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Sample records for candidatus pelagibacter ubique

  1. Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'

    Energy Technology Data Exchange (ETDEWEB)

    Sowell, Sarah M.; Norbeck, Angela D.; Lipton, Mary S.; Nicora, Carrie D.; Callister, Stephen J.; Smith, Richard D.; Barofsky, Douglas F.; Giovannoni, Stephen J.

    2008-05-01

    Candidatus Pelagibacter ubique, an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome revealed no evidence of global regulatory adaptations to stationary phase. We used high-resolution capillary liquid chromatography (LC) coupled online to an LTQ mass spectrometer to build an Accurate Mass and Time (AMT) tag library, and employed the AMT tag approach to quantitatively examine proteome differences between exponentially growing and stationary phase Cand. P. ubique cells cultivated in a seawater medium. The AMT tag library represented 72% of the predicted protein coding genes. Stationary phase protein abundance increased for OsmC, which mitigates oxidative damage, and for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in rho-dependent transcription termination, and the signal transduction enzymes CheY-FisH and ChvG. Our findings indicate that Cand. P. ubique responds adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis, but does not undergo major proteome remodeling. We speculate that this limited response may enable Cand. P. ubique to cope with ambient conditions in which nutrients are often insufficient for short periods, and the ability to resume growth overrides the capacity for long term survival afforded by more comprehensive global stationary phase responses.

  2. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

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    Schwalbach Michael S

    2009-06-01

    Full Text Available Abstract Background Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content. Results To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc. shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. Conclusion This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.

  3. Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration.

    Directory of Open Access Journals (Sweden)

    Laura Steindler

    Full Text Available Previous studies have demonstrated that Candidatus Pelagibacter ubique, a member of the SAR11 clade, constitutively expresses proteorhodopsin (PR proteins that can function as light-dependent proton pumps. However, exposure to light did not significantly improve the growth rate or final cell densities of SAR11 isolates in a wide range of conditions. Thus, the ecophysiological role of PR in SAR11 remained unresolved. We investigated a range of cellular properties and here show that light causes dramatic changes in physiology and gene expression in Cand. P. ubique cells that are starved for carbon, but provides little or no advantage during active growth on organic carbon substrates. During logarithmic growth there was no difference in oxygen consumption by cells in light versus dark. Energy starved cells respired endogenous carbon in the dark, becoming spheres that approached the minimum predicted size for cells, and produced abundant pili. In the light, energy starved cells maintained size, ATP content, and higher substrate transport rates, and differentially expressed nearly 10% of their genome. These findings show that PR is a vital adaptation that supports Cand. P. ubique metabolism during carbon starvation, a condition that is likely to occur in the extreme conditions of ocean environments.

  4. Proteomic Analysis of Stationary Phase in the Marine Bacterium "Candidatus Pelagibacter ubique"

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    Sowell, S. M.; Norbeck, A. D.; Lipton, M. S.; Nicora, C. D.; Callister, S. J.; Smith, R. D.; Barofsky, D. F.; Giovannoni, S. J.

    2008-05-09

    The α-proteobacterium ‘Candidatus Pelagibacter ubique’ str. HTCC1062, and most other members of the SAR11 clade, lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined media containing either limiting or non-limiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured during exponential growth, immediately prior to stationary phase, and in late stationary phase. Two distinct responses were observed: one as DMSP became exhausted, and another as cells acclimated to a sulfur-limited environment. The first response was characterized by increased transcription and translation of all Ca. P. ubique genes downstream of previously confirmed S-adenosyl methionine (SAM) riboswitches: bhmT, mmuM, and metY. Proteins encoded by these genes were up to 33 times more abundant as DMSP became limiting. Their predicted function is to shunt all available sulfur to methionine. The secondary response, observed during sulfur-depleted stationary phase, was a 6-10 fold increase in transcription of the heme c shuttle ccmC and two small genes of unknown function (SAR11_1163 and SAR11_1164). This bacterium's strategy for coping with sulfur stress appears to be intracellular redistribution to support methionine biosynthesis, rather than increasing organosulfur import. Many of the genes and SAM riboswitches involved in this response are located in a hypervariable genome region (HVR). One of these HVR genes, ordL, is located downstream of a conserved motif that evidence suggests is a novel riboswitch.

  5. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.

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    Kalliopi Georgiades

    Full Text Available BACKGROUND: The evolution of the Alphaproteobacteria and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the Rickettsiales order. Ten years ago, the bacterium Odyssella thessalonicensis was isolated from Acanthamoeba spp., and the 16S rDNA phylogeny placed it within the Rickettsiales. Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins. METHODOLOGY/PRINCIPAL FINDINGS: The results suggested that the O. thessalonicensis emerged between the Rickettsiales and other Alphaproteobacteria. The mitochondrial proteins of the Reclinomonas americana have been used to locate the phylogenetic position of the mitochondrion ancestor within the Alphaproteobacteria tree. Using the K tree score method, nine mitochondrion-encoded proteins, whose phylogenies were congruent with the Alphaproteobacteria phylogenomic tree, have been selected and concatenated for Bayesian and Maximum Likelihood phylogenies. The Reclinomonas americana mitochondrion is a sister taxon to the free-living bacteria Candidatus Pelagibacter ubique, and together, they form a clade that is deeply rooted in the Rickettsiales clade. CONCLUSIONS/SIGNIFICANCE: The Reclinomonas americana mitochondrion phylogenomic study confirmed that mitochondria emerged deeply in the Rickettsiales clade and that they are closely related to Candidatus Pelagibacter ubique.

  6. Proteome Remodeling in Response to Sulfur Limitation in “ Candidatus Pelagibacter ubique”

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Daniel P.; Nicora, Carrie D.; Carini, Paul; Lipton, Mary S.; Norbeck, Angela D.; Smith, Richard D.; Giovannoni, Stephen J.; Wilmes, Paul

    2016-07-12

    The alphaproteobacterium “CandidatusPelagibacter ubique” strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined medium containing either limiting or nonlimiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured before, during, and after the transition from exponential growth to stationary phase. Two distinct responses were observed, one as DMSP became exhausted and another as the cells acclimated to a sulfur-limited environment. The first response was characterized by increased transcription and translation of all “Ca. Pelagibacter ubique” genes downstream from the previously confirmedS-adenosyl methionine (SAM) riboswitchesbhmT,mmuM, andmetY. The proteins encoded by these genes were up to 33 times more abundant as DMSP became limiting. Their predicted function is to shunt all available sulfur to methionine. The secondary response, observed during sulfur-limited stationary phase, was a 6- to 10-fold increase in the transcription of the hemecshuttle-encoding geneccmCand two small genes of unknown function (SAR11_1163andSAR11_1164). This bacterium’s strategy for coping with sulfur stress appears to be intracellular redistribution to support methionine biosynthesis rather than increasing organosulfur import. Many of the genes and SAM riboswitches involved in this response are located in a hypervariable genome region (HVR). One of these HVR genes,ordL, is located downstream from a conserved motif that evidence suggests is a novel riboswitch.

  7. Abundance of Two Pelagibacter ubique Bacteriophage Genotypes along a Latitudinal Transect in the North and South Atlantic Oceans

    Science.gov (United States)

    Eggleston, Erin M.; Hewson, Ian

    2016-01-01

    This study characterizes viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10 N–40 S. Overall viral abundance decreased with depth, on average there were 1.64 ± 0.71 × 107 virus like particles (VLPs) in surface waters, decreasing to an average of 6.50 ± 2.26 × 105 VLPs in Antarctic Bottom Water. This decrease was highly correlated to bacterial abundance. There are six major water masses in the Southern Tropical Atlantic Ocean, and inclusion of water mass, temperature and salinity variables explained a majority of the variation in total viral abundance. Recent discovery of phages infecting bacteria of the SAR11 clade of Alphaproteobacteria (i.e., pelagiphages) leads to intriguing questions about the roles they play in shaping epipelagic communities. Viral-size fraction DNA from epipelagic water was used to quantify the abundance of two pelagiphages, using pelagiphage-specific quantitative PCR primers and probes along the transect. We found that HTVC010P, a member of a podoviridae sub-family, was most abundant in surface waters. Copy numbers ranged from an average of 1.03 ± 2.38 × 105 copies ml−1 in surface waters, to 5.79 ± 2.86 × 103 in the deep chlorophyll maximum. HTVC008M, a T4-like myovirus, was present in the deep chlorophyll maximum (5.42 ± 2.8 × 103 copies ml−1 on average), although it was not as highly abundant as HTVC010P in surface waters (6.05 ± 3.01 × 103 copies ml−1 on average). Interestingly, HTVC008M was only present at a few of the most southern stations, suggesting latitudinal biogeography of SAR11 phages. PMID:27733846

  8. Dicty_cDB: Contig-U11762-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 10 ( CP000084 ) Candidatus Pelagibacter ubique HTCC1062, complete... 34 0.87 20 ( EF568108 ) Glossina pallidipes salivary gland hyper...trophy vi... 30 0.88 16 ( AF529435 ) Bombus morio 12S small subunit ribosomal RNA g

  9. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jing; Todd, Jonathan D.; Thrash, J. Cameron; Qian, Yanping; Qian, Michael C.; Temperton, Ben; Guo, Jiazhen; Fowler, Emily K.; Aldrich, Joshua T.; Nicora, Carrie D.; Lipton, Mary S.; Smith, Richard D.; De Leenheer, Patrick; Payne, Samuel H.; Johnston, Andrew W. B.; Davie-Martin, Cleo L.; Halsey, Kimberly H.; Giovannoni, Stephen J.

    2016-05-16

    Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year1,2, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS)3,4. SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur5,6. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a DMSP lyase, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of DMS as the supply of DMSP exceeds cellular sulfur demands for biosynthesis. These findings suggest that DMSP supply and demand relationships in Pelagibacter metabolism are important to determining rates of oceanic DMS production.

  10. Abundance of two Pelagibacter ubique bacteriophage genotypes along a latitudinal transect in the North and South Atlantic Oceans

    Directory of Open Access Journals (Sweden)

    Erin M Eggleston

    2016-09-01

    Full Text Available This study characterizes viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10N to 40S. Overall viral abundance decreased with depth, on average there were 1.64 ± 0.71 x107 virus like particles (VLPs in surface waters, decreasing to an average of 6.50 ± 2.26 x105 VLPs in Antarctic Bottom Water. This decrease was highly correlated to bacterial abundance. There are six major water masses in the Southern Tropical Atlantic Ocean, and inclusion of water mass, temperature and salinity variables explained a majority of the variation in total viral abundance. Recent discovery of phages infecting bacteria of the SAR11 clade of Alphaproteobacteria (i.e. pelagiphages leads to intriguing questions about the roles they play in shaping epipelagic communities. Viral-size fraction DNA from epipelagic water was used to quantify the abundance of two pelagiphages, using pelagiphage-specific quantitative PCR primers and probes along the transect. We found that HTVC010P, a member of a podoviridae sub-family, was most abundant in surface waters. Copy numbers ranged from an average of 1.03 ± 2.38 x 105 copies ml-1 in surface waters, to 5.79 ± 2.86 x103 in the deep chlorophyll maximum. HTVC008M, a T4-like myovirus, was present in the deep chlorophyll maximum (5.42±2.8x103 copies ml-1 on average, although it was not as highly abundant as HTVC010P in surface waters (6.05±3.01x103 copies ml-1 on average. Interestingly, HTVC008M was only present at a few of the most southern stations, suggesting latitudinal biogeography of SAR11 phages.

  11. Packet Reordering Procedure with Ubiquous Communication Systems

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    Giridhar Akula

    2012-11-01

    Full Text Available Satellite links are going to play a vital role in the deployment of ubiquous broad band systems. Non- Geostationary (NGEO satellite communication systems are more advantageous than terrestrial satellites. This paper presents an exchange of information on cooperation status among neiboring satellites. The new explicit load balancing scheme is used to avoid congestion and packet drops at the satellite. A TTL based algorithm is used for packet reordering.

  12. Species in Wolbachia? Proposal for the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxteri', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylori', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitum' for the different species within Wolbachia supergroups.

    Science.gov (United States)

    Ramírez-Puebla, Shamayim T; Servín-Garcidueñas, Luis E; Ormeño-Orrillo, Ernesto; Vera-Ponce de León, Arturo; Rosenblueth, Mónica; Delaye, Luis; Martínez, Julio; Martínez-Romero, Esperanza

    2015-09-01

    Wolbachia are highly extended bacterial endosymbionts that infect arthropods and filarial nematodes and produce contrasting phenotypes on their hosts. Wolbachia taxonomy has been understudied. Currently, Wolbachia strains are classified into phylogenetic supergroups. Here we applied phylogenomic analyses to study Wolbachia evolutionary relationships and examined metrics derived from their genome sequences such as average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, and synteny to shed light on the taxonomy of these bacteria. Draft genome sequences of strains wDacA and wDacB obtained from the carmine cochineal insect Dactylopius coccus were included. Although all analyses indicated that each Wolbachia supergroup represents a distinct evolutionary lineage, we found that some of the analyzed supergroups showed enough internal heterogeneity to be considered as assemblages of more than one species. Thus, supergroups would represent supraspecific groupings. Consequently, Wolbachia pipientis nomen species would apply only to strains of supergroup B and we propose the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxterii', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylorii', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitis' for other supergroups.

  13. Ubiquity of bisphenol A in the atmosphere.

    Science.gov (United States)

    Fu, Pingqing; Kawamura, Kimitaka

    2010-10-01

    Bisphenol A (BPA) is a suspected endocrine disruptor in the environment. However, little is known about its distribution and transport in the atmosphere. Here, the concentrations of BPA in the atmospheric aerosols from urban, rural, marine, and the polar regions were measured using solvent extraction/derivatization and gas chromatography/mass spectrometry technique. The concentrations of BPA (1-17,400 pg m(-3)) ranged over 4 orders of magnitude in the world with a declining trend from the continent (except for the Antarctica) to remote sites. A positive correlation was found between BPA and 1,3,5-triphenylbenzene, a tracer for plastic burning, in urban regions, indicating that the open burning of plastics in domestic waste should be a significant emission source of atmospheric BPA. Our results suggest that the ubiquity of BPA in the atmosphere may raise a requirement for the evaluation of health effects of BPA in order to control its emission sources, for example, from plastic burning.

  14. The ubiquity of deception and the ethics of deceptive research.

    Science.gov (United States)

    Benham, Bryan

    2008-03-01

    Does the fact that deception is widely practised - even though there is a general prohibition against deception - provide insight into the ethics of deceptive methods in research, especially for social-behavioral research? I answer in the affirmative. The ubiquity of deception argument, as I will call it, points to the need for a concrete and nuanced understanding of the variety of deceptive practices, and thus promises an alternative route of analysis for why some deception may be permissible in social-behavioral research. As an alternative argument it also promises to break the stalemate that emerges in debates on the ethics of deceptive methods in social-behavioral research. In the current paper I (1) motivate and articulate the ubiquity argument in order to clarify the significance of ubiquity and discharge some initial objections. Then, on the recommendations of the ubiquity argument, I (2) highlight the importance of interpersonal relationships for understanding the ethics of deception. Following this insight I (3) provide an analysis of several features of the researcher-participant relationship relevant to the understanding of the ethics of deception in research. I then (4) conclude the argument with some recommendations for the ethical use of deceptive methods in social-behavioral research.

  15. Mammonist Capitalism – Ubiquity, Immanence, Acceleration. And the Social Consequences

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    Bo Isenberg

    2013-06-01

    Full Text Available This essay attempts at a general understanding of contemporary capitalism and some of its social and mental consequences. It works through combinations and variations of concepts from classical and contemporary social theory. Some key concepts are Mammonism, acceleration, ubiquity, self-dynamics, precariat, inertia, conformity, flexibility, specter of uselessness. The text refers to classical modern thinkers like Marx, Simmel, Musil, Benjamin, and to contemporary ideas in the works of Deleuze, Rosa, Crouch, Illouz, Standing, Hochschild. It is summoned up by asking some important, complex questions that regard democracy, community and autonomy.

  16. Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification.

    Science.gov (United States)

    Jezbera, Jan; Jezberová, Jitka; Brandt, Ulrike; Hahn, Martin W

    2011-04-01

    The subspecies Polynucleobacter necessarius asymbioticus (> 99% 16S rRNA similarity) has a cosmopolitan distribution and a ubiquitous occurrence in lentic freshwater habitats. We tested if the observed ubiquity of these free-living planktonic freshwater bacteria results from a euryoecious (generalist) adaptation of P. n. asymbioticus strains, or from ecological diversification within the subspecies. We developed a reverse line blot hybridization assay enabling the cultivation-independent detection of 13 groups within the subspecies in environmental samples. A set of 121 lentic freshwater habitats, spanning a broad variety of habitat types (e.g. pH levels ranging from 3.8 to 8.5) was investigated for the presence of these 13 P. n. asymbioticus groups. Statistical analyses of the reverse line blot hybridization detections revealed pronounced differences in habitat preferences of several of the groups. Their preferences differed regarding pH, conductivity, dissolved organic carbon and oxygen concentration of habitats. For some groups, differences in environmental preferences resulted even in complete niche separation between them. The revealed differences in habitat preferences suggest that the previously reported ubiquity of P. n. asymbioticus results from ecological diversification within the taxon and not from generalist adaptation of strains.

  17. Medicoscapes: on mobile ubiquity effects and ICT4D

    DEFF Research Database (Denmark)

    Michelsen, Anders Ib

    2012-01-01

    on use of resources of the global civil society emerging in global ‘transformations’ related to migration, media and ‘the social work of the imagination’. Whereas much new media debate departs from the assumption of media ubiquity affecting our notions of reality, the article will attempt a different...... perspective. It will ponder issues of collective imagination as exerted by way of such effects, i.e. in cultural forms that emerge out of media-roles in the ‘complex connectivity’ in globalisation processes.......The Article presents theoretical comments on the theme of ‘media ubiquity’, as an introduction to the presentation of an information and communication technology ‘4’ development (ICT4D) project in the Republic of Somaliland: The Somaliland Telemedical System for Psychiatry. This project is based...

  18. Isolation of Candidatus Rickettsia asemboensis from Ctenocephalides Fleas.

    Science.gov (United States)

    Luce-Fedrow, Alison; Maina, Alice N; Otiang, Elkanah; Ade, Fredrick; Omulo, Sylvia; Ogola, Eric; Ochieng, Linus; Njenga, M Kariuki; Richards, Allen L

    2015-04-01

    Candidatus Rickettsia asemboensis was identified molecularly in fleas collected in 2009 from Asembo, Kenya. Multilocus sequence typing using the 17-kD antigen gene, rrs, gltA, ompA, ompB, and sca4 demonstrated that Candidatus R. asemboensis is closely related to Rickettsia felis but distinct enough to be considered for separate species classification. Following this molecular characterization of Candidatus R. asemboensis, the in vitro cultivation of this bacterium was then performed. We used Ctenocephalides canis and Ctenocephalides felis fleas removed from dogs in Kenya to initiate the in vitro isolation of Candidatus R. asemboensis. Successful cultures were obtained using Drosophila melanogaster S2 and Aedes albopictus C6/36 cell lines. Cytological staining and quantitative real-time PCR (qPCR) assays were used to visualize/confirm the culture of the bacteria in both cell lines. Sequencing of fragments of the 17-kD antigen gene, gltA, and ompB genes confirmed the identity of our Candidatus R. asemboensis isolates. To date, we have passaged Candidatus R. asemboensis 12 times through S2 and C6/36 cells, and active and frozen cultures are currently being maintained. This is the first time that a R. felis-like organism has been grown and maintained in culture and is therefore the first time that one of them, Candidatus R. asemboensis, has been characterized beyond molecular typing.

  19. Hierarchy, causation and explanation: ubiquity, locality and pluralism.

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    Love, Alan C

    2012-02-06

    The ubiquity of top-down causal explanations within and across the sciences is prima facie evidence for the existence of top-down causation. Much debate has been focused on whether top-down causation is coherent or in conflict with reductionism. Less attention has been given to the question of whether these representations of hierarchical relations pick out a single, common hierarchy. A negative answer to this question undermines a commonplace view that the world is divided into stratified 'levels' of organization and suggests that attributions of causal responsibility in different hierarchical representations may not have a meaningful basis for comparison. Representations used in top-down and bottom-up explanations are primarily 'local' and tied to distinct domains of science, illustrated here by protein structure and folding. This locality suggests that no single metaphysical account of hierarchy for causal relations to obtain within emerges from the epistemology of scientific explanation. Instead, a pluralist perspective is recommended-many different kinds of top-down causation (explanation) can exist alongside many different kinds of bottom-up causation (explanation). Pluralism makes plausible why different senses of top-down causation can be coherent and not in conflict with reductionism, thereby illustrating a productive interface between philosophical analysis and scientific inquiry.

  20. Human attribute concepts: relative ubiquity across twelve mutually isolated languages.

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    Saucier, Gerard; Thalmayer, Amber Gayle; Bel-Bahar, Tarik S

    2014-07-01

    It has been unclear which human-attribute concepts are most universal across languages. To identify common-denominator concepts, we used dictionaries for 12 mutually isolated languages-Maasai, Supyire Senoufo, Khoekhoe, Afar, Mara Chin, Hmong, Wik-Mungkan, Enga, Fijian, Inuktitut, Hopi, and Kuna-representing diverse cultural characteristics and language families, from multiple continents. A composite list of every person-descriptive term in each lexicon was closely examined to determine the content (in terms of English translation) most ubiquitous across languages. Study 1 identified 28 single-word concepts used to describe persons in all 12 languages, as well as 41 additional terms found in 11 of 12. Results indicated that attribute concepts related to morality and competence appear to be as cross-culturally ubiquitous as basic-emotion concepts. Formulations of universal-attribute concepts from Osgood and Wierzbicka were well-supported. Study 2 compared lexically based personality models on the relative ubiquity of key associated terms, finding that 1- and 2-dimensional models draw on markedly more ubiquitous terms than do 5- or 6-factor models. We suggest that ubiquitous attributes reflect common cultural as well as common biological processes.

  1. Thermodynamic Explanation for the Cosmic Ubiquity of Organic Pigments

    CERN Document Server

    Michaelian, Karo

    2016-01-01

    There is increasingly more evidence being accumulated for the occurrence of large amounts of organic material in the cosmos, particularly in the form of aromatic compounds. These molecules can be found on the surface of Earth and Mars, in the atmospheres of the larger planets and on many of their satellites, on asteroids, comets, meteorites, the atmospheres of red giant stars, interstellar nebulae, and in the spiral arms of galaxies. Many of these environments are expected to be of low temperature and pressure, implying that the Gibbs free energy for the formation of these complex molecules should be positive and large, suggesting that their existence could only be attributed to non-equilibrium thermodynamic processes. In this article we first review the evidence for the abundance of these molecules in the cosmos and then describe how the ubiquity can be explained from within the framework of non-equilibrium thermodynamics on the basis of the catalytic properties of these pigment molecules in dissipating phot...

  2. Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Coates, J.D.; Michaelidou, U.; Bruce, R.A.; O' Connor, S.M.; Crespi, J.N.; Achenbach, L.A.

    1999-12-01

    Environmental contamination with compounds containing oxyanions of chlorine, such as perchlorate or chlorate [(per)chlorate] or chlorine dioxide, has been a constantly growing problem over the last 100 years. Although the fact that microbes reduce these compounds has been recognized for more than 50 years, only six organisms which can obtain energy for growth by this metabolic process have been described. As part of a study to investigate the diversity and ubiquity of microorganisms involved in the microbial reduction of (per) chlorate, the authors enumerated the (per) chlorate-reducing bacteria (ClRB) in very diverse environments, including pristine and hydrocarbon-contaminated soils, aquatic sediments, paper mill waste sludges, and farm animal waste lagoons. In all of the environments tested, the acetate-oxidizing ClRB represented a significant population, whose size ranged from 2.31 x 10{sup 3} to 2.4 x 10{sup 6} cells per g of sample. In addition, the authors isolated 13 ClRB from these environments. All of these organisms could grow anaerobically by coupling complete oxidation of acetate to reduction of (per) chlorate. Chloride was the sole end product of this reductive metabolism. All of the isolates could also use oxygen as a sole electron acceptor, and most, but not all, could use nitrate. The alternative electron donors included simple volatile fatty acids, such as propionate, butyrate, or valerate, as well as simple organic acids, such as lactate or pyruvate. Oxidized-minus-reduced difference spectra of washed whole-cell suspensions of the isolates had absorbance maxima close to 425, 525, and 550 nm, which are characteristic of type c cytochromes. In addition, washed cell suspensions of all of the ClRB isolates could dismutate chlorite, an intermediate in the reductive metabolism of (per) chlorate, into chloride and molecular oxygen.

  3. Two rrn DNAs from periwinkle infected by Candidatus Liberibacter asiaticus

    Science.gov (United States)

    Huanglongbing (HLB, ex. greening,) is a highly destructive disease threatening citrus production worldwide. In southern China, HLB is currently believed to be caused by infection by Candidatus Liberibacter asiaticus. The pathogen is not culturable in vitro. We have been maintaining a strain o...

  4. First report of "Candidatus Liberibacter solanacearum" on pepper in Honduras

    Science.gov (United States)

    In 2012, bell pepper (Capsicum annuum) plants exhibiting symptoms that resembled those of the bacterium “Candidatus Liberibacter solanacearum” infection were observed in commercial pepper fields in several departments in Honduras, including Francisco Morazán, Ocotepeque, El Paraíso, and Olancho. Man...

  5. First report of 'Candidatus Liberibacter solanacearum' on tomato in Honduras

    Science.gov (United States)

    In April of 2012, tomato plants grown in several departments of Honduras, were observed with symptoms resembling those of “Candidatus Liberibacter solanacearum” (Lso) infection. The symptoms include overall chlorosis, severe stunting, leaf cupping, excessive branching of axillary shoots, and leaf pu...

  6. Complete genome sequence of ‘Candidatus Liberibacter africanus’

    Science.gov (United States)

    The complete genome sequence of ‘Candidatus Liberibacter africanus’ (Laf), strain ptsapsy, was obtained by an Illumina HiSeq 2000. The Laf genome comprises 1,192,232 nucleotides, 34.5% GC content, 1,141 predicted coding sequences, 44 tRNAs, 3 complete copies of ribosomal RNA genes (16S, 23S and 5S) ...

  7. Ubiquity of non-diffusive momentum transport in JET H-modes

    NARCIS (Netherlands)

    Weisen, H.; Camenen, Y.; Salmi, A.; Versloot, T. W.; de Vries, P. C.; Maslov, M.; Tala, T.; Beurskens, M.; Giroud, C.; JET-EFDA Contributors,

    2012-01-01

    A broad survey of the experimental database of neutral beam heated baseline H-modes and hybrid scenarios in the JET tokamak has established the ubiquity of non-diffusive momentum transport mechanisms in rotating plasmas. As a result of their presence, the normalized angular frequency gradient R &

  8. A mathematical explanation via "intelligent" PID controllers of the strange ubiquity of PIDs

    CERN Document Server

    Novel, Brigitte D'Andrea; Join, Cédric; Mounier, Hugues; Steux, Bruno

    2010-01-01

    The ubiquity of PID controllers in the industry has remained mysterious until now. We provide here a mathematical explanation of this strange phenomenon by comparing their sampling with the the one of "intelligent" PID controllers, which were recently introduced. Some computer simulations nevertheless confirm the superiority of the new intelligent feedback design.

  9. Microbiology of ‘Candidatus Accumulibacter’ in activated sludge

    OpenAIRE

    He, Shaomei; McMahon, Katherine D.

    2011-01-01

    Summary ‘Candidatus Accumulibacter’ is a biotechnologically important bacterial group that can accumulate large amounts of intracellular polyphosphate, contributing to biological phosphorus removal in wastewater treatment. Since its first molecular identification more than a decade ago, this bacterial group has drawn significant research attention due to its high abundance in many biological phosphorus removal systems. In the past 6 years, our understanding of Accumulibacter microbiology and ...

  10. High prevalence of "Candidatus Rickettsia andeanae" and apparent exclusion of Rickettsia parkeri in adult Amblyomma maculatum (Acari: Ixodidae) from Kansas and Oklahoma.

    Science.gov (United States)

    Paddock, Christopher D; Denison, Amy M; Dryden, Michael W; Noden, Bruce H; Lash, R Ryan; Abdelghani, Sarah S; Evans, Anna E; Kelly, Aubree R; Hecht, Joy A; Karpathy, Sandor E; Ganta, Roman R; Little, Susan E

    2015-04-01

    Amblyomma maculatum (the Gulf Coast tick), an aggressive, human-biting, Nearctic and Neotropical tick, is the principal vector of Rickettsia parkeri in the United States. This pathogenic spotted fever group Rickettsia species has been identified in 8-52% of questing adult Gulf Coast ticks in the southeastern United States. To our knowledge, R. parkeri has not been reported previously from adult specimens of A. maculatum collected in Kansas or Oklahoma. A total of 216 adult A. maculatum ticks were collected from 18 counties in Kansas and Oklahoma during 2011-2014 and evaluated by molecular methods for evidence of infection with R. parkeri. No infections with this agent were identified; however, 47% of 94 ticks collected from Kansas and 73% of 122 ticks from Oklahoma were infected with "Candidatus Rickettsia andeanae" a spotted fever group Rickettsia species of undetermined pathogenicity. These preliminary data suggest that "Ca. R. andeanae" is well-adapted to survival in populations of A. maculatum in Kansas and Oklahoma, and that its ubiquity in Gulf Coast ticks in these states may effectively exclude R. parkeri from their shared arthropod host, which could diminish markedly or preclude entirely the occurrence of R. parkeri rickettsiosis in this region of the United States.

  11. Influence of study in hee on ubiquity and strength of students’ computer gambling

    Directory of Open Access Journals (Sweden)

    Kudryavtsev M.D.

    2016-06-01

    Full Text Available Purpose: to clear up effectiveness of learning-education process for counteraction of students’ harmful passion to computer games’ ubiquity. Material: 1st - 3rd year students (main health group were the objects of the research. In total they were 952 boys and 523 girls. In 1st year students’ academic groups testing was carried out ant the beginning of academic year (October; in academic groups of 1st-3rd year students the testing was at the end of academic year (May. Results: it was found that among 1st year boy students ubiquity of computer gaming as well as time losses, connected with it are higher than among girl students. Educational process is not sufficiently effective in struggle against computer gaming. For girls, this passion is not dangerous in general. In the course of study at HEE, the strength of this passion reduces independent on sex. Conclusions: for increase of educational process’s effectiveness and improvement of students’ life quality it is necessary to consider personal features of boy students as well as to organize health related measures with the help of health related physical culture means.

  12. Effect of chronic feline immunodeficiency infection, and efficacy of marbofloxacin treatment, on 'Candidatus Mycoplasma haemominutum' infection.

    Science.gov (United States)

    Tasker, Séverine; Caney, Sarah M A; Day, Michael J; Dean, Rachel S; Helps, Chris R; Knowles, Toby G; Lait, Philippa J P; Pinches, Mark D G; Gruffydd-Jones, Timothy J

    2006-03-01

    The purpose of this study was to investigate the effect of chronic feline immunodeficiency virus (FIV) infection, and efficacy of marbofloxacin treatment, on 'Candidatus Mycoplasma haemominutum' infection. Six cats chronically infected with FIV-Glasgow8 (group A) and six FIV-free cats (group B) were infected with 'Candidatus M. haemominutum' on day 0 by intravenous inoculation of blood. From day 0 to 105 post-infection (pi), blood samples were collected for 'Candidatus M. haemominutum' and FIV provirus quantitative real-time polymerase chain reaction (PCR) and haematological examination. Three of the six cats in each of the groups were randomly selected to receive marbofloxacin treatment (2mg/kg PO SID) from day 49 to day 76 pi, with the remaining cats being untreated controls. Maximum 'Candidatus M. haemominutum' copy number was reached around day 30 pi. No overt cycling or marked variation in copy number was observed. No significant effect of FIV infection on 'Candidatus M. haemominutum' copy number kinetics or anaemia indices was found. No correlation was found between FIV provirus copy number and 'Candidatus M. haemominutum' copy number or haematological variables. Although marbofloxacin treatment was associated with a significant decrease in 'Candidatus M. haemominutum' copy number, the copy number plateaued during treatment, with no negative PCR results. Additionally, after termination of marbofloxacin treatment the copy numbers of the treated cats increased to reach levels similar to those of the untreated cats within 7-10 days. This study documents, for the first time, the infection kinetics and antibiotic responsiveness of 'Candidatus M. haemominutum' infection.

  13. Candidatus ‘Rickettsia senegalensis’ in cat fleas in Senegal

    Directory of Open Access Journals (Sweden)

    O. Mediannikov

    2015-01-01

    Full Text Available Epidemiological studies of Rickettsia felis and related bacteria are very important, because the natural cycle of this important infection has not yet been established. The recent emergence of R. felis-associated febrile diseases in West and East Africa demands insightful epidemiological studies of the vectors and reservoirs of this bacterium in Africa. Twenty-nine cat fleas, Ctenocephalides felis, were tested for the presence of rickettsiae, including R. felis, bartonellae, and borreliae, with specific quantitative real-time PCR assays. Supporting our previous studies, R. felis was not detected in the fleas collected. In addition, neither Bartonella nor Borrelia was found. In five (17% examined fleas, we found another species of rickettsia. We isolated three rickettsial strains, and genetic analysis demonstrated that these strains represent a probable new species, provisionally called Candidatus Rickettsia senegalensis here.

  14. Rickettsia africae and Candidatus Rickettsia barbariae in ticks in Israel.

    Science.gov (United States)

    Waner, Trevor; Keysary, Avi; Eremeeva, Marina E; Din, Adi Beth; Mumcuoglu, Kosta Y; King, Roni; Atiya-Nasagi, Yafit

    2014-05-01

    DNA of several spotted fever group rickettsiae was found in ticks in Israel. The findings include evidence for the existence of Rickettsia africae and Candidatus Rickettsia barbariae in ticks in Israel. The DNA of R. africae was detected in a Hyalomma detritum tick from a wild boar and DNA of C. Rickettsia barbariae was detected in Rhipicephalus turanicus and Rhipicephalus sanguineus collected from vegetation. The DNA of Rickettsia massiliae was found in Rh. sanguineus and Haemaphysalis erinacei, whereas DNA of Rickettsia sibirica mongolitimonae was detected in a Rhipicephalus (Boophilus) annulatus. Clinicians should be aware that diseases caused by a variety of rickettsiae previously thought to be present only in other countries outside of the Middle East may infect residents of Israel who have not necessarily traveled overseas. Furthermore, this study reveals again that the epidemiology of the spotted fever group rickettsiae may not only involve Rickettsia conorii but may include other rickettsiae.

  15. Molecular Detection of Candidatus Bartonella hemsundetiensis in Bats.

    Science.gov (United States)

    Lilley, Thomas M; Veikkolainen, Ville; Pulliainen, Arto T

    2015-11-01

    Although bats have been implicated as reservoir hosts for a number of zoonotic and life-threatening viruses, the bat bacterial flora and its zoonotic threat remain elusive. However, members of the vector-borne bacterial genera Bartonella causing various human as well as animal diseases have recently been isolated or detected from bats and their ectoparasites. In this study, we sampled 124 insectivorous microbats (Daubenton's bat, Myotis daubentonii) for peripheral blood in southwestern Finland in 2010. A Bartonella-specific PCR targeting rpoB (RNA polymerase β-subunit) was positive with blood samples from 46 bats (prevalence 37%). Scaled mass indexes of the infected and noninfected bats did not differ (p = 0.057). One rpoB sequence was identical with the rpoB sequence of B. naantaliensis strain 2574/1, previously isolated from bats in Finland. The rest of the sequences were highly similar to each other with nucleotide identity scores of 96% or higher. Nucleotide identity scores to the previously described type strain sequences of Bartonella or other database entries were no higher than 87%. Sequence analyses of another gene, gltA (citrate synthase), gave no higher than 90% nucleotide identity scores. On the basis of the conventional 95% sequence similarity cutoff in bacterial species delineation, a novel species of Bartonella was detected. We propose a species name Candidatus B. hemsundetiensis. Phylogenetic analyses based on rpoB and gltA sequences indicate that Candidatus B. hemsundetiensis clusters in a deep-branching position close to the ancestral species B. tamiae and B. bacilliformis. Our study reinforces the importance of bats as reservoirs of Bartonella.

  16. Phylogeny, physiology and distribution of 'Candidatus Microthrix calida', a new Microthrix species isolated from industrial activated sludge wastewater treatment plants.

    Science.gov (United States)

    Levantesi, Caterina; Rossetti, Simona; Thelen, Karin; Kragelund, Caroline; Krooneman, Janneke; Eikelboom, Dick; Nielsen, Per Halkjaer; Tandoi, Valter

    2006-09-01

    Twelve strains of filamentous bacteria morphologically identified as 'Microthrix parvicella' were isolated from industrial activated sludge wastewater treatment plants. 16S rRNA gene sequences analysis showed that these strains were all closely related to 'Candidatus Microthrix parvicella'. Six of them, however, had a 16S rRNA gene similarity of only 95.7% and 96.7% to 'Candidatus Microthrix parvicella' suggesting the presence of a new species. The name 'Candidatus Microthrix calida' is proposed for this new microorganism. The physiological properties of these six isolates supported the description of a new taxon. The 'Candidatus Microthrix calida' strains produced thin filaments (0.3-0.7 microm diameter), they did not grow on the media supporting the growth of 'Candidatus Microthrix parvicella' and could be cultivated at higher temperature (up to 36.5 degrees C). Preliminary data on substrate uptake were obtained by microautoradiography on pure culture. Two new fluorescence in situ hybridization (FISH) probes, Mpa-T1-1260 specific for 'Candidatus Microthrix calida' and Mpa-all-1410 targeting both Microthrix species, were designed. The presence of Microthrix spp. was investigated in 114 activated sludge plants. 'Microthrix parvicella' morphotype was detected in 23% of the analysed samples and FISH analysis revealed that 'Candidatus Microthrix calida' was present in 5% of them. The remaining 'M. parvicella' filaments were positive with probe Mpa-all-1410 but could not all be identified as 'Candidatus Microthrix parvicella' suggesting the presence of more hitherto undescribed biodiversity within this morphotype.

  17. 'Candidatus Tenderia electrophaga', an uncultivated electroautotroph from a biocathode enrichment.

    Science.gov (United States)

    Eddie, Brian J; Wang, Zheng; Malanoski, Anthony P; Hall, Richard J; Oh, Steve D; Heiner, Cheryl; Lin, Baochuan; Strycharz-Glaven, Sarah M

    2016-06-01

    Biocathode communities are of interest for a variety of applications, including electrosynthesis, bioremediation, and biosensors, yet much remains to be understood about the biological processes that occur to enable these communities to grow. One major difficulty in understanding these communities is that the critical autotrophic organisms are difficult to cultivate. An uncultivated, electroautotrophic bacterium previously identified as an uncultivated member of the family Chromatiaceae appears to be a key organism in an autotrophic biocathode microbial community. Metagenomic, metaproteomic and metatranscriptomic characterization of this community indicates that there is likely a single organism that utilizes electrons from the cathode to fix CO2, yet this organism has not been obtained in pure culture. Fluorescence in situ hybridization reveals that the organism grows as rod-shaped cells approximately 1.8 × 0.6 µm, and forms large clumps on the cathode. The genomic DNA G+C content was 59.2 mol%. Here we identify the key features of this organism and propose 'Candidatus Tenderia electrophaga', within the Gammaproteobacteria on the basis of low nucleotide and predicted protein sequence identity to known members of the orders Chromatiales and Thiotrichales.

  18. First report of 'Candidatus Liberibacter solanacearum' on tomato in El Salvador

    Science.gov (United States)

    In April of 2012, tomato plants grown near the town of Yuroconte in the municipality of La Palma in El Salvador, were observed with symptoms resembling those of “Candidatus Liberibacter solanacearum” (Lso) infection. Disease incidence in several fields in the area ranged from 40 to 60%. Heavy infes...

  19. First detection of tick-borne "Candidatus Neoehrlichia mikurensis" in Denmark 2011

    DEFF Research Database (Denmark)

    Fertner, Mette Ely; Mølbak, Lars; Pihl, Thomas Peter Boye;

    2012-01-01

    This is the first reporting of the tick-borne zoonotic bacterium "Candidatus Neoehrlichia mikurensis" in Denmark. A total of 2,625 Ixodes ricinus ticks from 58 locations in Denmark were collected and analysed for "Ca. Neoehrlichia mikurensis". A nested PCR revealed the presence of the bacterium...... at three geographically separate locations, which indicates that it is widely established in ticks....

  20. Pyrosequencing analyses of endophytic bacterial populations in tomato leaves infected by ‘Candidatus Liberibacter solanacearum’

    Science.gov (United States)

    Candidatus Liberibacter solanacearum’ (CLso) is associated with zebra Chip (ZC) disease of potato. The bacterium is currently not culturable and commonly maintained in plant hosts for characterization. In this study, CLso was graft-transmitted to tomato plants. A maximum of over 200-fold increase i...

  1. SSR-based Genetic Analysis of “Candidatus Liberibacter asiaticus” isolates from Multiple Continents.

    Science.gov (United States)

    Huanglongbing (HLB) is one of the most devastating citrus diseases that threaten citrus production worldwide. The causal agents are believed to be Candidatus Liberibacter spp. Although substantial efforts have been made toward detection of the presumed pathogens, information regarding to the patho...

  2. Multilocus microsatellite analysis of ‘Candidatus Liberibacter asiaticus’ associated with citrus Huanglongbing worldwide

    Science.gov (United States)

    Huanglongbing (HLB) is one of the most destructive citrus diseases worldwide. In the United States (US), HLB is typically associated with the presence of a fastidious phloem-limited bacterium named ‘Candidatus Liberibacter asiaticus’, though other Liberibacter species also have been associated with ...

  3. Draft Genome Sequence of "Candidatus Liberibacter asiaticus" from a Citrus Tree in San Gabriel, California.

    Science.gov (United States)

    Wu, F; Kumagai, L; Liang, G; Deng, X; Zheng, Z; Keremane, M; Chen, J

    2015-12-23

    The draft genome sequence of "Candidatus Liberibacter asiaticus" strain SGCA5 from an orange citrus tree in San Gabriel, California, is reported here. SGCA5 has a genome size of 1,201,445 bp, a G+C content of 36.4%, 1,152 predicted open reading frames (ORFs), and 42 RNA genes.

  4. Scanning electron microscopy of “Candidatus Liberibacter solanacearum” in infected tomato phloem tissue

    Science.gov (United States)

    Candidatus Liberibacter solanacearum” is an alpha-proteobacterium associated with potato zebra-chip disease. The bacterium is currently non-cultureable. Very little is known about the bacterial morphology, an important characteristic of a complete bacterial description. In this study, “Ca. L. so...

  5. First report of 'Candidatus Liberibacter solanacearum' associated with psyllid-affected carrots in Sweden

    Science.gov (United States)

    Carrot (Daucus carota) plants with symptoms resembling those of the carrot psyllid Trioza apicalis and “Candidatus Liberibacter solanacearum” damage were observed in 70% of commercial fields in southern Sweden in August 2011; all cultivars grown were affected, at about 1 to 45% symptomatic plants pe...

  6. Factors affecting transmission rates of 'Candidatus Liberibacter asiaticus' by Asian citrus psyllid

    Science.gov (United States)

    The Asian citrus psyllid (ACP), Diaphorina citri, is an important pest because it transmits a bacterium ‘Candidatus Liberibacter asiaticus’ (CLas) responsible for a serious disease of citrus known as Asiatic huanglongbing (citrus greening disease). USDA-ARS researchers recently established a program...

  7. First report of 'Candidatus Liberibacter solanacearum' associated with psylllid-affected tobacco in Honduras

    Science.gov (United States)

    Tobacco plants with symptoms resembling those associated with the psyllid Bactericera cockerelli and the bacterium “Candidatus Liberibacter solanacearum” (Lso) were observed in April of 2012 in heavily B. cockerelli-infested commercial fields in the Department of El-Paraíso, Honduras; all cultivars ...

  8. Complete genome sequence of chinese strain of ‘Candidatus Liberibacter asiaticus’

    Science.gov (United States)

    The complete genome sequence of ‘Candidatus Liberibacter asiaticus’ strain (Las) Guangxi-1(GX-1) was obtained by an Illumina HiSeq 2000. The GX-1 genome comprises 1,268,237 nucleotides, 36.5 % GC content, 1,141 predicted coding sequences, 44 tRNAs, 3 complete copies of ribosomal RNA genes (16S, 23S ...

  9. First report of 'Candidatus Liberibacter solanacearum' associated with psyllid-affected carrots in Norway

    Science.gov (United States)

    Carrot (Daucus carota) plants with symptoms resembling those associated with the carrot psyllid Trioza apicalis and the bacterium “Candidatus Liberibacter solanacearum” were observed in 70-80% of commercial fields and experimental plots in southeastern Norway from late July to mid-September 2011; al...

  10. First Report of Candidatus Liberibacter solanacearum in Pepper Plants in Mexico

    Science.gov (United States)

    Bell pepper (Capsicum annuum) plants exhibiting symptoms that resemble those of potato psyllid damage and/or ‘Candidatus Liberibacter solanacearum’ infection were observed in La Cruz de Elota, Sinaloa, México in March 2009. The plants had chlorotic or pale green leaves and exhibited leaf cupping, sh...

  11. Draft Genome Sequence of the Bactrocera oleae Symbiont “Candidatus Erwinia dacicola”

    Science.gov (United States)

    Blow, Frances; Gioti, Anastasia; Starns, David; Ben-Yosef, Michael; Pasternak, Zohar; Jurkevitch, Edouard; Vontas, John

    2016-01-01

    Candidatus Erwinia dacicola” is a Gammaproteobacterium that forms a symbiotic association with the agricultural pest Bactrocera oleae. Here, we present a 2.1-Mb draft hybrid genome assembly for “Ca. Erwinia dacicola” generated from single-cell and metagenomic data. PMID:27634990

  12. Candidatus Bartonella merieuxii, a Potential New Zoonotic Bartonella Species in Canids from Iraq

    Science.gov (United States)

    2012-09-27

    one pool from salivary glands from female ticks and one gut content pool collected two dogs PCR positive for Candidatus B. merieuxii [19]. Therefore...23. Chomel BB, Abbott C, Kasten RW, Floyd-Hawkins KA, Kass PH , et al. (1995) Bartonella henselae prevalence in domestic cats in California: Risk

  13. Low incidence of Candidatus Liberibacter asiaticus in Diaphorina citri and its host plant Murraya paniculata

    Science.gov (United States)

    Huanglongbing (HLB) is one of the most devastating diseases of citrus worldwide. Candidatus Liberibacter asiaticus is the prevalent species of three HLB-associated Liberibacter species, which is vectored by the psyllid Diaphorina citri. The vector and the bacteria have host plants outside Citrus, ...

  14. Candidatus Neoehrlichia mikurensis in Ticks from Migrating Birds in Sweden.

    Science.gov (United States)

    Labbé Sandelin, Lisa; Tolf, Conny; Larsson, Sara; Wilhelmsson, Peter; Salaneck, Erik; Jaenson, Thomas G T; Lindgren, Per-Eric; Olsen, Björn; Waldenström, Jonas

    2015-01-01

    Candidatus Neoehrlichia mikurensis (CNM; family Anaplasmataceae) was recently recognized as a potential tick-borne human pathogen. The presence of CNM in mammals, in host-seeking Ixodes ticks and in ticks attached to mammals and birds has been reported recently. We investigated the presence of CNM in ornithophagous ticks from migrating birds. A total of 1,150 ticks (582 nymphs, 548 larvae, 18 undetermined ticks and two adult females) collected from 5,365 birds captured in south-eastern Sweden was screened for CNM by molecular methods. The birds represented 65 different species, of which 35 species were infested with one or more ticks. Based on a combination of morphological and molecular species identification, the majority of the ticks were identified as Ixodes ricinus. Samples were initially screened by real-time PCR targeting the CNM 16S rRNA gene, and confirmed by a second real-time PCR targeting the groEL gene. For positive samples, a 1260 base pair fragment of the 16S rRNA gene was sequenced. Based upon bacterial gene sequence identification, 2.1% (24/1150) of the analysed samples were CNM-positive. Twenty-two out of 24 CNM-positive ticks were molecularly identified as I. ricinus nymphs, and the remaining two were identified as I. ricinus based on morphology. The overall CNM prevalence in I. ricinus nymphs was 4.2%. None of the 548 tested larvae was positive. CNM-positive ticks were collected from 10 different bird species. The highest CNM-prevalences were recorded in nymphs collected from common redpoll (Carduelis flammea, 3/7), thrush nightingale (Luscinia luscinia, 2/29) and dunnock (Prunella modularis, 1/17). The 16S rRNA sequences obtained in this study were all identical to each other and to three previously reported European strains, two of which were obtained from humans. It is concluded that ornithophagous ticks may be infected with CNM and that birds most likely can disperse CNM-infected ticks over large geographical areas.

  15. Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.

    Science.gov (United States)

    Borrel, Guillaume; Harris, Hugh M B; Parisot, Nicolas; Gaci, Nadia; Tottey, William; Mihajlovski, Agnès; Deane, Jennifer; Gribaldo, Simonetta; Bardot, Olivier; Peyretaillade, Eric; Peyret, Pierre; O'Toole, Paul W; Brugère, Jean-François

    2013-07-11

    "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1 is a methanogenic archaeon found in the human gut and is a representative of the novel order of methanogens related to Thermoplasmatales. Its complete genome sequence is presented here.

  16. 'Candidatus Phytoplasma hispanicum', a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus.

    Science.gov (United States)

    Davis, Robert E; Harrison, Nigel A; Zhao, Yan; Wei, Wei; Dally, Ellen L

    2016-09-01

    Mexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first known member of phytoplasma group 16SrXIII, and a new subgroup (16SrXIII-A) was established to accommodate MPV phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MPV represents a lineage distinct from previously described 'CandidatusPhytoplasma' species. Nucleotide sequence alignments revealed that strain MPV shared less than 97.5 % 16S rRNA gene sequence similarity with all previously described 'Ca.Phytoplasma' species. Based on unique properties of the DNA, we propose recognition of Mexican periwinkle virescence phytoplasma strain MPV as representative of a novel taxon, 'CandidatusPhytoplasma hispanicum'.

  17. Molecular typing of "Candidatus Bartonella ancashi," a new human pathogen causing verruga peruana.

    Science.gov (United States)

    Mullins, Kristin E; Hang, Jun; Jiang, Ju; Leguia, Mariana; Kasper, Matthew R; Maguiña, Ciro; Jarman, Richard G; Blazes, David L; Richards, Allen L

    2013-11-01

    A recently described clinical isolate, "Candidatus Bartonella ancashi," was obtained from a blood sample of a patient presenting with verruga peruana in the Ancash region of Peru. This sample and a second isolate obtained 60 days later from the same patient were molecularly typed using multilocus sequence typing (MLST) and multispacer sequence typing (MST). The isolates were 100% indistinguishable from each other but phylogenetically distant from Bartonella bacilliformis and considerably divergent from other known Bartonella species, confirming their novelty.

  18. 'Candidatus Phytoplasma lycopersici', a phytoplasma associated with 'hoja de perejil' disease in Bolivia.

    Science.gov (United States)

    Arocha, Yaima; Antesana, Olivia; Montellano, Ernesto; Franco, Pablo; Plata, G; Jones, Phil

    2007-08-01

    New diseases known locally as 'hoja de perejil' of tomato (Lycopersicon esculentum Mill) and 'brotes grandes' of potato (Solanum tuberosum L.) were first recognized in surveys of production fields in Bolivia during 2000-2003. Alfalfa (Medicago sativa) witches' broom and little leaf diseases of native weeds Morrenia variegata and mora-mora (Serjania perulacea) were also identified near to production fields. Phytoplasma aetiology was attributed to each of these diseases following detection and initial identification of aster yellows group (16SrI) phytoplasmas in all five diseased plant species. While potato, alfalfa and mora-mora plants contained indistinguishable 16SrI-B strains, 'hoja de perejil' (THP) and morrenia little leaf (MVLL)-associated phytoplasma strains shared 97.5 % 16S rRNA gene sequence similarity with 'Candidatus Phytoplasma asteris' and related strains and <95 % similarity with all other 'Candidatus Phytoplasma' species. Phylogenetic analysis of 16S rRNA gene sequences indicated that the THP and MVLL phytoplasmas represent a novel lineage within the aster yellows (16SrI) group and, on the basis of unique 16S rRNA gene sequences, we propose that THP and MVLL phytoplasmas represent 'Candidatus Phytoplasma lycopersici', with THP as the reference strain.

  19. Isolation of the rickettsial agent genetically similar to Candidatus Rickettsia kotlanii, from Haemaphysalis megaspinosa in Japan.

    Science.gov (United States)

    Andoh, Masako; Ogasawara, Yumiko; Sakata, Akiko; Ito, Takuya; Fujita, Hiromi; Kawabata, Hiroki; Ando, Shuji

    2014-09-01

    Two rickettsial isolates, HM-1 and HM-2, were isolated from Haemaphysalis megaspinosa collected in Japan in 2006 and 2011, respectively. The isolates were analyzed by DNA sequences of the outer membrane protein A gene, the outer membrane protein B gene, the citrate synthase gene, the genus Rickettsia-specific outer membrane protein 17-kDa gene, the 16S ribosome RNA gene, and the PS120 protein gene ("geneD"). HM-1 was identified as Rickettsia tamurae. HM-2 matched most closely with 'Candidatus Rickettsia kotlanii' DNA, which has only been reported from H. concinna in Hungary. This is the first report of isolation in Japan of the agent genetically similar to 'Candidatus R. kotlanii,' which belongs phylogenetically to the spotted fever group Rickettsia. Our study shows the possibility that 'Candidatus R. kotlanii' can be carried by at least two tick species. Furthermore, because the Rickettsia sp. has been found two distant countries, Hungary and Japan, it has potential for wider distribution.

  20. Diversity of the citrus HLB bacterium, ‘Candidatus Liberibacter asiaticus’, in psyllids (Diaphorina citri) collected from Murraya paniculata and citrus spp. in Thailand

    Science.gov (United States)

    Candidatus Liberibacter asiaticus’ (Las) is a phloem inhabiting bacterium that causes huanglongbing disease (HLB), also known as citrus greening associated with three species of a-Proteobacteria in the genus ‘Candidatus Liberibacter sp’. Prophage is an important genetic element of bacterial genomes...

  1. Genomes of Candidatus Wolbachia bourtzisii wDacA and Candidatus Wolbachia pipientis wDacB from the Cochineal Insect Dactylopius coccus (Hemiptera: Dactylopiidae)

    Science.gov (United States)

    Ramírez-Puebla, Shamayim T.; Ormeño-Orrillo, Ernesto; Vera-Ponce de León, Arturo; Lozano, Luis; Sanchez-Flores, Alejandro; Rosenblueth, Mónica; Martínez-Romero, Esperanza

    2016-01-01

    Dactylopius species, known as cochineal insects, are the source of the carminic acid dye used worldwide. The presence of two Wolbachia strains in Dactylopius coccus from Mexico was revealed by PCR amplification of wsp and sequencing of 16S rRNA genes. A metagenome analysis recovered the genome sequences of Candidatus Wolbachia bourtzisii wDacA (supergroup A) and Candidatus Wolbachia pipientis wDacB (supergroup B). Genome read coverage, as well as 16S rRNA clone sequencing, revealed that wDacB was more abundant than wDacA. The strains shared similar predicted metabolic capabilities that are common to Wolbachia, including riboflavin, ubiquinone, and heme biosynthesis, but lacked other vitamin and cofactor biosynthesis as well as glycolysis, the oxidative pentose phosphate pathway, and sugar uptake systems. A complete tricarboxylic acid cycle and gluconeogenesis were predicted as well as limited amino acid biosynthesis. Uptake and catabolism of proline were evidenced in Dactylopius Wolbachia strains. Both strains possessed WO-like phage regions and type I and type IV secretion systems. Several efflux systems found suggested the existence of metal toxicity within their host. Besides already described putative virulence factors like ankyrin domain proteins, VlrC homologs, and patatin-like proteins, putative novel virulence factors related to those found in intracellular pathogens like Legionella and Mycobacterium are highlighted for the first time in Wolbachia. Candidate genes identified in other Wolbachia that are likely involved in cytoplasmic incompatibility were found in wDacB but not in wDacA. PMID:27543297

  2. Genomes of Candidatus Wolbachia bourtzisii wDacA and Candidatus Wolbachia pipientis wDacB from the Cochineal Insect Dactylopius coccus (Hemiptera: Dactylopiidae

    Directory of Open Access Journals (Sweden)

    Shamayim T. Ramírez-Puebla

    2016-10-01

    Full Text Available Dactylopius species, known as cochineal insects, are the source of the carminic acid dye used worldwide. The presence of two Wolbachia strains in Dactylopius coccus from Mexico was revealed by PCR amplification of wsp and sequencing of 16S rRNA genes. A metagenome analysis recovered the genome sequences of Candidatus Wolbachia bourtzisii wDacA (supergroup A and Candidatus Wolbachia pipientis wDacB (supergroup B. Genome read coverage, as well as 16S rRNA clone sequencing, revealed that wDacB was more abundant than wDacA. The strains shared similar predicted metabolic capabilities that are common to Wolbachia, including riboflavin, ubiquinone, and heme biosynthesis, but lacked other vitamin and cofactor biosynthesis as well as glycolysis, the oxidative pentose phosphate pathway, and sugar uptake systems. A complete tricarboxylic acid cycle and gluconeogenesis were predicted as well as limited amino acid biosynthesis. Uptake and catabolism of proline were evidenced in Dactylopius Wolbachia strains. Both strains possessed WO-like phage regions and type I and type IV secretion systems. Several efflux systems found suggested the existence of metal toxicity within their host. Besides already described putative virulence factors like ankyrin domain proteins, VlrC homologs, and patatin-like proteins, putative novel virulence factors related to those found in intracellular pathogens like Legionella and Mycobacterium are highlighted for the first time in Wolbachia. Candidate genes identified in other Wolbachia that are likely involved in cytoplasmic incompatibility were found in wDacB but not in wDacA.

