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Sample records for burkholderia species causal

  1. Antibiotic resistance in Burkholderia species.

    Science.gov (United States)

    Rhodes, Katherine A; Schweizer, Herbert P

    2016-09-01

    The genus Burkholderia comprises metabolically diverse and adaptable Gram-negative bacteria, which thrive in often adversarial environments. A few members of the genus are prominent opportunistic pathogens. These include Burkholderia mallei and Burkholderia pseudomallei of the B. pseudomallei complex, which cause glanders and melioidosis, respectively. Burkholderia cenocepacia, Burkholderia multivorans, and Burkholderia vietnamiensis belong to the Burkholderia cepacia complex and affect mostly cystic fibrosis patients. Infections caused by these bacteria are difficult to treat because of significant antibiotic resistance. The first line of defense against antimicrobials in Burkholderia species is the outer membrane penetration barrier. Most Burkholderia contain a modified lipopolysaccharide that causes intrinsic polymyxin resistance. Contributing to reduced drug penetration are restrictive porin proteins. Efflux pumps of the resistance nodulation cell division family are major players in Burkholderia multidrug resistance. Third and fourth generation β-lactam antibiotics are seminal for treatment of Burkholderia infections, but therapeutic efficacy is compromised by expression of several β-lactamases and ceftazidime target mutations. Altered DNA gyrase and dihydrofolate reductase targets cause fluoroquinolone and trimethoprim resistance, respectively. Although antibiotic resistance hampers therapy of Burkholderia infections, the characterization of resistance mechanisms lags behind other non-enteric Gram-negative pathogens, especially ESKAPE bacteria such as Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa. PMID:27620956

  2. Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

    Science.gov (United States)

    Peeters, Charlotte; Meier-Kolthoff, Jan P.; Verheyde, Bart; De Brandt, Evie; Cooper, Vaughn S.; Vandamme, Peter

    2016-01-01

    Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317T = CCUG 68412T), Burkholderia hypogeia sp. nov. (type strain LMG 29322T = CCUG 68407T), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326T = CCUG 68403T), Burkholderia glebae sp. nov. (type strain LMG 29325T = CCUG 68404T), Burkholderia pedi sp. nov. (type strain LMG 29323T = CCUG 68406T), Burkholderia arationis sp. nov. (type strain LMG 29324T = CCUG 68405T), Burkholderia fortuita sp. nov. (type strain LMG 29320T = CCUG 68409T), Burkholderia temeraria sp. nov. (type strain LMG 29319T = CCUG 68410T), Burkholderia calidae sp. nov. (type strain LMG 29321T = CCUG 68408T), Burkholderia concitans sp. nov. (type strain LMG 29315T = CCUG 68414T), Burkholderia turbans sp. nov. (type strain LMG 29316T = CCUG 68413T), Burkholderia catudaia sp. nov. (type strain LMG 29318T = CCUG 68411T) and Burkholderia peredens sp. nov. (type strain LMG 29314T = CCUG

  3. Differentiation of Species Combined into the Burkholderia cepacia Complex and Related Taxa on the Basis of Their Fatty Acid Patterns

    OpenAIRE

    Krejčí, Eva; Kroppenstedt, Reiner M.

    2006-01-01

    Using the established commercial system Sherlock (MIDI, Inc.), cellular fatty acid methyl ester analysis for differentiation among Burkholderia cepacia complex species was proven. The identification key based on the diagnostic fatty acids is able to discern phenotypically related Ralstonia pickettii and Pandoraea spp. and further distinguish Burkholderia pyrrocinia, Burkholderia ambifaria, and Burkholderia vietnamiensis.

  4. The Tomato Rhizosphere, an Environment Rich in Nitrogen-Fixing Burkholderia Species with Capabilities of Interest for Agriculture and Bioremediation▿

    OpenAIRE

    Caballero-Mellado, Jesús; Onofre-Lemus, Janette; Estrada-De Los Santos, Paulina; Martínez-Aguilar, Lourdes

    2007-01-01

    Burkholderia strains are promising candidates for biotechnological applications. Unfortunately, most of these strains belong to species of the Burkholderia cepacia complex (Bcc) involved in human infections, hampering potential applications. Novel diazotrophic Burkholderia species, phylogenetically distant from the Bcc species, have been discovered recently, but their environmental distribution and relevant features for agro-biotechnological applications are little known. In this work, the oc...

  5. Mechanisms of Disease: Host-Pathogen Interactions between Burkholderia Species and Lung Epithelial Cells

    OpenAIRE

    David, Jonathan; Bell, Rachel E.; Clark, Graeme C.

    2015-01-01

    Members of the Burkholderia species can cause a range of severe, often fatal, respiratory diseases. A variety of in vitro models of infection have been developed in an attempt to elucidate the mechanism by which Burkholderia spp. gain entry to and interact with the body. The majority of studies have tended to focus on the interaction of bacteria with phagocytic cells with a paucity of information available with regard to the lung epithelium. However, the lung epithelium is becoming more widel...

  6. Multivariate Analyses of Burkholderia Species in Soil: Effect of Crop and Land Use History

    OpenAIRE

    Salles, J.F.; Veen, van, R.; Elsas, van, J.D.

    2004-01-01

    The assessment of Burkholderia diversity in agricultural areas is important considering the potential use of this genus for agronomic and environmental applications. Therefore, the aim of this work was to ascertain how plant species and land use management drive the diversity of the genus Burkholderia. In a greenhouse experiment, different crops, i.e., maize, oat, barley, and grass, were planted in pots containing soils with different land use histories, i.e., maize monoculture, crop rotation...

