52,53 330(59 100.59m) 54 1,000 0.2 Bean: Field and garden 7 1 23 0...

  8. 7 CFR 201.76 - Minimum Land, Isolation, Field, and Seed Standards.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... contaminating source. The figures in the “Field” column indicate the minimum number of plants or heads in which one plant or head of another variety is permitted. The figure in the “Seed” column indicate the... Hybrid (Chemically assisted) 57 0 52,53 330(59 100.59m) 54 1,000 0.2 Bean: Field and garden 7 1 23 0...

  9. 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.

  10. Phylogeographic analysis of a temperate-deciduous forest restricted plant (Bupleurum longiradiatum Turcz.) reveals two refuge areas in China with subsequent refugial isolation promoting speciation.

    PubMed

    Zhao, Cai; Wang, Chang-Bao; Ma, Xiang-Guang; Liang, Qian-Long; He, Xing-Jin

    2013-09-01

    This study investigates the influence of climate-induced oscillations and complicated geological conditions on the evolutionary processes responsible for species formation in presently fragmented temperate forest habitats, located in continental East Asia. In addition to this, we also investigate the heavily debated issue of whether temperate forests migrated southwards during such glacial periods or, alternatively, whether there existed refugia within north China, enabling localized survival of temperate forests within this region. In order to achieve these, we surveyed the phylogeography of Bupleurum longiradiatum Turcz. (a herbaceous plant solely confined to temperate forests) constructed from sequence variation in three chloroplast (cp) DNA fragments: trnL-trnF, psbA-trnH and rps16. Our analyses show high genetic diversity within species (h(T)=0.948) and pronounced genetic differentiation among groups (yellow and purple flowers) with a significant phylogeographical pattern (N(ST)>G(ST), P<0.05). Forty-three haplotypes were identified and clustered into two lineages (the purple-flowered lineage and the yellow-flowered lineage). Two corresponding refuge areas, one in Qinling and its adjacent regions and one in the Changbai Mountains/eastern China, were revealed across the entire distribution ranges of Bupleurum longiradiatum. These results provide evidence for the hypothesis that independent refugia were maintained across the range of temperate forests in northern China during the last glacial maximum or earlier cold periods. Bupleurum longiradiatum var. porphyranthum formed a single taxon based on molecular data. This specific formation process suggests that the historical vicariance factors, i.e. climate-induced eco-geographic isolation through the biotic displacement of temperate-deciduous forest habitats, enhanced the divergence of the yellow and purple flower lineages at different spatial-temporal scales and over glacial and interglacial periods

  11. Phylogeographic analysis of a temperate-deciduous forest restricted plant (Bupleurum longiradiatum Turcz.) reveals two refuge areas in China with subsequent refugial isolation promoting speciation.

    PubMed

    Zhao, Cai; Wang, Chang-Bao; Ma, Xiang-Guang; Liang, Qian-Long; He, Xing-Jin

    2013-09-01

    This study investigates the influence of climate-induced oscillations and complicated geological conditions on the evolutionary processes responsible for species formation in presently fragmented temperate forest habitats, located in continental East Asia. In addition to this, we also investigate the heavily debated issue of whether temperate forests migrated southwards during such glacial periods or, alternatively, whether there existed refugia within north China, enabling localized survival of temperate forests within this region. In order to achieve these, we surveyed the phylogeography of Bupleurum longiradiatum Turcz. (a herbaceous plant solely confined to temperate forests) constructed from sequence variation in three chloroplast (cp) DNA fragments: trnL-trnF, psbA-trnH and rps16. Our analyses show high genetic diversity within species (h(T)=0.948) and pronounced genetic differentiation among groups (yellow and purple flowers) with a significant phylogeographical pattern (N(ST)>G(ST), P<0.05). Forty-three haplotypes were identified and clustered into two lineages (the purple-flowered lineage and the yellow-flowered lineage). Two corresponding refuge areas, one in Qinling and its adjacent regions and one in the Changbai Mountains/eastern China, were revealed across the entire distribution ranges of Bupleurum longiradiatum. These results provide evidence for the hypothesis that independent refugia were maintained across the range of temperate forests in northern China during the last glacial maximum or earlier cold periods. Bupleurum longiradiatum var. porphyranthum formed a single taxon based on molecular data. This specific formation process suggests that the historical vicariance factors, i.e. climate-induced eco-geographic isolation through the biotic displacement of temperate-deciduous forest habitats, enhanced the divergence of the yellow and purple flower lineages at different spatial-temporal scales and over glacial and interglacial periods

  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.

  13. 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

  14. 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

  15. Effect of drugs, hormones and electrical field stimulation on isolated muscle strips from human choledochoduodenal junction.

    PubMed

    McKirdy, H C; Marshall, R W; Griffin, P

    1987-04-01

    The behaviour of in vitro strips from the human choledochoduodenal junction would appear to be related to the anatomical location of origin of the strip. Strips from the papillary region showed low tone and obvious spontaneous rhythmic contractions (0 X 5-6/min). Strips from the region of the inferior choledochal sphincter showed, in ten out of fifteen specimens, spontaneous myogenic tone and gave a relaxation or a biphasic response (relaxation followed by contraction) to electrical field stimulation (0 X 3 ms pulses at 10 Hz for 5 s). All strips from human choledochoduodenal junction are remarkably insensitive to a variety of gastrointestinal hormones and to opioid agents.

  16. 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.

  17. High-resolution melt PCR analysis for rapid identification of Chlamydia abortus live vaccine strain 1B among C. abortus strains and field isolates.

    PubMed

    Vorimore, Fabien; Cavanna, Noémie; Vicari, Nadia; Magnino, Simone; Willems, Hermann; Rodolakis, Annie; Siarkou, Victoria I; Laroucau, Karine

    2012-09-01

    We describe a novel high-resolution melt assay that clearly differentiates Chlamydia abortus live vaccine strain 1B from field C. abortus strains and field wild-type isolates based on previously described single nucleotide polymorphisms. This modern genotyping technique is inexpensive, easy to use, and less time-consuming than PCR-RFLP.

  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