  3. Global ubiquity and local endemism of free-living terrestrial protists: phylogeographic assessment of the streptophyte alga Klebsormidium.

    Science.gov (United States)

    Ryšánek, David; Hrčková, Kristýna; Škaloud, Pavel

    2015-03-01

    Despite considerable research attention during the last 10 years, the distribution and biogeography of protists remain as highly controversial issues. The presumably huge population sizes and unlimited dispersal capabilities should result in protist ubiquity. However, recent molecular investigations suggest that protist communities exhibit strong biogeographic patterns. Here, we examined the biogeographic pattern of a very common green algal genus Klebsormidium. We evaluated the geographic distribution of rbcL genotypes for 190 isolates sampled in six sampling regions located in Europe, North America and Asia. Measures of correlation between genetic and geographic distance matrices revealed a differential distribution pattern on two geographic levels. Globally, the populations were genetically homogeneous; locally, the genotypes were patchily distributed. We hypothesized that a local fine-scale structuring of genotypes may be caused by various ecological factors, in particular, by the habitat differentiation of particular genotypes. Our investigations also identified a large number of new, previously unrecognized lineages. A total of 44 genotypes were identified and more than 66% of these were reported for the first time.

  4. Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes.

    Science.gov (United States)

    Boo, Sung Min; Kim, Han Soon; Shin, Woongghi; Boo, Ga Hun; Cho, Sung Mi; Jo, Bok Yeon; Kim, Jee-Hwan; Kim, Jin Hee; Yang, Eun Chan; Siver, Peter A; Wolfe, Alexander P; Bhattacharya, Debashish; Andersen, Robert A; Yoon, Hwan Su

    2010-10-01

    The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically relevant geological time (10⁷-10⁸ years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood.

  5. 'Candidatus Phytoplasma malaysianum', a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus).

    Science.gov (United States)

    Nejat, Naghmeh; Vadamalai, Ganesan; Davis, Robert E; Harrison, Nigel A; Sijam, Kamaruzaman; Dickinson, Matthew; Abdullah, Siti Nor Akmar; Zhao, Yan

    2013-02-01

    This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytoplasma distinguished the phytoplasma from all previously described 'Candidatus Phytoplasma' species. Pairwise sequence similarity scores, calculated through alignment of full-length 16S rRNA gene sequences, revealed that the MaPV phytoplasma 16S rRNA gene shared 96.5 % or less sequence similarity with that of previously described 'Ca. Phytoplasma' species, justifying the recognition of the MaPV phytoplasma as a reference strain of a novel taxon, 'Candidatus Phytoplasma malaysianum'. The 16S rRNA gene F2nR2 fragment from the MaPV phytoplasma exhibited a distinct restriction fragment length polymorphism (RFLP) profile and the pattern similarity coefficient values were lower than 0.85 with representative phytoplasmas classified in any of the 31 previously delineated 16Sr groups; therefore, the MaPV phytoplasma was designated a member of a new 16Sr group, 16SrXXXII. Phytoplasmas affiliated with this novel taxon and the new group included diverse strains infecting periwinkle, coconut palm and oil palm in Malaysia. Three phytoplasmas were characterized as representatives of three distinct subgroups, 16SrXXXII-A, 16SrXXXII-B and 16SrXXXII-C, respectively.

  6. Proteomic analysis of the purple sulfur bacterium Candidatus "Thiodictyon syntrophicum" strain Cad16T isolated from Lake Cadagno

    DEFF Research Database (Denmark)

    Storelli, Nicola; Saad, Maged M.; Frigaard, Niels-Ulrik;

    2014-01-01

    Lake Cadagno is characterised by a compact chemocline with high concentrations of purple sulfur bacteria (PSB). 2D-DIGE was used to monitor the global changes in the proteome of Candidatus "Thiodictyon syntrophicum" strain Cad16T both in the presence and absence of light. This study aimed...

  7. Increase of “Candidatus Liberibacter solanacearum” titer in aging tomato leaves and pyrosequencing analyses of endophyte populations

    Science.gov (United States)

    This project studied changes in titer of “Candidatus Liberibacter solanacearum” (Lso) in tomato leaves of different cultivars with the goal of searching for factors associated with Lso enrichment. Lso titers, as monitored by qPCR, were observed to increase in tomato leaf cultures, which involved mai...

  8. Low-level detection of Candidatus Liberibacter solanacearum in extracted Bactericera cockerelli (Hemiptera: Triozidae) DNA by 454 pyrosequencing

    Science.gov (United States)

    Accurate detection and quantification of Candidatus Liberibacter solanacearum, the putative causal agent of zebra chip disease of potato (Solanum tuberosum), in the potato psyllid, Bactericera cockerelli, has become necessary to better understand the biology of the disease cycle. Studies on the tran...

  9. Novel Molecular Technique for Rapid Cloning of Unknown Sequences From Unculturable Huanglongbing (HLB) Associated Bacterium, Candidatus Liberibacter

    Science.gov (United States)

    Huanglongbing (HLB), previously known as citrus greening disease, is one of the most destructive citrus diseases worldwide. Recent occurrence of citrus Huanglongbing(HLB)in Florida has dramatically increased the threat to the entire US citrus industry. The disease is associated with Candidatus Liber...

  10. Transgenic Carrizo expressing 'Candidatus Liberibacter asiaticus' effector P235 displays huanglongbing-like symptom and alters some gene expression

    Science.gov (United States)

    Candidatus Liberibacter asiaticus’ (Las) is the agent causing destructive citrus huanglongbing worldwide. A hypothetical protein (P235) was identified in Las genome prophage region, which encodes a 123aa protein with a molecular weight of 14.19kD. Green fluorescence protein (GFP)-fused with P235 ap...

  11. Zebra Chip disease and potato biochemistry: Tuber physiological changes in response to ‘Candidatus Liberibacter solanacearum’ infection over time

    Science.gov (United States)

    Zebra chip disease (ZC), putatively caused by ‘Candidatus Liberibacter solanacearum’ (Lso), is of increasing concern to potato production in Mexico, the United States, and New Zealand. However, little is known about host tuber physiological changes that result in ZC symptom formation. This study exp...

  12. Extraction of DNA from orange juice and detection of bacterium Candidatus Liberibacter asiaticus by real-time PCR

    Science.gov (United States)

    Orange juice processed from Huanglongbing (HLB) affected fruit is often associated with bitter taste and/or off-flavor. HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem limited bacterium. The current standard to confirm CLas for citrus trees is to take sam...

  13. Detection of 16S rDNA of Candidatus Liberibacter asiaticus by quantitative real-time PCR

    Science.gov (United States)

    Orange juice processed from Huanglongbing (HLB) infected fruit is often associated with bitter taste and/or off-flavor. The widely spread HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem limited bacterium. The current standard to diagnose HLB for citrus tr...

  14. "Candidatus Hepatobacter penaei," an intracellular pathogenic enteric bacterium in the hepatopancreas of the marine shrimp Penaeus vannamei (Crustacea: Decapoda).

    Science.gov (United States)

    Nunan, Linda M; Pantoja, Carlos R; Gomez-Jimenez, Silvia; Lightner, Donald V

    2013-02-01

    The bacteria that cause necrotizing hepatopancreatitis in Penaeus vannamei adversely affect penaeid shrimp cultured in the western hemisphere. 16S rRNA and gyrase B gene analyses determined the taxonomic position of these bacteria. The name "Candidatus Hepatobacter penaei" is proposed for these pathogenic bacteria, which are members of the Rickettsiales order.

  15. Draft Genome Sequence of "Candidatus Hepatoplasma crinochetorum" Ps, a Bacterial Symbiont in the Hepatopancreas of the Terrestrial Isopod Porcellio scaber.

    Science.gov (United States)

    Collingro, Astrid; Kostanjšek, Rok; Toenshoff, Elena R; Schulz, Frederik; Schuster, Lisa; Domann, Daryl; Horn, Matthias

    2015-08-13

    "Candidatus Hepatoplasma crinochetorum" Ps is an extracellular symbiont residing in the hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is highly similar to that of the close relative "Ca. Hepatoplasma crinochetorum" Av from Armadillidium vulgare. However, instead of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction modification system.

  16. Autotrophic Carbon Dioxide Fixation via the Calvin-Benson-Bassham Cycle by the Denitrifying Methanotroph "Candidatus Methylomirabilis oxyfera"

    NARCIS (Netherlands)

    Rasigraf, O.; Kool, D.M.; Jetten, M.S.M.; Ettwig, K.F.; Sinninghe Damsté, J.S.

    2014-01-01

    Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "Candidatus Methylomirabilis oxyfera" is a

  17. Candidatus Liberibacter asiaticus is present in orange jasmine and Asian citrus psyllid reared from jasmine at low titers

    Science.gov (United States)

    Orange jasmine, Murraya paniculata, is a common horticultural plant in Florida, and an alternate host of the Asian citrus psyllid, Diaphorina citri Kuwayama. Orange jasmine has also been reported to harbor the bacteria Candidatus Liberibacter asiaticus, the causal agent of huanglongbing disease. We ...

  18. Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes.

    Science.gov (United States)

    Kumar, Manjeet; Balaji, Petety V

    2011-05-01

    Glycosylation of proteins in prokaryotes has been known for the last few decades. Glycan structures and/or the glycosylation pathways have been experimentally characterized in only a small number of prokaryotes. Even this has become possible only during the last decade or so, primarily due to technological and methodological developments. Glycosylated proteins are diverse in their function and localization. Glycosylation has been shown to be associated with a wide range of biological phenomena. Characterization of the various types of glycans and the glycosylation machinery is critical to understand such processes. Such studies can help in the identification of novel targets for designing drugs, diagnostics, and engineering of therapeutic proteins. In view of this, the experimentally characterized pgl system of Campylobacter jejuni, responsible for N-linked glycosylation, has been used in this study to identify glycosylation loci in 865 prokaryotes whose genomes have been completely sequenced. Results from the present study show that only a small number of organisms have homologs for all the pgl enzymes and a few others have homologs for none of the pgl enzymes. Most of the organisms have homologs for only a subset of the pgl enzymes. There is no specific pattern for the presence or absence of pgl homologs vis-à-vis the 16S rRNA sequence-based phylogenetic tree. This may be due to differences in the glycan structures, high sequence divergence, horizontal gene transfer or non-orthologous gene displacement. Overall, the presence of homologs for pgl enzymes in a large number of organisms irrespective of their habitat, pathogenicity, energy generation mechanism, etc., hints towards the ubiquity of N-linked glycosylation in prokaryotes.

  19. Molecular detection of Rickettsia felis and Candidatus Rickettsia asemboensis in fleas from human habitats, Asembo, Kenya.

    Science.gov (United States)

    Jiang, Ju; Maina, Alice N; Knobel, Darryn L; Cleaveland, Sarah; Laudisoit, Anne; Wamburu, Kabura; Ogola, Eric; Parola, Philippe; Breiman, Robert F; Njenga, M Kariuki; Richards, Allen L

    2013-08-01

    The flea-borne rickettsioses murine typhus (Rickettsia typhi) and flea-borne spotted fever (FBSF) (Rickettsia felis) are febrile diseases distributed among humans worldwide. Murine typhus has been known to be endemic to Kenya since the 1950s, but FBSF was only recently documented in northeastern (2010) and western (2012) Kenya. To characterize the potential exposure of humans in Kenya to flea-borne rickettsioses, a total of 330 fleas (134 pools) including 5 species (Xenopsylla cheopis, Ctenocephalides felis, Ctenocephalides canis, Pulex irritans, and Echidnophaga gallinacea) were collected from domestic and peridomestic animals and from human dwellings within Asembo, western Kenya. DNA was extracted from the 134 pooled flea samples and 89 (66.4%) pools tested positively for rickettsial DNA by 2 genus-specific quantitative real-time PCR (qPCR) assays based upon the citrate synthase (gltA) and 17-kD antigen genes and the Rfelis qPCR assay. Sequences from the 17-kD antigen gene, the outer membrane protein (omp)B, and 2 R. felis plasmid genes (pRF and pRFd) of 12 selected rickettsia-positive samples revealed a unique Rickettsia sp. (n=11) and R. felis (n=1). Depiction of the new rickettsia by multilocus sequence typing (MLST) targeting the 16S rRNA (rrs), 17-kD antigen gene, gltA, ompA, ompB, and surface cell antigen 4 (sca4), shows that it is most closely related to R. felis but genetically dissimilar enough to be considered a separate species provisionally named Candidatus Rickettsia asemboensis. Subsequently, 81 of the 134 (60.4%) flea pools tested positively for Candidatus Rickettsia asemboensis by a newly developed agent-specific qPCR assay, Rasemb. R. felis was identified in 9 of the 134 (6.7%) flea pools, and R. typhi the causative agent of murine typhus was not detected in any of 78 rickettsia-positive pools assessed using a species-specific qPCR assay, Rtyph. Two pools were found to contain both R. felis and Candidatus Rickettsia asemboensis DNA and 1 pool

  20. Influence of photoperiod duration and phloem disruption through scoring on growth, disease symptoms and bacterial titer in citrus graft-inoculated with Candidatus Liberibacter asiaticus

    Science.gov (United States)

    Plants inoculated with the huanglongbing (HLB)-associated bacterium, Candidatus Liberibacter asiaticus (CLas) are typically monitored for 8-10 months to identify differences in susceptibility between genotypes. A previous report indicated that continuous light accelerated development of HLB symptoms...

  1. Draft Genome Sequence of Anammox Bacterium "Candidatus Scalindua brodae," Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments

    NARCIS (Netherlands)

    Speth, Daan R; Russ, Lina; Kartal, Boran; Op den Camp, Huub J M; Dutilh, Bas E; Jetten, Mike S M

    2015-01-01

    We present the draft genome of anammox bacterium "Candidatus Scalindua brodae," which at 282 contigs is a major improvement over the highly fragmented genome assembly of related species "Ca. Scalindua profunda" (1,580 contigs) which was previously published.

  2. Pathogenic potential of a Costa Rican strain of 'Candidatus Rickettsia amblyommii' in guinea pigs (Cavia porcellus) and protective immunity against Rickettsia rickettsii.

    Science.gov (United States)

    Rivas, Juan J; Moreira-Soto, Andrés; Alvarado, Gilberth; Taylor, Lizeth; Calderón-Arguedas, Olger; Hun, Laya; Corrales-Aguilar, Eugenia; Morales, Juan Alberto; Troyo, Adriana

    2015-09-01

    'Candidatus Rickettsia amblyommii' is a spotted fever group rickettsia that is not considered pathogenic, although there is serologic evidence of possible infection in animals and humans. The aim of this study was to evaluate the pathogenic potential of a Costa Rican strain of 'Candidatus R. amblyommii' in guinea pigs and determine its capacity to generate protective immunity against a subsequent infection with a local strain of Rickettsia rickettsii isolated from a human case. Six guinea pigs were inoculated with 'Candidatus R. amblyommii' strain 9-CC-3-1 and two controls with cell culture medium. Health status was evaluated, and necropsies were executed at days 2, 4, and 13. Blood and tissues were processed by PCR to detect the gltA gene, and end titers of anti-'Candidatus R. amblyommii' IgG were determined by indirect immunofluorescence. To evaluate protective immunity, another 5 guinea pigs were infected with 'Candidatus R. amblyommii' (IGPs). After 4 weeks, these 5 IGPs and 3 controls (CGPs) were inoculated with pathogenic R. rickettsii. Clinical signs and titers of anti-Rickettsia IgG were determined. IgG titers reached 1:512 at day 13 post-infection with 'Candidatus R. amblyommii'. On day 2 after inoculation, two guinea pigs had enlarged testicles and 'Candidatus R. amblyommii' DNA was detected in testicles. Histopathology confirmed piogranulomatous orchitis with perivascular inflammatory infiltrate in the epididymis. In the protective immunity assay, anti-Rickettsia IgG end titers after R. rickettsii infection were lower in IGPs than in CGPs. IGPs exhibited only transient fever, while CGP showed signs of severe disease and mortality. R. rickettsii was detected in testicles and blood of CGPs. Results show that the strain 9-CC-3-1 of 'Candidatus R. amblyommii' was able to generate pathology and an antibody response in guinea pigs. Moreover, its capacity to generate protective immunity against R. rickettsii may modulate the epidemiology and severity of Rocky

  3. The ubiquity of iron.

    Science.gov (United States)

    Frey, Perry A; Reed, George H

    2012-09-21

    The importance of iron in living systems can be traced to the many complexes within which it is found, to its chemical mobility in undergoing oxidation-reduction reactions, and to the abundance of iron in Earth's crust. Iron is the most abundant element, by mass, in the Earth, constituting about 80% of the inner and outer cores of Earth. The molten outer core is about 8000 km in diameter, and the solid inner core is about 2400 km in diameter. Iron is the fourth most abundant element in Earth's crust. It is the chemically functional component of mononuclear iron complexes, dinuclear iron complexes, [2Fe-2S] and [4Fe-4S] clusters, [Fe-Ni-S] clusters, iron protophorphyrin IX, and many other complexes in protein biochemistry. Metals such as nickel, cobalt, copper, and manganese are present in the crust and could in principle function chemically in place of iron, but they are scarce in Earth's crust. Iron is plentiful because of its nuclear stability in stellar nuclear fusion reactions. It seems likely that other solid planets, formed by the same processes as Earth, would also foster the evolution of life and that iron would be similarly important to life on those planets as it is on Earth.

  4. The Ubiquity Of Crossover

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    If the word 'crossover' is unfamiliar to you, perhaps it is time to get to grips with this modern phenomenon. It is one of those vague words that one is never quite clear about; how did it start? What exactly does it mean? Crossover seems to have infiltrated our lives without us even noticing.

  5. Candidatus Rickettsia andeanae, a spotted fever group agent infecting Amblyomma parvum ticks in two Brazilian biomes.

    Science.gov (United States)

    Nieri-Bastos, Fernanda Aparecida; Lopes, Marcos Gomes; Cançado, Paulo Henrique Duarte; Rossa, Giselle Ayres Razera; Faccini, João Luiz Horácio; Gennari, Solange Maria; Labruna, Marcelo Bahia

    2014-04-01

    Adult ticks of the species Amblyomma parvum were collected from the vegetation in the Pantanal biome (state of Mato Grosso do Sul) and from horses in the Cerrado biome (state of Piauí) in Brazil. The ticks were individually tested for rickettsial infection via polymerase chain reaction (PCR) targeting three rickettsial genes, gltA, ompA and ompB. Overall, 63.5% (40/63) and 66.7% (2/3) of A. parvum ticks from Pantanal and Cerrado, respectively, contained rickettsial DNA, which were all confirmed by DNA sequencing to be 100% identical to the corresponding fragments of the gltA, ompA and ompB genes of Candidatus Rickettsia andeanae. This report is the first to describe Ca. R. andeanae in Brazil.

  6. Chemical compounds effective against the citrus Huanglongbing bacterium 'Candidatus Liberibacter asiaticus' in planta.

    Science.gov (United States)

    Zhang, Muqing; Powell, Charles A; Zhou, Lijuan; He, Zhenli; Stover, Ed; Duan, Yongping

    2011-09-01

    Citrus Huanglongbing (HLB) is one of the most destructive diseases of citrus worldwide and is threatening the survival of the Floridian citrus industry. Currently, there is no established cure for this century-old and emerging disease. As a possible control strategy for citrus HLB, therapeutic compounds were screened using a propagation test system with 'Candidatus Liberibacter asiaticus'-infected periwinkle and citrus plants. The results demonstrated that the combination of penicillin and streptomycin (PS) was effective in eliminating or suppressing the 'Ca. L. asiaticus' bacterium and provided a therapeutically effective level of control for a much longer period of time than when administering either antibiotic separately. When treated with the PS, 'Ca. L. asiaticus'-infected periwinkle cuttings achieved 70% of regeneration rates versus citrus plants. This may provide a useful tool for the management of citrus HLB and other Liberibacter-associated diseases.

  7. Candidate gene markers for Candidatus Liberibacter asiaticus for detecting citrus greening disease.

    Science.gov (United States)

    Nageswara-Rao, Madhugiri; Irey, Mike; Garnsey, Stephen M; Gowda, Siddarame

    2013-06-01

    Citrus Huanglongbing (HLB) also known as citrus greening is one of the most devastating diseases of citrus worldwide. The disease is caused by Candidatus Liberibacter bacterium, vectored by the psyllid Diaphorina citri Kuwayama and Trioza erytreae Del Guercio. Citrus plants infected by the HLB bacterium may not show visible symptoms sometimes for years following infection. The aim of this study was to develop effective gene-specific primer pairs for polymerase chain reaction based method for quick screening of HLB disease. Thirty-two different gene-specific primer pairs, across the Ca. Liberibacter asiaticus genome, were successfully developed. The possibility of these primer pairs for cross-genome amplification across 'Ca. Liberibacter africanus' and 'Ca. Liberibacter americanus' were tested. The applicability of these primer pairs for detection and differentiation of Ca Liberibacter spp. is discussed.

  8. Candidate gene markers for Candidatus Liberibacter asiaticus for detecting citrus greening disease

    Indian Academy of Sciences (India)

    Madhugiri Nageswara-Rao; Mike Irey; Stephen M Garnsey; Siddarame Gowda

    2013-06-01

    Citrus Huanglongbing (HLB) also known as citrus greening is one of the most devastating diseases of citrus worldwide. The disease is caused by Candidatus Liberibacter bacterium, vectored by the psyllid Diaphorina citri Kuwayama and Trioza erytreae Del Guercio. Citrus plants infected by the HLB bacterium may not show visible symptoms sometimes for years following infection. The aim of this study was to develop effective gene-specific primer pairs for polymerase chain reaction based method for quick screening of HLB disease. Thirty-two different gene-specific primer pairs, across the Ca. Liberibacter asiaticus genome, were successfully developed. The possibility of these primer pairs for cross-genome amplification across `Ca. Liberibacter africanus’ and `Ca. Liberibacter americanus’ were tested. The applicability of these primer pairs for detection and differentiation of Ca Liberibacter spp. is discussed.

  9. Candidatus Liberibacter asiaticus’, Causal Agent of Citrus Huanglongbing, Is Reduced by Treatment with Brassinosteroids

    Science.gov (United States)

    Hernández, Ingrid; Portieles, Roxana; Rodríguez García, Mayra; López, Yunior; Aranguren, Miguel; Alonso, Eugenio; Delgado, Roger; Luis, Maritza; Batista, Lochy; Paredes, Camilo; Rodríguez, Meilyn; Pujol, Merardo; Ochagavia, María Elena; Falcón, Viviana; Terauchi, Ryohei; Matsumura, Hideo; Ayra-Pardo, Camilo; Llauger, Raixa; Pérez, María del Carmen; Núñez, Mirian; Borrusch, Melissa S.; Walton, Jonathan D.; Silva, Yussuan; Pimentel, Eulogio; Borroto, Carlos; Borrás-Hidalgo, Orlando

    2016-01-01

    Huanglongbing (HLB) constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, ‘Candidatus Liberibacter asiaticus’. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with next generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. The results demonstrate that epibrassinolide may provide a useful tool for the management of HLB. PMID:26731660

  10. 'Candidatus Liberibacter asiaticus', Causal Agent of Citrus Huanglongbing, Is Reduced by Treatment with Brassinosteroids.

    Directory of Open Access Journals (Sweden)

    Eduardo Canales

    Full Text Available Huanglongbing (HLB constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, 'Candidatus Liberibacter asiaticus'. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with next generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. The results demonstrate that epibrassinolide may provide a useful tool for the management of HLB.

  11. Genome sequence of "Candidatus Walczuchella monophlebidarum" the flavobacterial endosymbiont of Llaveia axin axin (Hemiptera: Coccoidea: Monophlebidae).

    Science.gov (United States)

    Rosas-Pérez, Tania; Rosenblueth, Mónica; Rincón-Rosales, Reiner; Mora, Jaime; Martínez-Romero, Esperanza

    2014-03-01

    Scale insects (Hemiptera: Coccoidae) constitute a very diverse group of sap-feeding insects with a large diversity of symbiotic associations with bacteria. Here, we present the complete genome sequence, metabolic reconstruction, and comparative genomics of the flavobacterial endosymbiont of the giant scale insect Llaveia axin axin. The gene repertoire of its 309,299 bp genome was similar to that of other flavobacterial insect endosymbionts though not syntenic. According to its genetic content, essential amino acid biosynthesis is likely to be the flavobacterial endosymbiont's principal contribution to the symbiotic association with its insect host. We also report the presence of a γ-proteobacterial symbiont that may be involved in waste nitrogen recycling and also has amino acid biosynthetic capabilities that may provide metabolic precursors to the flavobacterial endosymbiont. We propose "Candidatus Walczuchella monophlebidarum" as the name of the flavobacterial endosymbiont of insects from the Monophlebidae family.

  12. Candidatus Rickettsia andeanae, a spotted fever group agent infecting Amblyomma parvum ticks in two Brazilian biomes

    Directory of Open Access Journals (Sweden)

    Fernanda Aparecida Nieri-Bastos

    2014-04-01

    Full Text Available Adult ticks of the species Amblyomma parvum were collected from the vegetation in the Pantanal biome (state of Mato Grosso do Sul and from horses in the Cerrado biome (state of Piauí in Brazil. The ticks were individually tested for rickettsial infection via polymerase chain reaction (PCR targeting three rickettsial genes, gltA, ompA and ompB. Overall, 63.5% (40/63 and 66.7% (2/3 of A. parvum ticks from Pantanal and Cerrado, respectively, contained rickettsial DNA, which were all confirmed by DNA sequencing to be 100% identical to the corresponding fragments of the gltA, ompA and ompB genes of Candidatus Rickettsia andeanae. This report is the first to describe Ca. R. andeanae in Brazil.

  13. 'Candidatus Phytoplasma costaricanum' a novel phytoplasma associated with an emerging disease in soybean (Glycine max).

    Science.gov (United States)

    Lee, I-M; Bottner-Parker, K D; Zhao, Y; Villalobos, W; Moreira, L

    2011-12-01

    A novel phytoplasma, designated strain SoyST1c1, associated with a newly emerging disease in soybean (Glycine max), known as soybean stunt (SoyST), was found in 2002 in a soybean plantation in Alajuela Province, Costa Rica. The same phytoplasma, or a very closely related strain, also infected sweet pepper (Capsicum annuum) with purple vein syndrome (SwPPV) and passion fruit vine (Passiflora edulis) with bud proliferation disease (PasFBP) in the same region. Sequence analysis of cloned 16S rRNA gene sequences (GenBank accession nos FJ226068-FJ226073 and HQ225624-HQ225635) indicated that all three affected plants were infected by phytoplasmas that shared <97.5% sequence similarity with previously described phytoplasmas. The SoyST-causing phytoplasma represents a new taxon, most closely related to phytoplasma group 16SrI and 16SrXII strains. Virtual RFLP analysis indicated that the SoyST-causing phytoplasma and its closely related strains represent a novel 16Sr group, designated 16SrXXXI. Phylogenetic analysis of 16S rRNA gene sequences from the new phytoplasma strains, those previously described as 'Candidatus Phytoplasma spp.' and other distinct, as yet unnamed, phytoplasmas indicated that the SoyST-causing phytoplasma represents a distinct lineage within the aster yellows/stolbur branch on the phylogenetic tree. On the basis of its unique 16S rRNA gene sequence and biological properties, strain SoyST1c1 represents a novel taxon, for which the name 'Candidatus Phytoplasma costaricanum' is proposed with SoyST1c1 as the reference strain.

  14. Dealing with the ubiquity of phthalates in the laboratory when determining plasticizers by gas chromatography/mass spectrometry and PARAFAC.

    Science.gov (United States)

    Oca, M L; Rubio, L; Sarabia, L A; Ortiz, M C

    2016-09-16

    Determining plasticizers and other additives migrated from plastic materials becomes a hard task when these substances are already present in the laboratory environment. This work dealt with this drawback in the multiresidue determination of four plasticizers (2,6-di-tert-butyl-4-methyl-phenol (BHT), diisobutyl phthalate (DiBP), bis(2-ethylhexyl) adipate (DEHA) and diisononyl phthalate (DiNP)) and a UV stabilizer (benzophenone (BP)) by gas chromatography/mass spectrometry (GC/MS) using DiBP-d4 as internal standard. The ubiquity of DiBP by a non-constant leaching process in the laboratory was detected, which could not guarantee the achievement of a trustworthy quantification. To handle this, the assessment of the level of DiBP in solvent blanks having fixed the probabilities of false non-compliance (α) and false compliance (β) at 0.01 was performed. On the other hand, another special case was that of DiNP, in whose chromatogram finger peaks appear because of an array of possible C9 isomers. PARAFAC, used for the identification and quantification of all the substances, is a useful chemometric tool that enabled a more reliable determination of this analyte since no peak areas were considered but chromatographic and spectral loadings. Since phthalates may migrate from rubber latex items, an evaluation of the existence of matrix effects on the determination of the five analytes was conducted prior to an extraction with hexane from a dummy for infants. As matrix effects were present, the quantification of the compounds under study was performed following the standard addition method using PARAFAC sample loadings as response variable. As a result, the presence of BHT was confirmed, being its concentration equal to 37.87μgL(-1). Calibrations based on PARAFAC yielded the following values for the decision limit (CCα): 1.16μgL(-1) for BHT, 1.34μgL(-1) for BP, 1.84μgL(-1) for DEHA and 51.42μgL(-1) for DiNP(for α=0.05 and two replicates).

  15. Candidatus Liberibacter asiaticus causes damage to citrus fibrous roots before visual decline of Huanglongbing-infected citrus trees

    OpenAIRE

    Graham, J. H.; Johnson, E.G.; Gottwald, T. R.; Irey, M. S.

    2014-01-01

    Huanglongbing (HLB), associated with Candidatus Liberibacter asiaticus (Las), was first detected in Florida in late 2005 and is now widely distributed throughout the commercial citrus-growing regions. In recent seasons, concurrent with freeze and drought episodes, symptomatic HLB-infected trees were much more affected by the extremes of temperature and moisture than trees without HLB. Symptoms exhibited by the stressed trees were excessive leaf loss and premature fruit drop even when HLB-infe...

  16. Guidelines for Selection of Tissues for Electron Microscopy Confirmation of Candidatus Liberibacter spp. in Huanglongbing-affected Citrus

    OpenAIRE

    Achor, Diann; Davis, Craig L.; Brlansky, Ronald H.; Folimonova, Svetlana Y.

    2014-01-01

    Polymerase chain reaction (PCR) with the pathogen-specific primers and electron microscopy are the two techniques of choice that have been used for detection and identification of Candidatus Liberibacter spp. in the Huanglongbing (HLB)-affected citrus. Due to the low population and uneven distribution of Liberibacter in the diseased citrus trees finding the bacteria with transmission electron microscopy has been a challenge. Work with samples from HLB-affected citrus during the past 5 years h...

  17. Molecular detection of Ehrlichia canis, Anaplasma bovis, Anaplasma platys, Candidatus Midichloria mitochondrii and Babesia canis vogeli in ticks from Israel.

    Science.gov (United States)

    Harrus, S; Perlman-Avrahami, A; Mumcuoglu, K Y; Morick, D; Eyal, O; Baneth, G

    2011-03-01

    : Ticks are vectors of important pathogens of human and animals. Therefore, their microbial carriage capacity is constantly being investigated. The aim of this study was to characterize the diversity of domestic animal pathogens in ticks collected from vegetation and the ground, from different parts of Israel. Non-engorged questing adult ticks were collected from 13 localities. A total of 1196 ticks in 131 pools-83 pools of Rhipicephalus turanicus and 48 of Rhipicephalus sanguineus (with two to ten ticks per pool)-were included in this study. In addition, 13 single free-roaming Hyalomma spp. ticks were collected. Screening by molecular techniques revealed the presence of Ehrlichia canis, Anaplasma platys, Anaplasma bovis and Babesia canis vogeli DNA in R. turanicus ticks. E. canis, A. bovis, B. canis vogeli and Candidatus Midichloria mitochondrii DNA sequences were detected in R. sanguineus ticks. Candidatus Midichloria mitochondrii DNA was also detected in Hyalomma spp. ticks. Neither Hepatozoon spp. nor Bartonella spp. DNA was detected in any of the ticks examined. This study describes the first detection of E. canis in the tick R. turanicus, which may serve as a vector of this canine pathogen; E. canis was the most common pathogen detected in the collected questing ticks. It also describes the first detection of A. bovis and Candidatus Midichloria mitochondrii in Israel. To the best of the author's knowledge, this is the first report describing the detection of DNA of the latter two pathogens in R. sanguineus, and of A. bovis in R. turanicus.

  18. Transmission and Propagation of 'Candidatus Liberibacter asiaticus' by Grafting with Individual Citrus Leaves.

    Science.gov (United States)

    Hilf, Mark E; Lewis, Reid S

    2016-05-01

    Huanglongbing (HLB) is a chronic, progressive decline disease in citrus associated with a systemic infection by the bacterium 'Candidatus Liberibacter asiaticus'. Transmission of the bacterium in the field is by the Asian citrus psyllid, Diaphorina citri Kuwayama. Experimental propagation of 'Ca. L. asiaticus' is done primarily by grafting pieces of bud wood from an infected plant. To produce a small-scale model system for investigation of pathogen biology, we investigated grafting single leaves from infected citrus plants as sources of inoculum for propagation of the bacterium. In total, 162 plants ranging in age from 3 to 18 months were grafted. Grafting with intact asymptomatic and HLB-symptomatic leaves resulted in 61 of 78 (78%) and 35 of 41 (85%) of the plants infected with 'Ca. L. asiaticus', respectively. Inoculum consisting of the leaf petiole only or only an inoculum tissue remnant under the bark of the receptor tree resulted in 6 of 12 (50%) and 7 of 31 (23%) infected trees, respectively. Real-time polymerase chain reaction (qPCR) assays verified the infection in plants, a majority of which developed the foliar blotchy mottle symptom considered diagnostic for HLB, while some plants also displayed the stunted, chlorotic shoots for which the disease is named. The qPCR data together with the symptoms displayed demonstrated that individual leaves from infected trees can serve as effective inoculum sources for transmission and propagation of 'Ca. L. asiaticus' via grafting.

  19. Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus pongiarum"

    KAUST Repository

    Gao, Zhao-Ming

    2014-04-01

    "Candidatus Synechococcus spongiarum" is a cyanobacterial symbiont widely distributed in sponges, but its functions at the genome level remain unknown. Here, we obtained the draft genome (1.66 Mbp, 90% estimated genome recovery) of "Ca. Synechococcus spongiarum" strain SH4 inhabiting the Red Sea sponge Carteriospongia foliascens. Phylogenomic analysis revealed a high dissimilarity between SH4 and free-living cyanobacterial strains. Essential functions, such as photosynthesis, the citric acid cycle, and DNA replication, were detected in SH4. Eukaryoticlike domains that play important roles in sponge-symbiont interactions were identified exclusively in the symbiont. However, SH4 could not biosynthesize methionine and polyamines and had lost partial genes encoding low-molecular-weight peptides of the photosynthesis complex, antioxidant enzymes, DNA repair enzymes, and proteins involved in resistance to environmental toxins and in biosynthesis of capsular and extracellular polysaccharides. These genetic modifications imply that "Ca. Synechococcus spongiarum" SH4 represents a low-light-adapted cyanobacterial symbiont and has undergone genome streamlining to adapt to the sponge\\'s mild intercellular environment. 2014 Gao et al.

  20. 'Candidatus Erwinia dacicola', a coevolved symbiotic bacterium of the olive fly Bactrocera oleae (Gmelin).

    Science.gov (United States)

    Capuzzo, Caterina; Firrao, Giuseppe; Mazzon, Luca; Squartini, Andrea; Girolami, Vincenzo

    2005-07-01

    The taxonomic identity of the hereditary prokaryotic symbiont of the olive fly Bactrocera oleae (Diptera: Tephritidae) was investigated. In order to avoid superficial microbial contaminants and loosely associated saprophytic biota, flies were surface-sterilized at the larval stage and reared under aseptic conditions until adult emergence. B. oleae flies originating from different geographical locations and collected at different times of the year were tested. Bacterial isolation was undertaken from the cephalic oesophageal bulb, which is known to be a specific site of accumulation for the hosted microsymbionts in the adult insect. Despite evidence of multiplication cycles taking place within the insect, attempts at cultivation of the isolated bacteria ex situ were not productive at any stage, leading to the choice of unculturable status definition. PCR amplification and nucleotide sequencing of the entire 16S rRNA gene consistently yielded a single sequence that displayed marked similarity with enterobacterial lineages, with closest matches (97%) to Erwinia persicina and Erwinia rhapontici. The novel taxon differs from common intestinal bacterial species of fruit flies and from instances of culturable bacteria previously described in B. oleae raised without sterility precautions, which we also observed as minority occupants or occasional contaminants. The symbiont's identity is also distinct from Pseudomonas savastanoi. In all observations, the numerically dominant inhabitant of the olive fly oesophageal organ was the same unculturable organism, whose presence at later stages was also regularly observed in the midgut. A novel species is proposed, by virtue of its unique properties, under the designation 'Candidatus Erwinia dacicola'.

  1. Reaction of sweet orange cultivars expressing the attacin A gene to 'Candidatus Liberibacter asiaticus' infection

    Directory of Open Access Journals (Sweden)

    Rafaella Teles Arantes Felipe

    2013-11-01

    Full Text Available The objective of this work was to evaluate the reaction of four sweet orange cultivars expressing the attacin A gene to 'Candidatus Liberibacter asiaticus' (Las infection, a bacterium associated to huanglongbing (HLB disease. Transgenic sweet orange plants of Hamlin, Natal, Pêra, and Valência cultivars, as well as nontransgenic controls received inocula by grafting budwood sections of HLB-infected branches. Disease progression was evaluated through observations of leaf symptoms and by polymerase chain reaction (PCR analysis, eight months after inoculation. A completely randomized design was used, with four experiments (one for each cultivar performed simultaneously. Bacteria title was estimated by quantitative PCR (qPCR. HLB symptoms and Las titers were present in nontransgenic and transgenic plants expressing the attacin A gene of the four sweet orange cultivars, eight months after bacteria inoculation. Five transgenic lines (transformation events of 'Pêra' sweet orange expressing the attacin A gene have significantly lower Las titers in comparison with nontransgenic plants of this cultivar.

  2. Changes in Variable Number of Tandem Repeats in 'Candidatus Liberibacter asiaticus' through Insect Transmission.

    Directory of Open Access Journals (Sweden)

    Hiroshi Katoh

    Full Text Available Citrus greening (huanglongbing is the most destructive citrus disease worldwide. The disease is associated with three species of 'Candidatus Liberibacter' among which 'Ca. Liberibacter asiaticus' has the widest distribution. 'Ca. L. asiaticus' is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of 'Ca. L. asiaticus' were clearly differentiated by variable number of tandem repeat (VNTR profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a 'Ca. L. asiaticus' strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of 'Ca. L. asiaticus' change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively.

  3. Unique features of a Japanese 'Candidatus Liberibacter asiaticus' strain revealed by whole genome sequencing.

    Directory of Open Access Journals (Sweden)

    Hiroshi Katoh

    Full Text Available Citrus greening (huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with phloem-limited bacteria of three species of α-Proteobacteria, namely, 'Candidatus Liberibacter asiaticus', 'Ca. L. americanus', and 'Ca. L. africanus'. Recent findings suggested that some Japanese strains lack the bacteriophage-type DNA polymerase region (DNA pol, in contrast to the Floridian psy62 strain. The whole genome sequence of the pol-negative 'Ca. L. asiaticus' Japanese isolate Ishi-1 was determined by metagenomic analysis of DNA extracted from 'Ca. L. asiaticus'-infected psyllids and leaf midribs. The 1.19-Mb genome has an average 36.32% GC content. Annotation revealed 13 operons encoding rRNA and 44 tRNA genes, but no typical bacterial pathogenesis-related genes were located within the genome, similar to the Floridian psy62 and Chinese gxpsy. In contrast to other 'Ca. L. asiaticus' strains, the genome of the Japanese Ishi-1 strain lacks a prophage-related region.

  4. The complete genome sequence of 'Candidatus Liberibacter americanus', associated with Citrus huanglongbing.

    Science.gov (United States)

    Wulff, Nelson A; Zhang, Shujian; Setubal, João C; Almeida, Nalvo F; Martins, Elaine C; Harakava, Ricardo; Kumar, Dibyendu; Rangel, Luiz Thiberio; Foissac, Xavier; Bové, Joseph M; Gabriel, Dean W

    2014-02-01

    Liberibacter spp. form a Rhizobiaceae clade of phloem-limited pathogens of limited host range. Two obligately parasitic species have been sequenced: 'Candidatus Liberibacter asiaticus', which causes citrus huanglongbing (HLB) worldwide, and 'Ca. L. solanacearum', which causes potato "zebra chip" disease. A third (proposed) species, Liberibacter crescens, was isolated from mountain papaya, grown in axenic culture, and sequenced. In an effort to identify common host determinants, the complete genomic DNA sequence of a second HLB species, 'Ca. L. americanus' strain 'São Paulo' was determined. The circular genome of 1,195,201 bp had an average 31.12% GC content and 983 predicted protein encoding genes, 800 (81.4%) of which had a predicted function. There were 658 genes common to all sequenced Liberibacter spp. and only 8 genes common to 'Ca. L. americanus' and 'Ca. L. asiaticus' but not found in 'Ca. L. solanacearum'. Surprisingly, most of the lipopolysaccharide biosynthetic genes were missing from the 'Ca. L. americanus' genome, as well as OmpA and a key regulator of flagellin, all indicating a 'Ca. L. americanus' strategy of avoiding production of major pathogen-associated molecular patterns present in 'Ca. L. asiaticus' and 'Ca. L. solanacearum'. As with 'Ca. L. asiaticus', one of two 'Ca. L. americanus' prophages replicated as an excision plasmid and carried potential lysogenic conversion genes that appeared fragmentary or degenerated in 'Ca. L. solanacearum'.

  5. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics.

    Science.gov (United States)

    Duan, Yongping; Zhou, Lijuan; Hall, David G; Li, Wenbin; Doddapaneni, Harshavardhan; Lin, Hong; Liu, Li; Vahling, Cheryl M; Gabriel, Dean W; Williams, Kelly P; Dickerman, Allan; Sun, Yijun; Gottwald, Tim

    2009-08-01

    Citrus huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with a low-titer, phloem-limited infection by any of three uncultured species of alpha-Proteobacteria, 'Candidatus Liberibacter asiaticus', 'Ca. L. americanus', and 'Ca. L. africanus'. A complete circular 'Ca. L. asiaticus' genome has been obtained by metagenomics, using the DNA extracted from a single 'Ca. L. asiaticus'-infected psyllid. The 1.23-Mb genome has an average 36.5% GC content. Annotation revealed a high percentage of genes involved in both cell motility (4.5%) and active transport in general (8.0%), which may contribute to its virulence. 'Ca. L. asiaticus' appears to have a limited ability for aerobic respiration and is likely auxotrophic for at least five amino acids. Consistent with its intracellular nature, 'Ca. L. asiaticus' lacks type III and type IV secretion systems as well as typical free-living or plant-colonizing extracellular degradative enzymes. 'Ca. L. asiaticus' appears to have all type I secretion system genes needed for both multidrug efflux and toxin effector secretion. Multi-protein phylogenetic analysis confirmed 'Ca. L. asiaticus' as an early-branching and highly divergent member of the family Rhizobiaceae. This is the first genome sequence of an uncultured alpha-proteobacteria that is both an intracellular plant pathogen and insect symbiont.

  6. FIRST REPORT OF 'CANDIDATUS PHYTOPLASMA ULMI' IN ULMUS LAEVIS IN GERMANY.

    Science.gov (United States)

    Eisold, A M; Kube, M; Holz, S; Büttner, C

    2015-01-01

    The wall-less bacteria of the provisory taxon 'Candidatus Phytoplasma' are obligate parasites and associated to diseases in many important crops and trees worldwide. 'Ca. Phytoplasma ulmi', assigned to 16SrV-A subgroup, is a quarantine pest and described to be associated to elm phloem necrosis, leaf yellowing, stunting, witches broom and decline in various elm species. Elm yellows phytoplasmas (EY) have been reported in several European countries but not in Ulmus laevis in Germany so far. Leaf samples from European white elms (Ulmus leavis PALL.) with and without chlorotic symptoms were investigated for EYs infection in Berlin and Brandenburg, Germany, through performing diagnostic nested PCR targeting partial rRNA operon of phytoplasmas. Specific PCR-products were obtained from 30 out of 59 samples. Partial 16S-rDNA sequences were assigned to 'Ca. P. ulmi' through sequence analysis, while sequence variation was observed. This is the first report of U. laevis infected with 'Ca. P. ulmi' in Germany.

  7. Proteomic analysis of the Mexican lime tree response to "Candidatus Phytoplasma aurantifolia" infection.

    Science.gov (United States)

    Taheri, Farzan; Nematzadeh, Ghorbanali; Zamharir, Maryam Ghayeb; Nekouei, Mojtaba Khayam; Naghavi, Mohammadreza; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

    2011-11-01

    "Candidatus Phytoplasma aurantifolia" is the causative agent of witches' broom disease in the Mexican lime tree (Citrus aurantifolia L.), and is responsible for major tree losses in Southern Iran and Oman. The pathogen is strictly biotrophic, and, therefore, completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. We applied a proteomics approach to analyse gene expression in Mexican limes infected with "Ca. Phytoplasma aurantifolia". Leaf samples were collected from healthy and infected plants and were analysed using 2-DE coupled with MS. Among 800 leaf proteins that were detected reproducibly in eight biological replicates of healthy and eight biological replicates of infected plants, 55 showed a significant response to the disease. MS resulted in identification of 39 regulated proteins, which included proteins that were involved in oxidative stress defence, photosynthesis, metabolism, and the stress response. Our results provide the first proteomic view of the molecular basis of the infection process and identify genes that could help inhibit the effects of the pathogen.

  8. Shotgun proteomic analysis of the Mexican lime tree infected with "CandidatusPhytoplasma aurantifolia".

    Science.gov (United States)

    Monavarfeshani, Aboozar; Mirzaei, Mehdi; Sarhadi, Elham; Amirkhani, Ardeshir; Khayam Nekouei, Mojtaba; Haynes, Paul A; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

    2013-02-01

    Infection of Mexican lime trees (Citrus aurantifolia L.) with the specialized bacterium "CandidatusPhytoplasma aurantifolia" causes witches' broom disease. Witches' broom disease has the potential to cause significant economic losses throughout western Asia and North Africa. We used label-free quantitative shotgun proteomics to study changes in the proteome of Mexican lime trees in response to infection by "Ca. Phytoplasma aurantifolia". Of 990 proteins present in five replicates of healthy and infected plants, the abundances of 448 proteins changed significantly in response to phytoplasma infection. Of these, 274 proteins were less abundant in infected plants than in healthy plants, and 174 proteins were more abundant in infected plants than in healthy plants. These 448 proteins were involved in stress response, metabolism, growth and development, signal transduction, photosynthesis, cell cycle, and cell wall organization. Our results suggest that proteomic changes in response to infection by phytoplasmas might support phytoplasma nutrition by promoting alterations in the host's sugar metabolism, cell wall biosynthesis, and expression of defense-related proteins. Regulation of defense-related pathways suggests that defense compounds are induced in interactions with susceptible as well as resistant hosts, with the main differences between the two interactions being the speed and intensity of the response.

  9. Development of Quantitative Real-time PCR Assays for Different Clades of “Candidatus Accumulibacter”

    Science.gov (United States)

    Zhang, An Ni; Mao, Yanping; Zhang, Tong

    2016-05-01

    We designed novel quantitative real-time polymerase chain reaction (qPCR) primers for the polyphosphate kinase 1 (ppk1) gene, targeting eight individual “Candidatus Accumulibacter” (referred to as Accumulibacter) clades. An evaluation of primer sets was conducted regarding the coverage, specificity, and PCR efficiency. (i) All primer sets were designed to cover all available sequences of the target clade. (ii) The phylogenetic analysis of the sequences retrieved from the qPCR products by each primer set demonstrated a high level of specificity. (iii) All calibration curves presented high PCR efficiencies in the range of 85–112% (R2 = 0.962–0.998). In addition, the possible interference of non-target amplicons was individually examined using the qPCR assay for 13 Accumulibacter clades, which were either undetected or showed negligible detection. With the primers designed by other research groups, a highly selective and sensitive qPCR-based method was developed to quantify all Accumulibacter clades, with the exception of Clade IE, in one assay, which enables more comprehensive insights into the community dynamics. The applicability to environmental samples was demonstrated by profiling the Accumulibacter clades in activated sludge samples of nine full-scale wastewater treatment plants.

  10. Detection of Babesia venatorum, Anaplasma phagocytophilum and Candidatus Neoehrlichia mikurensis in Ixodes persulcatus ticks from Mongolia.

    Science.gov (United States)

    Karnath, Carolin; Obiegala, Anna; Speck, Stephanie; Essbauer, Sandra; Derschum, Henri; Scholz, Holger; Kiefer, Daniel; Tserennorov, Damdindorj; Dashdavaa, Otgonbataar; Tsogbadrakh, Nyamdorj; Jigjav, Battsetseg; Pfeffer, Martin

    2016-03-01

    Information about the prevalence and geographical distribution of tick-borne pathogens Anaplasma phagocytophilum, Candidatus Neoehrlichia mikurensis, and Babesia spp. is still rare in Mongolia. We tested 275 Ixodes persulcatus ticks for A. phagocytophilum, Cand. N. mikurensis and Babesia spp. and 125 Dermacentor nuttalli ticks especially for Babesia spp. using different PCR methods. Ticks were collected from three provinces (Selenge, Arkhangai, Khentii) in Mongolia. DNA of A. phagocytophilum, Cand. N. mikurensis and Babesia spp. were found with a prevalence of 6.2%, 1.5% and 3.3% in each case in I. persulcatus ticks. This is the first time Cand. N. mikurensis was found in ticks from Mongolia. Sequence analysis of Babesia spp.-positive amplicons showed exclusively B. venatorum, which had also not been mentioned in Mongolia before. On the contrary, all D. nuttalli ticks tested negatively for Babesia spp. This study demonstrates that all three zoonotic pathogens are present in I. persulcatus ticks in Mongolia, and justify the need for further investigations of a more detailed genetic characterization of these pathogens.

  11. Neoehrlichiosis: an emerging tick-borne zoonosis caused by Candidatus Neoehrlichia mikurensis.

    Science.gov (United States)

    Silaghi, Cornelia; Beck, Relja; Oteo, José A; Pfeffer, Martin; Sprong, Hein

    2016-03-01

    Candidatus Neoehrlichia mikurensis is an emerging tick-borne pathogen causing a systemic inflammatory syndrome mostly in persons with underlying hematologic or autoimmune diseases. As it is neither well-known nor well-recognized, it might be misdiagnosed as recurrence of the underlying disease or as an unrelated arteriosclerotic vascular event. The pathogen is transmitted by hard ticks of the genus Ixodes and is closely associated with rodents in which transplacental transmission occurs. Transovarial transmission in ticks has not yet been shown. Infection rates vary greatly in ticks and rodents, but the causes for its spatiotemporal variations are largely unknown. This review summarizes the current state of knowledge on the geographical distribution and clinical importance of Ca. N. mikurensis. By elucidating the life history traits of this pathogen and determining more accurately its incidence in the human population, a better assessment of its public health relevance can be made. Most urgent research needs are the in vitro-cultivation of the pathogen, the development of specific serological tests, the determination of the full genomic sequence, the routine implementation of molecular diagnosis in diseased patients with a particular panel of underlying diseases, and promoting the knowledge about neoehrlichiosis among general practitioners, hospital physicians and the risk groups such as forest workers or immune-compromised people to raise awareness about this disease that can easily be treated when correctly diagnosed.

  12. Molecular characterization of 'Candidatus Rickettsia vini' in Ixodes arboricola from the Czech Republic and Slovakia.

    Science.gov (United States)

    Novakova, Marketa; Bulkova, Alexandra; Costa, Francisco B; Kristin, Anton; Krist, Milos; Krause, Frantisek; Liznarova, Eva; Labruna, Marcelo B; Literak, Ivan

    2015-04-01

    The aim of this study was to analyze the prevalence of rickettsiae in the tree-hole tick Ixodes arboricola in the Czech Republic and Slovakia. During May to September of 2009 and 2013, bird boxes belonging to three different areas were screened for ticks. In total, 454 nestlings and 109 nests of 10 hole-breeding bird species were examined. Ticks were found on Ficedula albicollis, Parus major, Cyanistes caeruleus and Sitta europaea and/or in their nests. In total, 166 ticks (17 nymphs, 10 males and 139 females) were found at 3 areas (arithmetic mean±standard error: 55.3±45.9). All ticks were tested for the presence of Rickettsia species by polymerase chain reaction targeting the rickettsial genes gltA, ompA, ompB and htrA and amplicon sequencing. All individuals except 3 nymphs were infected with 'Candidatus Rickettsia vini'. Multilocus sequence typing showed closest proximity to Rickettsia japonica and Rickettsia heilongjiangensis cluster. The presence of 'Ca. R. vini' is reported for the first time in Slovakia.

  13. Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'.

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    Brewer, Tess E; Handley, Kim M; Carini, Paul; Gilbert, Jack A; Fierer, Noah

    2016-10-31

    Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name 'Candidatus Udaeobacter copiosus'. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

  14. "Candidatus Mesochlamydia elodeae" (Chlamydiae: Parachlamydiaceae), a novel chlamydia parasite of free-living amoebae.

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    Corsaro, Daniele; Müller, Karl-Dieter; Wingender, Jost; Michel, Rolf

    2013-02-01

    Vannella sp. isolated from waterweed Elodea sp. was found infected by a chlamydia-like organism. This organism behaves like a parasite, causing the death through burst of its host. Once the vannellae degenerated, the parasite was successfully kept in laboratory within a Saccamoeba sp. isolated from the same waterweed sample, which revealed in fine through electron microscopy to harbor two bacterial endosymbionts: the chlamydial parasite we introduce and another endosymbiont initially and naturally present in the host. Herein, we provide molecular-based identification of both the amoeba host and its two endosymbionts, with special focus on the chlamydia parasite. High sequence similarity values of the 18S rDNA permitted to assign the amoeba to the species Saccamoeba lacustris (Amoebozoa, Tubulinea). The bacterial endosymbiont naturally harbored by the host belonged to Sphingomonas koreensis (Alpha-Proteobacteria). The chlamydial parasite showed a strict specificity for Saccamoeba spp., being unable to infect a variety of other amoebae, including Acanthamoeba, and it was itself infected by a bacteriophage. Sequence similarity values of the 16S rDNA and phylogenetic analysis indicated that this strain is a new member of the family Parachlamydiaceae, for which we propose the name "Candidatus Mesochlamydia elodeae."

  15. Relación entre Bactericera cockerelli y presencia de Candidatus Liberibacter psyllaurous en lotes comerciales de papa Relation between Bactericera cockerelli and presence of Candidatus Liberibacter psyllaurous in commercial fields of potato

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    Oswaldo Ángel Rubio-Covarrubias

    2011-02-01

    Full Text Available La brotación anormal de los tubérculos (sin brotes o brotes ahilados y el pardeamiento interno de los tubérculos, son síntomas de una enfermedad que está afectando la producción de papa en México, en el suroeste de Estados Unidos y América central. Esta enfermedad ha sido asociada con el psilido de la papa Bactericera cockerelli Sulc. Con el objetivo de dilucidar las causas de esta enfermedad, en 2007 se llevó a cabo un muestreo en 11 lotes comerciales de papa localizados en un transecto altitudinal entre 2 600 y 3 500 m en la región productora de papa de Toluca. La población de B. cockerelli fue determinada mediante muestreos semanales de los insectos adultos atrapados en trampas amarillas pegajosas. Al final del periodo de crecimiento del cultivo, los tubérculos producidos en cada lote fueron muestreados y almacenados por 6 meses. Después de este tiempo, se determinó el porcentaje de tubérculos con brotación anormal y se hicieron análisis con PCR para determinar la presencia de Candidatus Liberibacter psyllaurous y de fitoplasmas en los tubérculos. Los resultados indican que la población de B. cockerelli y de los síntomas de la punta morada de la papa disminuyeron con la altura, en alturas superiores a 3 200 msnm no se presentaron problemas significativas de la enfermedad. El 36% de los tubérculos con brotes finos presentó el pardeamiento interno y 58% de los tubérculos sin brotes presentó el mismo síntoma. El 54% de los tubérculos con brotación anormal fue positivo a Candidatus Liberibacter psyllaurous y sólo 3.5% a fitoplasmas. Estos resultados indican que Candidatus Liberibacter psyllaurous está asociada con los síntomas de la punta morada de la papa en la región de Toluca.The abnormal sprouting of tubers (without sprouts or with threadlike sprouts and the internal browning of the potatoes are symptoms of a disease which is affecting the potato production in Mexico, in southwestern United States and Central

  16. Effective antibiotics against 'Candidatus Liberibacter asiaticus' in HLB-affected citrus plants identified via the graft-based evaluation.