  7. Molecular Signatures and Phylogenomic Analysis of the Genus Burkholderia: Proposal for Division of this Genus into the Emended Genus Burkholderia Containing Pathogenic Organisms and a New Genus Paraburkholderia gen. nov. Harboring Environmental Species

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    Aman eSawana

    2014-12-01

    Full Text Available The genus Burkholderia contains large number of diverse species which are not reliably distinguished by the available biochemical or molecular characteristics. We report here results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus Burkholderia. In phylogenetic trees based upon concatenated sequences for 21 conserved proteins as well as 16S rRNA gene sequences, Burkholderia species grouped into two major clades. Within these main clades a number of smaller clades were also clearly distinguished. Our comparative analysis of protein sequences from Burkholderia spp. has identified 42 highly specific molecular markers in the form of conserved sequence indels (CSIs that are uniquely found in different clades of Burkholderia spp. Six of these CSIs are specific for a group of Burkholderia spp. (referred to as Clade I which contains all clinically relevant members of the genus as well as the phytopathogenic Burkholderia species. The second main clade (Clade II composed of the environmental Burkholderia species, is also distinguished by 2 of the identified CSIs. Additionally, our work has also identified 3 CSIs that are specific for the Burkholderia cepacia complex, 4 CSIs that are uniquely found in the Burkholderia pseudomallei group, 5 CSIs that are specific for the phytopathogenic Burkholderia spp. and 22 other CSI that distinguish two groups within Clade II. The described molecular markers provide highly specific means for the demarcation of different groups of Burkholderia spp. and for development of novel diagnostic assays for the clinically important members of the group. Based upon the results from different lines of studies, a division of the genus Burkholderia into two genera is proposed. In this new proposal, the emended genus Burkholderia will contain only the clinically relevant and phytopathogenic Burkholderia species, whereas all other Burkholderia spp. are transferred to a new genus

  8. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia.

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    Jennifer L Ginther

    Full Text Available Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area.

  9. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species

    OpenAIRE

    Sawana, Amandeep; Adeolu, Mobolaji; Gupta, Radhey S.

    2014-01-01

    The genus Burkholderia contains large number of diverse species which include many clinically important organisms, phytopathogens, as well as environmental species. However, currently, there is a paucity of biochemical or molecular characteristics which can reliably distinguish different groups of Burkholderia species. We report here the results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus Burkholderia. In phylogenetic trees based upon concate...

  10. Polyphasic characterisation of Burkholderia cepacia complex species isolated from children with cystic fibrosis

    Science.gov (United States)

    Vicenzi, Fernando José; Pillonetto, Marcelo; de Souza, Helena Aguilar Peres Homem de Mello; Palmeiro, Jussara Kasuko; Riedi, Carlos Antônio; Rosario-Filho, Nelson Augusto; Dalla-Costa, Libera Maria

    2016-01-01

    Cystic fibrosis (CF) patients with Burkholderia cepacia complex (Bcc) pulmonary infections have high morbidity and mortality. The aim of this study was to compare different methods for identification of Bcc species isolated from paediatric CF patients. Oropharyngeal swabs from children with CF were used to obtain isolates of Bcc samples to evaluate six different tests for strain identification. Conventional (CPT) and automatised (APT) phenotypic tests, polymerase chain reaction (PCR)-recA, restriction fragment length polymorphism-recA, recAsequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) were applied. Bacterial isolates were also tested for antimicrobial susceptibility. PCR-recA analysis showed that 36 out of the 54 isolates were Bcc. Kappa index data indicated almost perfect agreement between CPT and APT, CPT and PCR-recA, and APT and PCR-recA to identify Bcc, and MALDI-TOF and recAsequencing to identify Bcc species. The recAsequencing data and the MALDI-TOF data agreed in 97.2% of the isolates. Based on recA sequencing, the most common species identified were Burkholderia cenocepacia IIIA (33.4%),Burkholderia vietnamiensis (30.6%), B. cenocepaciaIIIB (27.8%), Burkholderia multivorans (5.5%), and B. cepacia (2.7%). MALDI-TOF proved to be a useful tool for identification of Bcc species obtained from CF patients, although it was not able to identify B. cenocepacia subtypes. PMID:26814642

  11. Multivariate Analyses of Burkholderia species in soil: effect of crop and land use history.

    NARCIS (Netherlands)

    Salles, J.F.; Veen, van J.A.; Elsas, van J.D.

    2004-01-01

    The assessment of Burkholderia diversity in agricultural areas is important considering the potential use of this genus for agronomic and environmental applications. Therefore, the aim of this work was to ascertain how plant species and land use management drive the diversity of the genus Burkholder

  12. Multivariate analyses of Burkholderia species in soil : Effect of crop and land use history

    NARCIS (Netherlands)

    Salles, JF; van Veen, JA; van Elsas, JD

    2004-01-01

    The assessment of Burkholderia diversity in agricultural areas is important considering the potential use of this genus for agronomic and environmental applications. Therefore, the aim of this work was to ascertain how plant species and land use management drive the diversity of the genus Burkholder

  13. Multivariate analyses of Burkholderia species in soil: effect of crop and land use history

    NARCIS (Netherlands)

    Salles, J.F.; Van Veen, J.A.; van Elsas, J.D.

    2004-01-01

    The assessment of Burkholderia diversity in agricultural areas is important considering the potential use of this genus for agronomic and environmental applications. Therefore, the aim of this work was to ascertain how plant species and land use management drive the diversity of the genus Burkholder

  14. Draft Genome Sequences of Burkholderia contaminans, a Burkholderia cepacia Complex Species That Is Increasingly Recovered from Cystic Fibrosis Patients

    OpenAIRE

    Bloodworth, Ruhi A M; Selin, Carrie; López De Volder, Maria Agustina; Drevinek, Pavel; Galanternik, Laura; Degrossi, José; Cardona, Silvia T.

    2015-01-01

    Burkholderia contaminans belongs to the Burkholderia cepacia complex (BCC), a group of bacteria that are ubiquitous in the environment and capable of infecting the immunocompromised and people with cystic fibrosis. We report here draft genome sequences for the B. contaminans type strain LMG 23361 and an Argentinian cystic fibrosis sputum isolate.

  15. Genetic diversity of Burkholderia (Proteobacteria) species from the Caatinga and Atlantic rainforest biomes in Bahia, Brazil.

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    Santini, A C; Santos, H R M; Gross, E; Corrêa, R X

    2013-03-11

    The genus Burkholderia (β-Proteobacteria) currently comprises more than 60 species, including parasites, symbionts and free-living organisms. Several new species of Burkholderia have recently been described showing a great diversity of phenotypes. We examined the diversity of Burkholderia spp in environmental samples collected from Caatinga and Atlantic rainforest biomes of Bahia, Brazil. Legume nodules were collected from five locations, and 16S rDNA and recA genes of the isolated microorganisms were analyzed. Thirty-three contigs of 16S rRNA genes and four contigs of the recA gene related to the genus Burkholderia were obtained. The genetic dissimilarity of the strains ranged from 0 to 2.5% based on 16S rDNA analysis, indicating two main branches: one distinct branch of the dendrogram for the B. cepacia complex and another branch that rendered three major groups, partially reflecting host plants and locations. A dendrogram designed with sequences of this research and those designed with sequences of Burkholderia-type strains and the first hit BLAST had similar topologies. A dendrogram similar to that constructed by analysis of 16S rDNA was obtained using sequences of the fragment of the recA gene. The 16S rDNA sequences enabled sufficient identification of relevant similarities and groupings amongst isolates and the sequences that we obtained. Only 6 of the 33 isolates analyzed via 16S rDNA sequencing showed high similarity with the B. cepacia complex. Thus, over 3/4 of the isolates have potential for biotechnological applications.

  16. Fatal Burkholderia pseudomallei Infection Initially Reported as a Bacillus Species, Ohio, 2013

    OpenAIRE

    Doker, Thomas J.; Quinn, Celia L.; Salehi, Ellen D.; Sherwood, Joshua J.; Benoit, Tina J.; Elrod, Mindy Glass; Gee, Jay E.; Shadomy, Sean V.; Bower, William A.; Hoffmaster, Alex R.; Walke, Henry T.; Blaney, David D.; DiOrio, Mary S.

    2014-01-01

    A fatal case of melioidosis was diagnosed in Ohio one month after culture results were initially reported as a Bacillus species. To identify a source of infection and assess risk in patient contacts, we abstracted patient charts; interviewed physicians and contacts; genetically characterized the isolate; performed a Burkholderia pseudomallei antibody indirect hemagglutination assay on household contacts and pets to assess seropositivity; and collected household plant, soil, liquid, and insect...

  17. Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India

    Science.gov (United States)

    Peddayelachagiri, Bhavani V.; Paul, Soumya; Nagaraj, Sowmya; Gogoi, Madhurjya; Sripathy, Murali H.; Batra, Harsh V.

    2016-01-01

    Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha

  18. Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India.

    Science.gov (United States)

    Peddayelachagiri, Bhavani V; Paul, Soumya; Nagaraj, Sowmya; Gogoi, Madhurjya; Sripathy, Murali H; Batra, Harsh V

    2016-09-01

    Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha

  19. Detection of Burkholderia pseudomallei O-antigen serotypes in near-neighbor species

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    Stone Joshua K

    2012-11-01

    Full Text Available Abstract Background Burkholderia pseudomallei is the etiological agent of melioidosis and a CDC category B select agent with no available effective vaccine. Previous immunizations in mice have utilized the lipopolysaccharide (LPS as a potential vaccine target because it is known as one of the most important antigenic epitopes in B. pseudomallei. Complicating this strategy are the four different B. pseudomallei LPS O-antigen types: A, B, B2, and rough. Sero-crossreactivity is common among O-antigens of Burkholderia species. Here, we identified the presence of multiple B. pseudomallei O-antigen types and sero-crossreactivity in its near-neighbor species. Results PCR screening of O-antigen biosynthesis genes, phenotypic characterization using SDS-PAGE, and immunoblot analysis showed that majority of B. mallei and B. thailandensis strains contained the typical O-antigen type A. In contrast, most of B. ubonensis and B. thailandensis-like strains expressed the atypical O-antigen types B and B2, respectively. Most B. oklahomensis strains expressed a distinct and non-seroreactive O-antigen type, except strain E0147 which expressed O-antigen type A. O-antigen type B2 was also detected in B. thailandensis 82172, B. ubonensis MSMB108, and Burkholderia sp. MSMB175. Interestingly, B. thailandensis-like MSMB43 contained a novel serotype B positive O-antigen. Conclusions This study expands the number of species which express B. pseudomallei O-antigen types. Further work is required to elucidate the full structures and how closely these are to the B. pseudomallei O-antigens, which will ultimately determine the efficacy of the near-neighbor B serotypes for vaccine development.

  20. Species Distribution and Ribotype Diversity of Burkholderia cepacia Complex Isolates from French Patients with Cystic Fibrosis

    OpenAIRE

    Brisse, Sylvain; Cordevant, Christophe; Vandamme, Peter; Bidet, Philippe; Loukil, Chawki; Chabanon, Gérard; Lange, Marc; Bingen, Edouard

    2004-01-01

    A total of 153 Burkholderia cepacia strains obtained from 153 French patients with cystic fibrosis were identified as Burkholderia multivorans (51.6%) or Burkholderia cenocepacia (45.1%). Eighty-two genotypes were identified using PvuII and EcoRI ribotyping. B. multivorans genotype A (found in 32 French patients) and two other genotypes were also identified among isolates from Austrian, German, Italian, and Canadian patients.

  1. Molecular Method To Assess the Diversity of Burkholderia Species in Environmental Samples

    OpenAIRE

    Salles, J; Souza, de, H.R.; Elsas, van, J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the Burkholderia diversity in soil samples. Primers specific for the genus Burkholderia were developed ...