    Science.gov (United States)

    Zhang, Muqing; Guo, Ying; Powell, Charles A; Doud, Melissa S; Yang, Chuanyu; Duan, Yongping

    2014-01-01

    Citrus huanglongbing (HLB), caused by three species of fastidious, phloem-limited 'Candidatus Liberibacter', is one of the most destructive diseases of citrus worldwide. To date, there is no established cure for this century-old and yet, newly emerging disease. As a potential control strategy for citrus HLB, 31 antibiotics were screened for effectiveness and phytotoxicity using the optimized graft-based screening system with 'Candidatus Liberibacter asiaticus' (Las)-infected citrus scions. Actidione and Oxytetracycline were the most phytotoxic to citrus with less than 10% of scions surviving and growing; therefore, this data was not used in additional analyses. Results of principal component (PCA) and hierarchical clustering analyses (HCA) demonstrated that 29 antibiotics were clustered into 3 groups: highly effective, partly effective, and not effective. In spite of different modes of actions, a number of antibiotics such as, Ampicillin, Carbenicillin, Penicillin, Cefalexin, Rifampicin and Sulfadimethoxine were all highly effective in eliminating or suppressing Candidatus Liberibacter asiaticus indicated by both the lowest Las infection rate and titers of the treated scions and inoculated rootstock. The non-effective group, including 11 antibiotics alone with three controls, such as Amikacin, Cinoxacin, Gentamicin, Kasugamycin, Lincomycin, Neomycin, Polymixin B and Tobramycin, did not eliminate or suppress Las in the tested concentrations, resulting in plants with increased titers of Las. The other 12 antibiotics partly eliminated or suppressed Las in the treated and graft-inoculated plants. The effective and non-phytotoxic antibiotics could be potential candidates for control of citrus HLB, either for the rescue of infected citrus germplasm or for restricted field application.

  17. Proteomic analysis of the purple sulfur bacterium Candidatus “Thiodictyon syntrophicum” strain Cad16T isolated from Lake Cadagno

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    Nicola Storelli

    2014-03-01

    Full Text Available Lake Cadagno is characterised by a compact chemocline with high concentrations of purple sulfur bacteria (PSB. 2D-DIGE was used to monitor the global changes in the proteome of Candidatus “Thiodictyon syntrophicum” strain Cad16T both in the presence and absence of light. This study aimed to disclose details regarding the dark CO2 assimilation of the PSB, as this mechanism is often observed but is not yet sufficiently understood. Our results showed the presence of 17 protein spots that were more abundant in the dark, including three enzymes that could be part of the autotrophic dicarboxylate/4-hydroxybutyrate cycle, normally observed in archaea.

  18. The transcriptional activator LdtR from 'Candidatus Liberibacter asiaticus' mediates osmotic stress tolerance.

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    Fernando A Pagliai

    2014-04-01

    Full Text Available The causal agent of Huanglongbing disease, 'Candidatus Liberibacter asiaticus', is a non-culturable, gram negative, phloem-limited α-proteobacterium. Current methods to control the spread of this disease are still limited to the removal and destruction of infected trees. In this study, we identified and characterized a regulon from 'Ca. L. asiaticus' involved in cell wall remodeling, that contains a member of the MarR family of transcriptional regulators (ldtR, and a predicted L,D-transpeptidase (ldtP. In Sinorhizobium meliloti, mutation of ldtR resulted in morphological changes (shortened rod-type phenotype and reduced tolerance to osmotic stress. A biochemical approach was taken to identify small molecules that modulate LdtR activity. The LdtR ligands identified by thermal shift assays were validated using DNA binding methods. The biological impact of LdtR inactivation by the small molecules was then examined in Sinorhizobium meliloti and Liberibacter crescens, where a shortened-rod phenotype was induced by growth in presence of the ligands. A new method was also developed to examine the effects of small molecules on the viability of 'Ca. Liberibacter asiaticus', using shoots from HLB-infected orange trees. Decreased expression of ldtRLas and ldtPLas was observed in samples taken from HLB-infected shoots after 6 h of incubation with the LdtR ligands. These results provide strong proof of concept for the use of small molecules that target LdtR, as a potential treatment option for Huanglongbing disease.

  19. Genetic diversity of Candidatus Liberibacter asiaticus based on two hypervariable effector genes in Thailand.

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    Thamrongjet Puttamuk

    Full Text Available Huanglongbing (HLB, also known as citrus greening, is one of the most destructive diseases of citrus worldwide. HLB is associated with three species of 'Candidatus Liberibacter' with 'Ca. L. asiaticus' (Las being the most widely distributed around the world, and the only species detected in Thailand. To understand the genetic diversity of Las bacteria in Thailand, we evaluated two closely-related effector genes, lasAI and lasAII, found within the Las prophages from 239 infected citrus and 55 infected psyllid samples collected from different provinces in Thailand. The results indicated that most of the Las-infected samples collected from Thailand contained at least one prophage sequence with 48.29% containing prophage 1 (FP1, 63.26% containing prophage 2 (FP2, and 19.38% containing both prophages. Interestingly, FP2 was found to be the predominant population in Las-infected citrus samples while Las-infected psyllids contained primarily FP1. The multiple banding patterns that resulted from amplification of lasAI imply extensive variation exists within the full and partial repeat sequence while the single band from lasAII indicates a low amount of variation within the repeat sequence. Phylogenetic analysis of Las-infected samples from 22 provinces in Thailand suggested that the bacterial pathogen may have been introduced to Thailand from China and the Philippines. This is the first report evaluating the genetic variation of a large population of Ca. L. asiaticus infected samples in Thailand using the two effector genes from Las prophage regions.

  20. Sexual transmission of a plant pathogenic bacterium, Candidatus Liberibacter asiaticus, between conspecific insect vectors during mating.

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    Rajinder S Mann

    Full Text Available Candidatus Liberibacter asiaticus is a fastidious, phloem-inhabiting, gram-negative bacterium transmitted by Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae. The bacterium is the presumed causal agent of huanglongbing (HLB, one of the most destructive and economically important diseases of citrus. We investigated whether Las is transmitted between infected and uninfected D. citri adults during courtship. Our results indicate that Las was sexually transmitted from Las-infected male D. citri to uninfected females at a low rate (<4% during mating. Sexual transmission was not observed following mating of infected females and uninfected males or among adult pairs of the same sex. Las was detected in genitalia of both sexes and also in eggs of infected females. A latent period of 7 days or more was required to detect the bacterium in recipient females. Rod shaped as well as spherical structures resembling Las were observed in ovaries of Las-infected females with transmission electron microscopy, but were absent in ovaries from uninfected D. citri females. The size of the rod shaped structures varied from 0.39 to 0.67 µm in length and 0.19 to 0.39 µm in width. The spherical structures measured from 0.61 to 0.80 µm in diameter. This investigation provides convincing evidence that a plant pathogenic bacterium is sexually transmitted from male to female insects during courtship and established evidence that bacteria persist in reproductive organs. Moreover, these findings provide an alternative sexually horizontal mechanism for the spread of Las within populations of D. citri, even in the absence of infected host trees.

  1. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing.

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    Lijuan Zhou

    Full Text Available Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB, a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and

  2. The intracellular citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' encodes two novel autotransporters.

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    Guixia Hao

    Full Text Available Proteins secreted by the type V secretion system (T5SS, known as autotransporters, are large extracellular virulence proteins localized to the bacterial poles. In this study, we characterized two novel autotransporter proteins of 'Candidatus Liberibacter asiaticus' (Las, and redesignated them as LasAI and LasAII in lieu of the previous names HyvI and HyvII. As a phloem-limited, intracellular bacterial pathogen, Las has a significantly reduced genome and causes huanglongbing (HLB, a devastating disease of citrus worldwide. Bioinformatic analyses revealed that LasAI and LasAII share the structural features of an autotransporter family containing large repeats of a passenger domain and a unique C-terminal translocator domain. When fused to the GFP gene and expressed in E. coli, the LasAI C-terminus and the full length LasAII were localized to the bacterial poles, similar to other members of autotransporter family. Despite the absence of a typical signal peptide, LasAI was found to localize at the cell surface by immuno-dot blot using a monoclonal antibody against the partial LasAI protein. Its surface localization was also confirmed by the removal of the LasAI antigen using a proteinase K treatment of the intact bacterial cells. When co-inoculated with a P19 gene silencing suppressor and transiently expressed in tobacco leaves, the GFP-LasAI translocator targeted to the mitochondria. This is the first report that Las encodes novel autotransporters that target to mitochondria when expressed in the plants. These findings may lead to a better understanding of the pathogenesis of this intracellular bacterium.

  3. The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease.

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    Hong Lin

    Full Text Available Zebra Chip (ZC is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with 'Candidatus Liberibacter solanacearum', a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for 'Ca. L. solanacearum'. Here we present the sequence of the 1.26 Mbp metagenome of 'Ca. L. solanacearum', based on DNA isolated from potato psyllids. The coding inventory of the 'Ca. L. solanacearum' genome was analyzed and compared to related Rhizobiaceae to better understand 'Ca. L. solanacearum' physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, 'Ca. L. solanacearum' is related to 'Ca. L. asiaticus', a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to 'Ca. L. asiaticus', 'Ca. L. solanacearum' probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes.

  4. Molecular characterization of a mosaic locus in the genome of 'Candidatus Liberibacter asiaticus'

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    Wang Xuefeng

    2012-01-01

    Full Text Available Abstract Background Huanglongbing (HLB is a highly destructive disease of citrus production worldwide. 'Candidatus Liberibacter asiaticus', an unculturable alpha proteobacterium, is a putative pathogen of HLB. Information about the biology and strain diversity of 'Ca. L. asiaticus' is currently limited, inhibiting the scope of HLB research and control. Results A genomic region (CLIBASIA_05640 to CLIBASIA_05650 of 'Ca. L. asiaticus' showing hyper-sequence variation or locus mosaicism was identified and investigated using 262 bacterial strains (188 from China and 74 from Florida. Based on the characteristic electrophoretic profiles of PCR amplicons generated by a specific primer set, eight electrophoretic types (E-types were identified, six E-types (A, B, C, D, E, and F in China and four E-types (A, C, G, and H in Florida. The 'Ca. L. asiaticus' strains from China consisted predominately of E-type A (71.3% and E-type B (19.7%. In contrast, the 'Ca. L. asiaticus' strains from Florida was predominated by E-type G (82.4%. Diversity of 'Ca. L. asiaticus' in China was also evidenced. Strains from the high altitude Yunnan Province consisted of five E-types with E-type B being the majority (62.8%, whereas strains from the low altitude coastal Guangdong Province consisted of only two E-types with E-type A as the majority (97.0%. Sequence analyses revealed that variation of DNA amplicons was due to insertion/deletion events at CLIBASIA_05650 and the downstream intergenic region. Conclusions This study demonstrated the genomic mosaicism of 'Ca. L. asiaticus' resulted from active DNA insertion/deletion activities. Analyses of strain variation depicted the significant inter- and intra-continent diversity of 'Ca. L. asiaticus'.

  5. Specific PCR and real-time PCR assays for detection and quantitation of 'Candidatus Phytoplasma phoenicium'.

    Science.gov (United States)

    Jawhari, Maan; Abrahamian, Peter; Sater, Ali Abdel; Sobh, Hana; Tawidian, Patil; Abou-Jawdah, Yusuf

    2015-02-01

    Almond witches' broom (AlmWB) is a fast-spreading lethal disease of almond, peach and nectarine associated with 'Candidatus Phytoplasma phoenicium'. The development of PCR and quantitative real-time PCR (qPCR) assays for the sensitive and specific detection of the phytoplasma is of prime importance for early detection of 'Ca. P. phoenicium' and for epidemiological studies. The developed qPCR assay herein uses a TaqMan(®) probe labeled with Black Hole Quencher Plus. The specificity of the PCR and that of the qPCR detection protocols were tested on 17 phytoplasma isolates belonging to 11 phytoplasma 16S rRNA groups, on samples of almond, peach, nectarine, native plants and insects infected or uninfected with the phytoplasma. The developed assays showed high specificity against 'Ca. P. phoenicium' and no cross-reactivity against any other phytoplasma, plant or insect tested. The sensitivity of the developed PCR and qPCR assays was similar to the conventional nested PCR protocol using universal primers. The qPCR assay was further validated by quantitating AlmWB phytoplasma in different hosts, plant parts and potential insect vectors. The highest titers of 'Ca. P. phoenicium' were detected in the phloem tissues of stems and roots of almond and nectarine trees, where they averaged from 10(5) to 10(6) genomic units per nanogram of host DNA (GU/ng of DNA). The newly developed PCR and qPCR protocols are reliable, specific and sensitive methods that are easily applicable to high-throughput diagnosis of AlmWB in plants and insects and can be used for surveys of potential vectors and alternative hosts.

  6. Transcriptional and microscopic analyses of citrus stem and root responses to Candidatus Liberibacter asiaticus infection.

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    Valente Aritua

    Full Text Available Huanglongbing (HLB is the most destructive disease that affects citrus worldwide. The disease has been associated with Candidatus Liberibacter. HLB diseased citrus plants develop a multitude of symptoms including zinc and copper deficiencies, blotchy mottle, corky veins, stunting, and twig dieback. Ca. L. asiaticus infection also seriously affects the roots. Previous study focused on gene expression of leaves and fruit to Ca. L. asiaticus infection. In this study, we compared the gene expression levels of stems and roots of healthy plants with those in Ca. L. asiaticus infected plants using microarrays. Affymetrix microarray analysis showed a total of 988 genes were significantly altered in expression, of which 885 were in the stems, and 111 in the roots. Of these, 551 and 56 were up-regulated, while 334 and 55 were down-regulated in the stem and root samples of HLB diseased trees compared to healthy plants, respectively. Dramatic differences in the transcriptional responses were observed between citrus stems and roots to Ca. L. asiaticus infection, with only 8 genes affected in both the roots and stems. The affected genes are involved in diverse cellular functions, including carbohydrate metabolism, cell wall biogenesis, biotic and abiotic stress responses, signaling and transcriptional factors, transportation, cell organization, protein modification and degradation, development, hormone signaling, metal handling, and redox. Microscopy analysis showed the depletion of starch in the roots of the infected plants but not in healthy plants. Collapse and thickening of cell walls were observed in HLB affected roots, but not as severe as in the stems. This study provides insight into the host response of the stems and roots to Ca. L. asiaticus infection.

  7. In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia.

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    Mohsen Mardi

    Full Text Available Witches' broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia. However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes with an average length of 530 nt. Of these, 41,805 (53.4% were annotated against the NCBI non-redundant (nr protein database using a BLASTx search (e-value ≤ 1e-5. When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5. These differentially expressed genes (DEGs were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

  8. In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia.

    Science.gov (United States)

    Mardi, Mohsen; Karimi Farsad, Laleh; Gharechahi, Javad; Salekdeh, Ghasem Hosseini

    2015-01-01

    Witches' broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia). However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes) with an average length of 530 nt. Of these, 41,805 (53.4%) were annotated against the NCBI non-redundant (nr) protein database using a BLASTx search (e-value ≤ 1e-5). When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5). These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

  9. Search for potential vectors of ‘Candidatus Liberibacter solanacearum’: population dynamics in host crops

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    Teresani, G.; Hernández, E.; Bertolini, E.; Siverio, F.; Marroquín, C.; Molina, J.; Hermoso de Mendoza, A.; Cambra, M.

    2015-07-01

    Candidatus Liberibacter solanacearum’ has recently been reported to be associated with vegetative disorders and economic losses in carrot and celery crops in Spain. The bacterium is a carrot seedborne pathogen and it is transmitted by psyllid vector species. From 2011 to 2014 seasonal and occasional surveys in carrot, celery and potato plots were performed. The sticky plant method was used to monitor the arthropods that visited the plants. The collected arthropods were classified into Aphididae and Cicadellidae, and the superfamily Psylloidea was identified to the species level. The superfamily Psylloidea represented 35.45% of the total arthropods captured on celery in Villena and 99.1% on carrot in Tenerife (Canary Islands). The maximum flight of psyllid species was in summer, both in mainland Spain and the Canary Islands, reaching a peak of 570 specimens in August in Villena and 6,063 in July in Tenerife. The main identified psyllid species were as follows: Bactericera trigonica Hodkinson, B. tremblayi Wagner and B. nigricornis Förster. B. trigonica represented more than 99% of the psyllids captured in the Canary Islands and 75% and 38% in 2011 and 2012 in Villena, respectively. In addition, Trioza urticae Linnaeus, Bactericera sp., Ctenarytaina sp., Cacopsylla sp., Trioza sp. and Psylla sp. were captured. ‘Ca. L. solanacearum’ targets were detected by squash real-time PCR in 19.5% of the psyllids belonging to the different Bactericera species. This paper reports at least three new psyllid species that carry the bacterium and can be considered as potential vectors. (Author)

  10. Candidatus Bartonella merieuxii, a potential new zoonotic Bartonella species in canids from Iraq.

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    Bruno B Chomel

    Full Text Available Bartonellae are emerging vector-borne pathogens infecting erythrocytes and endothelial cells of various domestic and wild mammals. Blood samples were collected from domestic and wild canids in Iraq under the United States Army zoonotic disease surveillance program. Serology was performed using an indirect immunofluorescent antibody test for B. henselae, B. clarridgeiae, B. vinsonii subsp. berkhoffii and B. bovis. Overall seroprevalence was 47.4% in dogs (n = 97, 40.4% in jackals (n = 57 and 12.8% in red foxes (n = 39. Bartonella species DNA was amplified from whole blood and representative strains were sequenced. DNA of a new Bartonella species similar to but distinct from B. bovis, was amplified from 37.1% of the dogs and 12.3% of the jackals. B. vinsonii subsp. berkhoffii was also amplified from one jackal and no Bartonella DNA was amplified from foxes. Adjusting for age, the odds of dogs being Bartonella PCR positive were 11.94 times higher than for wild canids (95% CI: 4.55-31.35, suggesting their role as reservoir for this new Bartonella species. This study reports on the prevalence of Bartonella species in domestic and wild canids of Iraq and provides the first detection of Bartonella in jackals. We propose Candidatus Bartonella merieuxii for this new Bartonella species. Most of the Bartonella species identified in sick dogs are also pathogenic for humans. Therefore, seroprevalence in Iraqi dog owners and bacteremia in Iraqi people with unexplained fever or culture negative endocarditis requires further investigation as well as in United States military personnel who were stationed in Iraq. Finally, it will also be essential to test any dog brought back from Iraq to the USA for presence of Bartonella bacteremia to prevent any accidental introduction of a new Bartonella species to the New World.

  11. Search for potential vectors of ‘Candidatus Liberibacter solanacearum’: population dynamics in host crops

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    Gabriela Teresani

    2015-03-01

    Full Text Available Candidatus Liberibacter solanacearum’ has recently been reported to be associated with vegetative disorders and economic losses in carrot and celery crops in Spain. The bacterium is a carrot seedborne pathogen and it is transmitted by psyllid vector species. From 2011 to 2014 seasonal and occasional surveys in carrot, celery and potato plots were performed. The sticky plant method was used to monitor the arthropods that visited the plants. The collected arthropods were classified into Aphididae and Cicadellidae, and the superfamily Psylloidea was identified to the species level. The superfamily Psylloidea represented 35.45% of the total arthropods captured on celery in Villena and 99.1% on carrot in Tenerife (Canary Islands. The maximum flight of psyllid species was in summer, both in mainland Spain and the Canary Islands, reaching a peak of 570 specimens in August in Villena and 6,063 in July in Tenerife. The main identified psyllid species were as follows: Bactericera trigonica Hodkinson, B. tremblayi Wagnerand B. nigricornis Förster. B. trigonica represented more than 99% of the psyllids captured in the Canary Islands and 75% and 38% in 2011 and 2012 in Villena, respectively. In addition, Trioza urticae Linnaeus, Bactericera sp.,Ctenarytaina sp., Cacopsylla sp., Trioza sp. and Psylla sp. were captured. ‘Ca. L. solanacearum’ targets were detected by squash real-time PCR in 19.5% of the psyllids belonging to the different Bactericera species. This paper reports at least three new psyllid species that carry the bacterium and can be considered as potential vectors.

  12. "Candidatus Fokinia solitaria", a Novel "Stand-Alone" Symbiotic Lineage of Midichloriaceae (Rickettsiales.

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    Franziska Szokoli

    Full Text Available Recently, the family Midichloriaceae has been described within the bacterial order Rickettsiales. It includes a variety of bacterial endosymbionts detected in different metazoan host species belonging to Placozoa, Cnidaria, Arthropoda and Vertebrata. Representatives of Midichloriaceae are also considered possible etiological agents of certain animal diseases. Midichloriaceae have been found also in protists like ciliates and amoebae. The present work describes a new bacterial endosymbiont, "Candidatus Fokinia solitaria", retrieved from three different strains of a novel Paramecium species isolated from a wastewater treatment plant in Rio de Janeiro (Brazil. Symbionts were characterized through the full-cycle rRNA approach: SSU rRNA gene sequencing and fluorescence in situ hybridization (FISH with three species-specific oligonucleotide probes. In electron micrographs, the tiny rod-shaped endosymbionts (1.2 x 0.25-0.35 μm in size were not surrounded by a symbiontophorous vacuole and were located in the peripheral host cytoplasm, stratified in the host cortex in between the trichocysts or just below them. Frequently, they occurred inside autolysosomes. Phylogenetic analyses of Midichloriaceae apparently show different evolutionary pathways within the family. Some genera, such as "Ca. Midichloria" and "Ca. Lariskella", have been retrieved frequently and independently in different hosts and environmental surveys. On the contrary, others, such as Lyticum, "Ca. Anadelfobacter", "Ca. Defluviella" and the presently described "Ca. Fokinia solitaria", have been found only occasionally and associated to specific host species. These last are the only representatives in their own branches thus far. Present data do not allow to infer whether these genera, which we named "stand-alone lineages", are an indication of poorly sampled organisms, thus underrepresented in GenBank, or represent fast evolving, highly adapted evolutionary lineages.

  13. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing.

    Science.gov (United States)

    Zhou, Lijuan; Powell, Charles A; Li, Wenbin; Irey, Mike; Duan, Yongping

    2013-01-01

    Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.

  14. Genetic diversity of European phytoplasmas of the 16SrV taxonomic group and proposal of 'Candidatus Phytoplasma rubi'.

    Science.gov (United States)

    Malembic-Maher, Sylvie; Salar, Pascal; Filippin, Luisa; Carle, Patricia; Angelini, Elisa; Foissac, Xavier

    2011-09-01

    In addition to the grapevine flavescence dorée phytoplasmas, other members of taxonomic group 16SrV phytoplasmas infect grapevines, alders and species of the genera Clematis and Rubus in Europe. In order to investigate which phytoplasmas constitute discrete, species-level taxa, several strains were analysed by comparing their 16S rRNA gene sequences and a set of five housekeeping genes. Whereas 16S rRNA gene sequence similarity values were >97.5 %, the proposed threshold to distinguish two 'Candidatus Phytoplasma' taxa, phylogenetic analysis of the combined sequences of the tuf, rplV-rpsC, rplF-rplR, map and uvrB-degV genetic loci showed that two discrete phylogenetic clusters could be clearly distinguished. The first cluster grouped flavescence dorée (FD) phytoplasmas, alder yellows (AldY) phytoplasmas, Clematis (CL) phytoplasmas and the Palatinate grapevine yellows (PGY) phytoplasmas. The second cluster comprised Rubus stunt (RS) phytoplasmas. In addition to the specificity of the insect vector, the Rubus stunt phytoplasma contained specific sequences in the 16S rRNA gene. Hence, the Rubus stunt phytoplasma 16S rRNA gene was sufficiently differentiated to represent a novel putative taxon: 'Candidatus Phytoplasma rubi'.

  15. 'Candidatus Megaira polyxenophila' gen. nov., sp. nov.: considerations on evolutionary history, host range and shift of early divergent rickettsiae.

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    Martina Schrallhammer

    Full Text Available "Neglected Rickettsiaceae" (i.e. those harboured by non-hematophagous eukaryotic hosts display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora; furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta. Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria.

  16. Presence, genetic variability, and potential significance of "Candidatus Midichloria mitochondrii" in the lone star tick Amblyomma americanum.

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    Williams-Newkirk, Amanda Jo; Rowe, Lori A; Mixson-Hayden, Tonya R; Dasch, Gregory A

    2012-11-01

    We used next generation sequencing to detect the bacterium "Candidatus Midichloria mitochondrii" for the first time in lone star ticks (Amblyomma americanum) from the eastern United States. 177 individuals and 11 tick pools from seven sites in four states were tested by pyrosequencing with barcoded 16S rRNA gene eubacterial primers targeting variable regions 5-3. Average infection prevalence was 0.15 across all surveyed populations (range 0-0.29) and only the site with the smallest sample size (n = 5) was negative. Three genotypes differing by 2.6-4.1 % in a 271 bp region of 16S rRNA gene were identified. Two variants co-occurred in sites in North Carolina and New York, but were not observed in the same tick at those sites. The third genotype was found only in Georgia. Phylogenetic analysis of this fragment indicated that the three variants are more closely related to "Candidatus Midichloria mitochondrii" genotypes from other tick species than to each other. This variation suggests that multiple independent introductions occurred in A. americanum which may provide insight into bacterial spread within its ecosystem and parasitism on this tick. Whether the presence of this bacterium affects acquisition or maintenance of other pathogens and symbionts in A. americanum or the survival, biology and evolution of the tick itself is unknown.

  17. A single prophage carrying a CRISPR/cas system in ‘Candidatus Liberibacter asiaticus’ strain A4 from Guangdong, China

    Science.gov (United States)

    Candidatus Liberibacter asiaticus” (CLas) is an unculturable a-proteobacterium associated with citrus huanglongbing (HLB, yellow shoot disease), a highly destructive disease that affects citrus production worldwide. HLB was observed in Guangdong Province of China over a hundred years ago and remain...

  18. Visualization of ‘Candidatus Liberibacter asiaticus’ cells in citrus seed coats with fluorescence in situ hybridization and transmission electron microscopy

    Science.gov (United States)

    Candidatus Liberibacter asiaticus’ is bacterium implicated as the causal agent of the economically damaging disease of citrus called huanglongbing (HLB). The bacterium is spread by movement of infected citrus propagation material and by the Asian citrus psyllid, Diaphorina citri Kuwayama. Seed tr...

  19. Complete Genome Sequences of the Obligate Symbionts "Candidatus Sulcia muelleri" and "Ca. Nasuia deltocephalinicola" from the Pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae).

    Science.gov (United States)

    Bennett, Gordon M; Abbà, Simona; Kube, Michael; Marzachì, Cristina

    2016-01-01

    Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus (Hemiptera: Cicadellidae), were fully sequenced. "Candidatus Sulcia muelleri" and "Ca. Nasuia deltocephalinicola" represent two of the smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome sequences are nearly identical to strains reported from the closely related host species, M. quadrilineatus.

  20. Zinc treatment increases the titre of ‘Candidatus Liberibacter asiaticus’ in Huanglongbing-affected citrus plants while affecting the bacterial microbiomes

    Science.gov (United States)

    Huanglongbing (HLB)-affected citrus often display zinc deficiency symptoms. In this study, supplemental zinc was applied to citrus to determine its effect on Candidatus Liberibacter asiaticus (Las) titer, HLB symptoms, and leaf microbiome. HLB-affected citrus were treated with various amounts of zi...

  1. Molecular detection of aster yellows phytoplasma and 'Candidatus Liberibacter solanacearum' in carrots affected by the psyllid Trioza apicalis (Hemiptera: triozidae) in Finland

    Science.gov (United States)

    Carrot psyllid (Trioza apicalis Förster) causes considerable damage to carrot (Daucus carota L.) in many parts of Europe. It was recently established that the new bacterium “Candidatus Liberibacter solanacearum” is associated with carrot psyllid and plants affected by this insect pest. No other path...

  2. Screening molecules for control of citrus Huanglongbing (HLB) using an optimized regeneration system for 'Candidatus Liberibacter asiaticus' infected periwinkle (Catharunthus roseus) cuttings

    Science.gov (United States)

    Citrus huanglongbing (HLB) ( also known as citrus greening) is one of the most destructive diseases of citrus worldwide. The disease is associated with three different species of Candidatus Liberibacter, of which, ‘Ca. L. asiaticus’ (Las) is the most widely-distributed. An improved system using HLB-...

  3. Localization and distribution of ‘Candidatus Liberibacter asiaticus’ in citrus and periwinkle by direct tissue blot immuno assay with an anti-OmpA polyclonal antibody

    Science.gov (United States)

    Candidatus Liberibacter asiaticus’ (CaLas), a non-cultured member of the a-proteobacteria, is the causal agent of citrus Huanglongbing (HLB). Due to the difficulties of in vitro culture, antibodies against CaLas have not been widely used in studies of this pathogen. We have used an anti-OmpA poly...

  4. Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov.

    Science.gov (United States)

    Sauer, C; Stackebrandt, E; Gadau, J; Hölldobler, B; Gross, R

    2000-09-01

    The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'.

  5. Draft Genome Sequence of “Candidatus Hepatoplasma crinochetorum” Ps, a Bacterial Symbiont in the Hepatopancreas of the Terrestrial Isopod Porcellio scaber

    Science.gov (United States)

    Kostanjšek, Rok; Toenshoff, Elena R.; Schulz, Frederik; Schuster, Lisa; Domann, Daryl; Horn, Matthias

    2015-01-01

    Candidatus Hepatoplasma crinochetorum” Ps is an extracellular symbiont residing in the hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is highly similar to that of the close relative “Ca. Hepatoplasma crinochetorum” Av from Armadillidium vulgare. However, instead of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction modification system. PMID:26272556

  6. A draft whole genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351 from Asian citrus psyllids in Texas, USA

    Science.gov (United States)

    The draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351 collected from ACP in South Texas has been determined. The TX2351 genome is 1,252,043 bp in size with a 36.5% G+C content, encoding 1,184 predicted open reading frames and 51 RNA genes....

  7. Use of Electrical Penetration Graph Technology to Examine Transmission of ‘Candidatus Liberibacter solanacearum’ to Potato by Three Haplotypes of Potato Psyllid (Bactericera cockerelli; Hemiptera: Triozidae)

    Science.gov (United States)

    The potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae), is a vector of the phloem-limited bacterium ‘Candidatus Liberibacter solanacearum’ (Lso), the putative causal agent of zebra chip disease of potato. Little is known about how potato psyllid transmits Lso to potato. We used ele...

  8. Association of ‘Candidatus Liberibacter asiaticus’, the causal agent of citrus huanglongbing in Murraya paniculata and Diaphorina citri in Thailand

    Science.gov (United States)

    Orange jasmine, Murraya paniculata, is a preferred alternative host for the Asian citrus psyllid, the primary vector of citrus Huanglongbing (HLB) disease caused by ‘Candidatus Liberibacter asiaticus’ (Las). M. paniculata plant samples and psyllids on the Murraya plants from ten diverse geographical...

  9. Transcriptome analyses of Bactericera cockerelli adults in response to "Candidatus Liberibacter solanacearum" infection.

    Science.gov (United States)

    Nachappa, Punya; Levy, Julien; Tamborindeguy, Cecilia

    2012-10-01

    The potato/tomato psyllid, Bactericera cockerelli (Šulc) is an economically important crop pest that not only causes damage through its feeding but also transmits the bacterium, "Candidatus Liberibacter solanacearum" (CLs), which causes zebra chip disease in potato. There is some information about the phenotypic effects of phytopathogenic bacteria on their insect vectors; however, there are no published reports of the molecular mechanisms underlying phytopathogenic bacteria-insect vector interaction. In order to investigate the effects of CLs infection on B. cockerelli, transcriptomic analyses of CLs-infected and uninfected adult psyllids that were reared on potato were performed. De novo assembly of cDNA sequences generated 136,518 and 109,983 contigs for infected and uninfected insect libraries with an average contig length of 514 bp. BlastX analysis against the NCBI-nr database revealed that 33.33 % had significant matches. Gene ontology data illustrated that the majority of the expressed psyllid genes are involved in metabolic process, biological regulation, binding and catalytic activity. The psyllid transcriptome had an abundance of genes such as vitellogenin, heat shock protein, ejaculatory bulb-specific protein, ferritin, and cytochrome oxidase. Notably absent in the psyllid transcriptome were innate immunity genes induced in response to Gram-negative bacteria (IMD pathway). Several functionally diverse contigs related to symbiotic bacteria including the primary endosymbiont Carsonella ruddii, Wolbachia, and CLs in the psyllid transcriptome were identified. A total of 247 contigs showed differential expression in response to CLs infection including immune and stress-related genes and vitellogenins. Expression analyses of selected psyllid genes were performed on psyllids that were exclusively reared on potato (host of the insects used for RNAseq) and psyllids exclusively reared on tomato (alternative host of psyllids). These genes showed similar expression

  10. Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

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    Beverly E. Flood

    2016-05-01

    Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

  11. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

    Science.gov (United States)

    Flood, Beverly E.; Fliss, Palmer; Jones, Daniel S.; Dick, Gregory J.; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  12. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

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    Islam Md-Sajedul

    2012-03-01

    Full Text Available Abstract Background Huanglongbing (HLB is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida, Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. Results A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Conclusions Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a

  13. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity.

    Science.gov (United States)

    Flood, Beverly E; Fliss, Palmer; Jones, Daniel S; Dick, Gregory J; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  14. The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'

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    Migdoll Alexander M

    2008-06-01

    Full Text Available Abstract Background Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class Mollicutes (trivial name mycoplasmas and are characterized by a small genome with a low GC content, and the lack of a firm cell wall. All mycoplasmas, including strains of 'Candidatus (Ca. Phytoplasma asteris' and 'Ca. P. australiense', examined so far have circular chromosomes, as is the case for almost all walled bacteria. Results Our work has shown that 'Ca. Phytoplasma mali', the causative agent of apple proliferation disease, has a linear chromosome. Linear chromosomes were also identified in the closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'. The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a GC content of 21.4%. The chromosome is further characterized by large terminal inverted repeats and covalently closed hairpin ends. Analysis of the protein-coding genes revealed that glycolysis, the major energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in 'Ca. P. mali'. Due to the apparent lack of other metabolic pathways present in mycoplasmas, it is proposed that maltose and malate are utilized as carbon and energy sources. However, complete ATP-yielding pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P. asteris' by a smaller genome, a lower GC content, a lower number of paralogous genes, fewer insertions of potential mobile DNA elements, and a strongly reduced number of ABC transporters for amino acids. In contrast, 'Ca. P. mali' has an extended set of genes for homologous recombination, excision repair and SOS response than 'Ca. P. asteris'. Conclusion The small linear chromosome with large terminal inverted repeats and covalently closed hairpin ends, the extremely low GC content and the limited metabolic capabilities reflect unique features of 'Ca

  15. Quantitative distribution of 'Candidatus Liberibacter asiaticus' in citrus plants with citrus huanglongbing.

    Science.gov (United States)

    Li, Wenbin; Levy, Laurene; Hartung, John S

    2009-02-01

    Citrus huanglongbing (HLB), or greening disease, is strongly associated with any of three nonculturable gram-negative bacteria belonging to 'Candidatus Liberibacter spp.' 'Ca. Liberibacter spp.' are transmitted by citrus psyllids to all commercial cultivars of citrus. The diseases can be lethal to citrus and have recently become widespread in both São Paulo, Brazil, and Florida, United States, the locations of the largest citrus industries in the world. Asiatic HLB, the form of the disease found in Florida, is associated with 'Ca. Liberibacter asiaticus' and is the subject of this report. The nonculturable nature of the pathogen has hampered research and little is known about the distribution of 'Ca. L. asiaticus' in infected trees. In this study, we have used a quantitative polymerase chain reaction assay to systematically quantify the distribution of 'Ca. L. asiaticus' genomes in tissues of six species of citrus either identified in the field during survey efforts in Florida or propagated in a greenhouse in Beltsville, MD. The populations of 'Ca. L. asiaticus' inferred from the distribution of 16S rDNA sequences specific for 'Ca. L. asiaticus' in leaf midribs, leaf blades, and bark samples varied by a factor of 1,000 among samples prepared from the six citrus species tested and by a factor of 100 between two sweet orange trees tested. In naturally infected trees, above-ground portions of the tree averaged 10(10) 'Ca. L. asiaticus' genomes per gram of tissue. Similar levels of 'Ca. L. asiaticus' genomes were observed in some but not all root samples from the same plants. In samples taken from greenhouse-inoculated trees, levels of 'Ca. L. asiaticus' genomes varied systematically from 10(4) genomes/g at the graft inoculation site to 10(10) genomes/g in some leaf petioles. Root samples from these trees also contained 'Ca. L. asiaticus' at 10(7) genomes/g. In symptomatic fruit tissues, 'Ca. L. asiaticus' genomes were also readily detected and quantified. The highest

  16. Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone

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    laura eVillanueva

    2014-02-01

    Full Text Available Anaerobic ammonium oxidizing (anammox bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to Candidatus Scalindua species. Recently the genome assembly of a marine anammox enrichment culture dominated by Candidatus Scalindua profunda became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones. Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep and center (600 m area of the oxygen minimum zone in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of Candidatus Scalindua profunda served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV analysis was performed to assess diversity of the Candidatus Scalindua populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA and hydrazine dehydrogenase (scal_03295, hdh, while other genes involved in anammox metabolism (narGH, nirS, amtB, focA and ACS had a lower coverage but could still be assembled and analyzed. The results show that Candidatus Scalindua is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.

  17. Genetic variability of Rickettsia spp. in Ixodes persulcatus/Ixodes trianguliceps sympatric areas from Western Siberia, Russia: Identification of a new Candidatus Rickettsia species.

    Science.gov (United States)

    Igolkina, Yana P; Rar, Vera A; Yakimenko, Valeriy V; Malkova, Marina G; Tancev, Aleksey K; Tikunov, Artem Yu; Epikhina, Tamara I; Tikunova, Nina V

    2015-08-01

    Rickettsia spp. are the causative agents of a number of diseases in humans. These bacteria are transmitted by arthropods, including ixodid ticks. DNA of several Rickettsia spp. was identified in Ixodes persulcatus ticks, however, the association of Ixodes trianguliceps ticks with Rickettsia spp. is unknown. In our study, blood samples of small mammals (n=108), unfed adult I. persulcatus ticks (n=136), and I. persulcatus (n=12) and I. trianguliceps (n=34) ticks feeding on voles were collected in two I. persulcatus/I. trianguliceps sympatric areas in Western Siberia. Using nested PCR, ticks and blood samples were studied for the presence of Rickettsia spp. Three distinct Rickettsia species were found in ticks, but no Rickettsia species were found in the blood of examined voles. Candidatus Rickettsia tarasevichiae DNA was detected in 89.7% of unfed I. persulcatus, 91.7% of engorged I. persulcatus and 14.7% of I. trianguliceps ticks. Rickettsia helvetica DNA was detected in 5.9% of I. trianguliceps ticks. In addition, a new Rickettsia genetic variant was found in 32.4% of I. trianguliceps ticks. Sequence analysis of the 16S rRNA, gltA, ompA, оmpB and sca4 genes was performed and, in accordance with genetic criteria, a new Rickettsia genetic variant was classified as a new Candidatus Rickettsia species. We propose to name this species Candidatus Rickettsia uralica, according to the territory where this species was initially identified. Candidatus Rickettsia uralica was found to belong to the spotted fever group. The data obtained in this study leads us to propose that Candidatus Rickettsia uralica is associated with I. trianguliceps ticks.

  18. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

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    Wilhelm Larry J

    2007-11-01

    Full Text Available Abstract Background One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium SAR11 ('Candidatus Pelagibacter ubique'; strain HTCC1062, obtained from the cold, productive Oregon coast, as a query sequence to study variation in SAR11 metagenome sequence data from the Sargasso Sea, a warm, oligotrophic ocean gyre. Results The average amino acid identity of SAR11 genes encoded by the metagenomic data to the query genome was only 71%, indicating significant evolutionary divergence between the coastal isolates and Sargasso Sea populations. However, an analysis of gene neighbors indicated that SAR11 genes in the Sargasso Sea metagenomic data match the gene order of the HTCC1062 genome in 96% of cases (> 85,000 observations, and that rearrangements are most frequent at predicted operon boundaries. There were no conserved examples of genes with known functions being found in the coastal isolates, but not the Sargasso Sea metagenomic data, or vice versa, suggesting that core regions of these diverse SAR11 genomes are relatively conserved in gene content. However, four hypervariable regions were observed, which may encode properties associated with variation in SAR11 ecotypes. The largest of these, HVR2, is a 48 kb region flanked by the sole 5S and 23S genes in the HTCC1062 genome, and mainly encodes genes that determine cell surface properties. A comparison of two closely related 'Candidatus Pelagibacter' genomes (HTCC1062 and HTCC1002 revealed a number of "gene indels" in core regions. Most of these were found to be polymorphic in the metagenomic data and showed evidence of purifying selection, suggesting that the same "polymorphic gene indels" are maintained in physically isolated SAR11 populations. Conclusion These findings suggest that natural selection has conserved many core features of SAR11

  19. Candidatus Renichlamydia lutjani, a Gram-negative bacterium in internal organs of blue striped snapper Lutjanus kasmira from Hawaii.

    Science.gov (United States)

    Corsaro, Daniele; Work, Thierry M.

    2012-01-01

    The blue-striped snapper Lutjanus kasmira (Perciformes, Lutjanidae) are cosmopolitan in the Indo-Pacific but were introduced into Oahu, Hawaii, USA, in the 1950s and have since colonized most of the archipelago. Studies of microparasites in blue-striped snappers from Hawaii revealed chlamydia-like organisms (CLO) infecting the spleen and kidney, characterized by intracellular basophilic granular inclusions containing Gram-negative and Gimenez-positive bacteria similar in appearance to epitheliocysts when seen under light microscopy. We provide molecular evidence that CLO are a new member of Chlamydiae, i.e. Candidatus Renichlamydia lutjani, that represents the first reported case of chlamydial infection in organs other than the gill in fishes.

  20. Phylogeny and FISH probe analysis of the “Candidatus Competibacter”-lineage in wastewater treatment systems

    DEFF Research Database (Denmark)

    Nittami, Tadashi; McIlroy, Simon Jon; Kanai, Eri

    . This study aimed at resolving the phylogeny and reassessing FISH probes for coverage of the diversity of the lineage in EBPR systems. Analysis of the level of 16S rRNA gene sequence diversity of lineage members (> 89%) suggests that it is more appropriately viewed as a family rather than a single genus......Our understanding of the microbial ecology of enhanced biological phosphorus removal (EBPR) wastewater treatment systems has been greatly advanced through the application of molecular methods such as fluorescence in situ hybridization (FISH). Considerable attention has been directed...... the gammaproteobacterial “Candidatus Competibacter”-lineage. The group is currently delineated by 8 FISH probe defined phylotypes, although further undescribed phylogenetic diversity beyond what is covered by these probes is evident. Where studied, marked differences in physiology between members are observed, including...

  1. One carbon metabolism in SAR11 pelagic marine bacteria.

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    Jing Sun

    Full Text Available The SAR11 Alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. Their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. Here we show that conserved genes in SAR11 subgroup Ia (Candidatus Pelagibacter ubique genomes encode pathways for the oxidation of a variety of one-carbon compounds and methyl functional groups from methylated compounds. These pathways were predicted to produce energy by tetrahydrofolate (THF-mediated oxidation, but not to support the net assimilation of biomass from C1 compounds. Measurements of cellular ATP content and the oxidation of (14C-labeled compounds to (14CO(2 indicated that methanol, formaldehyde, methylamine, and methyl groups from glycine betaine (GBT, trimethylamine (TMA, trimethylamine N-oxide (TMAO, and dimethylsulfoniopropionate (DMSP were oxidized by axenic cultures of the SAR11 strain Ca. P. ubique HTCC1062. Analyses of metagenomic data showed that genes for C1 metabolism occur at a high frequency in natural SAR11 populations. In short term incubations, natural communities of Sargasso Sea microbial plankton expressed a potential for the oxidation of (14C-labeled formate, formaldehyde, methanol and TMAO that was similar to cultured SAR11 cells and, like cultured SAR11 cells, incorporated a much larger percentage of pyruvate and glucose (27-35% than of C1 compounds (2-6% into biomass. Collectively, these genomic, cellular and environmental data show a surprising capacity for demethylation and C1 oxidation in SAR11 cultures and in natural microbial communities dominated by SAR11, and support the conclusion that C1 oxidation might be a significant conduit by which dissolved organic carbon is recycled to CO(2 in the upper ocean.

  2. Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

    KAUST Repository

    Skennerton, Connor T.

    2016-04-08

    Tenericutes are a unique class of bacteria that lack a cell wall and are typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA surveys have identified a number of tenericute clades in diverse environments, introducing the possibility that these Tenericutes may represent non-host-associated, free-living microorganisms. Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes-affiliated clade currently known as \\'NB1-n\\' (SILVA taxonomy) or \\'RF3\\' (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured members of the Mollicutes, these \\'NB1-n\\' representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. Notably, the genomes also contained a number of unique metabolic features including hydrogenases and a simplified electron transport chain containing an RNF complex, cytochrome bd oxidase and complex I. On the basis of the metabolic potential predicted from the annotated genomes, we devised an anaerobic enrichment media that stimulated the growth of these Tenericutes at 10 °C, resulting in a mixed culture where these organisms represented ∼60% of the total cells by targeted fluorescence in situ hybridization (FISH). Visual identification by FISH confirmed these organisms were not directly associated with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture confirmed an ultrastructure consistent with the defining phenotypic property of Tenericutes, with a single membrane and no cell wall. On the basis of their unique gene content, phylogenetic placement and ultrastructure, we propose these organisms represent a novel class within the Tenericutes, and suggest the names Candidatus \\'Izimaplasma sp. HR1\\' and Candidatus \\'Izimaplasma sp. HR2\\' for the two genome representatives.

  3. Deciphering the bacterial microbiome of citrus plants in response to 'Candidatus Liberibacter asiaticus'-infection and antibiotic treatments.

    Directory of Open Access Journals (Sweden)

    Muqing Zhang

    Full Text Available The bacterial microbiomes of citrus plants were characterized in response to 'Candidatus Liberibacter asiaticus' (Las-infection and treatments with ampicillin (Amp and gentamicin (Gm by Phylochip-based metagenomics. The results revealed that 7,407 of over 50,000 known Operational Taxonomic Units (OTUs in 53 phyla were detected in citrus leaf midribs using the PhyloChip™ G3 array, of which five phyla were dominant, Proteobacteria (38.7%, Firmicutes (29.0%, Actinobacteria (16.1%, Bacteroidetes (6.2% and Cyanobacteria (2.3%. The OTU62806, representing 'Candidatus Liberibacter', was present with a high titer in the plants graft-inoculated with Las-infected scions treated with Gm at 100 mg/L and in the water-treated control (CK1. However, the Las bacterium was not detected in the plants graft-inoculated with Las-infected scions treated with Amp at 1.0 g/L or in plants graft-inoculated with Las-free scions (CK2. The PhyloChip array demonstrated that more OTUs, at a higher abundance, were detected in the Gm-treated plants than in the other treatment and the controls. Pairwise comparisons indicated that 23 OTUs from the Achromobacter spp. and 12 OTUs from the Methylobacterium spp. were more abundant in CK2 and CK1, respectively. Ten abundant OTUs from the Stenotrophomonas spp. were detected only in the Amp-treatment. These results provide new insights into microbial communities that may be associated with the progression of citrus huanglongbing (HLB and the potential effects of antibiotics on the disease and microbial ecology.

  4. Molecular survey of Babesia microti, Ehrlichia species and Candidatus neoehrlichia mikurensis in wild rodents from Shimane Prefecture, Japan.

    Science.gov (United States)

    Tabara, Kenji; Arai, Satoru; Kawabuchi, Takako; Itagaki, Asao; Ishihara, Chiaki; Satoh, Hiroshi; Okabe, Nobuhiko; Tsuji, Masayoshi

    2007-01-01

    A significant number of patients are diagnosed with "fevers of unknown origin" (FUO) in Shimane Prefecture in Japan where tick-borne diseases are endemic. We conducted molecular surveys for Babesia microti, Ehrlichia species, and Candidatus Neoehrlichia mikurensis in 62 FUO cases and 62 wild rodents from Shimane Prefecture, Japan. PCR using primers specific for the Babesia 18S small-subunit rRNA (rDNA) gene and Anaplasmataceae groESL amplified products from 45% (28/62) and 25.8% (16/62) of captured mice, respectively. Of the 28 18S rDNA PCR positives, 23 and five samples were positive for Hobetsu- and Kobe-type B. microti, respectively. In contrast, of the 16 groESL PCR positives, eight, one and seven samples were positive for Ehrlichia muris, Ehrlichia sp. HF565 and Candidatus N. mikurensis, respectively. Inoculation of selected blood samples into Golden Syrian hamsters indicated the presence of Hobetsu- and Kobe-type B. microti in four and one sample, respectively. Isolation of the latter strain was considered important as previous studies suggested that the distribution of this type was so far confined to Awaji Island in Hyogo Prefecture, where the first case of transfusion-associated human babesiosis originated. DNA samples from 62 FUO human cases tested negative for B. microti 18S rDNA gene, Anaplasmataceae groESL gene, Rickettsia japonica 17K genus-common antigen gene and Orientia tsutsugamushi 56K antigen gene by PCRs. We also conducted seroepidemiological surveys on 62 human sera collected in Shimane Prefecture from the FUO patients who were suspected of carrying tick-borne diseases. However, indirect immunofluorescent antibody tests using B. microti- and E. muris-infected cells detected IgG against E. muris in only a single positive sample. This study demonstrates the presence of several potentially important tick-borne pathogens in Shimane Prefecture and suggests the need for further study on the causative agents of FUOs.

  5. Ubiquity of insect-derived nitrogen transfer to plants by endophytic insect-pathogenic fungi: an additional branch of the soil nitrogen cycle.

    Science.gov (United States)

    Behie, Scott W; Bidochka, Michael J

    2014-03-01

    The study of symbiotic nitrogen transfer in soil has largely focused on nitrogen-fixing bacteria. Vascular plants can lose a substantial amount of their nitrogen through insect herbivory. Previously, we showed that plants were able to reacquire nitrogen from insects through a partnership with the endophytic, insect-pathogenic fungus Metarhizium robertsii. That is, the endophytic capability and insect pathogenicity of M. robertsii are coupled so that the fungus acts as a conduit to provide insect-derived nitrogen to plant hosts. Here, we assess the ubiquity of this nitrogen transfer in five Metarhizium species representing those with broad (M. robertsii, M. brunneum, and M. guizhouense) and narrower insect host ranges (M. acridum and M. flavoviride), as well as the insect-pathogenic fungi Beauveria bassiana and Lecanicillium lecanii. Insects were injected with (15)N-labeled nitrogen, and we tracked the incorporation of (15)N into two dicots, haricot bean (Phaseolus vulgaris) and soybean (Glycine max), and two monocots, switchgrass (Panicum virgatum) and wheat (Triticum aestivum), in the presence of these fungi in soil microcosms. All Metarhizium species and B. bassiana but not L. lecanii showed the capacity to transfer nitrogen to plants, although to various degrees. Endophytic association by these fungi increased overall plant productivity. We also showed that in the field, where microbial competition is potentially high, M. robertsii was able to transfer insect-derived nitrogen to plants. Metarhizium spp. and B. bassiana have a worldwide distribution with high soil abundance and may play an important role in the ecological cycling of insect nitrogen back to plant communities.

  6. Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from Klebsiella pneumoniae.

    Science.gov (United States)

    Burmølle, Mette; Norman, Anders; Sørensen, Søren J; Hansen, Lars Hestbjerg

    2012-01-01

    Plasmids are a highly effective means with which genetic traits that influence human health, such as virulence and antibiotic resistance, are disseminated through bacterial populations. The IncX-family is a hitherto sparsely populated group of plasmids that are able to thrive within Enterobacteriaceae. In this study, a replicon-centric screening method was used to locate strains from wastewater sludge containing plasmids belonging to the IncX-family. A transposon aided plasmid capture method was then employed to transport IncX-plasmids from their original hosts (and co-hosted plasmids) into a laboratory strain (Escherichia coli Genehogs®) for further study. The nucleotide sequences of the three newly isolated IncX-plasmids (pLN126_33, pMO17_54, pMO440_54) and the hitherto un-sequenced type-plasmid R485 revealed a remarkable occurrence of whole or partial gene cassettes that promote biofilm-formation in Klebsiella pneumonia or E. coli, in all four instances. Two of the plasmids (R485 and pLN126_33) were shown to directly induce biofilm formation in a crystal violet retention assay in E. coli. Sequence comparison revealed that all plasmid-borne forms of the type 3 fimbriae encoding gene cassette mrkABCDF were variations of a composite transposon Tn6011 first described in the E. coli IncX plasmid pOLA52. In conclusion, IncX-plasmids isolated from Enterobacteriaceae over almost 40 years and on three different continents have all been shown to carry a type 3 fimbriae gene cassette mrkABCDF stemming from pathogenic K. pneumoniae. Apart from contributing general knowledge about IncX-plasmids, this study also suggests an apparent ubiquity of a mobile form of an important virulence factor and is an illuminating example of the recruitment, evolution and dissemination of genetic traits through plasmid-mediated horizontal gene transfer.

  7. Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from Klebsiella pneumoniae.

    Directory of Open Access Journals (Sweden)

    Mette Burmølle

    Full Text Available Plasmids are a highly effective means with which genetic traits that influence human health, such as virulence and antibiotic resistance, are disseminated through bacterial populations. The IncX-family is a hitherto sparsely populated group of plasmids that are able to thrive within Enterobacteriaceae. In this study, a replicon-centric screening method was used to locate strains from wastewater sludge containing plasmids belonging to the IncX-family. A transposon aided plasmid capture method was then employed to transport IncX-plasmids from their original hosts (and co-hosted plasmids into a laboratory strain (Escherichia coli Genehogs® for further study. The nucleotide sequences of the three newly isolated IncX-plasmids (pLN126_33, pMO17_54, pMO440_54 and the hitherto un-sequenced type-plasmid R485 revealed a remarkable occurrence of whole or partial gene cassettes that promote biofilm-formation in Klebsiella pneumonia or E. coli, in all four instances. Two of the plasmids (R485 and pLN126_33 were shown to directly induce biofilm formation in a crystal violet retention assay in E. coli. Sequence comparison revealed that all plasmid-borne forms of the type 3 fimbriae encoding gene cassette mrkABCDF were variations of a composite transposon Tn6011 first described in the E. coli IncX plasmid pOLA52. In conclusion, IncX-plasmids isolated from Enterobacteriaceae over almost 40 years and on three different continents have all been shown to carry a type 3 fimbriae gene cassette mrkABCDF stemming from pathogenic K. pneumoniae. Apart from contributing general knowledge about IncX-plasmids, this study also suggests an apparent ubiquity of a mobile form of an important virulence factor and is an illuminating example of the recruitment, evolution and dissemination of genetic traits through plasmid-mediated horizontal gene transfer.

  8. 巴西柑橘黄龙病相关细菌“Candidatus Liberibacter americanus”的基因组草图序列

    Institute of Scientific and Technical Information of China (English)

    Hong Lin; Helvecio D.Coletta-Filho; Cliff S.Han; 娄兵海; Edwin L.Civerolo; Marcos A.Machado; Goutam Gupta

    2014-01-01

    Hong Lin,Helvecio D.Coletta-Filho,CliffS.Han,Binghai Lou,EdwinL.Civerolo,Marcos A.Machado,and Goutam Gupta.Draft genome sequence of"Candidatus Liberibacter americanus" bacterium associated with citrus huanglongbing in Brazil.Genome Announcements,2013,1(3):e00275-13.在此,我们报道“Candidatus Liberibacter americanus" PW_SP株系基因组草图序列.大小为1,176,071bp的基因组,G+C含量为31.6%,包含948个开放阅读框,38个tRNA,3个完整的rRNA.

  9. Complete Genome Sequences of the Obligate Symbionts “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” from the Pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae)

    Science.gov (United States)

    Abbà, Simona; Kube, Michael; Marzachì, Cristina

    2016-01-01

    Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus (Hemiptera: Cicadellidae), were fully sequenced. “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” represent two of the smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome sequences are nearly identical to strains reported from the closely related host species, M. quadrilineatus. PMID:26798106

  10. Questing Amblyomma mixtum and Haemaphysalis juxtakochi (Acari: Ixodidae) Infected with Candidatus “Rickettsia amblyommii” from the Natural Environment in Panama Canal Basin, Panama

    OpenAIRE

    D., Angélica M. Castro; S., Gleidys G. García; Dzul-Rosado, Karla; Aguilar, Ana; Castillo,Juan; Gabster, Amanda; Trejos, Diomedes; Zavala-Castro, Jorge; Bermúdez C., Sergio E.

    2015-01-01

    This work emphasizes the detection of Candidatus “Rickettsia amblyommii” in questing Haemaphysalis juxtakochi and Amblyomma mixtum. From February 2009 to December 2012, questing ticks were collected from the vegetation and leaf-litter of four protected forests and two grassy areas around the Panama Canal basin. DNA was extracted from Amblyomma mixtum, Amblyomma naponense, Amblyomma oblongoguttatum, Amblyomma pecarium, Amblyomma tapirellum, Haemaphysalis juxtakochi, and unidentified immature A...

  11. The Ubiquity of Chronic Illness.

    Science.gov (United States)

    Fonseca, Claudia; Fleischer, Soraya; Rui, Taniele

    2016-01-01

    This is a review of five different books dealing with some aspect of what might be termed a "chronic illness" - Alzheimer's disease, lupus, addiction, erectile dysfunction, and leprosy. The array of different subjects examined in these books points to the negotiable limits of this hugely open category. What exactly constitutes an "illness"? Why not use a less biomedical term instead: "disturbance", "problem", or simply "condition"? And how are we to understand "chronic" - simply as the flipside of "acute" or "curable"?

  12. ICT, ubiquity and public policy

    Directory of Open Access Journals (Sweden)

    Woo-kung Huh

    2013-06-01

    Full Text Available After decades of strong industrial growth, advanced urban economies around the world now face a range of challenges associated with the shift to a knowledge based economy and its resultant information society. Economic change, globalization, and the role of information and communication technologies (IT blend to create both distress and opportunity. The challenges all involve transition, each with costs and benefits and the power to change the nature of urban life in advanced metropolitan ar...

  13. Questioning the ubiquity of neofunctionalization.

    Directory of Open Access Journals (Sweden)

    Todd A Gibson

    2009-01-01

    Full Text Available Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of ancestral functions between gene duplicates. With protein interactions as a surrogate for protein functions, evidence of prodigious neofunctionalization and subfunctionalization has been identified in analyses of empirical protein interactions and evolutionary models of protein interactions. However, we have identified three phenomena that have contributed to neofunctionalization being erroneously identified as a significant factor in protein interaction network evolution. First, self-interacting proteins are underreported in interaction data due to biological artifacts and design limitations in the two most common high-throughput protein interaction assays. Second, evolutionary inferences have been drawn from paralog analysis without consideration for concurrent and subsequent duplication events. Third, the theoretical model of prodigious neofunctionalization is unable to reproduce empirical network clustering and relies on untenable parameter requirements. In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions.

  14. Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

    Energy Technology Data Exchange (ETDEWEB)

    Challacombe, Jean F [ORNL; Eichorst, Stephanie A [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Xie, Gary [Los Alamos National Laboratory (LANL); Kuske, Cheryl R [Los Alamos National Laboratory (LANL)

    2011-01-01

    Members of the bacterial phylum Acidobacteria are widespread in soils and sediments worldwide, and are abundant in many soils. Acidobacteria are challenging to culture in vitro, and many basic features of their biology and functional roles in the soil have not been determined. Candidatus Solibacter usitatus strain Ellin6076 has a 9.9 Mb genome that is approximately 2 5 times as large as the other sequenced Acidobacteria genomes. Bacterial genome sizes typically range from 0.5 to 10 Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Our comparative genome analyses indicate that the Ellin6076 large genome has arisen by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, and widespread small-scale gene duplications, resulting in an increased number of paralogs. Low amino acid sequence identities among functional group members, and lack of conserved gene order and orientation in regions containing similar groups of paralogs, suggest that most of the paralogs are not the result of recent duplication events. The genome sizes of additional cultured Acidobacteria strains were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 3 had larger genomes than those of subdivision 1, but none were as large as the Ellin6076 genome. The large genome of Ellin6076 may not be typical of the phylum, and encodes traits that could provide a selective metabolic, defensive and regulatory advantage in the soil environment.

  15. Convenient detection of the citrus greening (huanglongbing bacterium 'Candidatus Liberibacter asiaticus' by direct PCR from the midrib extract.

    Directory of Open Access Journals (Sweden)

    Takashi Fujikawa

    Full Text Available A phloem-limited bacterium, 'Candidatus Liberibacter asiaticus' (Las is a major pathogen of citrus greening (huanglongbing, one of the most destructive citrus diseases worldwide. The rapid identification and culling of infected trees and budwoods in quarantine are the most important control measures. DNA amplification including conventional polymerase chain reaction (PCR has commonly been used for rapid detection and identification. However, long and laborious procedures for DNA extraction have greatly reduced the applicability of this method. In this study, we found that the Las bacterial cells in the midribs of infected leaves were extracted rapidly and easily by pulverization and centrifugation with mini homogenization tubes. We also found that the Las bacterial cells in the midrib extract were suitable for highly sensitive direct PCR. The performance of direct PCR using this extraction method was not inferior to that of conventional PCR. Thus, the direct PCR method described herein is characterized by its simplicity, sensitivity, and robustness, and is applicable to quarantine testing.

  16. Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes

    Science.gov (United States)

    Haapalainen, Minna; Schott, Thomas; Thompson, Sarah M.; Smith, Grant R.; Nissinen, Anne I.; Pirhonen, Minna

    2017-01-01

    Haplotypes A and B of ‘Candidatus Liberibacter solanacearum’ (CLso) are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), were obtained from carrot psyllids (Trioza apicalis) harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species. PMID:28158295

  17. Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding

    Science.gov (United States)

    Pavlidi, Nena; Gioti, Anastasia; Wybouw, Nicky; Dermauw, Wannes; Ben-Yosef, Michael; Yuval, Boaz; Jurkevich, Edouard; Kampouraki, Anastasia; Van Leeuwen, Thomas; Vontas, John

    2017-01-01

    The olive fruit fly, Bactrocera oleae, is the most destructive pest of olive orchards worldwide. The monophagous larva has the unique capability of feeding on olive mesocarp, coping with high levels of phenolic compounds and utilizing non-hydrolyzed proteins present, particularly in the unripe, green olives. On the molecular level, the interaction between B. oleae and olives has not been investigated as yet. Nevertheless, it has been associated with the gut obligate symbiotic bacterium Candidatus Erwinia dacicola. Here, we used a B.oleae microarray to analyze the gene expression of larvae during their development in artificial diet, unripe (green) and ripe (black) olives. The expression profiles of Ca. E. dacicola were analyzed in parallel, using the Illumina platform. Several genes were found overexpressed in the olive fly larvae when feeding in green olives. Among these, a number of genes encoding detoxification and digestive enzymes, indicating a potential association with the ability of B. oleae to cope with green olives. In addition, a number of biological processes seem to be activated in Ca. E. dacicola during the development of larvae in olives, with the most notable being the activation of amino-acid metabolism. PMID:28225009

  18. Comparative transcriptional and anatomical analyses of tolerant rough lemon and susceptible sweet orange in response to 'Candidatus Liberibacter asiaticus' infection.

    Science.gov (United States)

    Fan, Jing; Chen, Chunxian; Yu, Qibin; Khalaf, Abeer; Achor, Diann S; Brlansky, Ron H; Moore, Gloria A; Li, Zheng-Guo; Gmitter, Frederick G

    2012-11-01

    Although there are no known sources of genetic resistance, some Citrus spp. are reportedly tolerant to huanglongbing (HLB), presumably caused by 'Candidatus Liberibacter asiaticus'. Time-course transcriptional analysis of tolerant rough lemon (Citrus jambhiri) and susceptible sweet orange (C. sinensis) in response to 'Ca. L. asiaticus' infection showed more genes differentially expressed in HLB-affected rough lemon than sweet orange at early stages but substantially fewer at late time points, possibly a critical factor underlying differences in sensitivity to 'Ca. L. asiaticus'. Pathway analysis revealed that stress responses were distinctively modulated in rough lemon and sweet orange. Although microscopic changes (e.g., callose deposition in sieve elements and phloem cell collapse) were found in both infected species, remarkably, phloem transport activity in midribs of source leaves in rough lemon was much less affected by HLB than in sweet orange. The difference in phloem cell transport activities is also implicated in the differential sensitivity to HLB between the two species. The results potentially lead to identification of key genes and the genetic mechanism in rough lemon to restrain disease development and maintain (or recover) phloem transport activity. These potential candidate genes may be used for improving citrus tolerance (or even resistance) to HLB by genetic engineering.

  19. rRNA operons and genome size of 'Candidatus Liberibacter americanus', a bacterium associated with citrus huanglongbing in Brazil.

    Science.gov (United States)

    Wulff, N A; Eveillard, S; Foissac, X; Ayres, A J; Bové, J-M

    2009-08-01

    Huanglongbing is one of the most severe diseases of citrus worldwide and is associated with 'Candidatus (Ca.) Liberibacter africanus' in Africa, 'Ca. Liberibacter asiaticus' in Asia and the Americas (Brazil, USA and Cuba) and 'Ca. Liberibacter americanus' (Lam) in Brazil. In the absence of axenic cultures, genetic information on liberibacters is scarce. The sequences of the entire 23S rRNA and 5S rRNA genes from Lam have now been obtained, using a consensus primer designed on known tRNAMet sequences of rhizobia. The size of the Lam genome was determined by PFGE, using Lam-infected periwinkle plants for bacterial enrichment, and was found to be close to 1.31 Mbp. In order to determine the number of ribosomal operons on the Lam genome, probes designed to detect the 16S rRNA gene and the 3' end of the 23S rRNA gene were developed and used for Southern hybridization with I-CeuI-treated genomic DNA. Our results suggest that there are three ribosomal operons in a circular genome. Lam is the first liberibacter species for which such data are available.

  20. The destructive citrus pathogen, 'Candidatus Liberibacter asiaticus' encodes a functional flagellin characteristic of a pathogen-associated molecular pattern.

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    Huasong Zou

    Full Text Available Huanglongbing (HLB is presently the most devastating citrus disease worldwide. As an intracellular plant pathogen and insect symbiont, the HLB bacterium, 'Candidatus Liberibacter asiaticus' (Las, retains the entire flagellum-encoding gene cluster in its significantly reduced genome. Las encodes a flagellin and hook-associated protein (Fla of 452 amino acids that contains a conserved 22 amino acid domain (flg22 at positions 29 to 50 in the N-terminus. The phenotypic alteration in motility of a Sinorhizobium meliloti mutant lacking the fla genes was partially restored by constitutive expression of Fla(Las. Agrobacterium-mediated transient expression in planta revealed that Fla(Las induced cell death and callose deposition in Nicotiana benthamiana, and that the transcription of BAK1 and SGT1, which are associated with plant innate immunity, was upregulated. Amino acid substitution experiments revealed that residues 38 (serine and 39 (aspartate of Fla(Las were essential for callose induction. The synthetic flg22(Las peptide could not induce plant cell death but retained the ability to induce callose deposition at a concentration of 20 µM or above. This demonstrated that the pathogen-associated molecular pattern (PAMP activity of flg22 in Las was weaker than those in other well-studied plant pathogenic bacteria. These results indicate that Fla(Las acts as a PAMP and may play an important role in triggering host plant resistance to the HLB bacteria.

  1. The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" encodes an afp-like prophage possibly used for protein secretion.

    Science.gov (United States)

    Penz, Thomas; Horn, Matthias; Schmitz-Esser, Stephan

    2010-01-01

    The recently sequenced genome of the obligate intracellular amoeba symbiont 'Candidatus Amoebophilus asiaticus' is unique among prokaryotic genomes due to its extremely large fraction of genes encoding proteins harboring eukaryotic domains such as ankyrin-repeats, TPR/SEL1 repeats, leucine-rich repeats, as well as F- and U-box domains, most of which likely serve in the interaction with the amoeba host. Here we provide evidence for the presence of additional proteins which are presumably presented extracellularly and should thus also be important for host cell interaction. Surprisingly, we did not find homologues of any of the well-known protein secretion systems required to translocate effector proteins into the host cell in the A. asiaticus genome, and the type six secretion systems seems to be incomplete. Here we describe the presence of a putative prophage in the A. asiaticus genome, which shows similarity to the antifeeding prophage from the insect pathogen Serratia entomophila. In S. entomophila this system is used to deliver toxins into insect hosts. This putative antifeeding-like prophage might thus represent the missing protein secretion apparatus in A. asiaticus.

  2. Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding

    Science.gov (United States)

    Pavlidi, Nena; Gioti, Anastasia; Wybouw, Nicky; Dermauw, Wannes; Ben-Yosef, Michael; Yuval, Boaz; Jurkevich, Edouard; Kampouraki, Anastasia; van Leeuwen, Thomas; Vontas, John

    2017-02-01

    The olive fruit fly, Bactrocera oleae, is the most destructive pest of olive orchards worldwide. The monophagous larva has the unique capability of feeding on olive mesocarp, coping with high levels of phenolic compounds and utilizing non-hydrolyzed proteins present, particularly in the unripe, green olives. On the molecular level, the interaction between B. oleae and olives has not been investigated as yet. Nevertheless, it has been associated with the gut obligate symbiotic bacterium Candidatus Erwinia dacicola. Here, we used a B.oleae microarray to analyze the gene expression of larvae during their development in artificial diet, unripe (green) and ripe (black) olives. The expression profiles of Ca. E. dacicola were analyzed in parallel, using the Illumina platform. Several genes were found overexpressed in the olive fly larvae when feeding in green olives. Among these, a number of genes encoding detoxification and digestive enzymes, indicating a potential association with the ability of B. oleae to cope with green olives. In addition, a number of biological processes seem to be activated in Ca. E. dacicola during the development of larvae in olives, with the most notable being the activation of amino-acid metabolism.

  3. Prevalence of Candidatus Erwinia dacicola in wild and laboratory olive fruit fly populations and across developmental stages.

    Science.gov (United States)

    Estes, Anne M; Hearn, David J; Burrack, Hannah J; Rempoulakis, Polychronis; Pierson, Elizabeth A

    2012-04-01

    The microbiome of the olive fruit fly, Bactrocera oleae (Gmelin), a worldwide pest of olives (Olea europaea L.), has been examined for >100 yr as part of efforts to identify bacteria that are plant pathogens vectored by the fly or are beneficial endosymbionts essential for the fly's survival and thus targets for possible biological control. Because tephritid fruit flies feed on free-living bacteria in their environment, distinguishing between the transient, acquired bacteria of their diet and persistent, resident bacteria that are vertically transmitted endosymbionts is difficult. Several culture-dependent and -independent studies have identified a diversity of species in the olive fruit fly microbiome, but they have not distinguished the roles of the microbes. Candidatus Erwinia dacicola, has been proposed to be a coevolved endosymbiont of the olive fruit fly; however, this was based on limited samples from two Italian populations. Our study shows that C. Erwinia dacicola was present in all New and Old World populations and in the majority of individuals of all life stages sampled in 2 yr. Olive fruit flies reared on olives in the laboratory had frequencies of C. Erwinia dacicola similar to that of wild populations; however, flies reared on artificial diets containing antibiotics in the laboratory rarely had the endosymbiont. The relative abundance of C. Erwinia dacicola varied across development stages, being most abundant in ovipositing females and larvae. This uniform presence of C. Erwini dacicola suggests that it is a persistent, resident endosymbiont of the olive fruit fly.

  4. Extraction of DNA from orange juice, and detection of bacterium Candidatus Liberibacter asiaticus by real-time PCR.

    Science.gov (United States)

    Bai, Jinhe; Baldwin, Elizabeth; Liao, Hui-Ling; Zhao, Wei; Kostenyuk, Igor; Burns, Jacqueline; Irey, Mike

    2013-10-01

    Orange juice processed from Huanglongbing (HLB) affected fruit is often associated with bitter taste and/or off-flavor. HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacterium. The current standard to confirm CLas for citrus trees is to take samples from midribs of leaves, which are rich in phloem tissues, and use a quantitative real-time polymerase chain reaction (qPCR) test to detect the 16S rDNA gene of CLas. It is extremely difficult to detect CLas in orange juice because of the low CLas population, high sugar and pectin concentration, low pH, and possible existence of an inhibitor to DNA amplification. The objective of this research was to improve extraction of DNA from orange juice and detection of CLas by qPCR. Homogenization using a sonicator increased DNA yield by 86% in comparison to mortar and pestle extraction. It is difficult to separate DNA from pectin; however, DNA was successfully extracted by treating the juice with pectinase. Application of an elution column successfully removed the unidentified inhibitor to DNA amplification. This work provided a protocol to extract DNA from whole orange juice and detect CLas in HLB-affected fruit.

  5. Description of Hyalodiscus flabellus sp. nov. (Vampyrellida, Rhizaria) and Identification of its Bacterial Endosymbiont, "Candidatus Megaira polyxenophila" (Rickettsiales, Alphaproteobacteria).

    Science.gov (United States)

    Hess, Sebastian

    2017-02-01

    The genus Hyalodiscus Hertwig and Lesser, 1874 comprises naked freshwater amoebae with a unique set of characters, namely a vibrant orange-red colour, a discoid or fan-shaped morphology, and a characteristic rolling locomotion. Some species feed on the chloroplasts of green algae and were regarded as relatives of Vampyrella Cienkowski, 1865. However, because of striking morphological differences and the lack of molecular data, the exact relationship of Hyalodiscus to vampyrellids is still obscure. Here, I describe Hyalodiscus flabellus sp. nov., a bright orange, fan-shaped amoeba feeding on Oedogonium (Chlorophyceae), which likely is a close relative of the type species H. rubicundus Hertwig and Lesser, 1874. Sequence comparisons of the SSU rRNA gene revealed that H. flabellus belongs to a deep-branching, so far uncharacterised lineage of the order Vampyrellida (Rhizaria), here defined as family Hyalodiscidae POCHE, 1913. Based on these results, the systematic position of the genus Hyalodiscus could be finally clarified, accompanied by the revision of relevant diagnoses and a taxonomic summary. Furthermore, the work reports on endosymbiotic bacteria inhabiting the cytoplasm of H. flabellus, which were identified as "Candidatus Megaira polyxenophila" (Rickettsiales, Alphaproteobacteria) using the full cycle rRNA approach with newly designed FISH probes for this widespread endosymbiotic bacterium.

  6. "Candidatus Bacilloplasma," a novel lineage of Mollicutes associated with the hindgut wall of the terrestrial isopod Porcellio scaber (Crustacea: Isopoda).

    Science.gov (United States)

    Kostanjsek, Rok; Strus, Jasna; Avgustin, Gorazd

    2007-09-01

    Pointed, rod-shaped bacteria colonizing the cuticular surface of the hindgut of the terrestrial isopod crustacean Porcellio scaber (Crustacea: Isopoda) were investigated by comparative 16S rRNA gene sequence analysis and electron microscopy. The results of phylogenetic analysis, and the absence of a cell wall, affiliated these bacteria with the class Mollicutes, within which they represent a novel and deeply branched lineage, sharing less than 82.6% sequence similarity to known Mollicutes. The lineage has been positioned as a sister group to the clade comprising the Spiroplasma group, the Mycoplasma pneumoniae group, and the Mycoplasma hominis group. The specific signature sequence was identified and used as a probe in in situ hybridization, which confirmed that the retrieved sequences originate from the attached rod-shaped bacteria from the hindgut of P. scaber and made it possible to detect these bacteria in their natural environment. Scanning and transmission electron microscopy revealed a spherically shaped structure at the tapered end of the rod-shaped bacteria, enabling their specific and exclusive attachment to the tip of the cuticular spines on the inner surface of the gut. Specific adaptation to the gut environment, as well as phylogenetic positioning, indicate the long-term association and probable coevolution of the bacteria and the host. Taking into account their pointed, rod-shaped morphology and their phylogenetic position, the name "Candidatus Bacilloplasma" has been proposed for this new lineage of bacteria specifically associated with the gut surface of P. scaber.

  7. Metabolic Response of “Candidatus Accumulibacter Phosphatis” Clade II C to Changes in Influent P/C Ratio

    Science.gov (United States)

    Welles, Laurens; Abbas, Ben; Sorokin, Dimitry Y.; Lopez-Vazquez, Carlos M.; Hooijmans, Christine M.; van Loosdrecht, Mark C. M.; Brdjanovic, Damir

    2017-01-01

    The objective of this study was to investigate the ability of a culture highly enriched with the polyphosphate-accumulating organism, “Candidatus Accumulibacter phosphatis” clade IIC, to adjust their metabolism to different phosphate availabilities. For this purpose the biomass was cultivated in a sequencing batch reactor with acetate and exposed to different phosphate/carbon influent ratios during six experimental phases. Activity tests were conducted to determine the anaerobic kinetic and stoichiometric parameters as well as the composition of the microbial community. Increasing influent phosphate concentrations led to increased poly-phosphate content and decreased glycogen content of the biomass. In response to higher biomass poly-phosphate content, the biomass showed higher specific phosphate release rates. Together with the phosphate release rates, acetate uptake rates also increased up to an optimal poly-phosphate/glycogen ratio of 0.3 P-mol/C-mol. At higher poly-phosphate/glycogen ratios (obtained at influent P/C ratios above 0.051 P-mol/C-mol), the acetate uptake rates started to decrease. The stoichiometry of the anaerobic conversions clearly demonstrated a metabolic shift from a glycogen dominated to a poly-phosphate dominated metabolism as the biomass poly-phosphate content increased. FISH and DGGE analyses confirmed that no significant changes occurred in the microbial community, suggesting that the changes in the biomass activity were due to different metabolic behavior, allowing the organisms to proliferate under conditions with fluctuating phosphate levels. PMID:28111570

  8. Population genetic analysis reveals a low level of genetic diversity of 'Candidatus Phytoplasma aurantifolia' causing witches' broom disease in lime.

    Science.gov (United States)

    Al-Abadi, Shaikha Y; Al-Sadi, Abdullah M; Dickinson, Matthew; Al-Hammadi, Mohammed S; Al-Shariqi, Rashid; Al-Yahyai, Rashid A; Kazerooni, Elham A; Bertaccini, Assunta

    2016-01-01

    Witches' broom disease of lime (WBDL) is a serious phytoplasma disease of acid lime in Oman, the UAE and Iran. Despite efforts to study it, no systemic study attempted to characterize the relationship among the associated phytoplasma, 'Candidatus Phytoplasma aurantifolia', from the three countries. This study utilized sequences of the 16S rRNA, imp and secA genes to characterize 57 strains collected from Oman (38), the UAE (9) and Iran (10). Phylogenetic analysis based on the 16S rRNA gene showed that the 57 strains shared 98.5-100 % nucleotide similarity to each other and to strains of 'Ca. P. aurantifolia' available in GenBank. The level of genetic diversity was low based on the 16S rRNA (0-0.011), imp (0-0.002) and secA genes (0-0.015). The presence of low level of diversity among phytoplasma strains from Oman, the UAE and Iran can be explained by the movement of infected lime seedlings from one country to another through trading and exchange of infected plants. The study discusses implication of the findings on WBDL spread and management.

  9. The olive fly endosymbiont, "Candidatus Erwinia dacicola," switches from an intracellular existence to an extracellular existence during host insect development.

    Science.gov (United States)

    Estes, Anne M; Hearn, David J; Bronstein, Judith L; Pierson, Elizabeth A

    2009-11-01

    As polyphagous, holometabolous insects, tephritid fruit flies (Diptera: Tephritidae) provide a unique habitat for endosymbiotic bacteria, especially those microbes associated with the digestive system. Here we examine the endosymbiont of the olive fly [Bactrocera oleae (Rossi) (Diptera: Tephritidae)], a tephritid of great economic importance. "Candidatus Erwinia dacicola" was found in the digestive systems of all life stages of wild olive flies from the southwestern United States. PCR and microscopy demonstrated that "Ca. Erwinia dacicola" resided intracellularly in the gastric ceca of the larval midgut but extracellularly in the lumen of the foregut and ovipositor diverticulum of adult flies. "Ca. Erwinia dacicola" is one of the few nonpathogenic endosymbionts that transitions between intracellular and extracellular lifestyles during specific stages of the host's life cycle. Another unique feature of the olive fly endosymbiont is that unlike obligate endosymbionts of monophagous insects, "Ca. Erwinia dacicola" has a G+C nucleotide composition similar to those of closely related plant-pathogenic and free-living bacteria. These two characteristics of "Ca. Erwinia dacicola," the ability to transition between intracellular and extracellular lifestyles and a G+C nucleotide composition similar to those of free-living relatives, may facilitate survival in a changing environment during the development of a polyphagous, holometabolous host. We propose that insect-bacterial symbioses should be classified based on the environment that the host provides to the endosymbiont (the endosymbiont environment).

  10. Spatiotemporal distribution of the magnetotactic multicellular prokaryote Candidatus Magnetoglobus multicellularis in a Brazilian hypersaline lagoon and in microcosms.

    Science.gov (United States)

    Martins, Juliana L; Silveira, Thais S; Abreu, Fernanda; de Almeida, Fernando P; Rosado, Alexandre S; Lins, Ulysses

    2012-09-01

    Candidatus Magnetoglobus multicellularis is an unusual morphotype of magnetotactic prokaryotes. These microorganisms are composed of a spherical assemblage of gram-negative prokaryotic cells capable of swimming as a unit aligned along a magnetic field. While they occur in many aquatic habitats around the world, high numbers of Ca. M. multicellularis have been detected in Araruama Lagoon, a large hypersaline lagoon near the city of Rio de Janeiro, in Brazil. Here, we report on the spatiotemporal distribution of one such population in sediments of Araruama Lagoon, including its annual distribution and its abundance compared with the total bacterial community. In microcosm experiments, Ca. M. multicellularis was unable to survive for more than 45 days: the population density gradually decreased coinciding with a shift to the upper layers of the sediment. Nonetheless, Ca. M. multicellularis was detected throughout the year in all sites studied. Changes in the population density seemed to be related to the input of organic matter as well as to salinity. The population density of Ca. M. multicellularis did not correlate with the total bacterial counts; instead, changes in the microbial community structure altered their counts in the environment.

  11. Candidatus Phytoplasma brasiliense associado ao superbrotamento do hibisco (Hibiscus rosa-sinensis L. no Estado de São Paulo Candidatus Phytoplasma brasiliense associated with hibiscus witches' broom in the State of São Paulo-Brazil

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    Eliane Gonçalves da Silva

    2009-09-01

    Full Text Available Plantas de hibisco com superbrotamento e definhamento seguido de morte têm sido observadas nos municípios de São Paulo, Campinas e Piracicaba. Como os sintomas são sugestivos daqueles induzidos por fitoplasmas, o presente trabalho buscou identificar o possível fitoplasma associado com a doença. Assim, 14 plantas sintomáticas de hibisco foram coletadas em Piracicaba (SP e submetidas ao PCR duplo com os primers P1/Tint-R16F2n/R2 e ao exame em microscópio eletrônico de transmissão. A identificação foi realizada por análise de RFLP com as enzimas de restrição BfaI, DraI, HaeIII, HhaI, HpaII, MboI, MseI, RsaI e TaqI. Testes de transmissão foram conduzidos com enxertia de ramos e uso de Cuscuta subinclusa. Os resultados de nested-PCR revelaram a presença consistente de fitoplasmas em todas as plantas sintomáticas e foram confirmados pela observação de corpúsculos pleomórficos no floema, através da microscopia eletrônica. A análise de RFLP mostrou que o fitoplasma encontrado em hibisco pertence ao grupo 16SrXV, o mesmo grupo do Candidatus Phytoplasma brasiliense. O fitoplasma foi transmitido de planta doente para sadia, tanto pela enxertia como pela C. subinclusa, demonstrando ser o agente do superbrotamento do hibisco.Ornamental hibiscus have been affected by shoot proliferation and decline followed by death in several cities in São Paulo State, especially São Paulo, Campinas and Piracicaba. As the symptoms are suggestives of those induced by phytoplasmas, the present work aimed to identify the possible phytoplasma associated with the disease. Fourteen symptomatic hibiscus were sampled in Piracicaba, submitted to nested-PCR with the primers P1/Tint-R16F2n/R2 and processed by transmission electron microscopy. The identification was made by RFLP analyses with the restriction enzymes BfaI, DraI, HaeIII, HhaI, HpaII, MboI, MseI, RsaI, and TaqI. Transmission assays were performed by grafting and Cuscuta subinclusa. The presence

  12. How clonal is clonal? Genome plasticity across multicellular segments of a "Candidatus Marithrix sp." filament from sulfidic, briny seafloor sediments in the Gulf of Mexico

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    Verena Salman-Carvalho

    2016-08-01

    Full Text Available Candidatus Marithrix is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria. This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, Candidatus Marithrix was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the Candidatus Marithrix genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

  13. Phylogenetic analysis identifies a 'Candidatus Phytoplasma oryzae'-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India.

    Science.gov (United States)

    Ramaswamy, Manimekalai; Nair, Smita; Soumya, V P; Thomas, George V

    2013-04-01

    Yellow leaf disease (YLD) with phytoplasmal aetiology is a serious disease of arecanut palm in India. The present study was undertaken to characterize the 16S rRNA and secA gene sequences of the Indian arecanut YLD phytoplasma for 'Candidatus Phytoplasma' species assignment and 16Sr group/subgroup classification. Phytoplasma 16S rRNA genes were amplified using three sets of semi-nested/nested primers, 1F7/7R3-1F7/7R2, 4Fwd/3Rev-4Fwd/5Rev and P1/P7-R16F2n/R16R2, producing amplicons of 491, 1150 and 1250 bp, respectively, from diseased samples. The amplicons were cloned and sequenced. A blast search showed that the sequences had 99 % similarity with sugar cane white leaf phytoplasma (16SrXI) and Napier grass stunt phytoplasma (16SrXI). Phylogenetic analysis based on the 16S rRNA gene revealed the clustering of YLD phytoplasma with the rice yellow dwarf and Bermuda grass white leaf groups. The YLD phytoplasma F2nR2 sequence shared 97.5 % identity with that of 'Candidatus Phytoplasma oryzae' and 97.8 % identity with that of 'Candidatus Phytoplasma cynodontis'. Hence, for finer differentiation, we examined the secA gene-based phylogeny, where the YLD phytoplasma clustered with Napier grass stunt and sugar cane grassy shoot phytoplasmas, both belonging to the rice yellow dwarf group. Hence, we are assigning the Indian arecanut YLD phytoplasma as a 'Candidatus Phytoplasma oryzae'-related strain. Virtual RFLP analysis of a 1.2 kb fragment of the 16S rRNA gene (F2nR2 region) identified the Indian arecanut YLD phytoplasma as a member of 16SrXI-B subgroup. We name the phytoplasma Indian yellow leaf disease phytoplasma, to differentiate it from the Hainan YLD phytoplasma, which belongs to group 16SrI.

  14. Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera".

    Science.gov (United States)

    Rasigraf, Olivia; Kool, Dorien M; Jetten, Mike S M; Sinninghe Damsté, Jaap S; Ettwig, Katharina F

    2014-04-01

    Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "Candidatus Methylomirabilis oxyfera" is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase reaction. Previous genome analysis has suggested that, like the verrucomicrobial methanotrophs, "Ca. Methylomirabilis oxyfera" encodes and transcribes genes for the Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. Here we provide multiple independent lines of evidence for autotrophic carbon dioxide fixation by "Ca. Methylomirabilis oxyfera" via the CBB cycle. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme of the CBB cycle, in cell extracts from an "Ca. Methylomirabilis oxyfera" enrichment culture was shown to account for up to 10% of the total methane oxidation activity. Labeling studies with whole cells in batch incubations supplied with either (13)CH4 or [(13)C]bicarbonate revealed that "Ca. Methylomirabilis oxyfera" biomass and lipids became significantly more enriched in (13)C after incubation with (13)C-labeled bicarbonate (and unlabeled methane) than after incubation with (13)C-labeled methane (and unlabeled bicarbonate), providing evidence for autotrophic carbon dioxide fixation. Besides this experimental approach, detailed genomic and transcriptomic analysis demonstrated an operational CBB cycle in "Ca. Methylomirabilis oxyfera." Altogether, these results show that the CBB cycle is active and plays a major role in carbon assimilation by "Ca. Methylomirabilis oxyfera" bacteria. Our results suggest that autotrophy might be more widespread among methanotrophs than was previously assumed and implies that a methanotrophic

  15. Candidatus Gortzia shahrazadis”, a novel endosymbiont of Paramecium multimicronucleatum and a revision of the biogeographical distribution of Holospora-like bacteria

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    Valentina Serra

    2016-11-01

    Full Text Available Holospora spp. and Candidatus Gortzia infectiva, known as Holospora-like bacteria (HLB, are commonly found as nuclear endosymbionts of ciliates, especially the Paramecium genus. HLB are related by phylogenetic relationships, morphological features, and life cycles, which involve two alternating morphotypes: reproductive and infectious forms (RF, IF. In this paper we describe a novel species belonging to the Ca. Gortzia genus, detected in P. multimicronucleatum, a ciliate for which infection by an HLB has not been reported, discovered in India. This novel endosymbiont shows unusual and surprising features with respect to other HLB, such as large variations in IF morphology and the occasional ability to reproduce in the host cytoplasm. We propose the name of Candidatus Gortzia shahrazadis for this novel HLB . Moreover, we report two additional species of HLB from Indian Paramecium populations: Ca. Gortzia infectiva (from P. jenningsi, and H. obtusa (from P. caudatum; the latter is the first record of Holospora from a tropical country. Although tropical, we retrieved H. obtusa at an elevation of 706 m. corresponding to a moderate climate not unlike conditions where Holospora are normally found, suggesting the genus Holospora does exist in tropical countries, but restricted to higher elevations.

  16. Predominance of Single Prophage Carrying a CRISPR/cas System in "Candidatus Liberibacter asiaticus" Strains in Southern China.

    Science.gov (United States)

    Zheng, Zheng; Bao, Minli; Wu, Fengnian; Chen, Jianchi; Deng, Xiaoling

    2016-01-01

    "Candidatus Liberibacter asiaticus" (CLas) is an uncultureable α-proteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease), a highly destructive disease affecting citrus production worldwide. HLB was observed in Guangdong Province of China over a hundred years ago and remains endemic there. Little is known about CLas biology due to its uncultureable nature. This study began with the genome sequence analysis of CLas Strain A4 from Guangdong in the prophage region. Within the two currently known prophage types, Type 1 (SC1-like) and Type 2 (SC2-like), A4 genome contained only a Type 2 prophage, CGdP2, namely. An analysis on CLas strains collected in Guangdong showed that Type 2 prophage dominated the bacterial population (82.6%, 71/86). An extended survey covering five provinces in southern China also revealed the predominance of single prophage (Type 1 or Type 2) in the CLas population (90.4%, 169/187). CLas strains with two and no prophage types accounted for 7.2% and 2.8%, respectively. In silico analyses on CGdP2 identified a CRISPR (clustered regularly interspaced short palindromic repeats)/cas (CRISPR-associated protein genes) system, consisting of four 22 bp repeats, three 23 bp spacers and 9 predicted cas. Similar CRISPR/cas systems were detected in all 10 published CLas prophages as well as 13 CLas field strains in southern China. Both Type 1 and Type 2 prophages shared almost identical sequences in spacer 1 and 3 but not spacer 2. Considering that the function of a CRISPR/cas system was to destroy invading DNA, it was hypothesized that a pre-established CLas prophage could use its CRISPR/cas system guided by spacer 1 and/or 3 to defeat the invasion of the other phage/prophage. This hypothesis explained the predominance of single prophage type in the CLas population in southern China. This is the first report of CRISPR/cas system in the "Ca. Liberibacter" genera.

  17. Predominance of Single Prophage Carrying a CRISPR/cas System in "Candidatus Liberibacter asiaticus" Strains in Southern China.

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    Zheng Zheng

    Full Text Available "Candidatus Liberibacter asiaticus" (CLas is an uncultureable α-proteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease, a highly destructive disease affecting citrus production worldwide. HLB was observed in Guangdong Province of China over a hundred years ago and remains endemic there. Little is known about CLas biology due to its uncultureable nature. This study began with the genome sequence analysis of CLas Strain A4 from Guangdong in the prophage region. Within the two currently known prophage types, Type 1 (SC1-like and Type 2 (SC2-like, A4 genome contained only a Type 2 prophage, CGdP2, namely. An analysis on CLas strains collected in Guangdong showed that Type 2 prophage dominated the bacterial population (82.6%, 71/86. An extended survey covering five provinces in southern China also revealed the predominance of single prophage (Type 1 or Type 2 in the CLas population (90.4%, 169/187. CLas strains with two and no prophage types accounted for 7.2% and 2.8%, respectively. In silico analyses on CGdP2 identified a CRISPR (clustered regularly interspaced short palindromic repeats/cas (CRISPR-associated protein genes system, consisting of four 22 bp repeats, three 23 bp spacers and 9 predicted cas. Similar CRISPR/cas systems were detected in all 10 published CLas prophages as well as 13 CLas field strains in southern China. Both Type 1 and Type 2 prophages shared almost identical sequences in spacer 1 and 3 but not spacer 2. Considering that the function of a CRISPR/cas system was to destroy invading DNA, it was hypothesized that a pre-established CLas prophage could use its CRISPR/cas system guided by spacer 1 and/or 3 to defeat the invasion of the other phage/prophage. This hypothesis explained the predominance of single prophage type in the CLas population in southern China. This is the first report of CRISPR/cas system in the "Ca. Liberibacter" genera.

  18. Comparative Transcriptome and iTRAQ Proteome Analyses of Citrus Root Responses to Candidatus Liberibacter asiaticus Infection.

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    Yun Zhong

    Full Text Available Root samples of 'Sanhu' red tangerine trees infected with and without Candidatus Liberibacter asiaticus (CLas were collected at 50 days post inoculation and subjected to RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ to profile the differentially expressed genes (DEGs and proteins (DEPs, respectively. Quantitative real-time PCR was subsequently used to confirm the expression of 16 selected DEGs. Results showed that a total of 3956 genes and 78 proteins were differentially regulated by HLB-infection. Among the most highly up-regulated DEPs were sperm specific protein 411, copper ion binding protein, germin-like proteins, subtilisin-like proteins and serine carboxypeptidase-like 40 proteins whose transcript levels were concomitantly up-regulated as shown by RNA-seq data. Comparison between our results and those of the previously reported showed that known HLB-modulated biological pathways including cell-wall modification, protease-involved protein degradation, carbohydrate metabolism, hormone synthesis and signaling, transcription activities, and stress responses were similarly regulated by HLB infection but different or root-specific changes did exist. The root unique changes included the down-regulation in genes of ubiquitin-dependent protein degradation pathway, secondary metabolism, cytochrome P450s, UDP-glucosyl transferases and pentatricopeptide repeat containing proteins. Notably, nutrient absorption was impaired by HLB-infection as the expression of the genes involved in Fe, Zn, N and P adsorption and transportation were significantly changed. HLB-infection induced some cellular defense responses but simultaneously reduced the biosynthesis of the three major classes of secondary metabolites, many of which are known to have anti-pathogen activities. Genes involved in callose deposition were up-regulated whereas those involved in callose degradation were also up-regulated, indicating that the sieve tube

  19. "Candidatus Phlomobacter fragariae" Is the Prevalent Agent of Marginal Chlorosis of Strawberry in French Production Fields and Is Transmitted by the Planthopper Cixius wagneri (China).

    Science.gov (United States)

    Danet, Jean-Luc; Foissac, Xavier; Zreik, Leyla; Salar, Pascal; Verdin, Eric; Nourrisseau, Jean-Georges; Garnier, Monique

    2003-06-01

    ABSTRACT Marginal chlorosis has affected strawberry production in France for about 15 years. A phloem-restricted uncultured bacterium, "Candidatus Phlomobacter fragariae," is associated with the disease. A large-scale survey for marginal chlorosis in French strawberry production fields and nurseries by polymerase chain reaction amplification of "Ca. P. fragariae" 16S rDNA revealed that symptoms of marginal chlorosis were not always induced by "Ca. P. fragariae" and that the stolbur phytoplasma could induce identical symptoms. "Ca. P. fragariae" was found to be predominant in strawberry production fields, whereas the stolbur phytoplasma was predominantly detected in nurseries. Two transmission periods of the disease, one in spring and the other from late summer to early fall, were evident. Cixius wagneri planthoppers captured on infected strawberry plants were demonstrated to be efficient vectors of "Ca. P. fragariae." The involvement in natural disease spread of the whitefly Trialeurodes vaporariorum, previously shown to acquire and multiply "Ca. P. fragariae" under greenhouse conditions, remains uncertain.

  20. Questing Amblyomma mixtum and Haemaphysalis juxtakochi (Acari: Ixodidae) Infected with Candidatus "Rickettsia amblyommii" from the Natural Environment in Panama Canal Basin, Panama.

    Science.gov (United States)

    D, Angélica M Castro; S, Gleidys G García; Dzul-Rosado, Karla; Aguilar, Ana; Castillo, Juan; Gabster, Amanda; Trejos, Diomedes; Zavala-Castro, Jorge; Bermúdez C, Sergio E

    2015-12-01

    This work emphasizes the detection of Candidatus "Rickettsia amblyommii" in questing Haemaphysalis juxtakochi and Amblyomma mixtum. From February 2009 to December 2012, questing ticks were collected from the vegetation and leaf-litter of four protected forests and two grassy areas around the Panama Canal basin. DNA was extracted from Amblyomma mixtum, Amblyomma naponense, Amblyomma oblongoguttatum, Amblyomma pecarium, Amblyomma tapirellum, Haemaphysalis juxtakochi, and unidentified immature Amblyomma. Specific primers of citrate synthase gene gltA were used to detect and identify the rickettsiae. Amplicons with the expected band size were purified and sequenced. DNA of C. "R. amblyommii" was found in A. mixtum, H. juxtakochi and Amblyomma immatures. To our knowledge, these finding represent the first report of C. "R. amblyommii" in free-living ticks in the wilderness of Central America.

  1. The Mitochondrial Genomes of the Zoonotic Canine Filarial Parasites Dirofilaria (Nochtiella) repens and Candidatus Dirofilaria (Nochtiella) Honkongensis Provide Evidence for Presence of Cryptic Species

    Science.gov (United States)

    Yilmaz, Esra; Fritzenwanker, Moritz; Pantchev, Nikola; Lendner, Mathias; Wongkamchai, Sirichit; Otranto, Domenico; Kroidl, Inge; Dennebaum, Martin; Le, Thanh Hoa; Anh Le, Tran; Ramünke, Sabrina; Schaper, Roland; von Samson-Himmelstjerna, Georg; Poppert, Sven; Krücken, Jürgen

    2016-01-01

    Background Cutaneous dirofilariosis is a canine mosquito-borne zoonosis that can cause larva migrans disease in humans. Dirofilaria repens is considered an emerging pathogen occurring with high prevalence in Mediterranean areas and many parts of tropical Asia. In Hong Kong, a second species, Candidatus Dirofilaria hongkongensis, has been reported. The present study aimed to compare mitochondrial genomes from these parasites and to obtain population genetic information. Methods and Findings Complete mitochondrial genomes were obtained by PCR and Sanger sequencing or ILLUMINA sequencing for four worms. Cytochrome oxidase subunit 1 sequences identified three as D. repens (all from Europe) and one as C. D. hongkongensis (from India). Mitochondrial genomes have the same organization as in other spirurid nematodes but a higher preference for thymine in the coding strand. Phylogenetic analysis was in contradiction to current taxonomy of the Onchocercidae but in agreement with a recent multi-locus phylogenetic analysis using both mitochondrial and nuclear markers. D. repens and C. D. hongkongensis sequences clustered together and were the common sister group to Dirofilaria immitis. Analysis of a 2.5 kb mitochondrial genome fragment from macrofilaria or canine blood samples from Europe (42), Thailand (2), India (1) and Vietnam (1) revealed only small genetic differences in the D. repens samples including all European and the Vietnam sample. The Indian C. D. hongkongensis and the two Thai samples formed separate clusters and differences were comparatively large. Conclusion Genetic differences between Dirofilaria spp. causing cutaneous disease can be considerable whereas D. repens itself was genetically quite homogenous. C. D. hongkongensis was identified for the first time from the Indian subcontinent. The full mitochondrial genome sequence strengthens the hypothesis that it represents an independent species and the Thai samples might represent another cryptic species

  2. Pattern of association between endemic Hawaiian fruit flies (Diptera, Tephritidae) and their symbiotic bacteria: Evidence of cospeciation events and proposal of "Candidatus Stammerula trupaneae".

    Science.gov (United States)

    Viale, E; Martinez-Sañudo, I; Brown, J M; Simonato, M; Girolami, V; Squartini, A; Bressan, A; Faccoli, M; Mazzon, L

    2015-09-01

    Several insect lineages have evolved mutualistic association with symbiotic bacteria. This is the case of some species of mealybugs, whiteflies, weevils, tsetse flies, cockroaches, termites, carpenter ants, aphids and fruit flies. Some species of Tephritinae, the most specialized subfamily of fruit flies (Diptera: Tephritidae), harbour co-evolved vertically transmitted, bacterial symbionts in their midgut, known as "Candidatus Stammerula spp.". The 25 described endemic species of Hawaiian tephritids, plus at least three undescribed species, are taxonomically distributed among three genera: the cosmopolitan genus Trupanea (21 described spp.), the endemic genus Phaeogramma (2 spp.) and the Nearctic genus Neotephritis (2 spp.). We examined the presence of symbiotic bacteria in the endemic tephritids of the Hawaiian Islands, which represent a spectacular example of adaptive radiation, and tested the concordant evolution between host and symbiont phylogenies. We detected through PCR assays the presence of specific symbiotic bacteria, designated as "Candidatus Stammerula trupaneae", from 35 individuals of 15 species. The phylogeny of the insect host was reconstructed based on two regions of the mitochondrial DNA (16S rDNA and COI-tRNALeu-COII), while the bacterial 16S rRNA was used for the symbiont analysis. Host and symbiont phylogenies were then compared and evaluated for patterns of cophylogeny and strict cospeciation. Topological congruence between Hawaiian Tephritinae and their symbiotic bacteria phylogenies suggests a limited, but significant degree of host-symbiont cospeciation. We also explored the character reconstruction of three host traits, as island location, host lineage, and host tissue attacked, based on the symbiont phylogenies under the hypothesis of cospeciation.

  3. 'Candidatus Phytoplasma pruni', a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes.

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    Davis, Robert E; Zhao, Yan; Dally, Ellen L; Lee, Ing-Ming; Jomantiene, Rasa; Douglas, Sharon M

    2013-02-01

    X-disease is one of the most serious diseases known in peach (Prunus persica). Based on RFLP analysis of 16S rRNA gene sequences, peach X-disease phytoplasma strains from eastern and western United States and eastern Canada were classified in 16S rRNA gene RFLP group 16SrIII, subgroup A. Phylogenetic analyses of 16S rRNA gene sequences revealed that the X-disease phytoplasma strains formed a distinct subclade within the phytoplasma clade, supporting the hypothesis that they represented a lineage distinct from those of previously described 'Candidatus Phytoplasma' species. Nucleotide sequence alignments revealed that all studied X-disease phytoplasma strains shared less than 97.5 % 16S rRNA gene sequence similarity with previously described 'Candidatus Phytoplasma' species. Based on unique properties of the DNA, we propose recognition of X-disease phytoplasma strain PX11CT1(R) as representative of a novel taxon, 'Candidatus Phytoplasma pruni'. Results from nucleotide and phylogenetic analyses of secY and ribosomal protein (rp) gene sequences provided additional molecular markers of the 'Ca. Phytoplasma pruni' lineage. We propose that the term 'Ca. Phytoplasma pruni' be applied to phytoplasma strains whose 16S rRNA gene sequences contain the oligonucleotide sequences of unique regions that are designated in the formally published description of the taxon. Such strains include X-disease phytoplasma and--within the tolerance of a single base difference in one unique sequence--peach rosette, peach red suture, and little peach phytoplasmas. Although not employed for taxon delineation in this work, we further propose that secY, rp, and other genetic loci from the reference strain of a taxon, and where possible oligonucleotide sequences of unique regions of those genes that distinguish taxa within a given 16Sr group, be incorporated in emended descriptions and as part of future descriptions of 'Candidatus Phytoplasma' taxa.

  4. Candidatus Neoehrlichia mikurensis in rodents in an area with sympatric existence of the hard ticks Ixodes ricinus and Dermacentor reticulatus, Germany

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    Silaghi Cornelia

    2012-12-01

    Full Text Available Abstract Background Candidatus Neoehrlichia mikurensis (CNM has been described in the hard tick Ixodes ricinus and rodents as well as in some severe cases of human disease. The aims of this study were to identify DNA of CNM in small mammals, the ticks parasitizing them and questing ticks in areas with sympatric existence of Ixodes ricinus and Dermacentor reticulatus in Germany. Methods Blood, transudate and organ samples (spleen, kidney, liver, skin of 91 small mammals and host-attached ticks from altogether 50 small mammals as well as questing I. ricinus ticks (n=782 were screened with a real-time PCR for DNA of CNM. Results 52.7% of the small mammals were positive for CNM-DNA. The majority of the infected animals were yellow-necked mice (Apodemus flavicollis and bank voles (Myodes glareolus. Small mammals with tick infestation were more often infected with CNM than small mammals without ticks. Compared with the prevalence of ~25% in the questing I. ricinus ticks, twice the prevalence in the rodents provides evidence for their role as reservoir hosts for CNM. Conclusion The high prevalence of this pathogen in the investigated areas in both rodents and ticks points towards the need for more specific investigation on its role as a human pathogen.

  5. High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus’

    Institute of Scientific and Technical Information of China (English)

    WANG Xue-feng; CHEN Jiao-yue; TAN Jin; DUAN Suo; DENG Xiao-ling; CHEN Jian-chi; ZHOU Chang-yong

    2015-01-01

    Two miniature inverted-repeat transposable elements (MITEs), MCLas-A and MCLas-B, were recently identiifed from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yelow shoot disease). MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus’ isolates from China, the United States and Brazil. Out of the 12 sequence types, three (T4, T5-2, T6) were reported for the ifrst time. Recombination events were found in the two unique sequence types (T5-2 and T6) which were detected in al Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two wel supported clades including ifve subclades were identiifed, clearly relfecting the geographical origins of isolates, especialy that of Ruili isolates, São Paulo isolates and a few Florida isolates.

  6. Detection of citrus huanglongbing-associated 'Candidatus Liberibacter asiaticus' in citrus and Diaphorina citri in Pakistan, seasonal variability, and implications for disease management.

    Science.gov (United States)

    Razi, Muhammad F; Keremane, Manjunath L; Ramadugu, Chandrika; Roose, Mikeal; Khan, Iqrar A; Lee, Richard F

    2014-03-01

    We report the detection of the huanglongbing (HLB)-associated bacterium 'Candidatus Liberibacter asiaticus' from both plants and insects in Pakistan and the seasonal variability in the numbers of 'Ca. L. asiaticus'-positive psyllid vector, Diaphorina citri. Our studies showed that 'Ca. L. asiaticus' was detectable from trees in areas with maximum temperatures reaching nearly 50°C (average maximum of 42°C). However, the bacterium was present at very low levels in psyllids both in summer (June to August) and autumn (September to November) in contrast to reports from Florida, where the bacterium was detectable at very high levels during October to November. We hypothesize that hot summer temperatures in Pakistan may interfere with acquisition and replication of 'Ca. L. asiaticus' in psyllids and may lead to dead or non transmissible 'Ca. L. asiaticus' in plants. Psyllid counts were very low in both summer and winter, showed a population peak ('Ca. L. asiaticus'-positive vectors) in spring, and showed a larger peak ('Ca. L. asiaticus'-free psyllids) in autumn. Natural thermotherapy during hot summers and a low vector population during environmental extremes may have played a major role in long-term survival of the citrus industry in Pakistan. These results may be useful in developing management strategies for U.S. citrus industries in Texas and California.

  7. Screening molecules for control of citrus huanglongbing using an optimized regeneration system for 'Candidatus Liberibacter asiaticus'-infected periwinkle (Catharanthus roseus) cuttings.

    Science.gov (United States)

    Zhang, Muqing; Duan, Yongping; Zhou, Lijuan; Turechek, William W; Stover, Ed; Powell, Charles A

    2010-03-01

    Citrus huanglongbing is one of the most destructive diseases of citrus worldwide. The disease is associated with three different species of 'Candidatus Liberibacter', of which 'Ca. L. asiaticus' is the most widely distributed. An optimized system using 'Ca. L. asiaticus'-infected periwinkle cuttings was developed to screen chemical compounds effective for controlling the bacterial population while simultaneously assessing their phytotoxicity. The optimal regeneration conditions were determined to be the use of vermiculite as a growth medium for the cuttings, and a fertilization routine using half-strength Murashige and Tucker medium supplemented with both naphthalene acetic acid (4 microg/ml) and indole-3-butyric acid (4 microg/ml). This system allowed a plant regeneration rate of 60.6% for 'Ca. L. asiaticus'-infected cuttings in contrast to the periwinkle regeneration system. When treated with penicillin G sodium at 50 microg/ml, all plants regenerated from 'Ca. L. asiaticus'-infected cuttings were 'Ca. L. asiaticus' negative as determined by both nested polymerase chain reaction (PCR) and quantitative real-time PCR. In addition, DBNPA was also able to significantly reduce the percentage of 'Ca. L. asiaticus'-positive plants and the titer of the 'Ca. L. asiaticus' bacterium at 200 microl/liter.

  8. Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria.

    Science.gov (United States)

    MacGregor, Barbara J; Biddle, Jennifer F; Teske, Andreas

    2013-07-01

    The draft genome sequence of a single orange Beggiatoa ("Candidatus Maribeggiatoa") filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceae matches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

  9. Light effects on the multicellular magnetotactic prokaryote 'Candidatus Magnetoglobus multicellularis' are cancelled by radiofrequency fields: the involvement of radical pair mechanisms.

    Science.gov (United States)

    de Melo, Roger Duarte; Acosta-Avalos, Daniel

    2017-02-01

    'Candidatus Magnetoglobus multicellularis' is the most studied multicellular magnetotactic prokaryote. It presents a light-dependent photokinesis: green light decreases the translation velocity whereas red light increases it, in comparison to blue and white light. The present article shows that radio-frequency electromagnetic fields cancel the light effect on photokinesis. The frequency to cancel the light effect corresponds to the Zeeman resonance frequency (DC magnetic field of 4 Oe and radio-frequency of 11.5 MHz), indicating the involvement of a radical pair mechanism. An analysis of the orientation angle relative to the magnetic field direction shows that radio-frequency electromagnetic fields disturb the swimming orientation when the microorganisms are illuminated with red light. The analysis also shows that at low magnetic fields (1.6 Oe) the swimming orientation angles are well scattered around the magnetic field direction, showing that magnetotaxis is not efficiently in the swimming orientation to the geomagnetic field. The results do not support cryptochrome as being the responsible chromophore for the radical pair mechanism and perhaps two different chromophores are necessary to explain the radio-frequency effects.

  10. Seroprevalence of Rickettsia spp. in Equids and Molecular Detection of 'Candidatus Rickettsia amblyommii' in Amblyomma cajennense Sensu Lato Ticks From the Pantanal Region of Mato Grosso, Brazil.

    Science.gov (United States)

    Alves, Alvair Da S; Melo, Andréia L T; Amorim, Marcus V; Borges, Alice M C M; Gaíva E Silva, Lucas; Martins, Thiago F; Labruna, Marcelo B; Aguiar, Daniel M; Pacheco, Richard C

    2014-11-01

    The aim of the study was to evaluate exposure of equids to rickettsial agents (Rickettsia rickettsii, Rickettsia parkeri, 'Candidatus Rickettsia amblyommii', Rickettsia rhipicephali, and Rickettsia bellii) and rickettsial infection in ticks of a Pantanal region of Brazil. Sera of 547 equids (500 horses and 47 donkeys) were evaluated by indirect immunofluorescence assay. In total, 665 adults and 106 nymphal pools of Amblyomma cajennense F. sensu lato, 10 Dermacentor nitens Neumann ticks, and 88 larval pools of Amblyomma sp. were tested by polymerase chain reaction (PCR). Overall, 337 (61.6%) equids were reactive (titer ≥64) to at least one antigen of Rickettsia spp. The prevalence values for Rickettsia were 66%, and the highest endpoint titers were observed for 'Ca. R. amblyommii'. By PCR 3 (0.45%) A. cajennense s.l. females were positive for 'Ca. R. amblyommii'. Minimum infection rates of 0.75% for nymphs and 0.34% for larvae were calculated. Positive samples of ticks have had a fragment of the 16S mitochondrial rRNA gene sequenced and sequences showed 99% identity to Amblyomma sculptum Berlese. This study reports a wide exposure of equids to Rickettsia agents, and PCR evidence of infection with 'Ca. R. amblyommii', for the first time, in A. sculptum.