  2. Fatal Burkholderia pseudomallei infection initially reported as a Bacillus species, Ohio, 2013.

    Science.gov (United States)

    Doker, Thomas J; Quinn, Celia L; Salehi, Ellen D; Sherwood, Joshua J; Benoit, Tina J; Glass Elrod, Mindy; Gee, Jay E; Shadomy, Sean V; Bower, William A; Hoffmaster, Alex R; Walke, Henry T; Blaney, David D; DiOrio, Mary S

    2014-10-01

    A fatal case of melioidosis was diagnosed in Ohio one month after culture results were initially reported as a Bacillus species. To identify a source of infection and assess risk in patient contacts, we abstracted patient charts; interviewed physicians and contacts; genetically characterized the isolate; performed a Burkholderia pseudomallei antibody indirect hemagglutination assay on household contacts and pets to assess seropositivity; and collected household plant, soil, liquid, and insect samples for culturing and real-time polymerase chain reaction testing. Family members and pets tested were seronegative for B. pseudomallei. Environmental samples were negative by real-time polymerase chain reaction and culture. Although the patient never traveled internationally, the isolate genotype was consistent with an isolate that originated in Southeast Asia. This investigation identified the fifth reported locally acquired non-laboratory melioidosis case in the contiguous United States. Physicians and laboratories should be aware of this potentially emerging disease and refer positive cultures to a Laboratory Response Network laboratory. PMID:25092821

  3. Transports of acetate and haloacetate in Burkholderia species MBA4 are operated by distinct systems

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    Su Xianbin

    2012-11-01

    Full Text Available Abstract Background Acetate is a commonly used substrate for biosynthesis while monochloroacetate is a structurally similar compound but toxic and inhibits cell metabolism by blocking the citric acid cycle. In Burkholderia species MBA4 haloacetate was utilized as a carbon and energy source for growth. The degradation of haloacid was mediated by the production of an inducible dehalogenase. Recent studies have identified the presence of a concomitantly induced haloacetate-uptake activity in MBA4. This uptake activity has also been found to transport acetate. Since acetate transporters are commonly found in bacteria it is likely that haloacetate was transported by such a system in MBA4. Results The haloacetate-uptake activity of MBA4 was found to be induced by monochloroacetate (MCA and monobromoacetate (MBA. While the acetate-uptake activity was also induced by MCA and MBA, other alkanoates: acetate, propionate and 2-monochloropropionate (2MCPA were also inducers. Competing solute analysis showed that acetate and propionate interrupted the acetate- and MCA- induced acetate-uptake activities. While MCA, MBA, 2MCPA, and butyrate have no effect on acetate uptake they could significantly quenched the MCA-induced MCA-uptake activity. Transmembrane electrochemical potential was shown to be a driving force for both acetate- and MCA- transport systems. Conclusions Here we showed that acetate- and MCA- uptake in Burkholderia species MBA4 are two transport systems that have different induction patterns and substrate specificities. It is envisaged that the shapes and the three dimensional structures of the solutes determine their recognition or exclusion by the two transport systems.

  4. ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity, a Widespread Trait in Burkholderia Species, and Its Growth-Promoting Effect on Tomato Plants▿

    OpenAIRE

    Onofre-Lemus, Janette; Hernández-Lucas, Ismael; Girard, Lourdes; Caballero-Mellado, Jesús

    2009-01-01

    The genus Burkholderia includes pathogens of plants and animals and some human opportunistic pathogens, such as the Burkholderia cepacia complex (Bcc), but most species are nonpathogenic, plant associated, and rhizospheric or endophytic. Since rhizobacteria expressing ACC (1-aminocyclopropane-1-carboxylate) deaminase may enhance plant growth by lowering plant ethylene levels, in this work we investigated the presence of ACC deaminase activity and the acdS gene in 45 strains, most of which are...

  5. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, J.; Souza, de F.A.; Elsas, van J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a pow

  6. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, J.F.; De Souza, F.A.; Van Elsas, J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient get electrophoresis (DGGE), a pow

  7. Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PLAT medium

    NARCIS (Netherlands)

    Salles, JF; Samyn, E; Vandamme, P; van Veen, JA; van Elsas, JD

    2006-01-01

    In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize monocultu

  8. Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PCAT medium

    NARCIS (Netherlands)

    Salles, J.F.; Samyn, E.; Vandamme, P.; Van Veen, J.A.; van Elsas, J.D.

    2006-01-01

    Abstract In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize

  9. Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus.

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    Partida-Martinez, Laila P; Groth, Ingrid; Schmitt, Imke; Richter, Walter; Roth, Martin; Hertweck, Christian

    2007-11-01

    Several strains of the fungus Rhizopus microsporus harbour endosymbiotic bacteria for the production of the causal agent of rice seedling blight, rhizoxin, and the toxic cyclopeptide rhizonin. R. microsporus and isolated endobacteria were selected for freeze-fracture electron microscopy, which allowed visualization of bacterial cells within the fungal cytosol by their two parallel-running envelope membranes and by the fine structure of the lipopolysaccharide layer of the outer membrane. Two representatives of bacterial endosymbionts were chosen for phylogenetic analyses on the basis of full 16S rRNA gene sequences, which revealed that the novel fungal endosymbionts formed a monophyletic group within the genus Burkholderia. Inter-sequence similarities ranged from 98.94 to 100%, and sequence similarities to members of the Burkholderia pseudomallei group, the closest neighbours, were 96.74-97.38%. In addition, the bacterial strains were distinguished from their phylogenetic neighbours by their fatty acid profiles and other biochemical characteristics. The phylogenetic studies based on 16S rRNA gene sequence data, together with conclusive DNA-DNA reassociation experiments, strongly support the proposal that these strains represent two novel species within the genus Burkholderia, for which the names Burkholderia rhizoxinica sp. nov. (type strain, HKI 454T=DSM 19002T=CIP 109453T) and Burkholderia endofungorum sp. nov. (type strain, HKI 456T=DSM 19003T=CIP 109454T) are proposed. PMID:17978222

  10. Investigating early stages of biocorrosion with XPS: AISI 304 stainless steel exposed to Burkholderia species

    Science.gov (United States)

    Johansson, Leena-Sisko; Saastamoinen, Tuomas

    1999-04-01

    We have investigated the interactions of an exopolymer-producing bacteria, Burkholderia sp. with polished AISI 304 stainless steel substrates using X-ray photoelectron spectroscopy (XPS). Steel coupons were exposed to the pure bacteria culture in a specially designed flowcell for 6 h during which the experiment was monitored in situ with an optical microscope. XPS results verified the formation of biofilm containing extracellular polymer on all the samples exposed to bacteria. Sputter results indicated that some ions needed for metabolic processes were trapped within the biofilm. Changes in the relative Fe concentration and Fe 2p peak shape indicated that also iron had accumulated into the biofilm.