  11. Genome and metabolic network of Candidatus Phaeomarinobacter ectocarpi Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

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    Simon M Dittami

    2014-07-01

    Full Text Available Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of Candidatus Phaeomarinobacter ectocarpi Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The Ca. P. ectocarpi genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, Ca. P. ectocarpi has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥ 97% identity have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus Phaeomarinobacter may comprise several species, which may colonize different niches.

  12. Ultrastructural characterization and multilocus sequence analysis (MLSA) of 'Candidatus Rickettsiella isopodorum', a new lineage of intracellular bacteria infecting woodlice (Crustacea: Isopoda).

    Science.gov (United States)

    Kleespies, Regina G; Federici, Brian A; Leclerque, Andreas

    2014-07-01

    The taxonomic genus Rickettsiella (Gammaproteobacteria; Legionellales) comprises intracellular bacteria associated with a wide range of arthropods including insects, arachnids and crustaceans. The present study provides ultrastructural together with genetic evidence for a Rickettsiella bacterium in the common rough woodlouse, Porcellio scaber (Isopoda, Porcellionidae), occurring in Germany, and shows that this bacterium is very closely related to one of the same genus occurring in California that infects the pill bug, Armadillidium vulgare (Isopoda, Armadillidiidae). Both bacterial isolates displayed the ultrastructural features described previously for crustacean-associated bacteria of the genus Rickettsiella, including the absence of well-defined associated protein crystals; occurrence of the latter is a typical characteristic of infection by this type of bacteria in insects, but has not been reported in crustaceans. A molecular systematic approach combining multilocus sequence analysis (MLSA) with likelihood-based significance testing demonstrated that despite their distant geographic origins, both bacteria form a tight sub-clade within the genus Rickettsiella. In the 16S rRNA gene trees, this sub-clade includes other bacterial sequences from woodlice. Moreover, the bacterial specimens from P. scaber and A. vulgare are found genetically or morphologically different from each of the four currently recognized Rickettsiella species. Therefore, the designation 'Candidatus Rickettsiella isopodorum' is introduced for this new lineage of isopod-associated Rickettsiella bacteria.

  13. "Candidatus Similichlamydia laticola", a novel Chlamydia-like agent of epitheliocystis in seven consecutive cohorts of farmed Australian barramundi, Lates calcarifer (Bloch.

    Directory of Open Access Journals (Sweden)

    Megan C Stride

    Full Text Available Six consecutively hatched cohorts and one cohort of pre-hatch eggs of farmed barramundi (Lates calcarifer from south Australia were examined for Chlamydia-like organisms associated with epitheliocystis. To identify and characterise the bacteria, 59 gill samples and three pre-hatch egg samples were processed for histology, in situ hybridisation and 16S rRNA amplification, sequencing and comprehensive phylogenetic analysis. Cases of epitheliocystis were observed microscopically and characterised by membrane-enclosed basophilic cysts filled with a granular material that caused hypertrophy of the epithelial cells. In situ hybridisation with a Chlamydiales-specific probe lead to specific labelling of the epitheliocystis inclusions within the gill epithelium. Two distinct but closely related 16S rRNA chlamydial sequences were amplified from gill DNA across the seven cohorts, including from pre-hatch eggs. These genotype sequences were found to be novel, sharing 97.1 - 97.5% similarity to the next closest 16S rRNA sequence, Ca. Similichlamydia latridicola, from Australian striped trumpeter. Comprehensive phylogenetic analysis of these genotype sequences against representative members of the Chlamydiales order and against other epitheliocystis agents revealed these Chlamydia-like organisms to be novel and taxonomically placed them within the recently proposed genus Ca. Similichlamydia. Following Fredricks and Relman's molecular postulates and based on these observations, we propose the epitheliocystis agents of barramundi to be known as "Candidatus Similichlamydia laticola" (sp. nov..

  14. The ubiquity and ancestry of insect doublesex.

    Science.gov (United States)

    Price, Dana C; Egizi, Andrea; Fonseca, Dina M

    2015-08-17

    The doublesex (dsx) gene functions as a molecular switch at the base of the insect sex determination cascade, and triggers male or female somatic sexual differentiation in Drosophila. Having been reported from only seven current insect orders, the exact phylogenetic distribution of dsx within the largest Arthropod sub-phylum, the Hexapoda, is unknown. To understand the evolution of this integral gene relative to other arthropods, we tested for the presence of dsx within public EST and genome sequencing projects representative of all 32 hexapod orders. We find the dsx gene to be ubiquitous, with putative orthologs recovered from 30 orders. Additionally, we recovered both alternatively spliced and putative paralogous dsx transcripts from several orders of hexapods, including basal lineages, indicating the likely presence of these characteristics in the hexapod common ancestor. Of note, other arthropods such as chelicerates and crustaceans express two dsx genes, both of which are shown to lack alternative splicing. Furthermore, we discovered a large degree of length heterogeneity in the common region of dsx coding sequences within and among orders, possibly resulting from lineage-specific selective pressures inherent to each taxon. Our work serves as a valuable resource for understanding the evolution of sex determination in insects.

  15. The ubiquity of small-world networks

    CERN Document Server

    Telesford, Qawi K; Hayasaka, Satoru; Burdette, Jonathan H; Laurienti, Paul J

    2011-01-01

    Small-world networks by Watts and Strogatz are a class of networks that are highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. These characteristics result in networks with unique properties of regional specialization with efficient information transfer. Social networks are intuitive examples of this organization with cliques or clusters of friends being interconnected, but each person is really only 5-6 people away from anyone else. While this qualitative definition has prevailed in network science theory, in application, the standard quantitative application is to compare path length (a surrogate measure of distributed processing) and clustering (a surrogate measure of regional specialization) to an equivalent random network. It is demonstrated here that comparing network clustering to that of a random network can result in aberrant findings and networks once thought to exhibit small-world properties may not. We propose a new small-world metric, {\\omega}...

  16. Relationship between the “Red Nose” Fruit of Shatangju Tangerine with Candidatus Liberibacter asiaticus%砂糖橘红鼻子果与韧皮部杆菌侵染相关性研究

    Institute of Scientific and Technical Information of China (English)

    张培; 关磊; 刘蕤; 蒲雪莲; 邓晓玲

    2011-01-01

    利用TaqMan实时荧光定量PCR技术对广东清远、四会、云浮地区砂糖橘90个红鼻子果样品进行检测.结果表明,韧皮部杆菌(Candidatus Liberiacter asiaticus)阳性检出率高达100%.分别对病树上无症状果实、斑驳叶片以及黄化叶片样品进行实时荧光定量PCR检测,阳性检出率分别为273%、91.8%、52.0%,因此,可将砂糖橘红鼻子果作为田间诊断黄龙病的典型症状.红鼻子果的果柄和果轴均可检测到病原,且果柄部位病原浓度明显高于果轴.对红鼻子果果柄韧皮部扫描电镜观察,发现果柄筛管中有大量淀粉粒沉积,且韧皮部筛管明显缢缩,阻碍了植株体内糖分和有机质向果实运输.%Citrus Huanglongbing (HLB) is difficult to identify in the field as the similar symptoms may also occur due to some physiological disorders and water stress, so in HLB management diagnosing HLB is of great importance. TaqMan quantative real -time PCR, targeting 16S rDNA sequence of ' Candidatus liberibacter asiaticus', was used to examine Shatangju tangerine (Citrus reticulate) "red nose" fruits, non-symptomatic fruits in the HLB infected trees, blotchy mottling leaves and yellowing leaves collected from Qingyuan, Sihui and Yunfu (Guangdong Province). The results showed that 100% of the " red nose" fruit samples were positive for 'Candidatus Liberibacter asiaticus', while 27.3% non-symptom fruits, 91.8% typical blotchy mottling leaves and 52.0% yellowing leaves were positive for 'Candidatus Liberibacter asiaticus'. Therefore, "red nose" fruit could be regarded as a typical symptom of HLB in Shatangju tangerine. The pathogen was detected in fruit axis and pedicle, but the latter one got a higher titer which maight be used as a material for the pathogen observation. A Scanning Electron Microscopy (SEM) showed no pathogen but a mass of starch grains was observed in the phloem sieve tubes of HLB Shatangju tangerine infected with HLB. The phloem was

  17. Expressão de genes das vias de jasmonato e etileno na resposta de plantas de citros às bactérias Candidatus Liberibacter spp., causadoras do Huanglongbing

    OpenAIRE

    Luciane Fender Coerini

    2014-01-01

    A citricultura destaca-se dentro do agronegócio brasileiro gerando dividendos diretos com exportações e empregos, e indiretos com arrecadação de impostos. No entanto, ainda padece com problemas fitossanitários, com destaque para o HLB (Huanglongbing, HLB, ex-greening), que nos últimos dez anos tem dizimado pomares e provocado o abandono da cultura por muitos produtores. Causada no Brasil pelas bactérias Candidatus Liberibacter asiaticus e Ca. Liberibacter americanus, é uma doença sistêmica, r...

  18. New excised-leaf assay method to test inoculativity of Asian citrus psyllid (Hemiptera: Psyllidae) with Candidatus Liberibacter asiaticus associated with citrus huanglongbing disease.

    Science.gov (United States)

    Ammar, El-Desouky; Walter, Abigail J; Hall, David G

    2013-02-01

    The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is the primary vector of Candidatus Liberibacter asiaticus (Las) associated with huanglongbing, or citrus greening, the most devastating citrus (Citrus spp.) disease worldwide. Here, we developed a new "excised-leaf assay" that can speed up Las-inoculativity tests on Asian citrus psyllid from the current 3-12 mo (when using whole citrus seedlings for inoculation) to only 2-3 wk. Young adults of Asian citrus psyllid that had been reared on Las-infected plants were caged on excised healthy sweet orange [Citrus sinensis (L.) Osbeck] leaves for a 1-2-wk inoculation access periods (IAP), and then both psyllids and leaves were tested later by quantitative polymerase chain reaction (PCR). When single adults were tested per leaf, percentages of Las-positive leaves averaged 2-6% by using HLBaspr primers and 10-20% by using the more sensitive LJ900 primers. Higher proportions of Las-positive leaves were obtained with 1) higher densities of inoculating psyllids (5-10 adults per leaf), 2) longer IAPs, and 3) incubation of leaves for 1 wk postinoculation before PCR. Logistic regression analysis indicated a positive correlation between Las titer in Asian citrus psyllid adults tested singly and the probability of detecting Las in the inoculated leaves, correlations that can be very useful in epidemiological studies. Comparison between excised leaves and whole seedlings, inoculated consecutively for 1 wk each by one or a group of psyllids, indicated no significant difference between Las detection in excised leaves or whole plants. This new excised-leaf assay method saves considerable time, materials, and greenhouse space, and it may enhance vector relation and epidemiological studies on Las and potentially other Liberibacter spp. associated with huanglongbing disease.

  19. Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity.

    Science.gov (United States)

    Vyas, Meenal; Fisher, Tonja W; He, Ruifeng; Nelson, William; Yin, Guohua; Cicero, Joseph M; Willer, Mark; Kim, Ryan; Kramer, Robin; May, Greg A; Crow, John A; Soderlund, Carol A; Gang, David R; Brown, Judith K

    2015-01-01

    The Asian citrus psyllid (ACP) Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the insect vector of the fastidious bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease, or Huanglongbing (HLB). The widespread invasiveness of the psyllid vector and HLB in citrus trees worldwide has underscored the need for non-traditional approaches to manage the disease. One tenable solution is through the deployment of RNA interference technology to silence protein-protein interactions essential for ACP-mediated CLas invasion and transmission. To identify psyllid interactor-bacterial effector combinations associated with psyllid-CLas interactions, cDNA libraries were constructed from CLas-infected and CLas-free ACP adults and nymphs, and analyzed for differential expression. Library assemblies comprised 24,039,255 reads and yielded 45,976 consensus contigs. They were annotated (UniProt), classified using Gene Ontology, and subjected to in silico expression analyses using the Transcriptome Computational Workbench (TCW) (http://www.sohomoptera.org/ACPPoP/). Functional-biological pathway interpretations were carried out using the Kyoto Encyclopedia of Genes and Genomes databases. Differentially expressed contigs in adults and/or nymphs represented genes and/or metabolic/pathogenesis pathways involved in adhesion, biofilm formation, development-related, immunity, nutrition, stress, and virulence. Notably, contigs involved in gene silencing and transposon-related responses were documented in a psyllid for the first time. This is the first comparative transcriptomic analysis of ACP adults and nymphs infected and uninfected with CLas. The results provide key initial insights into host-parasite interactions involving CLas effectors that contribute to invasion-virulence, and to host nutritional exploitation and immune-related responses that appear to be essential for successful ACP-mediated circulative, propagative CLas transmission.

  20. Use of Electrical Penetration Graph Technology to Examine Transmission of 'Candidatus Liberibacter solanacearum' to Potato by Three Haplotypes of Potato Psyllid (Bactericera cockerelli; Hemiptera: Triozidae.

    Directory of Open Access Journals (Sweden)

    Tariq Mustafa

    Full Text Available The potato psyllid, Bactericera cockerelli (Šulc (Hemiptera: Triozidae, is a vector of the phloem-limited bacterium 'Candidatus Liberibacter solanacearum' (Lso, the putative causal agent of zebra chip disease of potato. Little is known about how potato psyllid transmits Lso to potato. We used electrical penetration graph (EPG technology to compare stylet probing behaviors and efficiency of Lso transmission of three haplotypes of potato psyllid (Central, Western, Northwestern. All haplotypes exhibited the full suite of stylet behaviors identified in previous studies with this psyllid, including intercellular penetration and secretion of the stylet pathway, xylem ingestion, and phloem activities, the latter comprising salivation and ingestion. The three haplotypes exhibited similar frequency and duration of probing behaviors, with the exception of salivation into phloem, which was of higher duration by psyllids of the Western haplotype. We manipulated how long psyllids were allowed access to potato ("inoculation access period", or IAP to examine the relationship between phloem activities and Lso transmission. Between 25 and 30% of psyllids reached and salivated into phloem at an IAP of 1 hr, increasing to almost 80% of psyllids as IAP was increased to 24 h. Probability of Lso-transmission was lower across all IAP levels than probability of phloem salivation, indicating that a percentage of infected psyllids which salivated into the phloem failed to transmit Lso. Logistic regression showed that probability of transmission increased as a function of time spent salivating into the phloem; transmission occurred as quickly as 5 min following onset of salivation. A small percentage of infected psyllids showed extremely long salivation events but nonetheless failed to transmit Lso, for unknown reasons. Information from these studies increases our understanding of Lso transmission by potato psyllid, and demonstrates the value of EPG technology in

  1. Molecular and physiological properties associated with zebra complex disease in potatoes and its relation with Candidatus Liberibacter contents in psyllid vectors.

    Directory of Open Access Journals (Sweden)

    Veria Y Alvarado

    Full Text Available Zebra complex (ZC disease on potatoes is associated with Candidatus Liberibacter solanacearum (CLs, an α-proteobacterium that resides in the plant phloem and is transmitted by the potato psyllid Bactericera cockerelli (Šulc. The name ZC originates from the brown striping in fried chips of infected tubers, but the whole plants also exhibit a variety of morphological features and symptoms for which the physiological or molecular basis are not understood. We determined that compared to healthy plants, stems of ZC-plants accumulate starch and more than three-fold total protein, including gene expression regulatory factors (e.g. cyclophilin and tuber storage proteins (e.g., patatins, indicating that ZC-affected stems are reprogrammed to exhibit tuber-like physiological properties. Furthermore, the total phenolic content in ZC potato stems was elevated two-fold, and amounts of polyphenol oxidase enzyme were also high, both serving to explain the ZC-hallmark rapid brown discoloration of air-exposed damaged tissue. Newly developed quantitative and/or conventional PCR demonstrated that the percentage of psyllids in laboratory colonies containing detectable levels of CLs and its titer could fluctuate over time with effects on colony prolificacy, but presumed reproduction-associated primary endosymbiont levels remained stable. Potato plants exposed in the laboratory to psyllid populations with relatively low-CLs content survived while exposure of plants to high-CLs psyllids rapidly culminated in a lethal collapse. In conclusion, we identified plant physiological biomarkers associated with the presence of ZC and/or CLs in the vegetative potato plant tissue and determined that the titer of CLs in the psyllid population directly affects the rate of disease development in plants.

  2. Localization and Distribution of 'Candidatus Liberibacter asiaticus' in Citrus and Periwinkle by Direct Tissue Blot Immuno Assay with an Anti-OmpA Polyclonal Antibody.

    Science.gov (United States)

    Ding, Fang; Duan, Yongping; Paul, Cristina; Brlansky, Ronald H; Hartung, John S

    2015-01-01

    'Candidatus Liberibacter asiaticus' (CaLas), a non-cultured member of the α-proteobacteria, is the causal agent of citrus Huanglongbing (HLB). Due to the difficulties of in vitro culture, antibodies against CaLas have not been widely used in studies of this pathogen. We have used an anti-OmpA polyclonal antibody based direct tissue blot immunoassay to localize CaLas in different citrus tissues and in periwinkle leaves. In citrus petioles, CaLas was unevenly distributed in the phloem sieve tubes, and tended to colonize in phloem sieve tubes on the underside of petioles in preference to the upper side of petioles. Both the leaf abscission zone and the junction of the petiole and leaf midrib had fewer CaLas bacteria compared to the main portions of the petiole and the midribs. Colonies of CaLas in phloem sieve tubes were more frequently found in stems with symptomatic leaves than in stems with asymptomatic leaves with an uneven distribution pattern. In serial sections taken from the receptacle to the peduncle, more CaLas were observed in the peduncle sections adjacent to the stem. In seed, CaLas was located in the seed coat. Many fewer CaLas were found in the roots, as compared to the seeds and petioles when samples were collected from trees with obvious foliar symptoms. The direct tissue blot immuno assay was adapted to whole periwinkle leaves infected by CaLas. The pathogen was distributed throughout the lateral veins and the results were correlated with results of qPCR. Our data provide direct spatial and anatomical information for CaLas in planta. This simple and scalable method may facilitate the future research on the interaction of CaLas and host plant.

  3. Visualizing evolutionary relationships of multidomain proteins: An example from receiver (REC domains of sensor histidine kinases in the Candidatus Maribeggiatoa str. Orange Guaymas draft genome

    Directory of Open Access Journals (Sweden)

    Barbara J. MacGregor

    2016-11-01

    Full Text Available For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis. Recognition (REC domains are short (~125 amino acids and well conserved, simplifying sequence alignments and phylogenetic calculations. Over 100 of these were identified in the BOGUAY genome and found to have a wide range of inferred phylogenetic relationships. Two sets were chosen here for detailed study. One set of four BOGUAY ORFs has closest relatives among other Beggiatoaceae and Cyanobacteria. A second set of four has REC domains with more mixed affiliations, including other Beggiatoaceae, several sulfate-reducing Deltaproteobacteria and Firmicutes, magnetotactic Nitrospirae, one Shewanella and one Ferrimonas strain (both Gammaproteobacteria, and numerous Vibrio vulnificus and V. navarrensis strains (also Gammaproteobacteria. For an overview of the possible origins of the whole proteins and the surrounding genomic regions, color-coded BLASTP results were produced and displayed against cartoons showing protein domain structure of predicted genes. This is suggested as a visualization method for investigation of possible horizontally transferred regions, giving more detail than scans of DNA composition and codon usage but much faster than carrying out full phylogenetic analyses for multiple proteins. As expected, most of the predicted sensor histidine kinases investigated have two or more segments with distinct

  4. Localization and Distribution of 'Candidatus Liberibacter asiaticus' in Citrus and Periwinkle by Direct Tissue Blot Immuno Assay with an Anti-OmpA Polyclonal Antibody.

    Directory of Open Access Journals (Sweden)

    Fang Ding

    Full Text Available 'Candidatus Liberibacter asiaticus' (CaLas, a non-cultured member of the α-proteobacteria, is the causal agent of citrus Huanglongbing (HLB. Due to the difficulties of in vitro culture, antibodies against CaLas have not been widely used in studies of this pathogen. We have used an anti-OmpA polyclonal antibody based direct tissue blot immunoassay to localize CaLas in different citrus tissues and in periwinkle leaves. In citrus petioles, CaLas was unevenly distributed in the phloem sieve tubes, and tended to colonize in phloem sieve tubes on the underside of petioles in preference to the upper side of petioles. Both the leaf abscission zone and the junction of the petiole and leaf midrib had fewer CaLas bacteria compared to the main portions of the petiole and the midribs. Colonies of CaLas in phloem sieve tubes were more frequently found in stems with symptomatic leaves than in stems with asymptomatic leaves with an uneven distribution pattern. In serial sections taken from the receptacle to the peduncle, more CaLas were observed in the peduncle sections adjacent to the stem. In seed, CaLas was located in the seed coat. Many fewer CaLas were found in the roots, as compared to the seeds and petioles when samples were collected from trees with obvious foliar symptoms. The direct tissue blot immuno assay was adapted to whole periwinkle leaves infected by CaLas. The pathogen was distributed throughout the lateral veins and the results were correlated with results of qPCR. Our data provide direct spatial and anatomical information for CaLas in planta. This simple and scalable method may facilitate the future research on the interaction of CaLas and host plant.

  5. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

    Directory of Open Access Journals (Sweden)

    Kateryna V Zhalnina

    Full Text Available The activity of ammonia-oxidizing archaea (AOA leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

  6. The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria.

    Science.gov (United States)

    Schmitz-Esser, Stephan; Tischler, Patrick; Arnold, Roland; Montanaro, Jacqueline; Wagner, Michael; Rattei, Thomas; Horn, Matthias

    2010-02-01

    Protozoa play host for many intracellular bacteria and are important for the adaptation of pathogenic bacteria to eukaryotic cells. We analyzed the genome sequence of "Candidatus Amoebophilus asiaticus," an obligate intracellular amoeba symbiont belonging to the Bacteroidetes. The genome has a size of 1.89 Mbp, encodes 1,557 proteins, and shows massive proliferation of IS elements (24% of all genes), although the genome seems to be evolutionarily relatively stable. The genome does not encode pathways for de novo biosynthesis of cofactors, nucleotides, and almost all amino acids. "Ca. Amoebophilus asiaticus" encodes a variety of proteins with predicted importance for host cell interaction; in particular, an arsenal of proteins with eukaryotic domains, including ankyrin-, TPR/SEL1-, and leucine-rich repeats, which is hitherto unmatched among prokaryotes, is remarkable. Unexpectedly, 26 proteins that can interfere with the host ubiquitin system were identified in the genome. These proteins include F- and U-box domain proteins and two ubiquitin-specific proteases of the CA clan C19 family, representing the first prokaryotic members of this protein family. Consequently, interference with the host ubiquitin system is an important host cell interaction mechanism of "Ca. Amoebophilus asiaticus". More generally, we show that the eukaryotic domains identified in "Ca. Amoebophilus asiaticus" are also significantly enriched in the genomes of other amoeba-associated bacteria (including chlamydiae, Legionella pneumophila, Rickettsia bellii, Francisella tularensis, and Mycobacterium avium). This indicates that phylogenetically and ecologically diverse bacteria which thrive inside amoebae exploit common mechanisms for interaction with their hosts, and it provides further evidence for the role of amoebae as training grounds for bacterial pathogens of humans.

  7. Candidatus Bartonella antechini: a novel Bartonella species detected in fleas and ticks from the yellow-footed antechinus (Antechinus flavipes), an Australian marsupial.

    Science.gov (United States)

    Kaewmongkol, Gunn; Kaewmongkol, Sarawan; Owen, Helen; Fleming, Patricia A; Adams, Peter J; Ryan, Una; Irwin, Peter J; Fenwick, Stanley G

    2011-05-05

    Bartonella are fastidious, Gram-negative, aerobic bacilli belonging to the Alphaproteobacteria group. In the last ten years, the discovery of new Bartonella species from a variety of mammalian hosts, arthropod vectors and geographical areas has increased. More than 20 species of Bartonella have been identified, of which approximately thirteen are associated with disease in humans and animals. Recently, four novel species of Bartonella were isolated from mammalian hosts in Australia: Bartonella australis from eastern grey kangaroos (Macropus giganteus) and Bartonella rattaustraliani, Bartonella queenslandensis and Bartonella coopersplainsensis from rodents. Bartonella-like organisms have also been detected from Ixodes tasmani ticks collected from koalas (Phascolarctos cinereus). However, very little is known about Bartonella spp. in other marsupials in Australia. We report the identification of a novel Bartonella species detected from fleas (Acanthopsylla jordani) and ticks (Ixodes antechini) collected from a small carnivorous marsupial, Antechinus flavipes (Mardos or Yellow-footed antechinus) in the southwest of Western Australia. New nested-PCRs targeting the gltA gene and the ribosomal ITS region were developed as part of the present study. DNA sequencing of the 16S rRNA, gltA, ftsZ and rpoB genes and the ribosomal ITS region revealed that this detection is a distinct Bartonella species and is related to B. australis isolated from kangaroos. This is the first report of two different possible arthropod vectors in Australia (ticks and fleas) being infected with the same species of Bartonella. We propose the name Candidatus Bartonella antechini n. sp. for the recently characterized organism.

  8. Nested-quantitative PCR approach with improved sensitivity for the detection of low titer levels of Candidatus Liberibacter asiaticus in the Asian citrus psyllid, Diaphorina citri Kuwayama.

    Science.gov (United States)

    Coy, M R; Hoffmann, M; Kingdom Gibbard, H N; Kuhns, E H; Pelz-Stelinski, K S; Stelinski, L L

    2014-07-01

    Candidatus Liberibacter asiaticus (CLas) is a phloem-limited bacterium transmitted by the Asian citrus psyllid, Diaphorina citri, and the presumptive causal agent of citrus greening disease. The current method of detection for CLas within plant and insect samples is by a presence/absence qPCR assay using the CLas 16S rDNA gene target. Although qPCR is highly sensitive, low bacterial titers or suboptimal qPCR conditions can result in false-negatives. Using a nested qPCR assay, we determined the false-negative rate of the 16S presence/absence qPCR assay was greater than 50%. Studies to determine the performance parameters of the qPCR assays for CLas 16S and Wingless (Wg), the D. citri endogenous gene, using plasmid and psyllid DNA, revealed suboptimal and variable performance of the 16S assay in psyllid samples. Average efficiencies and sensitivity limits of the plasmid assays were 99.0% and 2.7 copies of template for Wg, respectively, and 98.5% and 2.2-22.1 copies for 16S, respectively. Variability in efficiency was significantly greater in psyllid samples for both gene targets compared to the corresponding plasmid assays, and efficiencies as low as 76% were obtained for 16S. A secondary structure analysis revealed the formation of two stem-loop structures that block the forward and probe binding sites in the 16S template, which could hinder amplification. In summary, our results suggest that suboptimal qPCR efficiency is not uncommon for the 16S presence/absence qPCR assay, which combined with lowCLas titers in some samples, could contribute significantly to the under-reporting of CLas infection in psyllid and plant samples.

  9. Efecto de antioxidantes y señalizadores en plantas de papa (Solanum tuberosum L. infectadas con Candidatus Liberibacter solanacearum bajo condiciones de invernadero

    Directory of Open Access Journals (Sweden)

    Isidro Humberto Almeyda León

    2014-12-01

    Full Text Available In Mexico, the losses caused by the purple top syndrome in potato range from 30 to 95%. This syndrome has been greatly associated with the bacterium Candidatus Liberibacter solaneacearum, which produces reduction in yield and in crop quality, the tubers have internal browning, which is not desirable either for fresh consumption or for the industry. Present study was conducted to evaluate the efficiency of three products that act as antioxidants and / or signs to reduce damage on potato caused by Ca. L. solanacearum under greenhouse conditions. Plants uninfected and infected with the bacterium, produced in vitro were used. The products evaluated were: dehydroascorbic acid (600 ppm, ascorbic acid (600 ppm and hydrogen peroxide (1 mM, and were applied to infected and uninfected plants twice a week. Infected and uninfected plants without application of antioxidants were used as control treatments. To avoid experimental error in the application of the products evaluated the experimental design was a randomized complete block. A reduction of potato damage by Ca. L solaneacearum was registered, and there were significant differences among treatments in the tubers production. The largest tuber number in treatments that included uninfected plants was obtained in the hydrogen peroxide application, which exceeded a 33 %, 48 % and 59 % to plants treated with dehydroascorbic acid, with ascorbic acid and the controls respectively. Similarly, the largest tuber number in treatments included infected plants was obtained by hydrogen peroxide, and it exceeded a 33 %, 17 % and 67 % to treatments with dehydroascorbic acid, with ascorbic acid and the controls respectively. These results show a potential effect of the products evaluated to protect potato plants against Ca. L. solanacearum, although its function is not to diminish the growth or development of bacteria.

  10. Enhanced Acquisition Rates of 'Candidatus Liberibacter asiaticus' by the Asian Citrus Psyllid (Hemiptera: Liviidae) in the Presence of Vegetative Flush Growth in Citrus.

    Science.gov (United States)

    Sétamou, Mamoudou; Alabi, Olufemi J; Kunta, Madhurababu; Jifon, John L; da Graça, John V

    2016-10-01

    The Asian citrus psyllid preferentially feeds and exclusively reproduces on young, newly emerged flush shoots of citrus. Asian citrus psyllid nymphs feed and complete their life stages on these flush shoots. Recent studies conducted under greenhouse conditions have shown that the transmission rates of 'Candidatus Liberibacter asiaticus' (CLas), the putative causal agent of huanglongbing disease of citrus, are enhanced when flush shoots are present. However, it is unclear if CLas acquisition by migrant adult Asian citrus psyllids is similarly enhanced. To address this knowledge gap, cohorts of Asian citrus psyllid adults were allowed 1-wk acquisition access period (AAP) on flushing and nonflushing shoots of qPCR-tested symptomatic (CLas+) and asymptomatic (CLas-) 10-yr-old sweet orange trees under field conditions. After the AAP, they were tested for CLas by qPCR. Progeny Asian citrus psyllid adults that emerged 4 wk post-AAP were similarly retrieved and tested. Eighty percent of flushing and 30% of nonflushing CLas+ trees produced infective Asian citrus psyllid adults, indicating that flush shoots have greater potential to be inoculum sources for CLas acquisition. Concomitantly, 21.1% and 6.0% infective adults were retrieved, respectively, from flushing and nonflushing CLas+ trees, indicating that Asian citrus psyllid adults acquire CLas more efficiently from flush shoots relative to mature shoots. In addition, 12.1% of infective Asian citrus psyllid adult progeny were obtained from 70% of flushing CLas+ trees. Significantly lower mean Ct values were also obtained from infective adults retrieved from flushing relative to nonflushing trees. The results underscore the role of flush shoots in CLas acquisition and the need to protect citrus trees from Asian citrus psyllid infestations during flush cycles.

  11. The phloem-sap feeding mealybug (Ferrisia virgata carries 'Candidatus Liberibacter asiaticus' populations that do not cause disease in host plants.

    Directory of Open Access Journals (Sweden)

    Marco Pitino

    Full Text Available 'Candidatus Liberibacter asiaticus' (Las is the primary causal agent of huanglongbing (HLB, the most devastating disease of citrus worldwide. There are three known insect vectors of the HLB-associated bacteria, and all are members of the Hemiptera: Diaphorina citri (Psyllidae, Trioza erytreae (Triozidae, and Cacopsylla (Psylla citrisuga (Psyllidae. In this study, we found that another hemipteran, the striped mealybug Ferrisia virgata (Cockerell (Hemiptera: Pseudococcidae, was able to acquire and retain Las bacteria. The bacterial titers were positively correlated with the feeding acquisition time on Las-infected leaf discs, with a two-weeks feeding period resulting in Ct values ranging from 23.1 to 36.1 (8.24 × 10(7 to 1.07 × 10(4 Las cells per mealybug. We further discovered that the prophage/phage populations of Las in the mealybugs were different from those of Las in psyllids based on Las prophage-specific molecular markers: infected psyllids harbored the Las populations with prophage/phage FP1 and FP2, while infected mealybugs carried the Las populations with the iFP3 being the dominant prophage/phage. As in the psyllids, Las bacteria were shown to move through the insect gut wall to the salivary glands after being ingested by the mealybug based on a time-course quantitative polymerase chain reaction (qPCR assay of the dissected digestive systems. However, Las populations transmitted by the mealybugs did not cause disease in host plants. This is the first evidence of genetic difference among Las populations harbored by different insect vectors and difference among Las populations with respect to whether or not they cause disease in host plants.

  12. The Phloem-Sap Feeding Mealybug (Ferrisia virgata) Carries ‘Candidatus Liberibacter asiaticus’ Populations That Do Not Cause Disease in Host Plants

    Science.gov (United States)

    Pitino, Marco; Hoffman, Michele T.; Zhou, Lijuan; Hall, David G.; Stocks, Ian C.; Duan, Yongping

    2014-01-01

    Candidatus Liberibacter asiaticus’ (Las) is the primary causal agent of huanglongbing (HLB), the most devastating disease of citrus worldwide. There are three known insect vectors of the HLB-associated bacteria, and all are members of the Hemiptera: Diaphorina citri (Psyllidae), Trioza erytreae (Triozidae), and Cacopsylla (Psylla) citrisuga (Psyllidae). In this study, we found that another hemipteran, the striped mealybug Ferrisia virgata (Cockerell) (Hemiptera: Pseudococcidae), was able to acquire and retain Las bacteria. The bacterial titers were positively correlated with the feeding acquisition time on Las-infected leaf discs, with a two-weeks feeding period resulting in Ct values ranging from 23.1 to 36.1 (8.24×107 to 1.07×104 Las cells per mealybug). We further discovered that the prophage/phage populations of Las in the mealybugs were different from those of Las in psyllids based on Las prophage-specific molecular markers: infected psyllids harbored the Las populations with prophage/phage FP1 and FP2, while infected mealybugs carried the Las populations with the iFP3 being the dominant prophage/phage. As in the psyllids, Las bacteria were shown to move through the insect gut wall to the salivary glands after being ingested by the mealybug based on a time-course quantitative polymerase chain reaction (qPCR) assay of the dissected digestive systems. However, Las populations transmitted by the mealybugs did not cause disease in host plants. This is the first evidence of genetic difference among Las populations harbored by different insect vectors and difference among Las populations with respect to whether or not they cause disease in host plants. PMID:24465578

  13. Crystal structure of a periplasmic solute binding protein in metal-free, intermediate and metal-bound states from Candidatus Liberibacter asiaticus.

    Science.gov (United States)

    Sharma, Nidhi; Selvakumar, Purushotham; Bhose, Sumit; Ghosh, Dilip Kumar; Kumar, Pravindra; Sharma, Ashwani Kumar

    2015-03-01

    The Znu system, a member of ABC transporter family, is critical for survival and pathogenesis of Candidatus Liberibacter asiaticus (CLA). Two homologues of this system have been identified in CLA. Here, we report high resolution crystal structure of a periplasmic solute binding protein from second of the two gene clusters of Znu system in CLA (CLas-ZnuA2) in metal-free, intermediate and metal-bound states. CLas-ZnuA2 showed maximum sequence identity to the Mn/Fe-specific solute binding proteins (SBPs) of cluster A-I family. The overall fold of CLas-ZnuA2 is similar to the related cluster A-I family SBPs. The sequence and structure analysis revealed the unique features of CLas-ZnuA2. The comparison of CLas-ZnuA2 structure in three states showed that metal binding and release is facilitated by a large displacement along with a change in orientation of the side chain for one of the metal binding residue (His39) flipped away from metal binding site in metal-free form. The crystal structure captured in intermediate state of metal binding revealed the changes in conformation and interaction of the loop hosting His39 during the metal binding. A rigid body movement of C-domain along with partial unfolding of linker helix at its C-terminal during metal binding, as reported for PsaA, was not observed in CLas-ZnuA2. The present results suggest that despite showing maximum sequence identity to the Mn/Fe-specific SBPs, the mechanistic resemblance of CLas-ZnuA2 seems to be closer to Zn-specific SBPs of cluster A-I family.

  14. Evidence of two lineages of the symbiont 'Candidatus Erwinia dacicola' in Italian populations of Bactrocera oleae (Rossi) based on 16S rRNA gene sequences.

    Science.gov (United States)

    Savio, Claudia; Mazzon, Luca; Martinez-Sañudo, Isabel; Simonato, Mauro; Squartini, Andrea; Girolami, Vincenzo

    2012-01-01

    The close association between the olive fly Bactrocera oleae (Rossi) (Diptera: Tephritidae) and bacteria has been known for more than a century. Recently, the presence of a host-specific, hereditary, unculturable symbiotic bacterium, designated 'Candidatus Erwinia dacicola', has been described inside the cephalic organ of the fly, called the oesophageal bulb. In the present study, the 16S rRNA gene sequence variability of 'Ca. E. dacicola' was examined within and between 26 Italian olive fly populations sampled across areas where olive trees occur in the wild and areas where cultivated olive trees have been introduced through history. The bacterial contents of the oesophageal bulbs of 314 olive flies were analysed and a minimum of 781 bp of the 16S rRNA gene was sequenced. The corresponding host fly genotype was assessed by sequencing a 776 bp portion of the mitochondrial genome. Two 'Ca. E. dacicola' haplotypes were found (htA and htB), one being slightly more prevalent than the other (57%). The two haplotypes did not co-exist in the same individuals, as confirmed by cloning. Interestingly, the olive fly populations of the two main Italian islands, Sicily and Sardinia, appeared to be represented exclusively by the htB and htA haplotypes, respectively, while peninsular populations showed both bacterial haplotypes in different proportions. No significant correlation emerged between the two symbiont haplotypes and the 16 host fly haplotypes observed, suggesting evidence for a mixed model of vertical and horizontal transmission of the symbiont during the fly life cycle.

  15. Unusual Five Copies and Dual Forms of nrdB in “Candidatus Liberibacter asiaticus”: Biological Implications and PCR Detection Application

    Science.gov (United States)

    Zheng, Zheng; Xu, Meirong; Bao, Minli; Wu, Fengnian; Chen, Jianchi; Deng, Xiaoling

    2016-01-01

    Candidatus Liberibacter asiaticus” (CLas), a non-culturable α-proteobacterium, is associated with citrus Huanglongbing (HLB, yellow shoot disease) currently threatening citrus production worldwide. Here, the whole genome sequence of CLas strain A4 from Guangdong of China was analyzed. Five copies of nrdB, encoding β-subunit of ribonucleotide reductase (RNR), a critical enzyme involving bacterial proliferation, were found. Three nrdB copies were in long form (nrdBL, 1,059 bp) and two were in short form (nrdBS, 378 bp). nrdBS shared >99% identity to 3′ end of nrdBL and had no active site. Sequences of CLas nrdB genes formed a distinct monophyletic lineage among eubacteria. To make use of the high copy number feature, a nrdB-based primer set RNRf/RNRr was designed and evaluated using real-time PCR with 262 HLB samples collected from China and USA. Compared to the current standard primer set HLBas/HLBr derived from the 16S rRNA gene, RNRf/RNRr had Ct value reductions of 1.68 (SYBR Green PCR) and 1.77 (TaqMan PCR), thus increasing the detection sensitivity three-fold. Meanwhile, RNRf/RNRr was more than twice the stability of primer set LJ900f/LJ900r derived from multi-copy prophage. The nrdB-based PCR thereby provides a sensitive and reliable CLas detection with broad application, especially for the early diagnosis of HLB. PMID:27958354

  16. Genome sequence of Candidatus Riesia pediculischaeffi, endosymbiont of chimpanzee lice, and genomic comparison of recently acquired endosymbionts from human and chimpanzee lice.

    Science.gov (United States)

    Boyd, Bret M; Allen, Julie M; de Crécy-Lagard, Valérie; Reed, David L

    2014-09-11

    The obligate-heritable endosymbionts of insects possess some of the smallest known bacterial genomes. This is likely due to loss of genomic material during symbiosis. The mode and rate of this erosion may change over evolutionary time: faster in newly formed associations and slower in long-established ones. The endosymbionts of human and anthropoid primate lice present a unique opportunity to study genome erosion in newly established (or young) symbionts. This is because we have a detailed phylogenetic history of these endosymbionts with divergence dates for closely related species. This allows for genome evolution to be studied in detail and rates of change to be estimated in a phylogenetic framework. Here, we sequenced the genome of the chimpanzee louse endosymbiont (Candidatus Riesia pediculischaeffi) and compared it with the closely related genome of the human body louse endosymbiont. From this comparison, we found evidence for recent genome erosion leading to gene loss in these endosymbionts. Although gene loss was detected, it was not significantly greater than in older endosymbionts from aphids and ants. Additionally, we searched for genes associated with B-vitamin synthesis in the two louse endosymbiont genomes because these endosymbionts are believed to synthesize essential B vitamins absent in the louse's diet. All of the expected genes were present, except those involved in thiamin synthesis. We failed to find genes encoding for proteins involved in the biosynthesis of thiamin or any complete exogenous means of salvaging thiamin, suggesting there is an undescribed mechanism for the salvage of thiamin. Finally, genes encoding for the pantothenate de novo biosynthesis pathway were located on a plasmid in both taxa along with a heat shock protein. Movement of these genes onto a plasmid may be functionally and evolutionarily significant, potentially increasing production and guarding against the deleterious effects of mutation. These data add to a growing

  17. 柑橘黄龙病菌核糖体蛋白基因的多态性及系统发育分析%Polymorphism and phylogenetic analysis of ribosomal protein genes of Candidatus Liberibacter asiaticus

    Institute of Scientific and Technical Information of China (English)

    鹿连明; 范国成; 姚锦爱; 胡秀荣; 陈国庆

    2011-01-01

    通过PCR扩增6个不同地区柑橘黄龙病(citrus huanglongbing,HLB)病原菌的核糖体蛋白基因,采用4种不同的限制性内切酶对PCR产物进行限制性片段长度多态性(RFLP)分析;并对核糖体蛋白基因克隆和测序后,使用DNAman和NCBI Blast等软件对基因序列进行比对分析,并通过软件Mega4.1构建其系统发育树.结果表明:6个分离物核糖体蛋白基因的RFLP指纹图谱有所差异,表现出一定的多态性;不同分离物核糖体蛋白基因的核酸序列和氨基酸序列均存在差异,但相互之间同源性很高,其中核酸序列与数据库中亚洲种(Candidatus Liberibacter asiaticus)的同源性高达99%~100%,与非洲种(Ca.L.africanus)的同源性为85%,与美洲种(Ca.L.americanus)的同源性为77%~80%;系统发育分析显示所有的Ca.L.asiaticus亲缘关系极近,归为一个类群,而后与Ca.L.africanus和Ca.L.americanus组成韧皮部杆菌属(Candidatus Liberibacter)一个大的类群.%Ribosomal protein genes of Candidatus Liberibacter asiaticus from six different geographical regions were amplified, and the restriction fragment length polymorphism (RFLP) of PCR products were analyzed. Then, the sequences of ribosomal protein genes were aligned with software DNAman and NCBI Blast, and the phylogenetic tree was constructed. The results showed that the ribosomal protein genes of six isolates had different RFLP fingerprints and showed some polymorphism, and the differences existed in the nucleotide sequences and amino acid sequences of ribosomal protein genes of different isolates, while the homology between each other was very high. Their homology level was from 99.0% to 100% with other Ca. L. asiaticus in GenBank, 85% with Ca. L. africanus, and 77% to 80%with Ca. L. americanus, respectively. Phylogenetic analysis suggested that all Ca. L. asiaticus were clustered into one group, and then clustered in a larger group as Candidatus Liberibacter with Ca. L.africanus and

  18. Candidatus Propionivibrio aalborgensis”

    DEFF Research Database (Denmark)

    Albertsen, Mads; McIlroy, Simon Jon; Stokholm-Bjerregaard, Mikkel

    2016-01-01

    Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater...

  19. 柑桔黄龙病的鉴定和柯赫氏定理%"Candidatus Liberibacter Species": Without Koch's Postulates Completed, Can the Bacterium be Considered as the Causal Agent of Citrus Huanglongbing (Yellow Shoot Disease) ?

    Institute of Scientific and Technical Information of China (English)

    Chen J; Deng X; Civerolo E L; Lee R F; Jones J B; Zhou C; Hartung J S; Manjunath K L; Brlansky R H

    2011-01-01

    Huanglongbing (HLB, yellow shoot disease) has been a destructive disease of citrus around the world for over a century, yet the etiology of the disease has not been definitively established. Based mainly on assays for 16S rRNA gene sequences, fastidious bacteria known as "Candidatus Liberibacter species" have been .ssociated with HLB. We are concerned that some current literature frequendy refers to "Ca. Liberibacter spp." as the causal or etiological agent of HLB. However, Koch' s postulates, either sensu stricto or modified, have not yet been completely fulfilled to establish that "Ca. Liberibacter spp." are the cause of HLB.Direct pathological interactions between the bacteria and citrus host have not been conclusively documented.We suggest there is a need for the literature to be precise on this point until the etiology of HLB is firmly established.%黄龙(梢)病被认为是世界柑橘生产上的毁灭性病害已超过一个世纪,但该病害的病原学至今还没有清晰地建立起来.根据16S rRNA基因序列分析,一组被称为"Candidatus Liberibacter species"的难培养细菌被认为与黄龙病相关.然而,要确定"Ca.Liberibacter spp."是黄龙病病原的柯赫氏定理并没有真正完成.令我们担忧的是,近年来有些文献频频指出"Ca.Liberibacter spp."是黄龙病的病原,其实该细菌与柑橘寄主的直接病理反应还没有完全确定.我们建议,在黄龙病病原学清楚之前,文献报道在这方面需要有准确的阐述.

  20. Characterization of copy numbers of 16S rDNA and 16S rRNA of Candidatus Liberibacter asiaticus and the implication in detection in planta using quantitative PCR

    Directory of Open Access Journals (Sweden)

    Wang Nian

    2009-03-01

    Full Text Available Abstract Background Citrus Huanglongbing (HLB is one of the most devastating diseases on citrus and is associated with Candidatus Liberibacter spp.. The pathogens are phloem limited and have not been cultured in vitro. The current management strategy of HLB is to remove infected citrus trees and reduce psyllid populations with insecticides to prevent the spreading. This strategy requires sensitive and reliable diagnostic methods for early detection. Results We investigated the copy numbers of the 16S rDNA and 16S rRNA of the HLB pathogen and the implication of improving the diagnosis of HLB for early detection using Quantitative PCR. We compared the detection of HLB with different Quantitative PCR based methods with primers/probe targeting either 16S rDNA, beta-operon DNA, 16S rRNA, or beta-operon RNA. The 16S rDNA copy number of Ca. Liberibacter asiaticus was estimated to be three times of that of the beta-operon region, thus allowing detection of lower titer of Ca. L. asiaticus. Quantitative reverse transcriptional PCR (QRT-PCR indicated that the 16S rRNA averaged 7.83 times more than that of 16S rDNA for the same samples. Dilution analysis also indicates that QRT-PCR targeting 16S rRNA is 10 time more sensitive than QPCR targeting 16S rDNA. Thus QRT-PCR was able to increase the sensitivity of detection by targeting 16S rRNA. Conclusion Our result indicates that Candidatus Liberibacter asiaticus contains three copies of 16S rDNA. The copy number of 16S rRNA of Ca. L. asiaticus in planta averaged about 7.8 times of 16S rDNA for the same set of samples tested in this study. Detection sensitivity of HLB could be improved through the following approaches: using 16S rDNA based primers/probe in the QPCR assays; and using QRT-PCR assays targeting 16S rRNA.

  1. Validation of 'variable number of tandem repeat'-based approach for examination of 'Candidatus Liberibacter asiaticus' diversity and its applications for the analysis of the pathogen populations in the areas of recent introduction.

    Directory of Open Access Journals (Sweden)

    Luis A Matos

    Full Text Available Citrus greening (Huanglongbing, HLB is one of the most destructive diseases of citrus worldwide. In South Asia HLB has been known for more than a century, while in Americas the disease was found relatively recently. HLB is associated with three species of 'Candidatus Liberibacter' among which 'Ca. Liberibacter asiaticus' (CLas has most wide distribution. Recently, a number of studies identified different regions in the CLas genome with variable number of tandem repeats (VNTRs that could be used for examination of CLas diversity. One of the objectives of the work presented here was to further validate the VNTR analysis-based approach by assessing the stability of these repeats upon multiplication of the pathogen in a host over an extended period of time and upon its passaging from a host to a host using CLas populations from Florida. Our results showed that the numbers of tandem repeats in the four loci tested display very distinguishable "signature profiles" for the two Florida-type CLas haplotype groups. Remarkably, the profiles do not change upon passage of the pathogen in citrus and psyllid hosts as well as after its presence within a host over a period of five years, suggesting that VNTR analysis-based approach represents a valid methodology for examination of the pathogen populations in various geographical regions. Interestingly, an extended analysis of CLas populations in different locations throughout Florida and in several countries in the Caribbean and Central America regions and in Mexico where the pathogen has been introduced recently demonstrated the dispersion of the same haplotypes of CLas. On the other hand, these CLas populations appeared to differ significantly from those obtained from locations where the disease has been present for a much longer time.

  2. 柑橘花器和种子中黄龙病菌的定量分布及应用%Quantitative distribution of Candidatus Liberibacter asiaticus in flowers and seeds of Shatian pummelo and its applications

    Institute of Scientific and Technical Information of China (English)

    娄兵海; 宋雅琴; 赵小龙; 白先进; 邓崇岭

    2014-01-01

    为准确、快速测定感病柑橘花器和种子中黄龙病菌(Candidatus Liberibacter asiaticus,Las)的含量,比较了SYBR Green Ⅰ实时荧光定量PCR (SGI-qPCR)和单管双引物对TaqMan探针qPCR(STDP-qPCR)的检测灵敏度,并用STDP-qPCR法定量检测了感病沙田柚花器和种子中的Las.结果显示,STDP-qPCR检测灵敏度为1×100拷贝/μL,比SGI-qPCR高100倍;花器中的雄蕊、花瓣、雌蕊和花粉等组织,以及种子的种皮和胚乳组织中均可检测到Las,但含量差异较大,其中种皮组织中Las含量最高,达到109842个细胞/μg DNA,花粉中的Las含量最低,为308个细胞/μg DNA,所有种壳中均未检测到Las;基于雄蕊组织的黄龙病分子诊断准确率达93.8%.表明Las在感病柑橘花器和种子中呈不均匀分布,基于雄蕊组织的黄龙病诊断方法可辅助用于该病害的高通量检测.

  3. Population Structure of‘Candidatus Liberibacter asiaticus’ in China Revealed by SSR Markers%基于SSR标记的中国亚洲韧皮杆菌种群结构研究

    Institute of Scientific and Technical Information of China (English)

    黄爱军; 苏华楠; 王雪峰; 唐科志; 李中安; 周常勇

    2014-01-01

    目的亚洲韧皮部杆菌是柑橘黄龙病病原。通过筛选SSR(Simple sequence repeat)位点,分析中国境内亚洲韧皮部杆菌(‘Candidatus Liberibacter asiaticus’)的群体结构。方法根据已报道亚洲韧皮部杆菌基因组上的25个SSR位点,使用中国不同地理来源的样品,对报道的SSR位点进行筛选,找出其中适宜进行中国样品群体结构分析的位点。应用PCR的方法,对收集的中国境内的285个亚洲韧皮部杆菌相应SSR位点进行扩增,聚丙烯酰胺凝胶电泳。所得电泳图导入软件Quantity One 4.5.0读取产物的碱基数。通过PopGen version 1.31软件评估选出的位点和不同地理来源的样品的多态性,分别使用软件Powermarker 3.25和structure 2.3.4进行聚类分析。结果共选出5个SSR位点可用于中国种群结构研究,Nei's多样性指数0.1542—0.9556。其中LasA位点多态性最高,有效等位基因数NE=22.5,Nei's多样性指数H=0.9556。通过这5个位点分析中国境内8个不同地理来源的样品,发现云南省样品存在较高多态性,NE=5.7,H=0.6580。8个地理种群间的遗传距离0.0236—0.5786,遗传相似度0.5607—0.9767,广西和四川遗传距离最大,遗传相似度最小。Powermarker软件以UPGMA方法进行聚类分析的结果显示,所有样品分为两个组群,四川和云南为一个组群;福建、浙江、贵州、广东、广西和江西为一个组群。Structure软件分析也得出了相似的结果,云南和四川样品的种群构成较为单一,90%以上个体为同一组群,而其他6个地理来源不同程度的为两个组群的混合。结论基于5个SSR位点分析中国境内的Ca. L. asiaticus表明其可能存在两种不同的群体结构,为进一步研究中国柑橘黄龙病的发生和流行规律提供了有价值的线索。%[Objective] ‘Candidatus Liberibacter asiaticus’ is the pathogeny of Citrus Huanglongbing. The purpose

  4. CONSTRAINTS ON THE UBIQUITY OF CORONAL X-RAY CYCLES

    Energy Technology Data Exchange (ETDEWEB)

    Hoffman, John [Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801 (United States); Guenther, Hans M.; Wright, Nicholas J., E-mail: hoffma24@illinois.edu, E-mail: guenther@head.cfa.harvard.edu, E-mail: nwright@cfa.harvard.edu [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2012-11-10

    Stellar activity cycles are known to be a widespread phenomenon amongst moderately active solar- and late-type stars from long-term periodic variations in chromospheric Ca II H and K emission lines, yet to date, only a handful of coronal X-ray cycles are known. We have surveyed serendipitously observed stellar sources in fields observed multiple times in the last decade by XMM-Newton and present our analysis of nine stars from six fields. Since our sample is flux-limited, it is strongly biased toward higher levels of X-ray activity. We fit a single temperature APEC spectrum to each source and search for significant periodicities using a Lomb-Scargle periodogram. We use a Monte Carlo (MC) algorithm to yield robust analysis of the statistical significance of cycle detections and non-detections. None of the nine stellar light curves show any convincing indications of periodicity. From MC simulations, we simulate the detection capabilities of our methodology and, assuming a uniform distribution of cycle periods and strengths over the domain searched, we conclude with 95% confidence that less than 72% of the stars represented by our sample of active stars have 5-13 year coronal X-ray cycles.

  5. Ubiquity of Kelvin-Helmholtz waves at Earth's magnetopause.

    Science.gov (United States)

    Kavosi, Shiva; Raeder, Joachim

    2015-05-11

    Magnetic reconnection is believed to be the dominant process by which solar wind plasma enters the magnetosphere. However, for periods of northward interplanetary magnetic field (IMF) reconnection is less likely at the dayside magnetopause, and Kelvin-Helmholtz waves (KHWs) may be important agents for plasma entry and for the excitation of ultra-low-frequency (ULF) waves. The relative importance of KHWs is controversial because no statistical data on their occurrence frequency exist. Here we survey 7 years of in situ data from the NASA THEMIS (Time History of Events and Macro scale Interactions during Substorms) mission and find that KHWs occur at the magnetopause ∼19% of the time. The rate increases with solar wind speed, Alfven Mach number and number density, but is mostly independent of IMF magnitude. KHWs may thus be more important for plasma transport across the magnetopause than previously thought, and frequently drive magnetospheric ULF waves.

  6. The ubiquity of mouthings in NGT : a corpus study

    NARCIS (Netherlands)

    Bank, R.

    2015-01-01

    When deaf signers of Sign Language of the Netherlands (NGT, Nederlandse Gebarentaal) sign among themselves, they often combine their signing with moutings: mouthed lexical items from spoken Dutch. Using a corpus of (semi-)spontaneous signing by deaf native signers, this dissertation investigates the

  7. The Hidden Cost of Ubiquity: Globalisation and Terrorism

    NARCIS (Netherlands)

    B. Krug (Barbara); P. Reinmoeller (Patrick)

    2003-01-01

    textabstractTerrorism is not a natural hazard outside the range of corporate decision-making. Simple micro-economic analysis shows how globalisation changed the supply of terrorist attacks and the costs for tolerating terrorist hazard. Approaches developed in organizational strategy help to single o

  8. PERSONAL-PRACTICES POLLUTANTS: UBIETY, UBIQUITY, SIGNIFICANCE, SOLUTIONS, STEWARDSHIP

    Science.gov (United States)

    The occurrence of pharmaceuticals and personal care products (PPCPS) as environmental pollutants is a multifaceted issue whose scope continues to become better delineated with the escalation of attention that began in the 1980s. PPCPs typically occur as trace environmental pollut...

  9. Ubiquity of Exciton Localization in Cryogenic Carbon Nanotubes.

    Science.gov (United States)

    Hofmann, Matthias S; Noé, Jonathan; Kneer, Alexander; Crochet, Jared J; Högele, Alexander

    2016-05-11

    We present photoluminescence studies of individual semiconducting single-wall carbon nanotubes at room and cryogenic temperatures. From the analysis of spatial and spectral features of nanotube photoluminescence, we identify characteristic signatures of unintentional exciton localization. Moreover, we quantify the energy scale of exciton localization potentials as ranging from a few to a few tens of millielectronvolts and stemming from both environmental disorder and shallow covalent side-wall defects. Our results establish disorder-induced crossover from the diffusive to the localized regime of nanotube excitons at cryogenic temperatures as a ubiquitous phenomenon in micelle-encapsulated and as-grown carbon nanotubes.