  11. Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans

    OpenAIRE

    Kost, Thomas; Stopnisek, Nejc; Agnoli, Kirsty; Eberl, Leo; Weisskopf, Laure

    2014-01-01

    Plant roots and shoots harbor complex bacterial communities. Early seed and plantlet colonization plays a key role in determining which bacterial populations will successfully invade plant tissues, yet the mechanisms enabling plants to select for beneficial rather than harmful populations are largely unknown. In this study, we demonstrate a role of oxalate as a determinant in this selection process, using members of the genus Burkholderia as model organisms. Oxalotrophy, i.e., the ability to ...

  12. Virulent Burkholderia species mimic host actin polymerases to drive actin-based motility

    Science.gov (United States)

    Benanti, Erin L.; Nguyen, Catherine M.; Welch, Matthew D.

    2015-01-01

    Summary Burkholderia pseudomallei and B. mallei are bacterial pathogens that cause melioidosis and glanders, while their close relative B. thailandensis is nonpathogenic. All use the trimeric autotransporter BimA to facilitate actin-based motility, host cell fusion and dissemination. Here, we show that BimA orthologs mimic different host actin-polymerizing proteins. B. thailandensis BimA activates the host Arp2/3 complex. In contrast, B. pseudomallei and B. mallei BimA mimic host Ena/VASP actin polymerases in their ability to nucleate, elongate and bundle filaments by associating with barbed ends, as well as in their use of WH2 motifs and oligomerization for activity. Mechanistic differences among BimA orthologs resulted in distinct actin filament organization and motility parameters, which affected the efficiency of cell fusion during infection. Our results identify bacterial Ena/VASP mimics and reveal that pathogens imitate the full spectrum of host actin-polymerizing pathways, suggesting that mimicry of different polymerization mechanisms influences key parameters of infection. PMID:25860613

  13. rpsU-based discrimination within the genus Burkholderia

    OpenAIRE

    Frickmann, H.; Neubauer, H.; Loderstaedt, U.; Derschum, H.; Hagen, R. M.

    2014-01-01

    Sequencing of the gene rpsU reliably delineates saprophytic Burkholderia (B.) thailandensis from highly pathogenic B. mallei and B. pseudomallei. We analyzed the suitability of this technique for the delineation of the B. pseudomallei complex from other Burkholderia species.

  14. Causality of the relationship between geographic distribution and species abundance

    DEFF Research Database (Denmark)

    Borregaard, Michael Krabbe; Rahbek, Carsten

    2010-01-01

    The positive relationship between a species' geographic distribution and its abundance is one of ecology's most well-documented patterns, yet the causes behind this relationship remain unclear. Although many hypotheses have been proposed to account for distribution-abundance relationships none ha......, in a framework that facilitates a comparison between them. We identify and discuss the central factors governing the individual mechanisms, and elucidate their effect on empirical patterns.......The positive relationship between a species' geographic distribution and its abundance is one of ecology's most well-documented patterns, yet the causes behind this relationship remain unclear. Although many hypotheses have been proposed to account for distribution-abundance relationships none have...... attained unequivocal support. Accordingly, the positive association in distribution-abundance relationships is generally considered to be due to a combination of these proposed mechanisms acting in concert. In this review, we suggest that much of the disparity between these hypotheses stems from...

  15. Complete Genome Sequence of the Fenitrothion-Degrading Burkholderia sp. Strain YI23

    OpenAIRE

    Lim, Jong Sung; Choi, Beom Soon; Choi, Ah Young; Kim, Kyung Duk; Kim, Dong In; Choi, Ik Young; Ka, Jong-Ok

    2012-01-01

    Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated from various environments have the potential to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was isolated from a golf course soil and identified as a fenitrothion-degrading bacterium. In this study, we report the complete genome sequence of Burkholderia sp. strain YI23.

  16. Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes.

    Science.gov (United States)

    De Meyer, Sofie E; Briscoe, Leah; Martínez-Hidalgo, Pilar; Agapakis, Christina M; de-Los Santos, Paulina Estrada; Seshadri, Rekha; Reeve, Wayne; Weinstock, George; O'Hara, Graham; Howieson, John G; Hirsch, Ann M

    2016-08-01

    Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.

  17. Species-Specific Detection and Identification of Fusarium Species Complex, the Causal Agent of Sugarcane Pokkah Boeng in China

    OpenAIRE

    Zhenyue Lin; Shiqiang Xu; Youxiong Que; Jihua Wang; Comstock, Jack C.; Jinjin Wei; McCord, Per H.; Baoshan Chen; Rukai Chen; Muqing Zhang

    2014-01-01

    BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological...

  18. Species-specific detection and identification of fusarium species complex, the causal agent of sugarcane pokkah boeng in China.

    Directory of Open Access Journals (Sweden)

    Zhenyue Lin

    Full Text Available BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. RESULT: Two Fusarium species (F. verticillioides and F. proliferatum that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. CONCLUSIONS/SIGNIFICANCE: This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng.