  10. The Ubiquity of Coeval Starbursts in Massive Galaxy Cluster Progenitors

    CERN Document Server

    Casey, Caitlin M

    2016-01-01

    The Universe's largest galaxy clusters likely built the majority of their massive $>10^{11} M_\\odot$ galaxies in simultaneous, short-lived bursts of activity well before virialization. This conclusion is reached from emerging datasets on $z>2$ proto-clusters and the characteristics of their member galaxies, in particular, rare starbursts and ultraluminous active galactic nuclei (AGN). The most challenging observational hurdle in identifying such structures is their very large volumes, $\\sim10^{4}$ comoving Mpc$^3$ at $z>2$, subtending areas $\\sim$half a degree on the sky. Thus the contrast afforded by an overabundance of very rare galaxies in comparison to the background can more easily distinguish overdense structures from the surrounding, normal density field. Five $210^{15} M_\\odot$ galaxy clusters in the nearby Universe, a factor of five larger than expected in some simulations. Some tension yet exists between measurements of their volume density of starburst-rich proto-clusters and the expectation that t...

  11. On the unnecessary ubiquity of hierarchical linear modeling.

    Science.gov (United States)

    McNeish, Daniel; Stapleton, Laura M; Silverman, Rebecca D

    2017-03-01

    In psychology and the behavioral sciences generally, the use of the hierarchical linear model (HLM) and its extensions for discrete outcomes are popular methods for modeling clustered data. HLM and its discrete outcome extensions, however, are certainly not the only methods available to model clustered data. Although other methods exist and are widely implemented in other disciplines, it seems that psychologists have yet to consider these methods in substantive studies. This article compares and contrasts HLM with alternative methods including generalized estimating equations and cluster-robust standard errors. These alternative methods do not model random effects and thus make a smaller number of assumptions and are interpreted identically to single-level methods with the benefit that estimates are adjusted to reflect clustering of observations. Situations where these alternative methods may be advantageous are discussed including research questions where random effects are and are not required, when random effects can change the interpretation of regression coefficients, challenges of modeling with random effects with discrete outcomes, and examples of published psychology articles that use HLM that may have benefitted from using alternative methods. Illustrative examples are provided and discussed to demonstrate the advantages of the alternative methods and also when HLM would be the preferred method. (PsycINFO Database Record

  12. The ubiquity of frequency effects in first language acquisition.

    Science.gov (United States)

    Ambridge, Ben; Kidd, Evan; Rowland, Caroline F; Theakston, Anna L

    2015-03-01

    This review article presents evidence for the claim that frequency effects are pervasive in children's first language acquisition, and hence constitute a phenomenon that any successful account must explain. The article is organized around four key domains of research: children's acquisition of single words, inflectional morphology, simple syntactic constructions, and more advanced constructions. In presenting this evidence, we develop five theses. (i) There exist different types of frequency effect, from effects at the level of concrete lexical strings to effects at the level of abstract cues to thematic-role assignment, as well as effects of both token and type, and absolute and relative, frequency. High-frequency forms are (ii) early acquired and (iii) prevent errors in contexts where they are the target, but also (iv) cause errors in contexts in which a competing lower-frequency form is the target. (v) Frequency effects interact with other factors (e.g. serial position, utterance length), and the patterning of these interactions is generally informative with regard to the nature of the learning mechanism. We conclude by arguing that any successful account of language acquisition, from whatever theoretical standpoint, must be frequency sensitive to the extent that it can explain the effects documented in this review, and outline some types of account that do and do not meet this criterion.

  13. The ubiquity of phenotypic plasticity in plants: a synthesis.

    Science.gov (United States)

    Palacio-López, Kattia; Beckage, Brian; Scheiner, Samuel; Molofsky, Jane

    2015-08-01

    Adaptation to heterogeneous environments can occur via phenotypic plasticity, but how often this occurs is unknown. Reciprocal transplant studies provide a rich dataset to address this issue in plant populations because they allow for a determination of the prevalence of plastic versus canalized responses. From 31 reciprocal transplant studies, we quantified the frequency of five possible evolutionary patterns: (1) canalized response-no differentiation: no plasticity, the mean phenotypes of the populations are not different; (2) canalized response-population differentiation: no plasticity, the mean phenotypes of the populations are different; (3) perfect adaptive plasticity: plastic responses with similar reaction norms between populations; (4) adaptive plasticity: plastic responses with parallel, but not congruent reaction norms between populations; and (5) nonadaptive plasticity: plastic responses with differences in the slope of the reaction norms. The analysis included 362 records: 50.8% life-history traits, 43.6% morphological traits, and 5.5% physiological traits. Across all traits, 52% of the trait records were not plastic, and either showed no difference in means across sites (17%) or differed among sites (83%). Among the 48% of trait records that showed some sort of plasticity, 49.4% showed perfect adaptive plasticity, 19.5% adaptive plasticity, and 31% nonadaptive plasticity. These results suggest that canalized responses are more common than adaptive plasticity as an evolutionary response to environmental heterogeneity.

  14. The Ubiquity and Dual Nature of Ultra Compact Dwarfs

    CERN Document Server

    Norris, Mark A

    2011-01-01

    We present the discovery of several Ultra Compact Dwarfs (UCDs) located in field/group environments. Examination of these objects, plus literature objects, confirms the existence of two distinct formation channels for UCDs. We find that the UCDs we have discovered around the group elliptical NGC3923 (and UCDs generally) have properties consistent with their being the most luminous members of the host galaxy's globular cluster (GC) system. We describe UCDs of this type as giant GCs (GGCs). In contrast, the UCD we have found associated with the isolated S0 NGC4546 is clearly the result of the stripping of a nucleated companion galaxy. The young age (~3.4 Gyr) of the UCD, the lack of a correspondingly young GC population, the apparently short dynamical friction decay timescale (~0.5 Gyr) of the UCD, and the presence of a counterrotating gas disc in the host galaxy (co-rotating with the UCD) together suggest that this UCD is the liberated nucleus remaining after the recent stripping of a companion by NGC4546. We ...

  15. Ubiquity and diversity of human-associated Demodex mites.

    Directory of Open Access Journals (Sweden)

    Megan S Thoemmes

    Full Text Available Demodex mites are a group of hair follicle and sebaceous gland-dwelling species. The species of these mites found on humans are arguably the animals with which we have the most intimate interactions. Yet, their prevalence and diversity have been poorly explored. Here we use a new molecular method to assess the occurrence of Demodex mites on humans. In addition, we use the 18S rRNA gene (18S rDNA to assess the genetic diversity and evolutionary history of Demodex lineages. Within our samples, 100% of people over 18 years of age appear to host at least one Demodex species, suggesting that Demodex mites may be universal associates of adult humans. A phylogenetic analysis of 18S rDNA reveals intraspecific structure within one of the two named human-associated Demodex species, D. brevis. The D. brevis clade is geographically structured, suggesting that new lineages are likely to be discovered as humans from additional geographic regions are sampled.

  16. The Ubiquity of Frequency Effects in First Language Acquisition

    Science.gov (United States)

    Ambridge, Ben; Kidd, Evan; Rowland, Caroline F.; Theakston, Anna L.

    2015-01-01

    This review article presents evidence for the claim that frequency effects are pervasive in children's first language acquisition, and hence constitute a phenomenon that any successful account must explain. The article is organized around four key domains of research: children's acquisition of single words, inflectional morphology, simple…

  17. On the Ubiquity and Utility of Cyclic Schemes

    CERN Document Server

    Abreu, M; Labbate, D; Napolitano, V

    2011-01-01

    Let $k,l,m,n$, and $\\mu$ be positive integers. A $\\mathbb{Z}_\\mu$--{\\it scheme of valency} $(k,l)$ and {\\it order} $(m,n)$ is a $m \\times n$ array $(S_{ij})$ of subsets $S_{ij} \\subseteq \\mathbb{Z}_\\mu$ such that for each row and column one has $\\sum_{j=1}^n |S_{ij}| = k $ and $\\sum_{i=1}^m |S_{ij}| = l$, respectively. Any such scheme is an algebraic equivalent of a $(k,l)$-semi-regular bipartite voltage graph with $n$ and $m$ vertices in the bipartition sets and voltages coming from the cyclic group $\\mathbb{Z}_\\mu$. We are interested in the subclass of $\\mathbb{Z}_\\mu$--schemes that are characterized by the property $a - b + c - d\\; \

  18. Ubiquity and diversity of human-associated Demodex mites.

    Science.gov (United States)

    Thoemmes, Megan S; Fergus, Daniel J; Urban, Julie; Trautwein, Michelle; Dunn, Robert R

    2014-01-01

    Demodex mites are a group of hair follicle and sebaceous gland-dwelling species. The species of these mites found on humans are arguably the animals with which we have the most intimate interactions. Yet, their prevalence and diversity have been poorly explored. Here we use a new molecular method to assess the occurrence of Demodex mites on humans. In addition, we use the 18S rRNA gene (18S rDNA) to assess the genetic diversity and evolutionary history of Demodex lineages. Within our samples, 100% of people over 18 years of age appear to host at least one Demodex species, suggesting that Demodex mites may be universal associates of adult humans. A phylogenetic analysis of 18S rDNA reveals intraspecific structure within one of the two named human-associated Demodex species, D. brevis. The D. brevis clade is geographically structured, suggesting that new lineages are likely to be discovered as humans from additional geographic regions are sampled.

  19. Ethographic ubiquity: original fake, expanded codex, transurban subject, performative doll

    Directory of Open Access Journals (Sweden)

    Massimo Canevacci

    2012-12-01

    Full Text Available My essay presents the emerging of fake as a concept that does not mean false, but a post-dualistic mix of false/truth. The relation between digital culture and ubiquitous subjectivity is fundamental during its process; in the same way, the relation between aura and reproducibility cannot be determined dialectically as Benjamin did. Digital auratic reproducibility is the contemporary context and communicational metropolis is characterized by spontaneous and public performance: so, my conclusion is an analysis of some “living” doll and their uncanny presence.

  20. Ubiquity of Benfords law and emergence of the reciprocal distribution

    CERN Document Server

    Friar, J L; Perez-Mercader, J

    2016-01-01

    We apply the Law of Total Probability to the construction of scale-invariant probability distribution functions (pdfs), and require that probability measures be dimensionless and unitless under a continuous change of scales. If the scale-change distribution function is scale invariant then the constructed distribution will also be scale invariant. Repeated application of this construction on an arbitrary set of (normalizable) pdfs results again in scale-invariant distributions. The invariant function of this procedure is given uniquely by the reciprocal distribution, suggesting a kind of universality. We separately demonstrate that the reciprocal distribution results uniquely from requiring maximum entropy for size-class distributions with uniform bin sizes.

  1. The ubiquity of model-based reinforcement learning.

    Science.gov (United States)

    Doll, Bradley B; Simon, Dylan A; Daw, Nathaniel D

    2012-12-01

    The reward prediction error (RPE) theory of dopamine (DA) function has enjoyed great success in the neuroscience of learning and decision-making. This theory is derived from model-free reinforcement learning (RL), in which choices are made simply on the basis of previously realized rewards. Recently, attention has turned to correlates of more flexible, albeit computationally complex, model-based methods in the brain. These methods are distinguished from model-free learning by their evaluation of candidate actions using expected future outcomes according to a world model. Puzzlingly, signatures from these computations seem to be pervasive in the very same regions previously thought to support model-free learning. Here, we review recent behavioral and neural evidence about these two systems, in attempt to reconcile their enigmatic cohabitation in the brain.

  2. Ubiquity and specificity of reinforcement signals throughout the human brain.

    Science.gov (United States)

    Vickery, Timothy J; Chun, Marvin M; Lee, Daeyeol

    2011-10-06

    Reinforcements and punishments facilitate adaptive behavior in diverse domains ranging from perception to social interactions. A conventional approach to understanding the corresponding neural substrates focuses on the basal ganglia and its dopaminergic projections. Here, we show that reinforcement and punishment signals are surprisingly ubiquitous in the gray matter of nearly every subdivision of the human brain. Humans played either matching-pennies or rock-paper-scissors games against computerized opponents while being scanned using fMRI. Multivoxel pattern analysis was used to decode previous choices and their outcomes, and to predict upcoming choices. Whereas choices were decodable from a confined set of brain structures, their outcomes were decodable from nearly all cortical and subcortical structures. In addition, signals related to both reinforcements and punishments were recovered reliably in many areas and displayed patterns not consistent with salience-based explanations. Thus, reinforcement and punishment might play global modulatory roles in the entire brain.

  3. Ubiquity of non-geometry in heterotic compactifications

    CERN Document Server

    García-Etxebarria, Iñaki; Massai, Stefano; Mayrhofer, Christoph

    2016-01-01

    We study the effect of quantum corrections on heterotic compactifications on elliptic fibrations away from the stable degeneration limit, elaborating on a recent observation by Malmendier and Morrison. We show that already for the simplest non-trivial elliptic fibration the effect is quite dramatic: the $I_1$ degeneration with trivial gauge background dynamically splits into two T-fects with monodromy around each T-fect being (conjugate to) T-duality along one of the legs of the $T^2$. This implies that almost every elliptic heterotic compactification becomes a non-geometric T-fold away from the stable degeneration limit. We also point out a subtlety due to this non-geometric splitting at finite fiber size. It arises when determining, via heterotic/F-theory duality, the SCFTs associated to a small number of pointlike instantons probing heterotic ADE singularities. Along the way we resolve various puzzles in the literature.

  4. Prosomes. Ubiquity and inter-species structural variation.

    Science.gov (United States)

    Martins de Sa, C; Grossi de Sa, M F; Akhayat, O; Broders, F; Scherrer, K; Horsch, A; Schmid, H P

    1986-02-20

    The "prosomes", a novel type of ubiquitous ribonucleoprotein particle of extraordinary stability and of defined electron microscopical structure, have been characterized in several cell types and species. Identified as a 19 S sub-component of free mRNA-protein complexes, including globin and other repressed mRNA, in the cytoplasm of duck, mouse and HeLa cells, they were previously found to inhibit protein synthesis in vitro. In all cells studied, electron microscopy shows an identical, seemingly ring-like but rather raspberry-shaped particle of 12 nm diameter, resistant to EDTA and 1% (w/v) Sarkosyl. Two-dimensional electrophoretic analysis of prosomal proteins shows a characteristic pattern in the 19,000 to 35,000 Mr range of pI 4 to 7, with an additional 56,000 Mr component specific to avian species. The prosomes found in globin mRNA-protein complexes contain about 25 protein components, 16 of which have identical molecular weight and pI values in duck and mouse, and which are also found in the prosomes of the heterogeneous free mRNPs of HeLa cells. Seral and monoclonal antibodies raised in mice against the prosomes of duck erythroblasts cross-react with some of the proteins of the mouse and HeLa cell particles. Prosomes isolated from duck and mouse globin mRNP, both contain small cytoplasmic RNAs of 70 to 90 nucleotides, which represent about 15% of the particle mass. The molecular weight and the 3'-terminal oligonucleotide of each one of these small cytoplasmic RNAs are identical in the two animal species; fingerprints of their oligonucleotides generated by RNase T1 show that more than 80% of spots are identical. In contrast, the prosomes of HeLa cells, associated with a large population of repressed mRNA, contain at least 12 small cytoplasmic RNA species. All prosomal RNAs tested so far hybridize to mRNA. The data available indicate that prosomes constitute a novel class of ubiquitous cellular ribonucleoprotein complexes, present in the nucleus and cytoplasm that, in its structural variations shown here, reflects function and species.

  5. Genetic variation analysis of an outer membrane protein gene of Candidatus Liberibacter asiaticus%柑橘黄龙病菌亚洲种外膜蛋白基因的遗传变异分析

    Institute of Scientific and Technical Information of China (English)

    鹿连明; 杜丹超; 程保平; 胡秀荣; 张利平; 陈国庆

    2014-01-01

    为了解柑橘黄龙病菌亚洲种(Candidatus Liberibacter asiaticus)的遗传多样性,对来源于国内外7个不同地区和浙江台州地区11个不同寄主品种的 Ca.L.asiaticus 的外膜蛋白(outer membrane protein,OMP)基因进行聚合酶链反应限制性片段长度多态性分析(polymerase chain reaction-restriction fragment length polymorphism,PCR-RFLP).PCR 产物经克隆测序后,利用 NCBI Blast 和 DNAMAN 软件对 omp 基因序列进行多重比对,并用 MEGA 软件构建系统发育树.结果显示:在浙江台州地区不同寄主品种上 Ca.L.asiaticus 各分离物的 omp 基因的酶切片段长度不具有多态性,其基因序列也完全一致;而不同地理来源的 Ca.L.asiaticus 的omp 基因经限制性内切酶消化后可产生不同的 RFLP 指纹图谱,其核酸序列和氨基酸序列均存在变异,表明 Ca. L.asiaticus 存在种内遗传多样性.在系统发育树上,所有的 Ca.L.asiaticus 分离物聚为1个分支,而 Ca.L. africanus 和 Ca.L.solanacearum 分别处于不同的分支上.%Summary Huanglongbing (HLB) is a destructive disease that represents a major threat to the world citrus industry.It was first reported from Chaoshan area of Guangdong Province in the early 20th century,and is now known to occur in next to 40 different Asian,African,Oceanian,South and North American countries and areas. Its pathogen is a phloem-limited,non-cultured,Gram-negative bacterium which belongs to the genus Candidatus Liberibacter.Three species,i.e.,Ca. L.asiaticus,Ca. L.americanus,and Ca. L.africanus with Ca. L. africanus subsp.capensis are currently known.So far,the pathogen of HLB disease discovered in China is only Ca.L.asiaticus,which distributes widely in almost all major citrus growing areas such as Guangdong,Guangxi, Fujian,Yunnan,Zhejiang and so on.This pathogen can be transmitted by grafting and Diaphorina citri and infect almost all fruit trees of Citrus Fortunella and Poncirus

  6. 中国柑橘黄龙病病原菌两个原噬菌体超变异基因遗传多样性%Genetic Diversity of Two Hypervariable Genes from Prophage Regions of‘Candidatus Liberibacter asiaticus’ in China

    Institute of Scientific and Technical Information of China (English)

    谭锦; 王雪峰; 苏华楠; 李中安; 周常勇

    2013-01-01

    [目的]通过原噬菌体区域高度变异的基因位点研究柑橘黄龙病病原菌亚洲种(‘Candidatus Liberibacter asiaticus’)的种群分化,探讨病原菌种群遗传多样性水平和遗传结构。[方法]基于2种原噬菌体类型(SC1和SC2)对应的超变异基因区域设计2对引物(Lap-TJ-F/Lap-TJ-R1和Lap-TJ-F/Lap-TJ-R2),对中国不同柑橘产区的224个‘Ca. L. asiaticus’株系进行PCR检测和序列分析。[结果]PCR扩增的条带类型呈多态性,具有4种条带类型(SC1-1、SC1-2、SC2-1和SC2-2),西南地区以SC1-1型为主,广东、广西地区以SC2-1型为主,福建、江西、浙江地区没有明显优势的扩增型。分析SC1-1和SC1-2对应序列表明,其差异系由于132 bp的卫星序列和24 bp的小卫星序列2种串联重复序列数不同引起,而SC2-1和SC2-2的差异系由原噬菌体内部基因重排引起。[结论]中国不同地理来源病原菌株系在原噬菌体区域具有较丰富的多态性,对该基因区域研究将有助于揭示中国‘Ca. L. asiaticus’种群的遗传多样性。%[Objective] Hypervariable genomic loci of prophage region were used to study population differentiation and genetic diversity of‘Candidatus Liberibacter asiaticus’, the putative casual agent of citrus Huanglongbing (HLB). [Method] Two primer sets (Lap-TJ-F/Lap-TJ-R1 and Lap-TJ-F/Lap-TJ-R2), targeted hypervariable genomic regions of two prophage types (SC1 and SC2), respectively, were used for PCR detection and sequence analysis of 224 ‘Ca. L. asiaticus’ strains from different citrus producing areas in China.[Result]PCR amplicon polymorphisms and four amplion types (SC1-1, SC1-2, SC2-1 and SC2-2) were observed, SC1-1 and SC2-1 were the predominant types in Southwestern region and Guangdong-Guangxi region, respectively, and no dominant types were found in Fujian-Jiangxi-Zhejiang region. The sequence differences in SC1-1/SC1-2 were mainly caused by different

  7. Homo ludicus. The ubiquity of play and its roles in present society

    Directory of Open Access Journals (Sweden)

    Peppino Ortoleva

    2012-05-01

    Full Text Available In the last decades new technologies, the rearrangement of living and labour time and other less visible cultural factors have brought some significant historical modifications to the traditionally separated area of the ludic. New types of games have emerged and the threshold between play and reality has been redefined to include aspects of social life that seemed to be unrelated to playing activities.

  8. Ubiquity and quantitative significance of detoxification catabolism of chlorophyll associated with protistan herbivory.

    Science.gov (United States)

    Kashiyama, Yuichiro; Yokoyama, Akiko; Kinoshita, Yusuke; Shoji, Sunao; Miyashiya, Hideaki; Shiratori, Takashi; Suga, Hisami; Ishikawa, Kanako; Ishikawa, Akira; Inouye, Isao; Ishida, Ken-ichiro; Fujinuma, Daiki; Aoki, Keisuke; Kobayashi, Masami; Nomoto, Shinya; Mizoguchi, Tadashi; Tamiaki, Hitoshi

    2012-10-23

    Chlorophylls are essential components of the photosynthetic apparati that sustain all of the life forms that ultimately depend on solar energy. However, a drawback of the extraordinary photosensitizing efficiency of certain chlorophyll species is their ability to generate harmful singlet oxygen. Recent studies have clarified the catabolic processes involved in the detoxification of chlorophylls in land plants, but little is understood about these strategies in aquatic ecosystem. Here, we report that a variety of heterotrophic protists accumulate the chlorophyll a catabolite 13(2),17(3)-cyclopheophorbide a enol (cPPB-aE) after their ingestion of algae. This chlorophyll derivative is nonfluorescent in solution, and its inability to generate singlet oxygen in vitro qualifies it as a detoxified catabolite of chlorophyll a. Using a modified analytical method, we show that cPPB-aE is ubiquitous in aquatic environments, and it is often the major chlorophyll a derivative. Our findings suggest that cPPB-aE metabolism is one of the most important, widely distributed processes in aquatic ecosystems. Therefore, the herbivorous protists that convert chlorophyll a to cPPB-aE are suggested to play more significant roles in the modern oceanic carbon flux than was previously recognized, critically linking microscopic primary producers to the macroscopic food web and carbon sequestration in the ocean.

  9. Ubiquity of organic nitrates from nighttime chemistry in the European submicron aerosol

    Science.gov (United States)

    Kiendler-Scharr, A.; Mensah, A. A.; Friese, E.; Topping, D.; Nemitz, E.; Prevot, A. S. H.; ńijälä, M.; Allan, J.; Canonaco, F.; Canagaratna, M.; Carbone, S.; Crippa, M.; Dall Osto, M.; Day, D. A.; De Carlo, P.; Di Marco, C. F.; Elbern, H.; Eriksson, A.; Freney, E.; Hao, L.; Herrmann, H.; Hildebrandt, L.; Hillamo, R.; Jimenez, J. L.; Laaksonen, A.; McFiggans, G.; Mohr, C.; O'Dowd, C.; Otjes, R.; Ovadnevaite, J.; Pandis, S. N.; Poulain, L.; Schlag, P.; Sellegri, K.; Swietlicki, E.; Tiitta, P.; Vermeulen, A.; Wahner, A.; Worsnop, D.; Wu, H.-C.

    2016-07-01

    In the atmosphere nighttime removal of volatile organic compounds is initiated to a large extent by reaction with the nitrate radical (NO3) forming organic nitrates which partition between gas and particulate phase. Here we show based on particle phase measurements performed at a suburban site in the Netherlands that organic nitrates contribute substantially to particulate nitrate and organic mass. Comparisons with a chemistry transport model indicate that most of the measured particulate organic nitrates are formed by NO3 oxidation. Using aerosol composition data from three intensive observation periods at numerous measurement sites across Europe, we conclude that organic nitrates are a considerable fraction of fine particulate matter (PM1) at the continental scale. Organic nitrates represent 34% to 44% of measured submicron aerosol nitrate and are found at all urban and rural sites, implying a substantial potential of PM reduction by NOx emission control.

  10. The fallacy of the average: on the ubiquity, utility and continuing novelty of Jensen's inequality.

    Science.gov (United States)

    Denny, Mark

    2017-01-15

    Biologists often cope with variation in physiological, environmental and ecological processes by measuring how living systems perform under average conditions. However, performance at average conditions is seldom equal to average performance across a range of conditions. This basic property of nonlinear averaging - known as 'Jensen's inequality' or 'the fallacy of the average' - has important implications for all of biology. For instance, a burgeoning awareness of Jensen's inequality has improved our ability to predict how plants and animals will respond to a warmer and more variable future climate. But for many biologists, the fallacy of the average is still a novel concept. Here, I highlight the importance of Jensen's inequality, provide a simple graphical approach to understanding its effects, and explore its consequences at atomic, molecular, organismal and ecological levels.

  11. Wish-fulfilling jewel pills: Tibetan medicines from exclusivity to ubiquity.

    Science.gov (United States)

    Blaikie, Calum

    2015-04-01

    Despite the recent growth of social science literature concerning the traditional medicine industry in Asia, insights into the contemporary dynamics of so-called 'classical formulae' remain relatively scant, as do studies of small-scale, less capitally intensive and technologically advanced modes of production. This paper seeks to address these gaps by considering a single Sowa Rigpa (Tibetan medicine) formula known as Samphel Norbu, or 'wish-fulfilling jewel', which appears in numerous texts and is today among the most popular Tibetan medicines in the world. Drawing primarily upon long-term fieldwork in Himalayan India, the paper follows Samphel Norbu's rise from exclusivity to popularity and examines the ways it has been transformed in the process, both materially and in its economic, social and clinical significance. The paper shows how Samphel Norbu acts as a marker of inequality between different groups of healers, and examines the role the medicine played in the development of commercial pharmacy and the proliferation of complex medicines. Tracing out wide variations in the medicine's formulation, composition, mode of production and pattern of circulation places the issue of multiplicity at the centre of analysis, and leads to a questioning of the assumptions that underpin the category 'classical formula'. The paper reflects upon the repositioning of such formulae within emergent configurations of knowledge, power, industry and market, and on their transformations and transformative effects both over time and in the present moment.

  12. MORPHOLOGY OF BLACK CARBON AEROSOLS AND UBIQUITY OF 50-NANOMETER BLACK CARBON AEROSOLS IN THE ATMOSPHERE

    Institute of Scientific and Technical Information of China (English)

    Fengfu Fu; Liangjun Xu; Wei Ye; Yiquan Chen; Mingyu Jiang; Xueqin Xu

    2006-01-01

    Different-sized aerosols were collected by an Andersen air sampler to observe the detailed morphology of the black carbon (BC) aerosols which were separated chemically from the other accompanying aerosols, using a Scanning Electron Microscope equipped with an Energy Dispersive X-ray Spectrometer (SEM-EDX). The results indicate that most BC aerosols are spherical particles of about 50 nm in diameter and with a homogeneous surface. Results also show that these particles aggregate with other aerosols or with themselves to form larger agglomerates in the micrometer range. The shape of these 50-nm BC spherical particles was found to be very similar to that of BC particles released from petroleum-powered vehicular internal combustion engines. These spherical BC particles were shown to be different from the previously reported fullerenes found using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS).

  13. The ubiquity of the rms-flux relation in black hole X-ray binaries

    NARCIS (Netherlands)

    Heil, L.M.; Vaughan, S.; Uttley, P.

    2012-01-01

    We have investigated the short-term linear relation between the rms variability and the flux in 1961 observations of nine black hole X-ray binaries. The rms-flux relation for the 1-10 Hz range is ubiquitously observed in any observation with good variability signal-to-noise ratio (>3 per cent, 1-10 

  14. Ubiquity, diversity and physiological characteristics of Geodermatophilaceae in Shapotou National Desert Ecological Reserve.

    Science.gov (United States)

    Sun, Hong-Min; Zhang, Tao; Yu, Li-Yan; Sen, Keya; Zhang, Yu-Qin

    2015-01-01

    The goal of this study was to gain insight into the diversity of culturable actinobacteria in desert soil crusts and to determine the physiological characteristics of the predominant actinobacterial group in these crusts. Culture-dependent method was employed to obtain actinobacterial strains from desert soil samples collected from Shapotou National Desert Ecological Reserve (NDER) located in Tengger Desert, China. A total of 376 actinobacterial strains were isolated and 16S rRNA gene sequences analysis indicated that these isolates belonged to 29 genera within 18 families, among which the members of the family Geodermatophilaceae were predominant. The combination of 16S rRNA gene information and the phenotypic data allowed these newly-isolated Geodermatophilaceae members to be classified into 33 "species clusters," 11 of which represented hitherto unrecognized species. Fermentation broths from 19.7% of the isolated strains showed activity in at least one of the six screens for antibiotic activity. These isolates exhibited bio-diversity in enzymatic characteristics and carbon utilization profiles. The physiological characteristics of the isolates from different types of crusts or bare sand samples were specific to their respective micro-ecological environments. Our study revealed that members of the family Geodermatophilaceae were ubiquitous, abundant, and diverse in Shapotou NDER, and these strains may represent a new major group of potential functional actinobacteria in desert soil.

  15. The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution.

    Science.gov (United States)

    Sakamaki, Kazuhiro; Shimizu, Kouhei; Iwata, Hiroaki; Imai, Kenichiro; Satou, Yutaka; Funayama, Noriko; Nozaki, Masami; Yajima, Mamiko; Nishimura, Osamu; Higuchi, Mayura; Chiba, Kumiko; Yoshimoto, Michi; Kimura, Haruna; Gracey, Andrew Y; Shimizu, Takashi; Tomii, Kentaro; Gotoh, Osamu; Akasaka, Koji; Sawasaki, Tatsuya; Miller, David J

    2014-12-01

    The caspases, a family of cysteine proteases, play multiple roles in apoptosis, inflammation, and cellular differentiation. Caspase-8 (Casp8), which was first identified in humans, functions as an initiator caspase in the apoptotic signaling mediated by cell-surface death receptors. To understand the evolution of function in the Casp8 protein family, casp8 orthologs were identified from a comprehensive range of vertebrates and invertebrates, including sponges and cnidarians, and characterized at both the gene and protein levels. Some introns have been conserved from cnidarians to mammals, but both losses and gains have also occurred; a new intron arose during teleost evolution, whereas in the ascidian Ciona intestinalis, the casp8 gene is intronless and is organized in an operon with a neighboring gene. Casp8 activities are near ubiquitous throughout the animal kingdom. Exogenous expression of a representative range of nonmammalian Casp8 proteins in cultured mammalian cells induced cell death, implying that these proteins possess proapoptotic activity. The cnidarian Casp8 proteins differ considerably from their bilaterian counterparts in terms of amino acid residues in the catalytic pocket, but display the same substrate specificity as human CASP8, highlighting the complexity of spatial structural interactions involved in enzymatic activity. Finally, it was confirmed that the interaction with an adaptor molecule, Fas-associated death domain protein, is also evolutionarily ancient. Thus, despite structural diversity and cooption to a variety of new functions, the ancient origins and near ubiquitous distribution of this activity across the animal kingdom emphasize the importance and utility of Casp8 as a central component of the metazoan molecular toolkit.

  16. Mini-review: Microbial coaggregation: ubiquity and implications for biofilm development.

    Science.gov (United States)

    Katharios-Lanwermeyer, S; Xi, C; Jakubovics, N S; Rickard, A H

    2014-01-01

    Coaggregation is the specific recognition and adherence of genetically distinct microorganisms. Because most biofilms are polymicrobial communities, there is potential for coaggregation to play an integral role in spatiotemporal biofilm development and the moderation of biofilm community composition. However, understanding of the mechanisms contributing to coaggregation and the relevance of coaggregation to biofilm ecology is at a very early stage. The purpose of this review is to highlight recent advances in the understanding of microbial coaggregation within different environments and to describe the possible ecological ramifications of such interactions. Bacteria that coaggregate with many partner species within different environments will be highlighted, including oral streptococci and oral bridging organisms such as fusobacteria, as well as the freshwater sphingomonads and acinetobacters. Irrespective of environment, it is proposed that coaggregation is essential for the orchestrated development of multi-species biofilms.

  17. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments.

    Science.gov (United States)

    Jiang, Xuexia; Dang, Hongyue; Jiao, Nianzhi

    2015-01-01

    Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.

  18. STED nanoscopy reveals the ubiquity of subcortical cytoskeleton periodicity in living neurons.

    Science.gov (United States)

    D'Este, Elisa; Kamin, Dirk; Göttfert, Fabian; El-Hady, Ahmed; Hell, Stefan W

    2015-03-03

    In the axons of cultured hippocampal neurons, actin forms various structures, including bundles, patches (involved in the preservation of neuronal polarity), and a recently reported periodic ring-like structure. Nevertheless, the overlaying organization of actin in neurons and in the axon initial segment (AIS) is still unclear, due mainly to a lack of adequate imaging methods. By harnessing live-cell stimulated emission depletion (STED) nanoscopy and the fluorescent probe SiR-Actin, we show that the periodic subcortical actin structure is in fact present in both axons and dendrites. The periodic cytoskeleton organization is also found in the peripheral nervous system, specifically at the nodes of Ranvier. The actin patches in the AIS co-localize with pre-synaptic markers. Cytosolic actin organization strongly depends on the developmental stage and subcellular localization. Altogether, the results of this study reveal unique neuronal cytoskeletal features.

  19. Ubiquity and persistance of Escherichia coli in a midwestern coastal stream

    Science.gov (United States)

    Byappanahalli, Muruleedhara N.; Fowler, Melanie; Shively, Dawn; Whitman, Richard

    2003-01-01

    Dunes Creek, a small Lake Michigan coastal stream that drains sandy aquifers and wetlands of Indiana Dunes, has chronically elevated Escherichia coli levels along the bathing beach near its outfall. This study sought to understand the sources ofE. coli in Dunes Creek's central branch. A systematic survey of random and fixed sampling points of water and sediment was conducted over 3 years. E. coliconcentrations in Dunes Creek and beach water were significantly correlated. Weekly monitoring at 14 stations during 1999 and 2000 indicated chronic loading of E. coli throughout the stream. Significant correlations between E. coli numbers in stream water and stream sediment, submerged sediment and margin, and margin and 1 m from shore were found. Median E. coli counts were highest in stream sediments, followed by bank sediments, sediments along spring margins, stream water, and isolated pools; in forest soils, E. coli counts were more variable and relatively lower. Sediment moisture was significantly correlated with E. colicounts. Direct fecal input inadequately explains the widespread and consistent occurrence of E. coli in the Dunes Creek watershed; long-term survival or multiplication or both seem likely. The authors conclude that (i) E. coli is ubiquitous and persistent throughout the Dunes Creek basin, (ii) E. coli occurrence and distribution in riparian sediments help account for the continuous loading of the bacteria in Dunes Creek, and (iii) ditching of the stream, increased drainage, and subsequent loss of wetlands may account for the chronically high E. coli levels observed.

  20. Ubiquity of density slope oscillations in the central regions of galaxy and cluster-sized systems

    CERN Document Server

    Young, Anthony M; Hjorth, Jens

    2016-01-01

    One usually thinks of a radial density profile as having a monotonically changing logarithmic slope, such as in NFW or Einasto profiles. However, in two different classes of commonly used systems, this is often not the case. These classes exhibit non-monotonic changes in their density profile slopes which we call oscillations for short. We analyze these two unrelated classes separately. Class 1 consists of systems that have density oscillations and that are defined through their distribution function $f(E)$, or differential energy distribution $N(E)$, such as isothermal spheres, King profiles, or DARKexp, a theoretically derived model for relaxed collisionless systems. Systems defined through $f(E)$ or $N(E)$ generally have density slope oscillations. Class 1 system oscillations can be found at small, intermediate, or large radii but we focus on a limited set of Class 1 systems that have oscillations in the central regions, usually at $\\log(r/r_{-2})\\lesssim -2$, where $r_{-2}$ is the largest radius where $d\\...

  1. Field-portable-XRF reveals the ubiquity of antimony in plastic consumer products.

    Science.gov (United States)

    Turner, Andrew; Filella, Montserrat

    2017-02-09

    Very little systematic information exists on the occurrence and concentrations of antimony (Sb) in consumer products. In this study, a Niton XL3t field-portable-X-ray fluorescence (FP-XRF) spectrometer was deployed in situ and in the laboratory to provide quantitative information on Sb dissipated in plastic items and fixtures (including rubber, textile and foamed materials) from the domestic, school, vehicular and office settings. The metalloid was detected in 18% of over 800 measurements performed, with concentrations ranging from about 60 to 60,000μgg(-1). The highest concentrations were encountered in white, electronic casings and in association with similar concentrations of Br, consistent with the use of antimony oxides (e.g. Sb2O3) as synergistic flame retardants. Concentrations above 1000μgg(-1), and with or without Br, were also encountered in paints, piping and hosing, adhesives, whiteboards, Christmas decorations, Lego blocks, document carriers, garden furniture, upholstered products and interior panels of private motor vehicles. Lower concentrations of Sb were encountered in a wide variety of items but its presence (without Br) in food tray packaging, single-use drinks bottles, straws and small toys were of greatest concern from a human health perspective. While the latter observations are consistent with the use of antimony compounds as catalysts in the production of polyethylene terephthalate, co-association of Sb and Br in many products not requiring flame retardancy suggests that electronic casings are widely recycled. Further research is required into the mobility of Sb when dissipated in new, recycled and aged polymeric materials.

  2. Social and spatial ubiquity of information and communication technology: a policy perspective

    NARCIS (Netherlands)

    Ouwersloot, Hans; Nijkamp, Peter

    1997-01-01

    In this paper, we analyze some fundamental impacts of the process of informatization. Inparticular, we address socio-economic and spatial impacts and discuss possible consequences for policy. Our objective is to discuss issues concerningthe desirability, necessity and possibility of government respo

  3. A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.

    Science.gov (United States)

    Zarecki, Raphy; Oberhardt, Matthew A; Reshef, Leah; Gophna, Uri; Ruppin, Eytan

    2014-07-01

    Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritional requirements and their ecological and genomic traits. We first show that nutritional requirements are more similar among species that co-habit many ecological niches. We then reveal three fundamental characteristics of microbial fastidiousness (i.e., complex and specific nutritional requirements): (1) more fastidious microorganisms tend to be more ecologically limited; (2) fastidiousness is positively associated with smaller genomes and smaller metabolic networks; and (3) more fastidious species grow more slowly and have less ability to cooperate with other species than more metabolically versatile organisms. These associations reflect the adaptation of fastidious microorganisms to unique niches with few cohabitating species. They also explain how non-fastidious species inhabit many ecological niches with high abundance rates. Taken together, these results advance our understanding microbial nutrition on a large scale, by presenting new nutrition-related associations that govern the distribution of microorganisms in nature.

  4. Testing for phylogenetic signal in biological traits: the ubiquity of cross-product statistics.

    Science.gov (United States)

    Pavoine, Sandrine; Ricotta, Carlo

    2013-03-01

    To evaluate rates of evolution, to establish tests of correlation between two traits, or to investigate to what degree the phylogeny of a species assemblage is predictive of a trait value so-called tests for phylogenetic signal are used. Being based on different approaches, these tests are generally thought to possess quite different statistical performances. In this article, we show that the Blomberg et al. K and K*, the Abouheif index, the Moran's I, and the Mantel correlation are all based on a cross-product statistic, and are thus all related to each other when they are associated to a permutation test of phylogenetic signal. What changes is only the way phylogenetic and trait similarities (or dissimilarities) among the tips of a phylogeny are computed. The definitions of the phylogenetic and trait-based (dis)similarities among tips thus determines the performance of the tests. We shortly discuss the biological and statistical consequences (in terms of power and type I error of the tests) of the observed relatedness among the statistics that allow tests for phylogenetic signal. Blomberg et al. K* statistic appears as one on the most efficient approaches to test for phylogenetic signal. When branch lengths are not available or not accurate, Abouheif's Cmean statistic is a powerful alternative to K*.

  5. Functional marker development is challenged by the ubiquity of endophytes-a practical perspective.

    Science.gov (United States)

    Arnholdt-Schmitt, Birgit; Valadas, Vera; Döring, Matthias

    2016-01-01

    Functional markers (FMs) are supposed to assist in diagnosis, disease treatment and turning plant and animal breeding more efficient. However, efficient FM application is challenged through current insights in the multi-organism nature of life. This letter aims to raise awareness for re-thinking concepts for FM development in plant breeding and proposes a novel perspective.

  6. Causal ubiquity in quantum physics. A superluminal and local-causal physical ontology

    Energy Technology Data Exchange (ETDEWEB)

    Neelamkavil, Raphael

    2014-07-01

    A fixed highest criterial velocity (of light) in STR (special theory of relativity) is a convention for a layer of physical inquiry. QM (Quantum Mechanics) avoids action-at-a-distance using this concept, but accepts non-causality and action-at-a-distance in EPR (Einstein-Podolsky-Rosen-Paradox) entanglement experiments. Even in such allegedly [non-causal] processes, something exists processually in extension-motion, between the causal and the [non-causal]. If STR theoretically allows real-valued superluminal communication between EPR entangled particles, quantum processes become fully causal. That is, the QM world is sub-luminally, luminally and superluminally local-causal throughout, and the Law of Causality is ubiquitous in the micro-world. Thus, ''probabilistic causality'' is a merely epistemic term.

  7. Ubiquity and impact of thin mid-level clouds in the tropics.

    Science.gov (United States)

    Bourgeois, Quentin; Ekman, Annica M L; Igel, Matthew R; Krejci, Radovan

    2016-08-17

    Clouds are crucial for Earth's climate and radiation budget. Great attention has been paid to low, high and vertically thick tropospheric clouds such as stratus, cirrus and deep convective clouds. However, much less is known about tropospheric mid-level clouds as these clouds are challenging to observe in situ and difficult to detect by remote sensing techniques. Here we use Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) satellite observations to show that thin mid-level clouds (TMLCs) are ubiquitous in the tropics. Supported by high-resolution regional model simulations, we find that TMLCs are formed by detrainment from convective clouds near the zero-degree isotherm. Calculations using a radiative transfer model indicate that tropical TMLCs have a cooling effect on climate that could be as large in magnitude as the warming effect of cirrus. We conclude that more effort has to be made to understand TMLCs, as their influence on cloud feedbacks, heat and moisture transport, and climate sensitivity could be substantial.

  8. Ubiquity: a framework for physiological/mechanism-based pharmacokinetic/pharmacodynamic model development and deployment.

    Science.gov (United States)

    Harrold, John M; Abraham, Anson K

    2014-04-01

    Practitioners of pharmacokinetic/pharmacodynamic modeling routinely employ various software packages that enable them to fit differential equation based mechanistic or empirical models to biological/pharmacological data. The availability and choice of different analytical tools, while enabling, can also pose a significant challenge in terms of both, implementation and transferability. A package has been developed that addresses these issues by creating a simple text-based format, which provides methods to reduce coding complexity and enables the modeler to describe the components of the model based on the underlying physiochemical processes. A Perl script builds the system for multiple formats (ADAPT, MATLAB, Berkeley Madonna, etc.), enabling analysis across several software packages and reducing the chance for transcription error. Workflows can then be built around this package, which can increase efficiency and model availability. As a proof of concept, tools are included that allow models constructed in this format to be run with MATLAB both at the scripting level and through a generic graphical application that can be compiled and run as a stand-alone application.

  9. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains.

    Science.gov (United States)

    Hughes, Colin E; Atchison, Guy W

    2015-07-01

    Alpine plant radiations are compared across the world's major mountain ranges and shown to be overwhelmingly young and fast, largely confined to the Pliocene and Pleistocene, and some of them apparently in the early explosive phase of radiation. Accelerated diversification triggered by island-like ecological opportunities following the final phases of mountain uplift, and in many cases enabled by the key adaptation of perennial habit, provides a general model for alpine plant radiations. Accelerated growth form evolution facilitated by perenniality provides compelling evidence of ecological release and suggests striking parallels between island-like alpine, and especially tropicalpine radiations, and island radiations more generally. These parallels suggest that the world's mountains offer an excellent comparative system for explaining evolutionary radiation.

  10. The possible ubiquity of energy injection in Gamma-Ray Burst afterglows

    CERN Document Server

    Panaitescu, A

    2012-01-01

    Since its launch in 2004, the Swift satellite has monitored the X-ray afterglows of several hundred Gamma-Ray Bursts, and revealed that their X-ray light-curves are more complex than previously thought, exhibiting up to three power-law segments. Energy injection into the relativistic blast-wave energizing the burst ambient medium has been proposed most often to be the reason for the X-ray afterglow complexity. We examine 117 light-curve breaks of 98 Swift X-ray afterglows, selected for their high-quality monitoring and well-constrained flux decay rates. Thirty percent of afterglows have a break that can be an adiabatic jet-break, in the sense that there is one variant of the forward-shock emission from a collimated outflow model that can account for both the pre- and post-break flux power-law decay indices, given the measured X-ray spectral slope. If allowance is made for a steady energy injection into the forward-shock, then another 56 percent of X-ray afterglows have a light-curve break that can be explaine...

  11. Confronting the Ubiquity of Electronic Communication and Social Media: Ethical and Legal Considerations for Psychoeducational Practice

    Science.gov (United States)

    Demers, Joseph A.; Sullivan, Amanda L.

    2016-01-01

    Most U.S. children and adults use computers and the Internet on a daily basis. The pervasiveness of electronic communication in a variety of contexts, including home and school, raises ethical and legal concerns for school psychologists and those in related fields of practice, because of the risks to privacy and confidentiality, boundaries,…

  12. PHARMACEUTICALS AND PERSONAL CARE PRODUCTS IN THE ENVIRONMENT: UBIETY, UBIQUITY, SIGNIFICANCE, SOLUTIONS, AND STEWARDSHIP

    Science.gov (United States)

    The OSU Water- Resources Seminar Series bm a 3 0-year history, serves as a meeting place for " graduate students and faculty with a common interest in water resource issues but diverse major fields - from sociology to civil engineering to public health to fisheries and wildlife."...

  13. STED Nanoscopy Reveals the Ubiquity of Subcortical Cytoskeleton Periodicity in Living Neurons

    Directory of Open Access Journals (Sweden)

    Elisa D’Este

    2015-03-01

    Full Text Available In the axons of cultured hippocampal neurons, actin forms various structures, including bundles, patches (involved in the preservation of neuronal polarity, and a recently reported periodic ring-like structure. Nevertheless, the overlaying organization of actin in neurons and in the axon initial segment (AIS is still unclear, due mainly to a lack of adequate imaging methods. By harnessing live-cell stimulated emission depletion (STED nanoscopy and the fluorescent probe SiR-Actin, we show that the periodic subcortical actin structure is in fact present in both axons and dendrites. The periodic cytoskeleton organization is also found in the peripheral nervous system, specifically at the nodes of Ranvier. The actin patches in the AIS co-localize with pre-synaptic markers. Cytosolic actin organization strongly depends on the developmental stage and subcellular localization. Altogether, the results of this study reveal unique neuronal cytoskeletal features.

  14. On the Ubiquity of Molecular Anions in the Dense Interstellar Medium

    Science.gov (United States)

    Cordiner, M. A.; Buckle, J. V.; Wirstroem, E. S.; Olofsson, A. O. H.; Charnley, S. B.

    2013-01-01

    Results are presented from a survey for molecular anions in seven nearby Galactic star-forming cores and molecular clouds. The hydrocarbon anion C6H(-) is detected in all seven target sources, including four sources where no anions have been previously detected: L1172, L1389, L1495B, and TMC-1C. The C6H(-) /C6H column density ratio is approx. > 1.0% in every source, with a mean value of 3.0% (and standard deviation 0.92%). Combined with previous detections, our results show that anions are ubiquitous in dense clouds wherever C6H is present. The C6H(-)/C6H ratio is found to show a positive correlation with molecular hydrogen number density, and with the apparent age of the cloud.We also report the first detection of C4H(-) in TMC-1 (at 4.8 sigma confidence), and derive an anion-to-neutral ratio C4H(-) /C4H = (1.2 +/- 0.4)×10(exp -5)(= 0.0012% +/- 0.0004%). Such a low value compared with C6H(-) highlights the need for a revised radiative electron attachment rate for C4H. Chemical model calculations show that the observed C4H(-) could be produced as a result of reactions of oxygen atoms with C5H(-) and C6H(-).

  15. Causal ubiquity in quantum physics a superluminal and local-causal physical ontology

    CERN Document Server

    Neelamkavil, Raphael

    2014-01-01

    A fixed highest criterial velocity (of light) in STR (special theory of relativity) is a convention for a layer of physical inquiry. QM (Quantum Mechanics) avoids action-at-a-distance using this concept, but accepts non-causality and action-at-a-distance in EPR (Einstein-Podolsky-Rosen-Paradox) entanglement experiments. Even in such allegedly non-causal processes, something exists processually in extension-motion, between the causal and the non-causal. If STR theoretically allows real-valued superluminal communication between EPR entangled particles, quantum processes become fully causal. That

  16. Ubiquity of Benford's law and emergence of the reciprocal distribution

    Energy Technology Data Exchange (ETDEWEB)

    Friar, J.L., E-mail: friar@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Goldman, T., E-mail: tjgoldman@post.harvard.edu [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Pérez-Mercader, J., E-mail: jperezmercader@fas.harvard.edu [Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138 (United States); Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501 (United States)

    2016-05-20

    We apply the Law of Total Probability to the construction of scale-invariant probability distribution functions (pdf's), and require that probability measures be dimensionless and unitless under a continuous change of scales. If the scale-change distribution function is scale invariant then the constructed distribution will also be scale invariant. Repeated application of this construction on an arbitrary set of (normalizable) pdf's results again in scale-invariant distributions. The invariant function of this procedure is given uniquely by the reciprocal distribution, suggesting a kind of universality. We separately demonstrate that the reciprocal distribution results uniquely from requiring maximum entropy for size-class distributions with uniform bin sizes. - Highlights: • We apply the Law of Total Probability to the construction of scale-invariant pdf's, and require that probability measures be dimensionless and unitless under a continuous change of scales. • Iterating this procedure for an arbitrary set of normalized pdf's again produces scale-invariant distributions. • The invariant function of this iteration is given uniquely by the reciprocal distribution, suggesting a kind of universality. • Requiring maximum entropy for uniformly binned size-class distributions also leads uniquely to the reciprocal distribution. • We discuss some applications of the above to computation and to the evolution of genomes.

  17. Infrared polarization images of star-forming regions. I - The ubiquity of bipolar structure

    Science.gov (United States)

    Tamura, M.; Gatley, Ian; Joyce, R. R.; Ueno, M.; Suto, H.; Sekiguchi, M.

    1991-01-01

    The inefficiency of the stellar formation process leads rather generally to high residual dust densities, and so to the existence of infrared reflection nebulosity (IRN), in regions of star formation. Polarization images of several star-forming regions with mass outflows (GSS 30, S255, GL 5180, GL 2591, GGD 27, and NGC 7538) presented here: (1) establish the universality of bipolarity and of shell or cavity structure in the IRN consistent with that of CO outflow; (2) identify the source of the mass outflow in each case; (3) show that the opening angle near this central source is large; and (4) demonstrate several instances of multiple shells, probably arising from episodic mass loss. Astrometry of 2.2-micron sources with arcsecond accuracy identifies the illuminating source of each IRN uniquely with a compact H II region or a bright IR source. The polarization images provide strong evidence for large-scale dust toroids around each of these sources. The density and mass of these disks are estimated from the extinction through the disk.

  18. ON THE UBIQUITY OF MOLECULAR ANIONS IN THE DENSE INTERSTELLAR MEDIUM

    Energy Technology Data Exchange (ETDEWEB)

    Cordiner, M. A.; Wirstroem, E. S.; Charnley, S. B. [Astrochemistry Laboratory and The Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Code 691, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States); Buckle, J. V. [Cavendish Astrophysics Group and Kavli Institute for Cosmology, Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HE (United Kingdom); Olofsson, A. O. H., E-mail: martin.cordiner@nasa.gov [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 92 Onsala (Sweden)

    2013-06-10

    Results are presented from a survey for molecular anions in seven nearby Galactic star-forming cores and molecular clouds. The hydrocarbon anion C{sub 6}H{sup -} is detected in all seven target sources, including four sources where no anions have been previously detected: L1172, L1389, L1495B, and TMC-1C. The C{sub 6}H{sup -}/C{sub 6}H column density ratio is {approx}> 1.0% in every source, with a mean value of 3.0% (and standard deviation 0.92%). Combined with previous detections, our results show that anions are ubiquitous in dense clouds wherever C{sub 6}H is present. The C{sub 6}H{sup -}/C{sub 6}H ratio is found to show a positive correlation with molecular hydrogen number density, and with the apparent age of the cloud. We also report the first detection of C{sub 4}H{sup -} in TMC-1 (at 4.8{sigma} confidence), and derive an anion-to-neutral ratio C{sub 4}H{sup -}/C{sub 4}H =(1.2 {+-} 0.4) Multiplication-Sign 10{sup -5}(= 0.0012% {+-} 0.0004%). Such a low value compared with C{sub 6}H{sup -} highlights the need for a revised radiative electron attachment rate for C{sub 4}H. Chemical model calculations show that the observed C{sub 4}H{sup -} could be produced as a result of reactions of oxygen atoms with C{sub 5}H{sup -} and C{sub 6}H{sup -}.

  19. Genomics of "Candidatus Synechococcus spongiarium", a Cyanobacterial Sponge Symbiont

    Energy Technology Data Exchange (ETDEWEB)

    Slaby, Beate M. [Univ. of Wuerzburg (Germany); Copeland, Alex [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Woyke, Tanja [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hentschel, Ute [Univ. of Wuerzburg (Germany)

    2014-03-21

    Marine sponges (Porifera): ancient metazoans of ecological importance, that produce bioactive secondary metabolites and interact with various microorganisms including cyanobacteria1: Marine Synechococcus spp.: cyanobacteria, important contributors to the global carbon cycle and major primary producers in the oceans2 Ca. S. spongiarum: an ecotype of this genus, widespread and abundant symbiont of various marine sponges around the world3, e.g. Aplysina aerophoba

  20. First report of "Candidatus Liberibacter solanacearum" infecting eggplant in Honduras

    Science.gov (United States)

    In May of 2012, eggplant (Solanum melongena) plants in an experimental research plot located at Zamorano in the Department of Francisco Morazán, Honduras, were observed with symptoms that included leaf chlorosis and cupping, overall stunting, and production of small and malformed fruits. The researc...

  1. Candidatus "Scalindua brodaea", spec. nov., Candidatus "Scalindua wagneri", spec. nov., two new species of anaerobic ammonium oxidizing bacteria

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Schmid, M.; Walsh, K.; Webb, R.; Rijpstra, W.I.C.; Pas-Schoonen, K. van de; Verbruggen, M.J.; Hill, T.; Moffett, B.; Fuerst, J.; Schouten, S.; Harris, James; Shaw, P.; Jetten, M.S.M.; Strous, M.

    2003-01-01

    Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply i

  2. Ubiquity of chaotic magnetic-field lines generated by three-dimensionally crossed wires in modern electric circuits.

    Science.gov (United States)

    Hosoda, M; Miyaguchi, T; Imagawa, K; Nakamura, K

    2009-12-01

    We investigate simple three-dimensionally crossed wires carrying electric currents which generate chaotic magnetic-field lines (CMFLs). As such wire systems, cross-ring and perturbed parallel-ring wires are studied, since topologically equivalent configurations to these systems can often be found in contemporary electric and integrated circuits. For realistic fundamental wire configurations, the conditions for wire dimensions (size) and current values to generate CMFLs are numerically explored under the presence of the weak but inevitable geomagnetic field. As a result, it is concluded that CMFLs can exist everywhere; i.e., they are ubiquitous in the modern technological world.

  3. Ubiquity of activated sludge ferricyanide-mediated BOD methods: a comparison of sludge seeds across wastewater treatment plants.

    Science.gov (United States)

    Jordan, Mark A; Welsh, David T; Teasdale, Peter R

    2014-07-01

    Many studies have described alternatives to the BOD5 standard method, with substantial decreases in incubation time observed. However, most of these have not maintained the features that make the BOD5 assay so relevant - a high level of substrate bio-oxidation and use of wastewater treatment plant (WWTP) sludge as the biocatalyst. Two recently described ferricyanide-mediated (FM)-BOD assays, one for trade wastes and one for WWTP influents and treated effluents, satisfy these criteria and were investigated further here for their suitability for use with diverse biocatalysts. Both FM-BOD assays responded proportionately to increasing substrate concentration with sludges from 11 different WWTPs and temporally (months to years) using sludges from a single WWTP, confirming the broad applicability of both assays. Sludges from four WWTPs were selected as biocatalysts for each FM-BOD assay to compare FM-BOD equivalent values with BOD5 (three different sludge seeds) measurements for 12 real wastewater samples (six per assay). Strong and significant relationships were established for both FM-BOD assays. This study has demonstrated that sludge sourced from many WWTPs may be used as the biocatalyst in either FM-BOD assay, as it is in the BOD5 assay. The industry potential of these findings is substantial given the widespread use of the BOD5 assay, the dramatically decreased incubation period (3-6h) and the superior analytical range of both assays compared to the standard BOD5 assay.

  4. 光系统的演变--无处不在的光%Evolution of the Photosystem-- Optical Ubiquity

    Institute of Scientific and Technical Information of China (English)

    朗讯科技

    2001-01-01

    迅速发展的光网络系统提供了日益强大的传输能力,尤为重要的是,光放大器和波分复用(WDM)技术的出现,不仅强化了光在网络中的地位,而且将其作用逐步扩大到网络边缘.朗讯科技正在着手实现包括软件控制的光波长增/减多路复用器在内的多点WDM环路系统的商业化,并将于近期推出大型光交叉连接.随着光纤价格的不断下降以及企业与家庭用户对带宽需求的持续增长,光纤系统将逐步从核心网和城域网扩展到接入网.

  5. Snapshot of viral infections in wild carnivores reveals ubiquity of parvovirus and susceptibility of Egyptian mongoose to feline panleukopenia virus.

    Science.gov (United States)

    Duarte, Margarida D; Henriques, Ana Margarida; Barros, Sílvia Carla; Fagulha, Teresa; Mendonça, Paula; Carvalho, Paulo; Monteiro, Madalena; Fevereiro, Miguel; Basto, Mafalda P; Rosalino, Luís Miguel; Barros, Tânia; Bandeira, Victor; Fonseca, Carlos; Cunha, Mónica V

    2013-01-01

    The exposure of wild carnivores to viral pathogens, with emphasis on parvovirus (CPV/FPLV), was assessed based on the molecular screening of tissue samples from 128 hunted or accidentally road-killed animals collected in Portugal from 2008 to 2011, including Egyptian mongoose (Herpestes ichneumon, n = 99), red fox (Vulpes vulpes, n = 19), stone marten (Martes foina, n = 3), common genet (Genetta genetta, n = 3) and Eurasian badger (Meles meles, n = 4). A high prevalence of parvovirus DNA (63%) was detected among all surveyed species, particularly in mongooses (58%) and red foxes (79%), along with the presence of CPV/FPLV circulating antibodies that were identified in 90% of a subset of parvovirus-DNA positive samples. Most specimens were extensively autolysed, restricting macro and microscopic investigations for lesion evaluation. Whenever possible to examine, signs of active disease were not present, supporting the hypothesis that the parvovirus vp2 gene fragments detected by real-time PCR possibly correspond to viral DNA reminiscent from previous infections. The molecular characterization of viruses, based on the analysis of the complete or partial sequence of the vp2 gene, allowed typifying three viral strains of mongoose and four red fox's as feline panleukopenia virus (FPLV) and one stone marten's as newCPV-2b type. The genetic similarity found between the FPLV viruses from free-ranging and captive wild species originated in Portugal and publicly available comparable sequences, suggests a closer genetic relatedness among FPLV circulating in Portugal. Although the clinical and epidemiological significance of infection could not be established, this study evidences that exposure of sympatric wild carnivores to parvovirus is common and geographically widespread, potentially carrying a risk to susceptible populations at the wildlife-domestic interface and to threatened species, such as the wildcat (Felis silvestris) and the critically endangered Iberian lynx (Lynx pardinus).

  6. Snapshot of viral infections in wild carnivores reveals ubiquity of parvovirus and susceptibility of Egyptian mongoose to feline panleukopenia virus.

    Directory of Open Access Journals (Sweden)

    Margarida D Duarte

    Full Text Available The exposure of wild carnivores to viral pathogens, with emphasis on parvovirus (CPV/FPLV, was assessed based on the molecular screening of tissue samples from 128 hunted or accidentally road-killed animals collected in Portugal from 2008 to 2011, including Egyptian mongoose (Herpestes ichneumon, n = 99, red fox (Vulpes vulpes, n = 19, stone marten (Martes foina, n = 3, common genet (Genetta genetta, n = 3 and Eurasian badger (Meles meles, n = 4. A high prevalence of parvovirus DNA (63% was detected among all surveyed species, particularly in mongooses (58% and red foxes (79%, along with the presence of CPV/FPLV circulating antibodies that were identified in 90% of a subset of parvovirus-DNA positive samples. Most specimens were extensively autolysed, restricting macro and microscopic investigations for lesion evaluation. Whenever possible to examine, signs of active disease were not present, supporting the hypothesis that the parvovirus vp2 gene fragments detected by real-time PCR possibly correspond to viral DNA reminiscent from previous infections. The molecular characterization of viruses, based on the analysis of the complete or partial sequence of the vp2 gene, allowed typifying three viral strains of mongoose and four red fox's as feline panleukopenia virus (FPLV and one stone marten's as newCPV-2b type. The genetic similarity found between the FPLV viruses from free-ranging and captive wild species originated in Portugal and publicly available comparable sequences, suggests a closer genetic relatedness among FPLV circulating in Portugal. Although the clinical and epidemiological significance of infection could not be established, this study evidences that exposure of sympatric wild carnivores to parvovirus is common and geographically widespread, potentially carrying a risk to susceptible populations at the wildlife-domestic interface and to threatened species, such as the wildcat (Felis silvestris and the critically endangered Iberian lynx (Lynx pardinus.

  7. Natural sunlight shapes crude oil-degradingbacterial communities in northern Gulf of Mexico surface waters

    Directory of Open Access Journals (Sweden)

    Hernando P Bacosa

    2015-12-01

    Full Text Available Following the Deepwater Horizon (DWH spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 d under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.

  8. Denitrification of nitrate and nitrite by 'Candidatus Accumulibacter phosphatis' clade IC.

    Science.gov (United States)

    Saad, Sondos A; Welles, Laurens; Abbas, Ben; Lopez-Vazquez, Carlos M; van Loosdrecht, Mark C M; Brdjanovic, Damir

    2016-11-15

    Phosphate accumulating organisms (PAO) are assumed to use nitrate as external electron acceptor, allowing an efficient integration of simultaneous nitrogen and phosphate removal with minimal organic carbon (COD) requirements. However, contradicting findings appear in literature regarding the denitrification capacities of PAO due to the lack of clade specific highly enriched PAO cultures. Whereas some studies suggest that only PAO clade I may be capable of using nitrate as external electron acceptor for anoxic P-uptake, other studies indicate that PAO clade II may be responsible for anoxic P-removal. In the present study, a highly enriched PAO clade IC culture (>99% according to FISH) was cultivated in an SBR operated under Anaerobic/Oxic conditions and subsequently exposed to Anaerobic/Anoxic/Oxic conditions using nitrate as electron acceptor. Before and after acclimatization to the presence of nitrate, the aerobic and anoxic (nitrate and nitrite) activities of the PAO I culture were assessed through the execution of batch tests using either acetate or propionate as electron donor. In the presence of nitrate, significant P-uptake by PAO I was not observed before or after acclimatization. Using nitrite as electron acceptor, limited nitrite removal rates were observed before acclimatization with lower rates in the acetate fed reactor without P-uptake and slightly higher in the propionate fed reactor with a marginal anoxic P-uptake. Only after acclimatization to nitrate, simultaneous P and nitrite removal was observed. This study suggests that PAO clade IC is not capable of using nitrate as external electron acceptor for anoxic P-removal. The elucidation of the metabolic capacities for individual PAO clades helps in better understanding and optimization of the relation between microbial ecology and process performance in enhanced biological phosphate removal processes.

  9. Candidatus Phytoplasma malaysianum, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus)

    Science.gov (United States)

    This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytopla...

  10. Is the striped mealybug, Ferrisia virgata, a vector of huanglongbing bacterium ‘Candidatus Liberibacter asiaticus’

    Science.gov (United States)

    This is the first report of ‘Ca. L. asiaticus’ (Las) present in striped mealybugs feeding on Las-infected periwinkle plants. In November 2010, specimens of a common greenhouse pest, the striped mealybug Ferrisia virgata (Cockerell) (Pseudococcidae; Hemiptera), were collected from Las-infected periw...

  11. DNA Barcoding for Identification of "Candidatus Phytoplasmas" Using a Fragment of the Elongation Factor Tu Gene

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta;

    2012-01-01

    barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases. Conclusions/Significance This study demonstrates that DNA barcoding principles can be applied...

  12. Comparative iTRAQ proteome and transcriptome analyses of sweet orange infected by "Candidatus Liberibacter asiaticus".

    Science.gov (United States)

    Fan, Jing; Chen, Chunxian; Yu, Qibin; Brlansky, Ronald H; Li, Zheng-Guo; Gmitter, Frederick G

    2011-11-01

    Citrus Huanglongbing (HLB) has been threatening citrus production worldwide. In this study, a comparative proteomic approach was applied to understand the pathogenic process of HLB in affected sweet orange leaves. Using the isobaric tags for relative and absolute quantification (iTRAQ) technique, we identified 686 unique proteins in the mature leaves of both mock-inoculated and diseased 'Madam Vinous' sweet orange plants. Of the identified proteins, 20 and 10 were differentially expressed in leaves with and without symptoms of HLB (fold change > 2.5), respectively, compared with mock-inoculated controls. Most significantly, upregulated proteins were involved in stress/defense response, such as four miraculin-like proteins, chitinase, Cu/Zn superoxide dismutase and lipoxygenase. Microarray analysis also showed that stress-related genes were significantly upregulated at the transcriptional level. For example, remarkable upregulations of miraculin-like proteins and Cu/Zn superoxide dismutase transcripts were observed. Moreover, the transcriptional patterns of miraculin-like protein 1 and Cu/Zn superoxide dismutase were examined at different stages of HLB disease development. Combined with the transcriptomic data, the proteomic data can provide an enhanced understanding of citrus stress/defense responses to HLB.

  13. Characterization of Candidatus Bartonella ancashi: A Novel Human Pathogen Associated with Carrins Disease

    Science.gov (United States)

    2015-03-12

    treatment trial. Phylogeny was created for a 240 bp fragment of gltA with Mega5 software , using the neighbor joining tree method (1,000 bootstrap replicates...Lima, Peru 5 Universidad Peruana Cayetano Heredia, Lima, Peru Published in Emerging Infectious Diseases Blazes DL, Mullins K, Smoak BL...Phylogenetic trees were created with MEGA5 software using the neighbor-joining tree method with 1,000 bootstrap replicates (234). Subsequent

  14. Candidatus Bartonella merieuxii, a Potential New Zoonotic Bartonella Species in Canids from Iraq

    OpenAIRE

    Chomel, Bruno B; Audrey C McMillan-Cole; Kasten, Rickie W.; Matthew J Stuckey; Shingo Sato; Soichi Maruyama; Diniz, Pedro P. V. P.; Breitschwerdt, Edward B

    2012-01-01

    Bartonellae are emerging vector-borne pathogens infecting erythrocytes and endothelial cells of various domestic and wild mammals. Blood samples were collected from domestic and wild canids in Iraq under the United States Army zoonotic disease surveillance program. Serology was performed using an indirect immunofluorescent antibody test for B. henselae, B. clarridgeiae, B. vinsonii subsp. berkhoffii and B. bovis. Overall seroprevalence was 47.4% in dogs (n = 97), 40.4% in jackals (n = 57) and...

  15. Novel Candidatus rickettsia species detected in nostril tick from human, Gabon, 2014.

    Science.gov (United States)

    Lopez-Velez, Rogelio; Palomar, Ana M; Oteo, José A; Norman, Francesca F; Pérez-Molina, José A; Portillo, Aránzazu

    2015-02-01

    We report the identification of a nymphal nostril tick (Amblyomma sp.) from a national park visitor in Gabon and subsequent molecular detection and characterization of tickborne bacteria. Our findings provide evidence of a potentially new Rickettsia sp. circulating in Africa and indicate that tick bites may pose a risk to persons visiting parks in the region.

  16. Hydroxylamine-dependent Anaerobic Ammonium Oxidation (Anammox) by “ Candidatus Brocadia sinica”

    KAUST Repository

    Oshiki, Mamoru

    2016-04-26

    Although metabolic pathways and associated enzymes of anaerobic ammonium oxidation (anammox) of “Ca. Kuenenia stuttgartiensis” have been studied, those of other anammox bacteria are still poorly understood. NO2- reduction to NO is considered to be the first step in the anammox metabolism of “Ca. K. stuttgartiensis”, however, “Ca. Brocadia” lacks the genes that encode canonical NO-forming nitrite reductases (NirS or NirK) in its genome, which is different from “Ca. K. stuttgartiensis”. Here, we studied the anammox metabolism of “Ca. Brocadia sinica”. 15N-tracer experiments demonstrated that “Ca. B. sinica” cells could reduce NO2- to NH2OH, instead of NO, with as yet unidentified nitrite reductase(s). Furthermore, N2H4 synthesis, downstream reaction of NO2- reduction, was investigated using a purified “Ca. B. sinica” hydrazine synthase (Hzs) and intact cells. Both the “Ca. B. sinica” Hzs and cells utilized NH2OH and NH4+, but not NO and NH4+, for N2H4 synthesis and further oxidized N2H4 to N2 gas. Taken together, the metabolic pathway of “Ca. B. sinica” is NH2OH-dependent and different from the one of “Ca. K. stuttgartiensis”, indicating metabolic diversity of anammox bacteria. This article is protected by copyright. All rights reserved.

  17. [The occurrence of "Candidatus Mycoplasma haemolamae" infections in clinically asymptomatic South American Camelids in Austria].

    Science.gov (United States)

    Franz, Sonja; Spergser, Joachim; Schwendenwein, Ilse; Stanitznig, Anna; Lambacher, Bianca; Tichy, Alexander; Wittek, Thomas

    2016-01-01

    Reports of CMhl infections in South American Camelids in Europe are only available from the United Kingdom and Switzerland. Knowing that CMhl infections can lead to severe disease resulting in death if combined with other diseases or stress, it was the aim of this study to assess prevalence data from camelids in Austria. In comparison to the previous studies a representative number of camelids was investigated nationwide. Data were assessed due to differences in geographical region, age, sex, species, and origin. A relatively high prevalence of 25.8% was recorded. CMhl was detected significantly more often in alpacas (Vicunja pacos) than in llamas (Lama glama) and more frequently in animals younger than 2 years. Additionally regional differences have been observed, which might be due to climatic differences and/or variations in insect vectors. In this study apperantly clinical healthy animals were shown to be infected with CMhl. Camelids infected with CMhl are a pathogen reservoir. The results of this study indicate different risk levels of infection between llamas and alpacas and between younger and older animals. The data presented underline the necessity of further studies on CMhlI infections in South American Camelids.

  18. Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Albertsen, Mads; Andresen, Eva Kammer;

    2014-01-01

    anaerobic-‘feast’: aerobic-‘famine’ regime of enhanced biological phosphorus removal (EBPR) wastewater treatment systems. As they do not contribute to phosphorus (P) removal, but compete for resources with the polyphosphate-accumulating organisms (PAO), thought responsible for P removal, their proliferation...... as for denitrification, nitrogen fixation, fermentation, trehalose synthesis and utilisation of glucose and lactate. Genetic comparison of P metabolism pathways with sequenced PAOs revealed the absence of the Pit phosphate transporter in the Competibacter-lineage genomes—identifying a key metabolic difference...... with the PAO physiology. These genomes are the first from any GAO organism and provide new insights into the complex interaction and niche competition between PAOs and GAOs in EBPR systems....

  19. Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Kristiansen, Rikke; Albertsen, Mads;

    2013-01-01

    acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment...

  20. Origin and Ubiquity of Short-Period Earth-like Planets: Evidence for the Sequential-Accretion Theory of Planet Formation

    CERN Document Server

    Zhou, J L; Lin, D N C; Nagasawa, M

    2005-01-01

    The formation of gas giant planets is assumed to be preceded by the emergence of solid cores in the conventional sequential-accretion paradigm. This hypothesis implies that the presence of earth-like planets can be inferred from the detection of gas giants. A similar prediction cannot be made with the gravitational instability (hereafter GI) model which assumes that gas giants (hereafter giants) formed from the collapse of gas fragments analogous to their host stars. We propose an observational test for the determination of the dominant planet-formation channel. Based on the sequential-accretion (hereafter SA) model, we identify several potential avenues which may lead to the prolific formation of a population of close-in earth-mass ($M_\\oplus$) planets (hereafter close-in earths) around stars with 1) short-period or 2) solitary eccentric giants and 3) systems which contain intermediate-period resonant giants. In contrast, these close-in earths are not expected to form in systems where giants originated rapid...

  1. Origin and Ubiquity of Short-Period Earth-like Planets: Evidence for the Sequential-Accretion Theory of Planet Formation

    OpenAIRE

    Zhou, J. L.; Aarseth, S. J.; Lin, D. N. C.; Nagasawa, M.

    2005-01-01

    The formation of gas giant planets is assumed to be preceded by the emergence of solid cores in the conventional sequential-accretion paradigm. This hypothesis implies that the presence of earth-like planets can be inferred from the detection of gas giants. A similar prediction cannot be made with the gravitational instability (hereafter GI) model which assumes that gas giants (hereafter giants) formed from the collapse of gas fragments analogous to their host stars. We propose an observation...

  2. Rest-Frame Optical Emission Lines in z~3.5 Lyman Break selected Galaxies: The Ubiquity of Unusually High [OIII]/Hbeta Ratios at 2 Gyr

    CERN Document Server

    Holden, B P; Gonzalez, V G; Illingworth, G D; Labbe, I; Bouwens, R; Franx, M; van Dokkum, P; Spitler, L

    2014-01-01

    We present K-band spectra of rest-frame optical emission lines for 24 star-forming galaxies at z~3.2-3.7 using MOSFIRE on the Keck 1 telescope. Strong rest-frame optical [O III] and Hbeta emission lines were detected in 18 LBGs. The median flux ratio of [O III]5007 to Hbeta is 5.1+/-0.5, a factor of 5-10x higher than in local galaxies with similar stellar masses. The observed Hbeta luminosities are in good agreement with expectations from the estimated star-formation rates, and none of our sources are detected in deep X-ray stacks, ruling out significant contamination by active galactic nuclei. Combining our sample with a variety of LBGs from the literature, including 49 galaxies selected in a very similar manner, we find a high median ratio of [OIII]/Hbeta = 4.8+0.8-1.7. This high ratio seems to be an ubiquitous feature of z~3-4 LBGs, very different from typical local star-forming galaxies at similar stellar masses. The only comparable systems at z~0 are those with similarly high specific star-formation rate...

  3. On the Ubiquity of Semantic Relations in Linguistic Activities%试论语言活动中语义关系的普遍性

    Institute of Scientific and Technical Information of China (English)

    冯春波

    2010-01-01

    词语不是一个凌乱的集合,也是不像词典中那样按照字母顺序排列的,而是按照语义关系相互联系的.语义关系在语言活动中无处不在.本文论述五种情况下的语义关系:自由回忆、智力测验、语言习得、词典定义、词典插图.

  4. 泛在感知网络的发展及趋势分析%Development Trend of Ambient Ubiquity Network

    Institute of Scientific and Technical Information of China (English)

    高歆雅

    2010-01-01

    从MarkWeise先生提出泛在网络以来,泛在网络无所不在的网络特性就常常为人们所讨论.泛在网络是一种以人为核心,强调了多种通信和感知技术的网络.本文阐述了泛在感知网络的基础技术模块,包括RFID技术、无线传感网络、云计算、近距离通信技术以及可能的泛在感知网体系架构.通过衡量不同的应用场景和可能的前景及当前的壁垒,文章讨论了泛在感知网对于通信产业的影响.泛在感知网的要素正代表了精确定位、有效识别和随时互联这3个对未来社会发展起决定作用的要素,泛在感知网络一定会成为未来5年或10年内推动商业发展的重要技术驱动力.

  5. Iron-centered ten-vertex germanium clusters: the ubiquity of low energy pentagonal prismatic structures with various skeletal electron counts.

    Science.gov (United States)

    Uţă, M M; Cioloboc, D; King, R B

    2012-09-13

    One of the most significant recent developments (in 2009) is the discovery of the clusters M@Ge10(3-) (M = Fe, Co) in which the outer Ge10 polyhedron is a pentagonal prism rather than a deltahedral structure of the type predicted by the Wade-Mingos rules. Consistent with this experimental observation, density functional theory shows the lowest energy structures to be pentagonal prisms for the iron-centered clusters Fe@Ge10(z) in all nine charge states ranging from -5 to +3. This contrasts with the previously studied cobalt-centered germanium clusters Co@Ge10(z) for which the lowest energy structures are pentagonal prisms only for the electron richest systems where z ranges from -3 to -5. The C3v structures derived from the tetracapped trigonal prism found as lowest energy structures of the electron poorer Co@Ge10(z) (z = 0, -1, -2) systems are higher energy structures for the iron-centered germanium clusters Fe@Ge10(z) (z = 0, -1, -2). The strong energetic preference for pentagonal prismatic structures in the Fe@Ge10(z) clusters can be attributed to the need for the larger volume of the pentagonal prism relative to other 10-vertex closed polyhedra to accommodate the interstitial iron atom.

  6. On the Ubiquity of Contradictions%矛盾无处不在——评《秀拉》中的二元对立现象

    Institute of Scientific and Technical Information of China (English)

    刘耘

    2006-01-01

    美国黑人作家托妮·莫瑞森在小说《秀拉》中,设置了众多矛盾,对传统的二元对立的创作思维模式提出了挑战,由此成功地塑造了秀拉等黑人人物.文章从《秀拉》中二元对立的矛盾冲突的角度,探讨小说所刻画的人物形象和所蕴涵的思想情感,试图总结出小说创作的新经验.

  7. The roles of Dmrt (Double sex/Male-abnormal-3 Related Transcription factor) genes in sex determination and differentiation mechanisms: Ubiquity and diversity across the animal kingdom.

    Science.gov (United States)

    Picard, Marion Anne-Lise; Cosseau, Céline; Mouahid, Gabriel; Duval, David; Grunau, Christoph; Toulza, Ève; Allienne, Jean-François; Boissier, Jérôme

    2015-07-01

    The Dmrt (Double sex/Male-abnormal-3 Related Transcription factor) genes have been intensively studied because they represent major transcription factors in the pathways governing sex determination and differentiation. These genes have been identified in animal groups ranging from cnidarians to mammals, and some of the genes functionally studied. Here, we propose to analyze (i) the presence/absence of various Dmrt gene groups in the different taxa across the animal kingdom; (ii) the relative expression levels of the Dmrt genes in each sex; (iii) the specific spatial (by organ) and temporal (by developmental stage) variations in gene expression. This review considers non-mammalian animals at all levels of study (i.e. no particular importance is given to animal models), and using all types of sexual strategy (hermaphroditic or gonochoric) and means of sex determination (i.e. genetic or environmental). To conclude this global comparison, we offer an analysis of the DM domains conserved among the different DMRT proteins, and propose a general sex-specific pattern for each member of the Dmrt gene family.

  8. 高校图书馆电子阅览泛在化建设研究%Research on the Construction of University Library's Electronic Reading Ubiquity

    Institute of Scientific and Technical Information of China (English)

    邓宗极; 赵桂玲; 张凤斌; 屈红军; 赵元洪; 何力; 肖荣荣

    2016-01-01

    解决高校电子阅览服务与需求不适应问题,建立泛在化电子阅览体系,实施升级发展是必由之路.以优化实体和虚拟两大阅览空间环境为突破口,通过架构云信息服务平台,拓展阅览渠道,整合服务功能,促进服务模式向多场所、多空问、复合型转变,为高校"十三五"电子阅览改革方向提供应用性参考.

  9. A ubiquidade das câmeras e a irrupção do real = The ubiquity of cameras and the eruption of the real into images

    Directory of Open Access Journals (Sweden)

    Polydoro, Felipe da Silva

    2014-01-01

    Full Text Available A disseminação de câmeras em dispositivos eletrônicos móveis e equipamentos de vigilância multiplica os registros visuais do mundo. Entre eles, estão os vídeos que captam a irrupção inesperada de um acontecimento alheio ao sujeito que filma, uma intromissão do real na cena que desorganiza os elementos e modifica até mesmo o estatuto da imagem. Neste texto, objetivamos conceituar tal tipo de imagem e, além disso, levantar referências teóricas para analisá-la, sobretudo com base no pensamento de Jacques Lacan. Além disso, analisamos alguns vídeos de acontecimentos de relevância midiática: o assassinato de Kennedy, o ataque terrorista de 11 de setembro, a queda de um meteorito na Rússia

  10. Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter asiaticus' and other Rhizobiales.

    Directory of Open Access Journals (Sweden)

    L David Kuykendall

    Full Text Available 'Ca. Liberibacter asiaticus,' an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called "HLB," is a member of the Rhizobiales along with nitrogen-fixing microsymbionts Sinorhizobium meliloti and Bradyrhizobium japonicum, plant pathogen Agrobacterium tumefaciens and facultative intracellular mammalian pathogen Bartonella henselae. Comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. Shared among all five species are 50 identical blocks of microsyntenous orthologous genes (MOGs, containing a total of 283 genes. While retaining highly conserved genomic blocks of microsynteny, divergent evolution, horizontal gene transfer and niche specialization have disrupted macrosynteny among the five circular chromosomes compared. Highly conserved microsyntenous gene clusters help define the Rhizobiales, an order previously defined by 16S RNA gene similarity and herein represented by the three families: Bartonellaceae, Bradyrhizobiaceae and Rhizobiaceae. Genes without orthologs in the other four species help define individual species. The circular chromosomes of each of the five Rhizobiales species examined had genes lacking orthologs in the other four species. For example, 63 proteins are encoded by genes of 'Ca. Liberibacter asiaticus' not shared with other members of the Rhizobiales. Of these 63 proteins, 17 have predicted functions related to DNA replication or RNA transcription, and some of these may have roles related to low genomic GC content. An additional 17 proteins have predicted functions relevant to cellular processes, particularly modifications of the cell surface. Seventeen unshared proteins have specific metabolic functions including a pathway to synthesize cholesterol encoded by a seven-gene operon. The remaining 12 proteins encoded by 'Ca. Liberibacter asiaticus' genes not shared with other Rhizobiales are of bacteriophage origin. 'Ca. Liberibacter asiaticus' shares 11 genes with only Sinorhizobium meliloti and 12 genes are shared with only Bartonella henselae.

  11. Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter' asiaticus and other rhizbiales

    Science.gov (United States)

    The intracellular plant pathogen ‘Ca. Liberibacter asiaticus’ is a member of the Rhizobiales, as are the nitrogen fixing Sinorhizobium meliloti and Bradyrhizobium japonicum, the plant pathogen Agrobacterium tumefaciens and the intracellular mammalian pathogen Bartonella henselae. Whole genome compar...

  12. Distribution of the Primary Endosymbiont (Candidatus Uzinura Diaspidicola Within Host Insects from the Scale Insect Family Diaspididae

    Directory of Open Access Journals (Sweden)

    Katharina Dittmar

    2012-02-01

    Full Text Available It has long been known that armored scale insects harbor endosymbiotic bacteria inside specialized cells called bacteriocytes. Originally, these endosymbionts were thought to be fungal symbionts but they are now known to be bacterial and have been named Uzinura diaspidicola. Bacteriocyte and endosymbiont distribution patterns within host insects were visualized using in situ hybridization via 16S rRNA specific probes. Images of scale insect embryos, eggs and adult scale insects show patterns of localized bacteriocytes in embryos and randomly distributed bacteriocytes in adults. The symbiont pocket was not found in the armored scale insect eggs that were tested. The pattern of dispersed bacteriocytes in adult scale insects suggest that Uzinura and Blattabacteria may share some homologous traits that coincide with similar life style requirements, such as dispersal in fat bodies and uric acid recycling.

  13. Candidatus Phytoplasma hispanicum’, a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus

    Science.gov (United States)

    Mexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first know...

  14. The giant ciliate Zoothamnium niveum and its thiotrophic epibiont Candidatus Thiobios zoothamnicoli: a model system to study interspecies cooperation

    Directory of Open Access Journals (Sweden)

    Monika eBright

    2014-04-01

    Full Text Available Symbioses between chemoautotrophic sulfur-oxidizing (thiotrophic bacteria and protists or animals are among the most diverse and prevalent in the ocean. They are extremely difficult to maintain in aquaria and no thiotrophic symbiosis involving an animal host has ever been successfully cultivated. In contrast, we have cultivated the giant ciliate Zoothamnium niveum and its obligate ectosymbiont Cand. Thiobios zoothamnicoli in small flow-through aquaria. This review provides an overview of the host and the symbiont and their phylogenetic relationships. We summarize our knowledge on the ecology, geographic distribution and life cycle of the host, on the vertical transmission of the symbiont, and on the cultivation of this symbiosis. We then discuss the benefits and costs involved in this cooperation compared with other thiotrophic symbioses and outline our view on the evolution and persistence of this byproduct mutualism.

  15. Leaf-disc grafting for the transmission of Candidatus Liberibacter asiaticus in citrus (Citrus sinensis; Rutaceae) seedlings1

    Science.gov (United States)

    Tabay Zambon, Flavia; Plant, Karen; Etxeberria, Ed

    2017-01-01

    Premise of the study: The search for resistance/tolerance to the devastating citrus huanglongbing disease (syn. HLB or citrus greening) is generating an increasing number of new plants of diverse genetic makeup. As the increasing number of new plants require more space, resources, and time, the need for faster and more efficient HLB screening tests becomes crucial. Methods and Results: The leaf-disc grafting system described here consists in replacing a disc of leaf tissue with a similar disc from an infected plant. This can be performed in young seedlings not yet big enough to endure other types of grafting. Graft success and infection rates average approximately 80%. Conclusions: We describe the successful adaptation of leaf-disc grafting as a powerful screening tool for HLB. The system requires minimal plant material and can be performed in seedlings at a very young age with increased efficiency in terms of time, space, and resources. PMID:28090406

  16. Distribution of the Primary Endosymbiont (Candidatus Uzinura Diaspidicola) Within Host Insects from the Scale Insect Family Diaspididae.

    Science.gov (United States)

    Gruwell, Matthew E; Flarhety, Meghan; Dittmar, Katharina

    2012-02-29

    It has long been known that armored scale insects harbor endosymbiotic bacteria inside specialized cells called bacteriocytes. Originally, these endosymbionts were thought to be fungal symbionts but they are now known to be bacterial and have been named Uzinura diaspidicola. Bacteriocyte and endosymbiont distribution patterns within host insects were visualized using in situ hybridization via 16S rRNA specific probes. Images of scale insect embryos, eggs and adult scale insects show patterns of localized bacteriocytes in embryos and randomly distributed bacteriocytes in adults. The symbiont pocket was not found in the armored scale insect eggs that were tested. The pattern of dispersed bacteriocytes in adult scale insects suggest that Uzinura and Blattabacteria may share some homologous traits that coincide with similar life style requirements, such as dispersal in fat bodies and uric acid recycling.

  17. RELACIÓN ENTRE Bactericera cockerelli Y PRESENCIA DE Candidatus Liberibacter psyllaurous EN LOTES COMERCIALES DE PAPA

    OpenAIRE

    Oswaldo Ángel Rubio-Covarrubias; Isidro Humberto Almeyda-León; Mateo Armando Cadena-Hinojosa; René Lobato-Sánchez

    2011-01-01

    La brotación anormal de los tubérculos (sin brotes o brotes ahilados) y el pardeamiento interno de los tubérculos, son síntomas de una enfermedad que está afectando la producción de papa en México, en el suroeste de Estados Unidos y América central. Esta enfermedad ha sido asociada con el psilido de la papa Bactericera cockerelli Sulc. Con el objetivo de dilucidar las causas de esta enfermedad, en 2007 se llevó a cabo un muestreo en 11 lotes comerciales de papa localizados en un transecto alt...

  18. Detection of a Potential New Bartonella Species “Candidatus Bartonella rondoniensis” in Human Biting Kissing Bugs (Reduviidae; Triatominae)

    Science.gov (United States)

    Laroche, Maureen; Berenger, Jean-Michel; Mediannikov, Oleg; Raoult, Didier; Parola, Philippe

    2017-01-01

    Background Among the Reduviidae family, triatomines are giant blood-sucking bugs. They are well known in Central and South America where they transmit Trypanosoma cruzi to mammals, including humans, through their feces. This parasitic protozoan is the causative agent of Chagas disease, a major public health issue in endemic areas. Because of the medical and economic impact of Chagas disease, the presence of other arthropod-borne pathogens in triatomines was rarely investigated. Methodology/Principal findings In this study, seven triatomines species involved in the transmission of T. cruzi were molecularly screened for the presence of known pathogens generally associated with arthropods, such as Rickettsia, Bartonella, Anaplasmataceae, Borrelia species and Coxiella burnetii. Of all included triatomine species, only Eratyrus mucronatus specimens tested positive for Bartonella species for 56% of tested samples. A new genotype of Bartonella spp. was detected in 13/23 Eratyrus mucronatus specimens, an important vector of T. cruzi to humans. This bacterium was further characterized by sequencing fragments of the ftsZ, gltA and rpoB genes. Depending on the targeted gene, this agent shares 84% to 91% of identity with B. bacilliformis, the agent of Carrion’s disease, a deadly sandfly-borne infectious disease endemic in South America. It is also closely related to animal pathogens such as B. bovis and B. chomelii. Conclusions As E. mucronatus is an invasive species that occasionally feeds on humans, the presence of potentially pathogenic Bartonella-infected bugs could present another risk for human health, along with the T. cruzi issue. PMID:28095503

  19. Candidate pathogenicity islands in the genome of ‘Candidatus Rickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

    Science.gov (United States)

    Wang, YaDong

    2016-01-01

    The bacterial genus Rickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus, R. grylliand R. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence for R. isopodorum, and performed a comparative genomic analysis with R. grylli. We found evidence for several candidate genomic island regions in R. isopodorum, none of which appear in the previously available R. grylli genome sequence.Furthermore, one of these genomic island candidates in R. isopodorum contained a gene that encodes a cytotoxin partially homologous to those found in Photorhabdus luminescensand Xenorhabdus nematophilus (Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity in Rickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis in R. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature. PMID:28028472

  20. Tissue localization of the endosymbiotic bacterium "Candidatus Blochmannia floridanus" in adults and larvae of the carpenter ant Camponotus floridanus.

    Science.gov (United States)

    Sauer, Christina; Dudaczek, Dieter; Hölldobler, Bert; Gross, Roy

    2002-09-01

    The distribution of endosymbiotic bacteria in different tissues of queens, males, and workers of the carpenter ant Camponotus floridanus was investigated by light and electron microscopy and by in situ hybridization. A large number of bacteria could be detected in bacteriocytes within the midguts of workers, young virgin queens, and males. Large amounts of bacteria were also found in the oocytes of workers and queens. In contrast, bacteria were not present in oocyte-associated cells or in the spermathecae of mature queens, although occasionally a small number of bacteria could be detected in the testis follicles of males. Interestingly, the number of bacteriocytes in mature queens was strongly reduced and the bacteriocytes contained only very few or no bacteria at all, although the endosymbionts were present in huge amounts in the ovaries of the same animals. During embryogenesis of the deposited egg, the bacteria were concentrated in a ring of endodermal tissue destined to become the midgut in later developmental stages. However, during larval development, bacteria could also be detected in other tissues although to a lesser extent. Only in the last-instar larvae were bacteria found exclusively in the midgut tissue within typical bacteriocytes. Tetracycline and rifampin efficiently cleansed C. floridanus workers of their symbionts and the bacteriocytes of these animals still remained empty several months after treatment had ceased. Despite the lack of their endosymbionts, these adult animals were able to survive without any obvious negative effect under normal cultivation conditions.

  1. A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones

    Digital Repository Service at National Institute of Oceanography (India)

    Woebken, D.; Lam, P.; Kuypers, M.M.M.; Naqvi, S.W.A; Kartal, B.; Strous, M.; Jetten, M.S.M.; Fuchs, B.M.; Amann, R.

    The anaerobic oxidation of ammonium (anammox) contributes significantly to the global loss of fixed nitrogen and is carried out by a deep branching monophyletic group of bacteria within the phylum Planctomycetes. Various studies have implicated...

  2. 'Candidatus Rhabdochlamydia porcellionis', an intracellular bacterium from the hepatopancreas of the terrestrial isopod Porcellio scaber (Crustacea: Isopoda).

    Science.gov (United States)

    Kostanjsek, Rok; Strus, Jasna; Drobne, Damjana; Avgustin, Gorazd

    2004-03-01

    Intracellular bacteria were observed in the hepatopancreas of the terrestrial isopod Porcellio scaber. Comparative 16S rRNA gene sequence analysis and electron microscopic observations were used to determine the taxonomic position of these intracellular bacteria. Phylogenetic analysis and a complex developmental cycle affiliate these bacteria to the order Chlamydiales, within which they form a distinctive lineage, close to the family Simkaniaceae. They share scaber.

  3. 'Candidatus Phytoplasma palmicola', associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique.

    Science.gov (United States)

    Harrison, Nigel A; Davis, Robert E; Oropeza, Carlos; Helmick, Ericka E; Narváez, María; Eden-Green, Simon; Dollet, Michel; Dickinson, Matthew

    2014-06-01

    In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100% identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0-99.6% identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d'Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d'Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.

  4. Survey of 'Candidatus Liberibacter solanacearum' in carrot crops affected by the psyllid Trioza apicalis (Hemiptera: Triozidae) in Norway

    Science.gov (United States)

    The carrot psyllid Trioza apicalis Förster (Hemiptera: Triozidae) is a serious insect pest of carrot (Daucus carota L.) in northern Europe, where it can cause up to 100% crop loss. Although it was long believed that T. apicalis causes damage to carrot by injection of toxins into the plant, it was re...

  5. "Candidatus phytoplasma costaricanum" a new phytoplasma associated with a newly emerging disease in soybean in Costa Rica

    Science.gov (United States)

    A new phytoplasma associated with a newly emerging disease, soybean stunt (SoyST), in soybean (Glycine max) was found in 2002 in a soybean plantation in Alajuela Province, Costa Rica. The same or very closely related phytoplasma also infected sweet pepper (Capsicum annuum) with purple vein syndrome ...

  6. Murraya paniculata (orange jasmine), a host and possible inoculum reservoir for Candidatus Liberibacter asiaticus, causal agent of Huanglongbing

    Science.gov (United States)

    Huanglongbing (HLB), considered the most serious vectored-pathogen of citrus, is transmitted in nature by the Asian citrus psyllid Diaphorina citri and the African citrus psyllid Trioza erytreae. In 1999, D. citri was discovered in southern Florida and has become established in FL and TX. Huanglon...

  7. Excitation Emission Matrix Spectra (EEMS) of Chromophoric Dissolved Organic Matter Produced during Microbial Incubation

    Science.gov (United States)

    McDonald, N.; Nelson, N. B.; Parsons, R.

    2013-12-01

    can be linked to this bacterial production. FISH analysis showed percentage abundance of Pelagibacter ubique (SAR 11) and of Alteromonas. On-going and future work will ascertain if specific microbial communities produce CDOM more readily than others, and if these different populations produce varying fluorescence peaks, thus indicating a range of chromophoric groups being produced by bacteria. An additional suite of probes will be used for further FISH analysis to identify percentages of other populations, and seasonal/temporal variations will be investigated.

  8. 泛在知识环境下图书馆服务泛在化研究%Research on the Ubiquity of Library Services in Ubiquitous Knowledge Environment

    Institute of Scientific and Technical Information of China (English)

    谢珍; 杨九龙

    2010-01-01

    泛在知识环境下图书馆服务应具有无所不在、透明、开放获取的特点.泛在图书馆的构建应倡导以用户为中心、主动服务、平等获取、开放共享的理念,坚持海量资源、质量保障、有序组织的资源建设与保障策略,加强网络技术、信息设备、智能交互的研究运用.向用户提供无所不在的知识服务.实体图书馆泛在化及网络服务泛在化是图书馆服务泛在化的实现路径.

  9. "健笔终存天地间":论邓拓与书生办报%Ubiquity of his forceful pen-DENG Tuo and "Press run by Scholars"

    Institute of Scientific and Technical Information of China (English)

    吴廷俊; 阳海洪

    2006-01-01

    1957年和1958年,毛泽东两次对邓拓和进行了严厉的批评,指斥邓拓为"书生办报".因为在毛泽东看来,"书生办报"和他在此时期所认可的"政治家办报"出现了相悖.本文清理了"书生办报的内涵"、"邓拓书生办报的发展"和"对邓拓书生办报的沉思",指出邓拓的书生办报的内核是强烈的责任感、求真精神、为民立言意识和理想情怀,并肯定了邓拓书生办报的历史意义.

  10. Rest-frame Optical Emission Lines in z ˜ 3.5 Lyman-break-selected Galaxies: The Ubiquity of Unusually High [OIII]/Hβ Ratios at 2 Gyr

    Science.gov (United States)

    Holden, B. P.; Oesch, P. A.; González, V. G.; Illingworth, G. D.; Labbé, I.; Bouwens, R.; Franx, M.; van Dokkum, P.; Spitler, L.

    2016-03-01

    We present K-band spectra of rest-frame optical emission lines for 24 star-forming galaxies at z ˜ 3.2-3.7 using MOSFIRE on the Keck I telescope. Strong rest-frame optical [O iii] and Hβ emission lines were detected in 18 Lyman break galaxies (LBGs). The median flux ratio of [O iii]λ5007 to Hβ is {5.1}-0.5+0.5. This is a factor of 5-10 times higher than in local galaxies with similar stellar masses. None of our sources are detected in deep X-ray stacks, ruling out significant contamination by active galactic nuclei. Combining our sample with a variety of LBGs from the literature, including 49 galaxies selected in a very similar manner, we find a high median ratio of [O iii]/Hβ = {4.8}-1.7+0.8. This high ratio seems to be a ubiquitous feature of z ˜ 3-4 LBGs, very different from typical local star-forming galaxies at similar stellar masses. The only comparable systems at z ˜ 0 are those with similarly high specific star formation rates (SSFRs), though ˜5 times lower stellar masses. High SSFRs may result in a higher ionization parameter, higher electron density, or harder ionizing radiation, which, combined different elemental abundances, result in a much higher [O iii]/Hβ line ratio. This implies a strong relation between a global property of a galaxy, the SSFR, and the local conditions of ISM in star-forming regions. Partially based on data obtained with the Hubble Space Telescope operated by AURA, Inc. for NASA under contract NAS5-26555. Partially based on observations with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under NASA contract 1407.

  11. Characterization of Xiphinema americanum group species (Nematoda: Dorylaimida) and co-evolution of bacteria from the genus ‘Candidatus Xiphinematobacter’ with these nematodes

    Science.gov (United States)

    The Xiphinema americanum group contains over two-dozen different species of nematode. They are economically important because they vector nepoviruses, which cause damage to several crops. Taxonomic differentiation among species of the X. americanum complex is problematic because many of the species ...

  12. First report of sweet cherry virescence disease in China and its association with infection by a ‘Candidatus Phytoplasma ziziphi’-related strain

    Science.gov (United States)

    Sweet cherry (Prunus avium L.) is a deciduous tree originating in the Black Sea/Caspian Sea region where Asia and Europe converge. Being highly valued for its timber and fruit, sweet cherry has been cultivated and naturalized on all continents. Over the past decade, the area of sweet cherry culti...

  13. Seed transmission of Candidatus Liberibacter asiaticus in periwinkle and dodder resulted in low bacterial titer and very mild disease in periwinkle

    Science.gov (United States)

    Canadidatus Liberibacter asiaticus (Las) is the most widely-distributed of three species of Liberibacter that are associated with citrus Huanglongbing (HLB), a lethal disease of citrus worldwide. In addition to citrus, periwinkle (Catharanthus roseus) and dodder (Cuscuta pentagona) are two experime...

  14. First Report of "Candidatus Liberibacter psyllaurous" (synonym "Ca. L. solanacearum") Associated with 'Tomato Vein-Greening' and 'Tomato psyllid yellows' Diseases in Commercial Greenhouses in Arizona

    Science.gov (United States)

    During 2006-2007, tomato plants in two independent, commercial greenhouses in Arizona were infested with potato psyllid Paratrioza cockerelli. Over 60% and ~20% of plants in GH-1 and GH-2, respectively, exhibited leaf curling, stunting, and shortened internodes, and GH-1 plants also showed vein-gree...

  15. Respuesta fisiológica y bioquímica de plantas de limón mexicano infectadas con Candidatus Liberibacter asiaticus

    OpenAIRE

    Soto Leal, Mónica Gisela

    2014-01-01

    Actualmente la enfermedad HLB está afectando seriamente la citricultura nacional. Hasta la fecha se ha reportado a Ca. Liberibacter spp. como el agente causal de la enfermedad HLB. La mayoría de las investigaciones se han basado en detectar al patógeno, ya que la principal limitante es que éste patógeno no se puede cultivar in vitro, los estudios sobre la respuesta fisiológica y bioquímica de la planta ante la infección por Ca. Liberibacter asiaticus son escasos. Por lo que, el objetivo de la...

  16. Carbon and sulfur cycling below the chemocline in a meromictic lake and the identification of a novel taxonomic lineage in the FCB superphylum, Candidatus Aegiribacteria

    Directory of Open Access Journals (Sweden)

    Trinity L Hamilton

    2016-04-01

    Full Text Available Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this ‘plate’, the euxinic hypolimnion is anoxic, eutrophic, saline, and rich in sulfide, polysulfides, elemental sulfur, and other sulfur intermediates. While much is known regarding microbial communities in sunlit portions of euxinic systems, the composition and genetic potential of organisms living at aphotic depths have rarely been studied. Metagenomic sequencing of samples from the hypolimnion and the underlying sediments of Mahoney Lake indicate that multiple taxa contribute to sulfate reduction below the chemocline and that the hypolimnion and sediments each support distinct populations of sulfate reducing bacteria (SRB different from the SRB populations observed in the chemocline. After assembling and binning the metagenomic datasets, we recovered near-complete genomes of dominant populations, including two Deltaproteobacteria. One of the deltaproteobacterial genomes encoded a 16S rRNA sequence that was most closely related to the sulfur-disproportionating genus Dissulfuribacter and the other encoded a 16S rRNA sequence that was most closely related to the fatty acid- and aromatic acid-degrading genus Syntrophus. We also recovered two near-complete genomes of Firmicutes species. Analysis of concatenated ribosomal protein trees suggests these genomes are most closely related to extremely alkaliphilic genera Alkaliphilus and Dethiobacter. Our metagenomic data indicate that these Firmicutes contribute to carbon cycling below the chemocline. Lastly, we recovered a nearly complete genome from the sediment metagenome which represents a new genus within the FCB (Fibrobacteres, Chlorobi, Bacteroidetes super phylum. Consistent with the geochemical data, we found little or no evidence for organisms capable of sulfide oxidation in the aphotic zone below the chemocline. Instead, comparison of functional genes below the chemocline are consistent with recovery of multiple populations capable of reducing oxidized sulfur. Our data support previous observations that at least some of the sulfide necessary to support the dense population of phototrophs in the chemocline is supplied from sulfate reduction in the hypolimnion and sediments. These studies provide key insights

  17. Candidatus Phytoplasma palmicola’, a novel taxon associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique

    Science.gov (United States)

    In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise sequence similarity values based on alignment of near full-length 16SrRNA genes (1530 bp) reve...

  18. First report of ‘Candidatus Phytoplasma asteris’ subgroup 16SrI-A associated with a disease of potato (Solanum tuberosum) in Lithuania

    Science.gov (United States)

    Symptoms of little leaf, witches’-broom, and abnormally small and deformed potatoes, suggestive of possible phytoplasmal infection, were observed in diseased potato (Solanum tuberosum var. Hannibal arba Kestrel) in the Vilnius region of Lithuania. DNA extracted from symptomatic leaves and shoots we...

  19. High-temperature EBPR process: the performance, analysis of PAOs and GAOs and the fine-scale population study of Candidatus "Accumulibacter phosphatis".

    Science.gov (United States)

    Ong, Ying Hui; Chua, Adeline Seak May; Fukushima, Toshikazu; Ngoh, Gek Cheng; Shoji, Tadashi; Michinaka, Atsuko

    2014-11-01

    The applicability of the enhanced biological phosphorus removal (EBPR) process for the removal of phosphorus in warm climates is uncertain due to frequent reports of EBPR deterioration at temperature higher than 25 °C. Nevertheless, a recent report on a stable and efficient EBPR process at 28 °C has inspired the present study to examine the performance of EBPR at 24 °C-32 °C, as well as the PAOs and GAOs involved, in greater detail. Two sequencing batch reactors (SBRs) were operated for EBPR in parallel at different temperatures, i.e., SBR-1 at 28 °C and SBR-2 first at 24 °C and subsequently at 32 °C. Both SBRs exhibited high phosphorus removal efficiencies at all three temperatures and produced effluents with phosphorus concentrations less than 1.0 mg/L during the steady state of reactor operation. Real-time quantitative polymerase chain reaction (qPCR) revealed Accumulibacter-PAOs comprised 64% of the total bacterial population at 24 °C, 43% at 28 °C and 19% at 32 °C. Based on fluorescent in situ hybridisation (FISH), the abundance of Competibacter-GAOs at both 24 °C and 28 °C was rather low (temperature could have contributed to the presence of a unique clade. The clade IIF was hypothesised to be able to perform the EBPR activity at high temperatures. The clade's robustness most likely helps it to fit the high-temperature EBPR sludge best and allows it not only to outcompete other Accumulibacter clades but coexist with GAOs without compromising EBPR activity.

  20. The relevance of Murraya paniculata and related species as potential hosts and inoculum reservoirs of Candidatus Liberibacter asiaticus, causal agent of Huanglongbing (HLB)

    Science.gov (United States)

    Huanglongbing (HLB), considered the most serious insect-vectored bacterial disease of citrus, is transmitted in nature by the Asian citrus psyllid Diaphorina citri and the African citrus psyllid Trioza erytreae. Diaphorina citri was discovered in southern Florida in 1998 and the HLB disease in 2005...

  1. NCBI nr-aa BLAST: CBRC-HSAP-05-0051 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-HSAP-05-0051 ref|YP_903576.1| nicotinate (nicotinamide) nucleotide adenylyltransferase [Candidatus Ruth...adenylyltransferase [Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)] YP_903576.1 1.1 34% ...

  2. NCBI nr-aa BLAST: CBRC-PTRO-06-0046 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-06-0046 ref|YP_903576.1| nicotinate (nicotinamide) nucleotide adenylyltransferase [Candidatus Ruth...adenylyltransferase [Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)] YP_903576.1 1.1 34% ...

  3. Prevalence of feline haemoplasma in cats in Denmark

    DEFF Research Database (Denmark)

    Rosenqvist, Maja Benedicte; Meilstrup, Ann-Katrine Helene; Larsen, Jesper;

    2016-01-01

    Background Infections with the three feline haemotropic mycoplasmas Mycoplasma haemofelis, Candidatus Mycoplasma haemominutum and Candidatus Mycoplasma turicensis cause feline infectious anemia. The purpose of this study was to investigate the prevalence of carriage of feline haemoplasma in Danis...

  4. Dicty_cDB: Contig-U14192-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 5e-22 CP001277_1252( CP001277 |pid:none) Candidatus Hamiltonella defensa... 106 ...|pid:none) Candidatus Hamiltonella defensa... 105 7e-22 AM180088_979( AM180088 |pid:none) Haloquadratum wals

  5. Use of digital PCR to improve early detection of CLas infection

    Science.gov (United States)

    Huanglongbing is a devastating disease of citrus caused by the bacterium Candidatus Liberibacter asiaticus. Huanglongbing has devastated the Florida citrus industry and is threatening citrus in Texas and California. Detection of Candidatus Liberibacter asiaticus infections as early as possible is ...

  6. 78 FR 76257 - Rural Call Completion

    Science.gov (United States)

    2013-12-17

    ... ubiquity and reliability of the nation's communications network and threaten commerce, public safety, and... completion problems adversely affect the ubiquity and reliability of the nation's telecommunications network...-distance call completion to rural areas. The ubiquity and reliability of the nation's...

  7. Hemoplasma prevalence and hematological abnormalities associated with infection in three different cat populations from Southern Brazil

    Directory of Open Access Journals (Sweden)

    Andrea Pires dos Santos

    2014-12-01

    Full Text Available Three hemoplasma species are recognized in domestic cats: Mycoplasma haemofelis, ‘Candidatus Mycoplasma haemominutum’ and ‘Candidatus Mycoplasma turicensis’. We report the prevalence and hematological abnormalities of hemoplasma infection in 369 domestic cats from three different populations (blood donors, hospitalized cats and shelter cats from Southern Brazil. Complete blood counts were performed at the time of blood collection, and DNA was extracted and tested by conventional PCR for each hemoplasma species. A total of 79 samples (21.40% were positive for at least one species. The most prevalent hemoplasma was ‘Candidatus Mycoplasma haemominutum’, with 50/369 (13.55% positive cats, followed by ‘Candidatus Mycoplasma turicensis’, 10/369 (2.71%, and Mycoplasma haemofelis, 8/369 (2.16%. Mycoplasma haemofelis and ‘Candidatus Mycoplasma haemominutum’ coinfection was observed in 4/369 (1.08%, whereas ‘Candidatus Mycoplasma haemominutum’ and ‘Candidatus Mycoplasma turicensis’ in 5/369 (1.35%. Three cats (0.81% were infected with all three hemoplasmas. There was no association between infection and the different populations. Anemia was associated with Mycoplasma haemofelis and ‘Candidatus Mycoplasma haemominutum’, but not with ‘Candidatus Mycoplasma turicensis’. Male cats and cats with outdoor access were more likely to be infected. Although ‘Candidatus Mycoplasma haemominutum’ is believed to cause minimal or no hematological alterations, the infected cats studied herein were more likely to be anemic.

  8. 论图书馆服务的泛在化——以用户为中心重构图书馆服务模式%The Ubiquity of the Library Services——Restructuring User-Centered Library Service Models

    Institute of Scientific and Technical Information of China (English)

    初景利; 吴冬曼

    2008-01-01

    泛在图书馆是全新的图书馆理念,表明图书馆新的发展方向.图书馆服务的泛在化体现在服务范围和服务对象的泛在化、服务内容和服务功能的泛在化、服务场所和服务空间的泛在化、以及服务手段和服务机制的泛在化.中国科学院国家科学图书馆的事实证明,在传统的图书馆服务以外,图书馆的服务具有广泛的需求和无限的发展空间.图书馆的服务只有融入到用户的场景和社区,才会显示图书馆更大的功能,才会有无限的发展潜力.

  9. Dicty_cDB: Contig-U15989-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available , chloroplastic;... 42 0.048 AF481102_20( AF481102 |pid:none) Candidatus Tremblaya princeps Mvi... 42 0.048 ...AF481103_6( AF481103 |pid:none) Candidatus Tremblaya princeps tran... 42 0.048 FM992695_127( FM992695 |pid:n...1 from Patent EP1104808. 40 0.11 AF481912_2( AF481912 |pid:none) Candidatus Tremblaya

  10. 'Candidatus Phytoplasmas pruni', a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes

    Science.gov (United States)

    X-disease is one of the most serious diseases known in peach (Prunus persica). Based on RFLP analysis of 16S rRNA gene sequences, peach X-disease phytoplasma strains from eastern and western United States and eastern Canada were classified in 16S rDNA RFLP group 16SrIII, subgroup A. Phylogenetic a...

  11. Dicty_cDB: Contig-U11379-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s embryo wh... 76 3e-12 EU021903_1( EU021903 |pid:none) Candidatus Hamiltonella defensa st... 76 4e-12 EU021...884_1( EU021884 |pid:none) Candidatus Hamiltonella defensa st... 76 4e-12 CP000489_2726( CP000489 |pid:none)...one) Candidatus Hamiltonella defensa st... 75 6e-12 AK314435_1( AK314435 |pid:non...e) Homo sapiens cDNA, FLJ95232, highl... 75 6e-12 EU021888_1( EU021888 |pid:none) Candidatus Hamiltonella defensa

  12. 78 FR 36725 - Numbering Policies for Modern Communications; IP-Enabled Services; Telephone Number Requirements...

    Science.gov (United States)

    2013-06-19

    ... number administration more generally. The memorability, ubiquity, convenience, and universality of... judicious management of telephone numbers and promote further innovation and competition, the NPRM...

  13. Dicty_cDB: SHB877 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 5 DQ163124 |DQ163124.1 Candidatus Hamiltonella defensa clone P010083 genomic sequ...ence. 38 0.080 2 DQ163419 |DQ163419.1 Candidatus Hamiltonella defensa clone P090011 genomic sequence. 38 0.0

  14. Dicty_cDB: Contig-U01609-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ted] - Nostoc ... 39 0.51 CP001277_1167( CP001277 |pid:none) Candidatus Hamiltonella defensa... 39 0.51 AL16...7 |pid:none) Candidatus Hamiltonella defensa... 38 0.66 CP000239_1978( CP000239 |pid:none) Synechococcus sp.