  19. Volatile-Sulfur-Compound Profile Distinguishes Burkholderia pseudomallei from Burkholderia thailandensis

    OpenAIRE

    Inglis, Timothy J J; Hahne, Dorothee R.; Merritt, Adam J.; Clarke, Michael W.

    2015-01-01

    Solid-phase microextraction gas chromatography-mass spectrometry (SPME-GCMS) was used to show that dimethyl sulfide produced by Burkholderia pseudomallei is responsible for its unusual truffle-like smell and distinguishes the species from Burkholderia thailandensis. SPME-GCMS can be safely used to detect dimethyl sulfide produced by agar-grown B. pseudomallei.

  20. Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

    Energy Technology Data Exchange (ETDEWEB)

    Moulin, Lionel [UMR, France; Klonowska, Agnieszka [UMR, France; Caroline, Bournaud [UMR, France; Booth, Kristina [University of Massachusetts; Vriezen, Jan A.C. [University of Massachusetts; Melkonian, Remy [UMR, France; James, Euan [James Hutton Institute, Dundee, United Kingdom; Young, Peter W. [University of York, United Kingdom; Bena, Gilles [UMR, France; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lizotte-Waniewski, Michelle [University of Massachusetts; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Riley, Monica [Woods Hole Oceanographic Institution (WHOI), Woods Hole

    2014-01-01

    Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

  1. CHROMOSOMAL MULTIPLICITY IN BURKHOLDERIA CEPACIA

    Science.gov (United States)

    We have used CHEF gel electrophoresis to screen preparations of large DNA from different Burkholderia cepacia isolates for the presence of DNA species corresponding to the linearized forms of the three chromosomes of 3.4,2.5, and 0.9 Mb identified in B. cepacia strain 17616. DNA ...

  2. Darwin's diagram of divergence of taxa as a causal model for the origin of species.

    Science.gov (United States)

    Bouzat, Juan L

    2014-03-01

    On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, thus representing a comprehensive model of Darwin's theory on the origin of species. I describe Darwin's Tree Diagram in relation to his argumentative strategy under the vera causa principle, and suggest that the testing of his theory based on the evidence from the geological record, the geographical distribution of organisms, and the mutual affinities of organic beings can be framed under the hypothetico-deductive method. Darwin's Diagram of Divergence of Taxa therefore represents a broad conceptual model that helps understanding the causal construction of Darwin's theory of evolution, the structure of his argumentative strategy, and the nature of his scientific methodology.

  3. Diagnostically and Experimentally Useful Panel of Strains from the Burkholderia cepacia Complex

    OpenAIRE

    Mahenthiralingam, Eshwar; Coenye, Tom; Chung, Jacqueline W.; Speert, David P.; Govan, John R. W.; Taylor, Peter; Vandamme, Peter

    2000-01-01

    Two new species, Burkholderia multivorans and Burkholderia vietnamiensis, and three genomovars (genomovars I, III, and IV) currently constitute the Burkholderia cepacia complex. A panel of 30 well-characterized strains representative of each genomovar and new species was assembled to assist with identification, epidemiological analysis, and virulence studies on this important group of opportunistic pathogens.

  4. An ancient but promiscuous host–symbiont association between Burkholderia gut symbionts and their heteropteran hosts

    OpenAIRE

    Kikuchi, Yoshitomo; Hosokawa, Takahiro; Fukatsu, Takema

    2010-01-01

    Here, we investigated 124 stinkbug species representing 20 families and 5 superfamilies for their Burkholderia gut symbionts, of which 39 species representing 6 families of the superfamilies Lygaeoidea and Coreoidea were Burkholderia-positive. Diagnostic PCR surveys revealed high frequencies of Burkholderia infection in natural populations of the stinkbugs, and substantial absence of vertical transmission of Burkholderia infection to their eggs. In situ hybridization confirmed localization of...

  5. Role of phages in the pathogenesis of Burkholderia or “Where are the toxin genes in Burkholderia phages?”

    OpenAIRE

    Summer, Elizabeth J.; Gill, Jason J.; Upton, Chris; Gonzalez, Carlos F.; Young, Ry

    2007-01-01

    Most bacteria of the genus Burkholderia are soil- and rhizosphere- associated, noted for their metabolic plasticity in the utilization of a wide range of organic compounds as carbon sources. Many Burkholderia species are also opportunistic human and plant pathogens and the distinction between environmental, plant, and human pathogens is not always clear. Burkholderia phages are not uncommon and multiple cryptic prophages are identifiable in the sequenced Burkholderia genomes. Phages have play...

  6. Characterization of the Poly-β-1,6-N-Acetylglucosamine Polysaccharide Component of Burkholderia Biofilms ▿

    OpenAIRE

    Yakandawala, Nandadeva; Gawande, Purushottam V.; LoVetri, Karen; Cardona, Silvia T.; Romeo, Tony; Nitz, Mark; Madhyastha, Srinivasa

    2011-01-01

    We demonstrated the production of poly-β-1,6-N-acetylglucosamine (PNAG) polysaccharide in the biofilms of Burkholderia multivorans, Burkholderia vietnamiensis, Burkholderia ambifaria, Burkholderia cepacia, and Burkholderia cenocepacia using an immunoblot assay for PNAG. These results were confirmed by further studies, which showed that the PNAG hydrolase, dispersin B, eliminated immunoreactivity of extracts from the species that were tested (B. cenocepacia and B. multivorans). Dispersin B als...

  7. Members of the genus Burkholderia: good and bad guys

    Science.gov (United States)

    Eberl, Leo; Vandamme, Peter

    2016-01-01

    In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains. PMID:27303639

  8. Evaluation of a latex agglutination assay for the identification of Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Duval, Brea D; Elrod, Mindy G; Gee, Jay E; Chantratita, Narisara; Tandhavanant, Sarunporn; Limmathurotsakul, Direk; Hoffmaster, Alex R

    2014-06-01

    Cases of melioidosis and glanders are rare in the United States, but the etiologic agents of each disease (Burkholderia pseudomallei and Burkholderia mallei, respectively) are classified as Tier 1 select agents because of concerns about their potential use as bioterrorism agents. A rapid, highly sensitive, and portable assay for clinical laboratories and field use is required. Our laboratory has further evaluated a latex agglutination assay for its ability to identify B. pseudomallei and B. mallei isolates. This assay uses a monoclonal antibody that specifically recognizes the capsular polysaccharide produced by B. pseudomallei and B. mallei, but is absent in closely related Burkholderia species. A total of 110 B. pseudomallei and B. mallei were tested, and 36 closely related Burkholderia species. The latex agglutination assay was positive for 109 of 110 (99.1% sensitivity) B. pseudomallei and B. mallei isolates tested.

  9. Multiplex qPCR for reliable detection and differentiation of Burkholderia mallei and Burkholderia pseudomallei

    OpenAIRE

    Janse Ingmar; Hamidjaja Raditijo A; Hendriks Amber CA; van Rotterdam Bart J

    2013-01-01

    Abstract Background Burkholderia mallei and B. pseudomallei are two closely related species of highly virulent bacteria that can be difficult to detect. Pathogenic Burkholderia are endemic in many regions worldwide and cases of infection, sometimes brought by travelers from unsuspected regions, also occur elsewhere. Rapid, sensitive methods for identification of B. mallei and B. pseudomallei are urgently needed in the interests of patient treatment and epidemiological surveillance. Methods Si...

  10. Burkholderia fungorum Septicemia

    OpenAIRE

    Gerrits, G. Peter; Klaassen, Corné; Coenye, Tom; Vandamme, Peter; Meis, Jacques F

    2005-01-01

    We report the first case of community-acquired bacteremia with Burkholderia fungorum, a newly described member of the Burkholderia cepacia complex. A 9-year-old girl sought treatment with septic arthritis in her right knee and ankle with soft tissue involvement. Commercial identification systems did not identify the causative microorganism.

  11. Recurrent Burkholderia Infection in Patients with Chronic Granulomatous Disease: 11-Year Experience at a Large Referral Center

    OpenAIRE

    Greenberg, David E.; Goldberg, Joanna B.; Stock, Frida; Murray, Patrick R.; Holland, Steven M.; LiPuma, John J.

    2009-01-01

    The epidemiology of Burkholderia infection in persons with chronic granulomatous disease is poorly understood. We used species-specific polymerase chain reaction–based assays and genotyping analyses to identify 32 strains representing 9 Burkholderia species among 50 isolates recovered from 18 patients with chronic granulomatous disease. We found that recurrent pulmonary infection with distinct Burkholderia strains is common in chronic granulomatous disease.

  12. Minocycline activity tested against Acinetobacter baumannii complex, Stenotrophomonas maltophilia, and Burkholderia cepacia species complex isolates from a global surveillance program (2013).

    Science.gov (United States)

    Flamm, Robert K; Castanheira, Mariana; Streit, Jennifer M; Jones, Ronald N

    2016-07-01

    Clinical isolates of Acinetobacter baumannii complex (1312), Stenotrophomonas maltophilia (464), and Burkholderia cepacia species complex (30) were selected from medical centers in the United States (USA), Europe and the Mediterranean (EU-M) region, Latin America, and Asia Pacific. Only one isolate per infected patient episode was included and local identifications were confirmed by the monitoring laboratory. Susceptibility testing was performed at the monitoring laboratory using the reference broth microdilution method as described by Clinical and Laboratory Standards Institute (CLSI). A. baumannii complex were classified as MDR (multi-drug resistant [MDR]; nonsusceptible to ≥1 agent in ≥3 antimicrobial classes) and extensively drug-resistant (XDR; nonsusceptible to ≥1 agent in all but ≤2 antimicrobial classes). A total of 81.6% of A. baumannii complex were MDR. Colistin was the most active agent against MDR A. baumannii complex. Minocycline was the most active "tetracycline" against these organisms based on susceptibility. Against B. cepacia, trimethoprim-sulfamethoxazole (MIC90, 2 μg/mL; 100.0% susceptible) was the most active agent tested. Overall, minocycline was the most active tetracycline tested against A. baumannii complex and S. maltophilia isolates collected from patients throughout EU-M, USA, Latin America, and the Asia-Pacific. Minocycline, particularly the intravenous formulation, has activity against several ESKAPE pathogens and merits consideration in seriously ill patients where treatment options may be limited due to the presence of MDR bacteria. PMID:27112832

  13. Development of a recA Gene-Based Identification Approach for the Entire Burkholderia Genus

    OpenAIRE

    Payne, George W.; Vandamme, Peter; Morgan, Sara H.; LiPuma, John J.; Coenye, Tom; Weightman, Andrew J.; Jones, T. Hefin; Mahenthiralingam, Eshwar

    2005-01-01

    Burkholderia is an important bacterial genus containing species of ecological, biotechnological, and pathogenic interest. With their taxonomy undergoing constant revision and the phenotypic similarity of several species, correct identification of Burkholderia is difficult. A genetic scheme based on the recA gene has greatly enhanced the identification of Burkholderia cepacia complex species. However, the PCR developed for the latter approach was limited by its specificity for the complex. By ...

  14. Draft Genome Sequence of the Organophosphorus Compound-Degrading Burkholderia zhejiangensis Strain CEIB S4-3

    OpenAIRE

    Hernández-Mendoza, Armando; Martínez-Ocampo, Fernando; Lozano-Aguirre Beltrán, Luis Fernando; Popoca-Ursino, Elida Carolina; Ortiz-Hernández, Laura; Sánchez-Salinas, Enrique; Dantán-González, Edgar

    2014-01-01

    Burkholderia species are widely distributed in the environment. A Burkholderia zhejiangensis strain was isolated from pesticide-contaminated soil from an agricultural field in Mexico and identified as an organophosphorus compound-degrading bacterium. In this study, we report the draft genome sequence of Burkholderia zhejiangensis strain CEIB S4-3.