  15. Dicty_cDB: Contig-U10184-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 000239 |pid:none) Synechococcus sp. JA-3-3Ab, comp... 83 8e-15 CP001277_66( CP001277 |pid:none) Candidatus Hamiltonella defensa...P001277_1866( CP001277 |pid:none) Candidatus Hamiltonella defensa... 72 2e-11 AE0

  16. Dicty_cDB: Contig-U12898-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available _741( CP001277 |pid:none) Candidatus Hamiltonella defensa ... 64 1e-08 CP000850_4205( CP000850 |pid:none) Sa...277 |pid:none) Candidatus Hamiltonella defensa ... 57 1e-06 (Q31WY3) RecName: Ful

  17. Dicty_cDB: Contig-U02155-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 02 CP001277_1866( CP001277 |pid:none) Candidatus Hamiltonella defensa... 47 0.002 CP000739_409( CP000739 |pi...enibacterium salmoninarum ATCC... 47 0.002 CP001277_66( CP001277 |pid:none) Candidatus Hamiltonella defens

  18. Dicty_cDB: Contig-U06605-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available harveyi ATCC BAA-1116 ch... 78 2e-13 CP001277_52( CP001277 |pid:none) Candidatus Hamiltonella defensa...001277 |pid:none) Candidatus Hamiltonella defensa... 38 0.18 CP000463_1604( CP000463 |pid:none) Rhodopseudom

  19. NCBI nr-aa BLAST: CBRC-VPAC-01-0381 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available yltransferase [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] gb|ACQ67332.1| UDP-3-O-(3-hydroxym...yristoyl)-glucosamine N-acyltransferase [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] YP_002923480.1 0.76 28% ...

  20. NCBI nr-aa BLAST: CBRC-TTRU-01-1371 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available ndent protein export [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] gb|ACQ68339.1| twin-arginin...e translocase subunit, sec-independent protein export [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] YP_002924487.1 0.89 24% ...

  1. NCBI nr-aa BLAST: CBRC-VPAC-01-0194 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available yltransferase [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] gb|ACQ67332.1| UDP-3-O-(3-hydroxym...yristoyl)-glucosamine N-acyltransferase [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] YP_002923480.1 0.58 29% ...

  2. NCBI nr-aa BLAST: CBRC-MDOM-11-0019 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available (LIV-II) (LIVCS family) [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] gb|ACQ67379.1| branched...-chain amino acid transport system II (LIV-II) (LIVCS family) [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)] YP_002923527.1 4.1 29% ...

  3. NCBI nr-aa BLAST: CBRC-CREM-01-1374 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1374 ref|YP_008913.1| hypothetical protein pc1914 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24638.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008913.1 0.29 20% ...

  4. NCBI nr-aa BLAST: CBRC-ACAR-01-0459 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0459 ref|YP_007081.1| hypothetical protein pc0082 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF22806.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_007081.1 1.4 39% ...

  5. NCBI nr-aa BLAST: CBRC-TTRU-01-0863 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0863 ref|YP_007184.1| hypothetical protein pc0185 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF22909.1| unknown protein [Candidatus Protochlamydia amoebophila UWE25] YP_007184.1 0.068 25% ...

  6. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008927.1| hypothetical protein pc1928 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24652.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008927.1 8e-14 30% ...

  7. NCBI nr-aa BLAST: CBRC-PCAP-01-0443 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PCAP-01-0443 ref|YP_008661.1| hypothetical protein pc1662 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24386.1| unknown protein [Candidatus Protochlamydia amoebophila UWE25] YP_008661.1 1.1 38% ...

  8. NCBI nr-aa BLAST: CBRC-MMUR-01-1593 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUR-01-1593 ref|YP_008914.1| hypothetical protein pc1915 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24639.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008914.1 7.7 41% ...

  9. NCBI nr-aa BLAST: CBRC-CREM-01-1374 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1374 ref|YP_008925.1| hypothetical protein pc1926 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24650.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008925.1 1.8 17% ...

  10. NCBI nr-aa BLAST: CBRC-SARA-01-2026 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-SARA-01-2026 ref|YP_008277.1| hypothetical protein pc1278 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24002.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008277.1 0.89 28% ...

  11. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008032.1| hypothetical protein pc1033 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23757.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008032.1 1e-16 30% ...

  12. NCBI nr-aa BLAST: CBRC-CREM-01-1339 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1339 ref|YP_008665.1| hypothetical protein pc1666 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24390.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008665.1 0.24 16% ...

  13. NCBI nr-aa BLAST: CBRC-CREM-01-1374 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1374 ref|YP_008665.1| hypothetical protein pc1666 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24390.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008665.1 0.075 18% ...

  14. NCBI nr-aa BLAST: CBRC-SARA-01-0159 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-SARA-01-0159 ref|YP_008619.1| hypothetical protein pc1620 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24344.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008619.1 7.8 27% ...

  15. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008506.1| hypothetical protein pc1507 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24231.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008506.1 1e-12 26% ...

  16. NCBI nr-aa BLAST: CBRC-PTRO-20-0007 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-20-0007 ref|YP_008665.1| hypothetical protein pc1666 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24390.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008665.1 1e-04 30% ...

  17. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008494.1| hypothetical protein pc1495 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24219.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008494.1 4e-12 28% ...

  18. NCBI nr-aa BLAST: CBRC-OPRI-01-0823 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OPRI-01-0823 ref|YP_007343.1| hypothetical protein pc0344 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23068.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_007343.1 1.8 27% ...

  19. NCBI nr-aa BLAST: CBRC-TTRU-01-0631 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0631 ref|YP_007980.1| hypothetical protein pc0981 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23705.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_007980.1 0.98 26% ...

  20. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008277.1| hypothetical protein pc1278 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24002.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008277.1 3e-15 27% ...

  1. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008141.1| hypothetical protein pc1142 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23866.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008141.1 2e-13 27% ...

  2. NCBI nr-aa BLAST: CBRC-CREM-01-1374 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1374 ref|YP_008032.1| hypothetical protein pc1033 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23757.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008032.1 9.2 19% ...

  3. NCBI nr-aa BLAST: CBRC-ETEL-01-1164 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ETEL-01-1164 ref|YP_008454.1| hypothetical protein pc1455 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24179.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008454.1 2e-06 19% ...

  4. NCBI nr-aa BLAST: CBRC-CREM-01-1339 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1339 ref|YP_008913.1| hypothetical protein pc1914 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24638.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008913.1 0.24 20% ...

  5. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008031.1| hypothetical protein pc1032 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23756.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008031.1 4e-13 29% ...

  6. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008914.1| hypothetical protein pc1915 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24639.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008914.1 4e-12 25% ...

  7. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_008271.1| hypothetical protein pc1272 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23996.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008271.1 2e-13 25% ...

  8. NCBI nr-aa BLAST: CBRC-SARA-01-2026 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-SARA-01-2026 ref|YP_008281.1| hypothetical protein pc1282 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24006.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008281.1 3.4 25% ...

  9. NCBI nr-aa BLAST: CBRC-CREM-01-1339 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1339 ref|YP_008032.1| hypothetical protein pc1033 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23757.1| hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008032.1 0.93 18% ...

  10. NCBI nr-aa BLAST: CBRC-CREM-01-1339 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1339 ref|YP_008925.1| hypothetical protein pc1926 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF24650.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_008925.1 1.2 17% ...

  11. NCBI nr-aa BLAST: CBRC-MLUC-01-0268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MLUC-01-0268 ref|YP_007991.1| hypothetical protein pc0992 [Candidatus Protochlamydia... amoebophila UWE25] emb|CAF23716.1| conserved hypothetical protein [Candidatus Protochlamydia amoebophila UWE25] YP_007991.1 8e-15 28% ...

  12. Steve Jobs and the User Psyche

    OpenAIRE

    Denning, Peter J.

    2011-01-01

    The article of record as published may be found at http://dx.doi.org/10.1145/2043155.2043157 Peter J. Denning reflects on a meeting he had with Steve Jobs in 1988. Published in ACM Ubiquity.Ubiquity Commentary

  13. Built-In Device Orientation Sensors for Ad-Hoc Pairing and Spatial Awareness

    DEFF Research Database (Denmark)

    Grønbæk, Jens Emil; O'Hara, Kenton

    Mobile devices are equipped with multiple sensors. The ubiquity of these sensors is key in their ability to support in-the-wild application and use. Building on the ubiquity we look at how we can use this existing sensing infrastructure combined with user mediation to support ad-hoc sharing with ...

  14. Dicty_cDB: Contig-U03315-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available um discoideum chromoso... 37 0.91 AY090469_1( AY090469 |pid:none) Candidatus Tremblaya princeps 23S ... 37 0...ompl... 36 2.7 AY079511_1( AY079511 |pid:none) Candidatus Tremblaya princeps from... 36 2.7 FN357504_16( FN3... 0.004 (A6VH19) RecName: Full=50S ribosomal protein L11P; &(A9A9N0) Re... 45 0.006 AF481103_7( AF481103 |pid:none) Candidatus Trembla...ya princeps tran... 45 0.006 CP000575_1076( CP000575 |pi

  15. Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm

    NARCIS (Netherlands)

    Barr, Jeremy J; Dutilh, Bas E; Skennerton, Connor T; Fukushima, Toshikazu; Hastie, Marcus L; Gorman, Jeffrey J; Tyson, Gene W; Bond, Philip L

    2015-01-01

    Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus remova

  16. Description of new filamentous toxic Cyanobacteria (Oscillatoriales) colonizing the sulfidic periphyton mat in marine mangroves.

    Science.gov (United States)

    Guidi-Rontani, Chantal; Jean, Maïtena R N; Gonzalez-Rizzo, Silvina; Bolte-Kluge, Susanne; Gros, Olivier

    2014-10-01

    In this multidisciplinary study, we combined morphological, physiological, and phylogenetic approaches to identify three dominant water bloom-forming Cyanobacteria in a tropical marine mangrove in Guadeloupe (French West Indies). Phylogenetic analysis based on 16S rRNA gene sequences place these marine Cyanobacteria in the genera Oscillatoria (Oscillatoria sp. clone gwada, strain OG) or Planktothricoides ('Candidatus Planktothricoides niger' strain OB and 'Candidatus Planktothricoides rosea' strain OP; both provisionally novel species within the genus Planktothricoides). Bioassays showed that 'Candidatus Planktothricoides niger' and 'Candidatus Planktothricoides rosea' are toxin-producing organisms. This is the first report of the characterization of Cyanobacteria colonizing periphyton mats of a tropical marine mangrove. We describe two novel benthic marine species and provide new insight into Oscillatoriaceae and their potential role in marine sulfide-rich environments such as mangroves.

  17. Annotation of the Asian citrus psyllid genome reveals a reduced innate immune system

    Science.gov (United States)

    Citrus production worldwide is currently facing significant losses due to citrus greening disease, also known as huanglongbing. The citrus greening bacteria, Candidatus Liberibacter asiaticus (CLas), is a persistent propagative pathogen transmitted by the Asian citrus psyllid, Diaphorina citri Kuway...

  18. Yeast Interacting Proteins Database: YNL311C, YKL001C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available -purification experiments; putative F-box protein; analysis of integrated high-throughput datasets predicts ...ments; putative F-box protein; analysis of integrated high-throughput datasets predicts involvement in ubiqu

  19. Muusika valib Tristan Priimägi / Tristan Priimägi

    Index Scriptorium Estoniae

    Priimägi, Tristan, 1976-

    2004-01-01

    Heliplaatidest: Roy Ayers "Virgin Ubiquity - Unreleased Recordings 1976-1981", "Ibadan People", "A Journey to the Dawn", The Matthew Herbert Big Band "Goodbye Swingtime", Amp Fiddler "Waltz of a Ghetto Fly"

  20. Gclust Server: 32698 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available egulatory X) domain-containing protein that interacts with Cdc48p, has a ubiquitin-associated (UBA) domain, interacts with ubiquity...lated proteins in vivo, and is required for degradation of a ubiquitylated model subs...interacts with Cdc48p, has a ubiquitin-associated (UBA) domain, interacts with ubiquity...lated proteins in vivo, and is required for degradation of a ubiquitylated model substrate Number of S

  1. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations.

    Science.gov (United States)

    Shilova, Irina N; Robidart, Julie C; DeLong, Edward F; Zehr, Jonathan P

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics.

  2. Distribution and activity of anaerobic ammonium-oxidising bacteria in natural freshwater wetland soils.

    Science.gov (United States)

    Shen, Li-dong; Wu, Hong-sheng; Gao, Zhi-qiu; Cheng, Hai-xiang; Li, Ji; Liu, Xu; Ren, Qian-qi

    2016-04-01

    Anaerobic ammonium oxidation (anammox) process plays a significant role in the marine nitrogen cycle. However, the quantitative importance of this process in nitrogen removal in wetland systems, particularly in natural freshwater wetlands, is still not determined. In the present study, we provided the evidence of the distribution and activity of anammox bacteria in a natural freshwater wetland, located in southeastern China, by using (15)N stable isotope measurements, quantitative PCR assays and 16S rRNA gene clone library analysis. The potential anammox rates measured in this wetland system ranged between 2.5 and 25.5 nmol N2 g(-1) soil day(-1), and up to 20% soil dinitrogen gas production could be attributed to the anammox process. Phylogenetic analysis of 16S rRNA genes showed that anammox bacteria related to Candidatus Brocadia, Candidatus Kuenenia, Candidatus Anammoxoglobus and two novel anammox clusters coexisted in the collected soil cores, with Candidatus Brocadia and Candidatus Kuenenia being the dominant anammox genera. Quantitative PCR of hydrazine synthase genes showed that the abundance of anammox bacteria varied from 2.3 × 10(5) to 2.2 × 10(6) copies g(-1) soil in the examined soil cores. Correlation analyses suggested that the soil ammonium concentration had significant influence on the activity of anammox bacteria. On the basis of (15)N tracing technology, it is estimated that a total loss of 31.1 g N m(-2) per year could be linked the anammox process in the examined wetland.

  3. Discovery of a novel methanogen prevalent in thawing permafrost.

    Science.gov (United States)

    Mondav, Rhiannon; Woodcroft, Ben J; Kim, Eun-Hae; McCalley, Carmody K; Hodgkins, Suzanne B; Crill, Patrick M; Chanton, Jeffrey; Hurst, Gregory B; VerBerkmoes, Nathan C; Saleska, Scott R; Hugenholtz, Philip; Rich, Virginia I; Tyson, Gene W

    2014-01-01

    Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.

  4. Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae).

    Science.gov (United States)

    Vandekerckhove, T T; Willems, A; Gillis, M; Coomans, A

    2000-11-01

    Numerous micro-organisms have been described as cytoplasmic symbionts of eukaryotes. Many so-called obligate endosymbionts rely exclusively on maternal (vertical or transovarial) transmission to maintain themselves, rendering them dependent on the host sex ratio, which they would tend to manipulate to their own advantage. The latter phenomenon is often associated with the presence of Wolbachia pipientis (alpha-Proteobacteria) in arthropods and nematodes. A potentially similar situation was discovered involving members of a new clade of Verrucomicrobia, another main line of descent in the Bacteria. Nematode species of the Xiphinema americanum group (Nematoda, Longidoridae), viz. Xiphinema americanum, Xiphinema rivesi and Xiphinema brevicollum, each harbour their own specific verrucomicrobial endosymbionts. They are exclusively maternally inherited and their hosts reproduce by thelytokous (mother-to-daughter) parthenogenesis, males being extremely rare. A new genus, 'Candidatus Xiphinematobacter' gen. nov., along with three new candidate verrucomicrobial species, 'Candidatus Xiphinematobacter americani' sp. nov., 'Candidatus Xiphinematobacter rivesi' sp. nov. and 'Candidatus Xiphinematobacter brevicolli' sp. nov., are described on the basis of transmission electron microscopy, scanning electron microscopy, DAPI (4',6-diamidino-2-phenylindole) epifluorescence microscopy and 16S rDNA sequence analysis. These are the first endosymbiotic species described among the Verrucomicrobia. They share a mean 16S rDNA similarity of about 93%, whereas similarity to their closest relative, clone WCHD3-88, is less than 87%. Thus, the endosymbionts form a homogeneous clade for which the new candidate genus 'Candidatus Xiphinematobacter' gen. nov. is proposed. The type species is 'Candidatus Xiphinematobacter brevicolli' sp. nov.

  5. High-throughput screening of tick-borne pathogens in Europe

    DEFF Research Database (Denmark)

    Michelet, Lorraine; Delannoy, Sabine; Devillers, Elodie

    2014-01-01

    , Bartonella, Candidatus Neoehrlichia, Coxiella, Francisella, Babesia, and Theileria genus) across 94 samples. We successfully determined the prevalence of expected (Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, Rickettsia helvetica, Candidatus Neoehrlichia mikurensis, Babesia divergens, Babesia...... was conducted on 7050 Ixodes ricinus nymphs collected from France, Denmark, and the Netherlands using a powerful new high-throughput approach. This advanced methodology permitted the simultaneous detection of 25 bacterial, and 12 parasitic species (including; Borrelia, Anaplasma, Ehrlichia, Rickettsia...... venatorum), unexpected (Borrelia miyamotoi) and rare (Bartonella henselae) pathogens in the three European countries. Moreover we detected Borrelia spielmanii, Borrelia miyamotoi, Babesia divergens, and Babesia venatorum for the first time in Danish ticks. This surveillance method represents a major...

  6. Gender differences and effect of photophase on Asian citrus psyllid (Diaphorina citri Kuwayama) feeding behavior

    Science.gov (United States)

    Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), thought to be primarily a phloem-feeding insect, transmits the presumptive pathogen for Huanglongbing, ‘Candidatus Liberibacter asiaticus’. Because this bacterium is restricted to the phloem and bacterial transmission is the res...

  7. Characterization of a recombinant Cathepsin B-Like cysteine peptidase from Diaphorina citri Kuwayama (Hemiptera: Liviidae): A putative target control of citrus huanglongbing

    Science.gov (United States)

    Huanglongbing (HLB) is one of the most destructive disease affecting citrus plants. The causal agent is associated with the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas) spread by the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae). Among the control strategies for H...

  8. Development of a Genome-Proxy Microarray for Profiling Marine Microbial Communities and its Application to a Time Series in Monterey Bay, California

    Science.gov (United States)

    2008-09-01

    Costas, A.M., Maresca, J.A., Chew, A.G., Klatt, C.G., Bateson , MM. et al. (2007) Candidatus Chloracidobacterium thermophilum: an aerobic...Microbiology 70: 4103-4110. Thyssen, M., Tarran, G.A., Zubkov, M.V., Holland, R.J., Gregori , G., Burkill, P.H., and Denis, M. (2008) The emergence of

  9. Verrucomicrobia subdivision 1 strains display a difference in the colonization of the leek (Allium porrum) rhizosphere

    NARCIS (Netherlands)

    da Rocha, Ulisses Nunes; van Elsas, Jan Dirk; van Overbeek, Leonard Simon

    2011-01-01

    Strains CHC12 and CHC8, belonging to, respectively, Luteolibacter and Candidatus genus Rhizospheria (Verrucomicrobia subdivision 1), were recently isolated from the leek rhizosphere. The key question addressed in this study was: does attraction to and colonization of the rhizosphere occur in the sam

  10. Verrucomicrobia subdivision 1 strains display a difference in colonization in the colonization of the leek (Allium porrum) rhizosphere

    NARCIS (Netherlands)

    Nunes da Rocha, U.; Elsas, van J.D.; Overbeek, van L.S.

    2011-01-01

    Strains CHC12 and CHC8, belonging to, respectively, Luteolibacter and Candidatus genus Rhizospheria (Verrucomicrobia subdivision 1), were recently isolated from the leek rhizosphere. The key question addressed in this study was: does attraction to and colonization of the rhizosphere occur in the sam

  11. Apparent tolerance to huanglongbing in citrus and citrus-related germplasm

    Science.gov (United States)

    In a Ft. Pierce, Florida field planting, growth and huanglongbing (HLB) severity were assessed as indicators of HLB-tolerance on progenies of 83 seed-source accessions of citrus and citrus-relatives from the Riverside, California genebank. The HLB-pathogen (Candidatus Liberibacter asiaticus) and vec...

  12. Early detection of HLB with metabolomics

    Science.gov (United States)

    Huanglongbing (HLB) is the most devastating of all citrus diseases and poses a serious threat to the U.S. citrus industry. Candidatus Liberibacter asiaticus (CLas) is a bacterium associated with, and believed to cause, HLB disease of citrus. Confirmation of CLas infection is crucial for regulatory a...

  13. Sulfate-dependent acetate oxidation under extremely natron-alkaline conditions by syntrophic associations from hypersaline soda lakes

    NARCIS (Netherlands)

    Sorokin, D.Y.; Abbas, B.; Tourova, T.P.; Bumazhkin, B.K.; Kolganova, T.V.; Muyzer, G.

    2014-01-01

    So far, anaerobic sulfate-dependent acetate oxidation at high pH has only been demonstrated for a low-salt-tolerant syntrophic association of a clostridium ‘Candidatus Contubernalis alkalaceticum’ and its hydrogenotrophic sulfate-reducing partner Desulfonatronum cooperativum. Anaerobic enrichments a

  14. Characterization of management and environmental factors associated with regional variations in potato zebra chip occurrence

    Science.gov (United States)

    Potato zebra chip (ZC) disease, putatively caused by the bacterial pathogen ‘Candidatus Liberibacter solanacearum’, which is vectored by the potato psyllid (Bactericera cockerelli), has caused widespread damage to the US potato production ever since its first discovery in south Texas in 2000. In t...

  15. Scanning electron microscopy and in vitro cultivation of endophytic bacteria from potato tubers related to Zebra Chip disease

    Science.gov (United States)

    Zebra chip disease (ZCD) drastically reduces the quality and market value of potatoes in North America. The disease is associated with a phloem-limited alpha-proteobacterium, “Candidatus Liberibacter solanacearum”. No effective measure is currently available to control ZCD. It is known that endoph...

  16. Procedure for collecting and packaging grapevine samples

    Science.gov (United States)

    Grapevine yellows (GY) is a term that is used to refer to any of several diseases of grapevine (Vitis vinifera) that are caused by phytoplasmas. Around the globe, diverse ‘Candidatus Phytoplasma’ species cause indistinguishable disease symptoms in V. vinifera and are spread by different species of ...

  17. Effects of soil-applied imidacloprid on Asian citrus psyllid (Hemiptera: Psyllidae) feeding behavior

    Science.gov (United States)

    The Asian citrus psyllid, Diaphorina citri Kuwayama is one of the most important pests of citrus due to its status as a vector of Candidatus Liberibacter asiaticus, the bacterium associated with huanglongbing (HLB) disease. The use of insecticides for vector control is the primary method of managing...

  18. A graft-based chemotherapy method for screening effective molecules and rescuing Huanglongbing (HLB)-affected citrus plants

    Science.gov (United States)

    Huanglongbing (HLB), the most devastating disease of citrus worldwide, is associated with three species of fastidious and phloem-limited a-Proteobacteria in the genus of ‘Candidatus Liberibacter’. We previously reported a regeneration-based chemical screening system using periwinkle cuttings. In ...

  19. Use of the entomopathogenic fungi Metarhizium anisopliae, Cordyceps bassiana and Isaria fumosorosea to control Diaphorina citri (Hemiptera: Psylidae) in Persian lime under field conditions

    Science.gov (United States)

    The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is a destructive insect pest in the citriculture, because it is an efficient vector of the proteobacteria, ‘Candidatus Liberibacter asiaticus’ (Las), ‘Ca. L. Africanus’ (Laf), and ‘Ca. L. Americanus’ (Lam). These bacteria c...

  20. Characterization and correlation of EPG waveforms of Bactericera cockerelli (Hemiptera: Triozidae): variability in waveform appearance in relation to applied signal

    Science.gov (United States)

    The potato psyllid, Bactericera cockerelli, was recently shown to be a vector of “Candidatus Liberibacter solanacearum” (Lso), a phloem-limited bacterium that is the putative causal agent of “Zebra Chip” in potato and unnamed diseases in other solanaceous species. Despite its importance, very little...

  1. Examining the role of tuber biochemistry in the development of zebra chip in stored potato tubers

    Science.gov (United States)

    Zebra chip disease (ZC), associated with infection by the bacterium ‘Candidatus Liberibacter solanacearum’ (Lso), is an emerging problem for potato growers in the United States, Mexico, and New Zealand. Although potato tubers exhibiting ZC symptoms will be rejected by processors, it remains possible...

  2. Variations in Zebra Chip disease expression and tuber biochemistry in response to vector density

    Science.gov (United States)

    This study examined effects of the number of ‘Candidatus Liberibacter solanacearum’ (Lso)-positive psyllids feeding on potatoes to Lso titers, zebra chip disease (ZC) symptom severity, and levels of amino acids, carbohydrates, and phenolics in tubers harvested weeks later. Red La Soda and Russet Nor...

  3. Dicty_cDB: Contig-U02594-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DL172026 ) Methods for Identifying the Target of a Compound ... 42 0.049 2 ( DJ377761 ) Identification of E...e cDNA clone:VS... 670 0.0 2 ( CU469464 ) Candidatus Phytoplasma mali strain AT complete ch... 34 0.015 11 (

  4. Effect of chemical compounds on the ‘Cadidatus Liberibacter asiaticus’ infected pomelo (Citrus maxima)

    Science.gov (United States)

    Huanglongbing (HLB), also known as citrus greening, is one of the most destructive diseases affecting Rutaceae plants in many parts of the world. HLB is associated with three species of ‘Candidatus Liberibacter’ with ‘Ca. L. asiaticus’ (Las), being the most widely distributed in Thailand and Asia. T...

  5. Chemical and behavioral analysis of the cuticular hydrocarbons from Asian citrus psyllid, Diaphorina citri

    Science.gov (United States)

    Huanglongbing (HLB) is the most destructive disease of citrus worldwide. Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is the vector of the phloem-inhabiting bacterium, Candidatus Liberibacter asiaticus, which is presumed to cause HLB. Laboratory and field studies were cond...

  6. The complete mitochondrial genome sequence of Bactericera cockerelli and its comparison with three other psylloidea species

    Science.gov (United States)

    Potato-tomato psyllid (Bactericera cockerelli) is an important pest of potatoes, tomato and peppers. A toxin secreted by nymphs results in serious phytotoxemia in some host plants. Over the past few years, B. cockerelli was shown to transmit “Candidatus Liberibacter solanacearum”, the putative bacte...

  7. Dicty_cDB: VSD442 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available atural-host Pachypsylla celtidis ATP synthase alpha subunit (atpA) gene, partial cds; ATP synthase gamma sub... from strain CLIB 210 of Kluyveromyces lactis. 46 0.86 1 AF267217 |AF267217.1 Candidatus Carsonella ruddii n

  8. High-throughput sequencing-based microbial characterization of size fractionated biomass in an anoxic anammox reactor for low-strength wastewater at low temperatures.

    Science.gov (United States)

    Liu, Wenru; Yang, Dianhai; Chen, Wenjing; Gu, Xiao

    2017-05-01

    The microbial characterization of three size-fractionated sludge obtained from a suspended-growth anoxic anammox reactor treating low-strength wastewater at low temperatures were investigated by using high-throughput sequencing. Particularly, the spatial variability in relative abundance of microorganisms involved in nitrogen metabolism were analyzed in detail. Results showed that population segregation did occur in the reactor. It was found, for the first time, that the genus Nitrotoga was enriched only in large granules (>400μm). Three anammox genus including Candidatus Jettenia, Brocadia and Kuenenia were detected. Among them, Candidatus Brocadia and Kuenenia preferred to grow in large-sized granules (>400μm), whereas Candidatus Jettenia dominated in small- and moderate-sized sludge (<400μm). The members of genus Candidatus Jettenia appeared to play the vital role in nitrogen removal, since sludge with diameters smaller than 400μm accounted for 81.55% of the total biomass. However, further studies are required to identify the activity of different-size sludge.

  9. Gut content analysis of a phloem-feeding insect, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae)

    Science.gov (United States)

    Potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae) is a key pest of potato (Solanum tuberosum L., Solanales: Solanaceae) and a vector of "Candidatus Liberibacter solanacearum," the pathogen associated with zebra chip disease. In addition to its presence on cultivated crops, the p...

  10. Novel Bartonella agent as cause of verruga peruana.

    Science.gov (United States)

    Blazes, David L; Mullins, Kristin; Smoak, Bonnie L; Jiang, Ju; Canal, Enrique; Solorzano, Nelson; Hall, Eric; Meza, Rina; Maguina, Ciro; Myers, Todd; Richards, Allen L; Laughlin, Larry

    2013-07-01

    While studying chronic verruga peruana infections in Peru from 2003, we isolated a novel Bartonella agent, which we propose be named Candidatus Bartonella ancashi. This case reveals the inherent weakness of relying solely on clinical syndromes for diagnosis and underscores the need for a new diagnostic paradigm in developing settings.

  11. Diversity and importance of filamentous bacteria in biological nutrient removal wastewater treatment plants – a worldwide survey

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Ziegler, Anja Sloth; McIlroy, Simon Jon;

    bacteria in full-scale nutrient removal WWTPs. 16S rRNA gene amplicon sequencing was applied to survey 24 Danish and 30 worldwide full-scale biological nutrient removal WWTPs (total of >550 samples), where all known bacterial genera possessing filamentous morphology were investigated. Candidatus Microthrix...

  12. Within-orchard edge effects of the azimuth of the sun on Diaphorina citri adults in mature orchards

    Science.gov (United States)

    Huanglongbing (HLB) has been considered the most devastating disease of citrus. The bacterium and vector associated with HLB in Florida are ‘Candidatus Liberibacter asiaticus’ and Diaphorina citri (Asian citrus psyllid), respectively. D. citri is positively phototropic, and higher populations have b...

  13. Novel rickettsia in ticks, Tasmania, Australia.

    Science.gov (United States)

    Izzard, Leonard; Graves, Stephen; Cox, Erika; Fenwick, Stan; Unsworth, Nathan; Stenos, John

    2009-10-01

    A novel rickettsia was detected in Ixodes tasmani ticks collected from Tasmanian devils. A total of 55% were positive for the citrate synthase gene by quantitative PCR. According to current criteria for rickettsia speciation, this new rickettsia qualifies as Candidatus Rickettsia tasmanensis, named after the location of its detection.

  14. Dicty_cDB: Contig-U14415-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1_119( CP001281 |pid:none) Thauera sp. MZ1T, complete genome. 43 0.015 CP001277_1694( CP001277 |pid:none) Candidatus Hamiltonella def...ensa... 42 0.020 CT573326_3376( CT573326 |pid:none) Pseudomonas entomophila str. L4

  15. Evidence for anaerobic ammonium oxidation process in freshwater sediments of aquaculture ponds.

    Science.gov (United States)

    Shen, Li-dong; Wu, Hong-sheng; Gao, Zhi-qiu; Ruan, Yun-jie; Xu, Xiang-hua; Li, Ji; Ma, Shi-jie; Zheng, Pei-hui

    2016-01-01

    The anaerobic ammonium oxidation (anammox) process, which can simultaneously remove ammonium and nitrite, both toxic to aquatic animals, can be very important to the aquaculture industry. Here, the presence and activity of anammox bacteria in the sediments of four different freshwater aquaculture ponds were investigated by using Illumina-based 16S rRNA gene sequencing, quantitative PCR assays and (15)N stable isotope measurements. Different genera of anammox bacteria were detected in the examined pond sediments, including Candidatus Brocadia, Candidatus Kuenenia and Candidatus Anammoxoglobus, with Candidatus Brocadia being the dominant anammox genus. Quantitative PCR of hydrazine synthase genes showed that the abundance of anammox bacteria ranged from 5.6 × 10(4) to 2.1 × 10(5) copies g(-1) sediment in the examined ponds. The potential anammox rates ranged between 3.7 and 19.4 nmol N2 g(-1) sediment day(-1), and the potential denitrification rates varied from 107.1 to 300.3 nmol N2 g(-1) sediment day(-1). The anammox process contributed 1.2-15.3% to sediment dinitrogen gas production, while the remainder would be due to denitrification. It is estimated that a total loss of 2.1-10.9 g N m(-2) per year could be attributed to the anammox process in the examined ponds, suggesting that this process could contribute to nitrogen removal in freshwater aquaculture ponds.

  16. Redox stratified biofilms to support completely autotrophic nitrogen removal: Principles and results

    DEFF Research Database (Denmark)

    Pellicer i Nàcher, Carles; Smets, Barth F.

    bacteria in compact reaction zones about 100 m thick separated by an intermediate zone with low or null metabolic activity. Both identified microbial communities showed a very low diversity and were dominated by halophilic and halotolerant Nitrosomonas sp. and Candidatus Brocadia anammoxidans...

  17. The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps

    Directory of Open Access Journals (Sweden)

    Sergio eLópez-Madrigal

    2015-06-01

    Full Text Available Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium Candidatus Tremblaya maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae, which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have Candidatus Tremblaya phenacola as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one where every Candidatus Tremblaya princeps cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, composed by Ca. Tremblaya princeps and Candidatus Moranella endobia, unveiled several atypical features of the former’s genome, including the concerted evolution of paralogous loci. Its comparison with the genome of Ca. Tremblaya phenacola PAVE, single endosymbiont of Phenacoccus avenae, suggests that the atypical reductive evolution of Ca. Tremblaya princeps could be linked to the acquisition of Ca. Moranella endobia, which possess an almost complete set of genes encoding proteins involved in homologous recombination. In order to test this hypothesis, we performed comparative genomics between Ca. Tremblaya phenacola and Ca. Tremblaya princeps and searched for the co-occurrence of concerted evolution and homologous recombination genes in endosymbiotic consortia from four unexplored mealybug species, Dysmicoccus boninsis, Planococcus ficus, Pseudococcus longispinus and Pseudococcus viburni. Our results support a link between concerted evolution and nested endosymbiosis.

  18. Prevalence, risk factor analysis, and hematological findings of hemoplasma infection in domestic cats from Valdivia, Southern Chile.

    Science.gov (United States)

    Walker Vergara, Romina; Morera Galleguillos, Francisco; Gómez Jaramillo, Marcelo; Pereira Almosny, Nadia Regina; Arauna Martínez, Pía; Grob Behne, Paulina; Acosta-Jamett, Gerardo; Müller, Ananda

    2016-06-01

    Four distinct cat hemoplasma species are recognized worldwide. However, this is the first study to investigate the prevalence, risk factors, and hematological findings of hemoplasmas in cats from Chile. Complete blood count and 16S rRNA real-time PCR for cat hemoplasma species were performed in 384 blood samples from domestic cats in Valdivia, Chile. Among the 384 samples the species-specific prevalence was as follows: 'Candidatus Mycoplasma haemominutum' (7.8%), Mycoplasma haemofelis (4.4%), 'Candidatus Mycoplasma turicensis' (1%), 'Ca. M. haemominutum'+M. haemofelis (0.78%), 'Ca. M. haemominutum'+'Ca. M. turicensis' (0.52%), 'Ca. M. haemominutum'+'Candidatus Mycoplasma haematoparvum' (0.26%) and 'Ca. M. haemominutum'+M. haemofelis+'Ca. M. haematoparvum' (0.26%). Male sex, older age, outdoor access, and FIV status were risk factors for hemoplasmosis. Mycoplasma haemofelis-positive cats had higher mean corpuscular volume and monocyte count. Four hemoplasma species circulate in the cat population of Valdivia. 'Candidatus M. turicensis' and 'Ca. M. haematoparvum' have been reported for the first time in Chilean cats.

  19. Dicty_cDB: Contig-U12038-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 8 ( CU469464 ) Candidatus Phytoplasma mali strain AT complete ch... 34 0.005 19 ( DW248180 ) pOP-EON00464_EST_C_1_pSK_SK EON (Oil... Palm Embryoi... 54 0.013 1 ( EY410093 ) pOP-EO07491_EST_C_1_pSK_SK EO (Oil

  20. The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps

    Science.gov (United States)

    López-Madrigal, Sergio; Latorre, Amparo; Moya, Andrés; Gil, Rosario

    2015-01-01

    Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium “Candidatus Tremblaya” maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae), which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have “Candidatus Tremblaya phenacola” as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one) where every “Candidatus Tremblaya princeps” cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, composed by “Ca. Tremblaya princeps” and “Candidatus Moranella endobia,” unveiled several atypical features of the former's genome, including the concerted evolution of paralogous loci. Its comparison with the genome of “Ca. Tremblaya phenacola” PAVE, single endosymbiont of Phenacoccus avenae, suggests that the atypical reductive evolution of “Ca. Tremblaya princeps” could be linked to the acquisition of “Ca. Moranella endobia,” which possess an almost complete set of genes encoding proteins involved in homologous recombination. In order to test this hypothesis, we performed comparative genomics between “Ca. Tremblaya phenacola” and “Ca. Tremblaya princeps” and searched for the co-occurrence of concerted evolution and homologous recombination genes in endosymbiotic consortia from four unexplored mealybug species, Dysmicoccus boninsis, Planococcus ficus, Pseudococcus longispinus, and Pseudococcus viburni. Our results support a link between concerted evolution and nested endosymbiosis. PMID:26161080

  1. Survey of endosymbionts in the Diaphorina citri metegenome and assembly of a Wolbachia wDi draft genome

    Science.gov (United States)

    Diaphorina citri, the Asian citrus psyllid,(Hemiptera) is the insect vector of Candidatus Liberibacter asiaticus, the presumed cause of citrus greening disease, known as huanglongbing. Sequencing of the Diaphorina citri metagenome has been initiated to gain better understanding of the biology of D. ...

  2. Cloning and expressing a highly functional and substrate specific farnesoic acid o-methyltransferase from the Asian citrus psyllid (Diaphorina citri Kuwayama)

    Science.gov (United States)

    The Asian citrus psyllid, Diaphorina citri, transmits a phloem-limited bacterium, Candidatus Liberibacter asiaticus that causes citrus greening disease. Because juvenile hormone (JH) plays an important role in adult and nymphal development, we studied the final steps in juvenile hormone biosynthesis...

  3. PROCENTAJE DE PSILIDOS PORTADORES DE Canidatus Liberibacter asiaticus Y SU RELACION CON LA INCIDENCIA DE HLB EN CINCO HUERTAS COMERCIALES DE LIMON MEXICANO {Citrus aurantifolia (Christm) Swingle} EN EL ESTADO DE COLIMA MEXICO

    Science.gov (United States)

    Asian citrus psyllids (Diaphorina citri) were individually analyzed by qPCR to detect Candidatus Liberibacter asiaticus (CLas). The psyllids were collected in Mexican lime (Citrus aurantifolia) trees in five commercial orchards in Tecomán and Manzanillo, Colima with severe symptoms of classical mott...

  4. Stylet penetration of Cacopsylla pyri; an electrical penetration graph (EPG) study

    NARCIS (Netherlands)

    Civolani, S.; Leis, M.; Grandi, G.; Garzo, E.; Pasqualini, E.; Musacchi, S.; Chicca, M.; Castaldelli, G.; Rossie, M.; Tjallingii, W.F.

    2011-01-01

    Detailed information on plant penetration activities by pear psylla Cacopsylla pyri L. (Hemiptera Psyllidae) is essential to study phytoplasma transmission of “Candidatus Phytoplasma pyri” responsible of pear decline disease (PD) and to trace and evaluate resistant traits in new pear tree selections

  5. First Report of Dodder Transmission of Huanglongbing from Naturally Infected Murraya paniculata to Citrus

    Science.gov (United States)

    Huanglongbing (HLB) or “greening” disease of citrus is caused by phloem-limited, uncultured bacteria in the genus “Candidatus Liberibacter”. HLB is one of the most destructive diseases of citrus worldwide and is considered so dangerous to a U.S. citrus production that the USDA has listed “Ca. Liberi...

  6. Titers of 'Ca. Liberibacter asiaticus' in Murraya paniculata and Murraya-reared Diaphorina citri are much lower than in citrus and citrus-reared psyllids

    Science.gov (United States)

    Huanglongbing, one of the most devastating diseases of citrus, is associated with the bacterium Candidatus Liberibacter asiaticus vectored by the Asian citrus psyllid, Diaphorina citri, in North America. Murraya paniculata is a common ornamental plant that is an alternate host of Ca. L. asiaticus an...

  7. Insecticidal Activity of Entomopathogenic Fungi (Hypocreales) for Potato Psyllid, Bactericera cockerelli (Hemiptera: Triozidae): Development of Bioassay Techniques, Effect of Fungal Species and Stage of the Psyllid

    Science.gov (United States)

    The potato psyllid, Bactericera cockerelli (Šulc), is a pest of potato, tomato, and some other solanaceous vegetables and has also been incriminated in the transmission of a bacterial pathogen, Candidatus Liberibacter solanacearum, resulting in a serious disease known as “zebra chip”. Although there...

  8. Assessment of bacterial endosymbiont diversity in Otiorhynchus spp. (Coleoptera: Curculionidae larvae using a multitag 454 pyrosequencing approach

    Directory of Open Access Journals (Sweden)

    Hirsch Jacqueline

    2012-01-01

    Full Text Available Abstract Background Weevils of the genus Otiorhynchus are regarded as devastating pests in a wide variety of horticultural crops worldwide. So far, little is known on the presence of endosymbionts in Otiorhynchus spp.. Investigation of endosymbiosis in this genus may help to understand the evolution of different reproductive strategies in these weevils (parthenogenesis or sexual reproduction, host-symbiont interactions, and may provide a future basis for novel pest management strategy development. Here, we used a multitag 454 pyrosequencing approach to assess the bacterial endosymbiont diversity in larvae of four economically important Otiorhynchus species. Results High-throughput tag-encoded FLX amplicon pyrosequencing of a bacterial 16S rDNA fragment was used to characterise bacterial communities associated with different Otiorhynchus spp. larvae. By sequencing a total of ~48,000 PCR amplicons, we identified 49 different operational taxonomic units (OTUs as bacterial endosymbionts in the four studied Otiorhynchus species. More than 90% of all sequence reads belonged either to the genus Rickettsia or showed homology to the phylogenetic group of “Candidatus Blochmannia” and to endosymbionts of the lice Pedicinus obtusus and P. badii. By using specific primers for the genera Rickettsia and “Candidatus Blochmannia”, we identified a new phylogenetic clade of Rickettsia as well as “Candidatus Nardonella” endosymbionts in Otiorhynchus spp. which are closely related to “Candidatus Blochmannia” bacteria. Conclusions Here, we used multitag 454 pyrosequencing for assessment of insect endosymbiotic communities in weevils. As 454 pyrosequencing generates only quite short sequences, results of such studies can be regarded as a first step towards identifying respective endosymbiotic species in insects. In the second step of our study, we analysed sequences of specific gene regions for a more detailed phylogeny of selected endosymbiont genera

  9. Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils.

    Science.gov (United States)

    Meng, Han; Wang, Yong-Feng; Chan, Ho-Wang; Wu, Ruo-Nan; Gu, Ji-Dong

    2016-09-01

    Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two new processes of recent discoveries linking the microbial nitrogen and carbon cycles. In this study, 16S ribosomal RNA (rRNA) gene of anammox bacteria and pmoA gene of n-damo bacteria were used to investigate their distribution and diversity in natural acidic and re-vegetated forest soils. The 16S rRNA gene sequences retrieved featured at least three species in two genera known anammox bacteria, namely Candidatus Brocadia anammoxidans, Candidatus Brocadia fulgida, and Candidatus Kuenenia stuttgartiensis while the pmoA gene amplified was affiliated with two species of known n-damo bacteria Candidatus Methylomirabilis oxyfera and a newly established Candidatus Methylomirabilis sp. According to the results, the diversity of anammox bacteria in natural forests was lower than in re-vegetated forests, but no significant difference was observed in n-damo community between them. Quantitative real-time PCR showed that both anammox and n-damo bacteria were more abundant in the lower layer (10-20 cm) than the surface layer (0-5 cm). The abundance of anammox bacteria varied from 2.21 × 10(5) to 3.90 × 10(6) gene copies per gram dry soil, and n-damo bacteria quantities were between 1.69 × 10(5) and 5.07 × 10(6) gene copies per gram dry soil in the two different layers. Both anammox and n-damo bacteria are reported for the first time to co-occur in acidic forest soil in this study, providing a more comprehensive information on more defined microbial processes contributing to C and N cycles in the ecosystems.

  10. Evolutionary relationships among primary endosymbionts of the mealybug subfamily phenacoccinae (hemiptera: Coccoidea: Pseudococcidae).

    Science.gov (United States)

    Gruwell, Matthew E; Hardy, Nate B; Gullan, Penny J; Dittmar, Katharina

    2010-11-01

    Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria ("Candidatus Tremblaya princeps") containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes, (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes, in a clade sister to cockroach endosymbionts (Blattabacterium), and (iii) the remaining Phenacoccinae within the Betaproteobacteria, forming a well-supported sister group to "Candidatus Tremblaya princeps." Names are proposed for two strongly supported lineages: "Candidatus Brownia rhizoecola" for P-endosymbionts of Rhizoecini and "Candidatus Tremblaya phenacola" for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria. Analyses also recovered a clade of Gammaproteobacteria, sister to the P-endosymbiont lineage of aphids ("Candidatus Buchnera aphidicola"), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups.

  11. Deans Speak out

    Science.gov (United States)

    Pitt, Alice; Dibbon, David; Sumara, Dennis; Wiens, John R.

    2011-01-01

    Calls for students to develop 21st-century competencies are gaining traction among educators and policymakers, driven by a number of factors including research on learning; the ubiquity of information and communications technologies; and globalization in its many forms. What does 21st-century teaching mean to those who prepare young people for…

  12. Semiflexible filamentous composites

    NARCIS (Netherlands)

    Huisman, E.M.; Heussinger, C.; Storm, C.; Barkema, G.T.

    2010-01-01

    Inspired by the ubiquity of composite filamentous networks in nature, we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains

  13. Using Information and Communication Technology (ICT) to the Maximum: Learning and Teaching Biology with Limited Digital Technologies

    Science.gov (United States)

    Van Rooy, Wilhelmina S.

    2012-01-01

    Background: The ubiquity, availability and exponential growth of digital information and communication technology (ICT) creates unique opportunities for learning and teaching in the senior secondary school biology curriculum. Digital technologies make it possible for emerging disciplinary knowledge and understanding of biological processes…

  14. Protecting Children from Chemical Exposure: Social Work and U.S. Social Welfare Policy.

    Science.gov (United States)

    Rogge, Mary E.; Combs-Orme, Terri

    2003-01-01

    Defines chemical contamination and reviews data regarding the ubiquity of toxic chemicals. Describes major risk pathways to fetuses and children at different developmental stages and discusses evidence regarding exposure and harm to children from chemical contamination. Reviews the roles for social workers in protecting current and future…

  15. Studies in Intelligence. Volume 55, Number 1, March 2011

    Science.gov (United States)

    2011-03-01

    illicit copies of Disney films in Moscow. Broker, Trader, Lawyer, Spy is well written and documented. The ubiquity of the corporate espi- onage...Studies in Intelligence Vol. 55, No. 1 (Extracts, March 2011) strated the ineffectiveness of Allied attacks on U-boat production facilities . Nesbit

  16. GETDB: 113105 [GETDB

    Lifescience Database Archive (English)

    Full Text Available f Genetics. FM7c Link to clone table - 1 159 Link to cluster table 159 1 Request - gut associated cells? ubiquitous gut, stripes...itous Larval X-gal gut, stripes in epi, Adult GFP internal Lethality - Also known...le 159 Num of clusters 1 Stock Request Request - Embryonic Expression gut associated cells? Larval GFP ubiqu

  17. Introduction to solitons

    Indian Academy of Sciences (India)

    Miki Wadati

    2001-11-01

    As an introduction to the special issue on nonlinear waves, solitons and their significance in physics are reviewed. The soliton is the first universal concept in nonlinear science. Universality and ubiquity of the soliton concept are emphasized.

  18. Developing Students' Professional Digital Identity

    Science.gov (United States)

    Cochrane, Thomas; Antonczak, Laurent

    2015-01-01

    In contrast to the myth of the "Digital Native" and the ubiquity of Facebook use, we have found that students' digital identities are predominantly social with their online activity beyond Facebook limited to being social media consumers rather than producers. Within a global economy students need to learn new digital literacy skills to…

  19. Design and Implementation of BusinessApp, a MALL Application to Make Successful Business Presentations

    Science.gov (United States)

    Calle-Martínez, Cristina; Yanes, Lourdes Pomposo; Pareja-Lora, Antonio

    2016-01-01

    Little by little, (or, simply, MALL) is taking force in the field of education, as it supports language blended learning and language learning ubiquity. The study presented here belongs in the Social Ontology-based Cognitively Augmented Language Learning Mobile Environment (SO-CALL-ME) research project, whose final aim is to design and create…

  20. Development of an electrochemical immunoassay for the detection of polybrominated diphenyl ethers (PBDEs)

    Science.gov (United States)

    Polybrominated diphenyl ethers (PBDEs) are persistent environmental substances that were commonly used as fire retardants in a wide number of commercial products. Their low reactivity, high hydrophobicity and bioaccumulative properties cause their ubiquity in the air, water, food and lead to extensi...

  1. Skew Pairs of Idempotents in Transformation Semigroups

    Institute of Scientific and Technical Information of China (English)

    T. S. BLYTH; M. H. ALMEIDA SANTOS

    2006-01-01

    An ordered pair (e, f) of idempotents of a regular semigroup is called a skew pair if ef is not idempotent whereas fe is idempotent. We have shown previously that there are four distinct types of skew pairs of idempotents. Here we investigate the ubiquity of such skew pairs in full transformation semigroups.

  2. AcEST: DK953958 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 1 tr|Q6UA12|Q6UA12_GOSBA Fiber polyubiquitin OS=Gossypium barbaden... 335 8e-91 tr|B2Z6R9|B2Z6R9_GOSHI Ubiqu...97 FAGKQLEDGRTLADYNIQKESTLHLVLRLRG 227 >tr|Q6UA12|Q6UA12_GOSBA Fiber polyubiquitin OS=Gossypium barbadense P

  3. PERKAM: Personalized Knowledge Awareness Map for Computer Supported Ubiquitous Learning

    Science.gov (United States)

    El-Bishouty, Moushir M.; Ogata, Hiroaki; Yano, Yoneo

    2007-01-01

    This paper introduces a ubiquitous computing environment in order to support the learners while doing tasks; this environment is called PERKAM (PERsonalized Knowledge Awareness Map). PERKAM allows the learners to share knowledge, interact, collaborate, and exchange individual experiences. It utilizes the RFID ubiquities technology to detect the…

  4. Collaborative development of embedded systems

    NARCIS (Netherlands)

    Verhoef, Marcel; Pierce, Kenneth; Gamble, Carl; Broenink, Jan; Fitzgerald, John; Larsen, Peter Gorm; Verhoef, Marcel

    2014-01-01

    This chapter presents motivation for taking a collaborative multi-disciplinary approach to the model-based development of embedded systems. Starting from a consideration of the ubiquity of embedded systems in daily life it identifies challenges faced by industry in developing products in a timely ma

  5. Camel spider (Solifugae) use of prairie dog colonies

    Science.gov (United States)

    Solifugids (camel spiders) are widespread throughout arid regions of western North America and are thought to be important in structuring desert arthropod communities. Despite the ubiquity of camel spiders, little is known about their ecology. Black-tailed prairie dogs (Cynomys ludovicianus) are als...

  6. Let Them Have Their Cell Phone (And Let Them Read to It Too): Technology, Writing Instruction and Textual Obsolescence

    Science.gov (United States)

    Shahar, Jed

    2012-01-01

    Cell phone ubiquity enables students to record and share audio file versions of their essays for proofreading purposes. Adopting this practice in community college developmental writing classes leads to an investigation of both writing as a technology and the influence of modern technology on composition and composition pedagogy.

  7. Bacterial Human Virulence Genes across Diverse Habitats As Assessed by In silico Analysis of Environmental Metagenomes

    DEFF Research Database (Denmark)

    Søborg, Ditte A; Hendriksen, Niels B; Kilian, Mogens;

    2016-01-01

    and glacial ice. Homologs to 16 bacterial human virulence genes, involved in urinary tract infections, gastrointestinal diseases, skin diseases, and wound and systemic infections, showed global ubiquity. A principal component analysis did not demonstrate clear trends across the metagenomes with respect...

  8. Reconceptualisation of Approaches to Teaching Evaluation in Higher Education

    Science.gov (United States)

    Tran, Nga D.

    2015-01-01

    The ubiquity of using Student Evaluation of Teaching (SET) in higher education is inherently controversial. Issues mostly resolve around whether the instrument is reliable and valid for the purpose for which it was intended. Controversies exist, in part, due to the lack of a theoretical framework upon which SETs can be based and tested for their…

  9. Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system

    Science.gov (United States)

    Bumble bees are a longstanding model system for studies on behavior, ecology, and evolution, due to their well-studied social lifestyle, invaluable roles as both wild and managed pollinators, and their ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of ...

  10. Genomics-Guided Discovery of Traits Contributing to Interactions of Pseudomonas fluorescens with Other Organisms

    Science.gov (United States)

    Pseudomonas fluorescens is a diverse bacterial species known for its ubiquity in natural habitats and the production of structurally diverse, bioactive secondary metabolites. The high degree of ecological and metabolic diversity represented in P. fluorescens is reflected in the genomic diversity di...

  11. Spectral characterization and surface complexation modeling of low molecular weight organics on hematite nanoparticles: Role of electrolytes in the binding mechanism

    Science.gov (United States)

    Given the ubiquity of organic-metal oxide interfaces in environmental and medical systems, it is incumbent to obtain mechanistic details at the molecular level from experimental procedures that mimic real systems and conditions. We report herein the adsorption pH envelopes (range 9-5) and isotherms...

  12. Costs and constraints conspire to produce honest signaling

    DEFF Research Database (Denmark)

    Holman, Luke

    2012-01-01

    Signal costs and evolutionary constraints have both been proposed as ultimate explanations for the ubiquity of honest signaling, but the interface between these two factors is unclear. Here, I propose a pluralistic interpretation, and use game theory to demonstrate that evolutionary constraints...

  13. Dead or gone? Bayesian inference on mortality for the dispersing sex

    DEFF Research Database (Denmark)

    Barthold, Julia; Packer, Craig; Loveridge, Andrew;

    2016-01-01

    a solution to the challenge of estimating mortality of the dispersing sex in species with data deficiency due to natal dispersal. Given the utility of sex-specific mortality estimates in biological and conservation research, and the virtual ubiquity of sex-biased dispersal, our model will be useful to a wide...

  14. Nation/non-nation

    DEFF Research Database (Denmark)

    Sonnichsen, André; Gad, Ulrik Pram

    2008-01-01

    Is nationality the only way of organizing political community? Given the ubiquity of the national principle, one might think so. But, in practice, the national principle is constantly challenged by what can be termed non-national identities. This article looks at manners in which such deviating...

  15. Museums, Environments, Information

    NARCIS (Netherlands)

    Koutamanis, A.

    2015-01-01

    Modern digital media already permeate the physical world. The portability of information devices and the ubiquity of networks allow us to access information practically anyplace, creating digital overlays on reality. This also allows us to bring information we routinely archive in museums and collec

  16. FESTERING FOOD: CHYTRIDIOMYCETE PATHOGEN REDUCES QUALITY OF DAPHNIA HOST AS A FOOD RESOURCE

    Science.gov (United States)

    When parasitic infections are severe or highly prevalent among prey, a significant component of the predator’s diet may consist of parasitized hosts. However, despite the ubiquity of parasites in most food webs, comparisons of the nutritional quality of prey as a function of inf...

  17. Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

    DEFF Research Database (Denmark)

    Croft, Laurence J; Szklarczyk, Damian; Jensen, Lars J;

    2012-01-01

    ABSTRACT: BACKGROUND: Transcription factors (TFs) have long been known to be principally activators of transcription in eukaryotes and prokaryotes. The growing awareness of the ubiquity of microRNAs (miRNAs) as suppressive regulators in eukaryotes, suggests the possibility of a mutual, preferential...

  18. Modeling fate and transport of "Contaminants of Emerging Concern" (CECs): is the Soil Water Assessment Tool (SWAT) the appropriate model?

    Science.gov (United States)

    Background/Question/Methods As the scientific and regulatory communities realize the significant environmental impacts and ubiquity of “contaminants of emerging concern” (CECs), it is increasingly imperative to develop quantitative assessment tools to evaluate and predict the fate and transport of...

  19. Ten Essential Questions Educators Should Ask when Using Video Annotation Tools

    Science.gov (United States)

    Rich, Peter J.; Trip, Tonya

    2011-01-01

    The increasing ease and ubiquity of video has resulted in a proliferation of video annotation tools used and designed for improving education. While similar, each tool has its relative strengths and weaknesses. Choosing the "right" tool can have an impact on the experience of teachers and the effectiveness of video as a means for improving…

  20. CLOSTRIDIUM PERFRINGENS

    Science.gov (United States)

    The incidence of C. perfringens food-poisoning is quite common and costly. Although somewhat fastidious in growth characteristics using synthetic laboratory media, the microorganism is very prolific when found in food products. Despite the pathogen’s ubiquity in the natural environment, foodborne i...