  15. Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil

    OpenAIRE

    Woo, Hannah L.; Utturkar, Sagar; Klingeman, Dawn; Simmons, Blake A.; DeAngelis, Kristen M; Brown, Steven D.; Hazen, Terry C.

    2014-01-01

    Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30.

  16. Multiplex qPCR for reliable detection and differentiation of Burkholderia mallei and Burkholderia pseudomallei

    Directory of Open Access Journals (Sweden)

    Janse Ingmar

    2013-02-01

    Full Text Available Abstract Background Burkholderia mallei and B. pseudomallei are two closely related species of highly virulent bacteria that can be difficult to detect. Pathogenic Burkholderia are endemic in many regions worldwide and cases of infection, sometimes brought by travelers from unsuspected regions, also occur elsewhere. Rapid, sensitive methods for identification of B. mallei and B. pseudomallei are urgently needed in the interests of patient treatment and epidemiological surveillance. Methods Signature sequences for sensitive, specific detection of pathogenic Burkholderia based on published genomes were identified and a qPCR assay was designed and validated. Results A single-reaction quadruplex qPCR assay for the detection of pathogenic Burkholderia, which includes a marker for internal control of DNA extraction and amplification, was developed. The assay permits differentiation of B. mallei and B. pseudomallei strains, and probit analysis showed a very low detection limit. Use of a multicopy signature sequence permits detection of less than 1 genome equivalent per reaction. Conclusions The new assay permits rapid detection of pathogenic Burkholderia and combines enhanced sensitivity, species differentiation, and inclusion of an internal control for both DNA extraction and PCR amplification.

  17. Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers.

    Science.gov (United States)

    Depoorter, Eliza; Bull, Matt J; Peeters, Charlotte; Coenye, Tom; Vandamme, Peter; Mahenthiralingam, Eshwar

    2016-06-01

    Burkholderia is an incredibly diverse and versatile Gram-negative genus, within which over 80 species have been formally named and multiple other genotypic groups likely represent new species. Phylogenetic analysis based on the 16S rRNA gene sequence and core genome ribosomal multilocus sequence typing analysis indicates the presence of at least three major clades within the genus. Biotechnologically, Burkholderia are well-known for their bioremediation and biopesticidal properties. Within this review, we explore the ability of Burkholderia to synthesise a wide range of antimicrobial compounds ranging from historically characterised antifungals to recently described antibacterial antibiotics with activity against multiresistant clinical pathogens. The production of multiple Burkholderia antibiotics is controlled by quorum sensing and examples of quorum sensing pathways found across the genus are discussed. The capacity for antibiotic biosynthesis and secondary metabolism encoded within Burkholderia genomes is also evaluated. Overall, Burkholderia demonstrate significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites. PMID:27115756

  18. Autotransporters and their role in the virulence of Burkholderia pseudomallei and Burkholderia mallei.

    Directory of Open Access Journals (Sweden)

    Natalie eLazar Adler

    2011-07-01

    Full Text Available Burkholderia pseudomallei and Burkholderia mallei are closely related Gram-negative bacteria responsible for the infectious diseases melioidosis and glanders, respectively. Autotransporters (ATs comprise a large and diverse family of secreted and outer membrane proteins that includes virulence-associated invasins, adhesins, proteases and actin-nucleating factors. The B. pseudomallei K96243 genome contains eleven predicted ATs, eight of which share homologues in the B. mallei ATCC 23344 genome. This review distils key findings from in silico, in vitro and in vivo studies on the ATs of B. pseudomallei and B. mallei. To date, the best characterized of the predicted ATs of B. pseudomallei and B. mallei is BimA, a predicted trimeric AT mediating actin-based motility which varies in sequence and mode of action between Burkholderia species. Of the remaining eight predicted B. pseudomallei trimeric autotransporters, five of which are also present in B. mallei, two (BoaA and BoaB, have been implicated in bacterial adhesion to epithelial cells. Several predicted Burkholderia ATs are recognized by human humoral and cell-mediated immunity, indicating that they are expressed during infection and may be useful for diagnosis and vaccine-mediated protection. Further studies on the mode of secretion and functions of Burkholderia ATs will facilitate the rational design of control strategies.

  19. Members of the genus Burkholderia: good and bad guys [version 1; referees: 3 approved

    OpenAIRE

    Leo Eberl; Peter Vandamme

    2016-01-01

    In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isol...

  20. Burkholderia Vaccines: Are We Moving Forward?

    Directory of Open Access Journals (Sweden)

    Leang-Chung eChoh

    2013-02-01

    Full Text Available The genus Burkholderia consists of diverse species which includes both ‘friends’ and ‘foes’. Some of the ‘friendly’ Burkholderia spp. are extensively used in the biotechnological and agricultural industry for bioremediation and biocontrol. However, several members of the genus including B. pseudomallei, B. mallei and B. cepacia, are known to cause fatal disease in both humans and animals. B. pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively, while B. cepacia infection is lethal to cystic fibrosis patients. Due to the high rate of infectivity and intrinsic resistance to many commonly used antibiotics, together with high mortality rate, B. mallei and B. pseudomallei are considered to be potential biological warfare agents. Treatments of the infections caused by these bacteria are often unsuccessful with frequent relapse of the infection. Thus, we are at a crucial stage of the need for Burkholderia vaccines. Although the search for a prophylactic therapy candidate continues, to date development of vaccines has not advanced beyond research to human clinical trials. In this article, we review the current research on development of safe vaccines with high efficacy against B. pseudomallei, B. mallei and B. cepacia. It can be concluded that further research will enable elucidation of the potential benefits and risks of Burkholderia vaccines.

  1. Burkholderia vaccines: are we moving forward?

    Science.gov (United States)

    Choh, Leang-Chung; Ong, Guang-Han; Vellasamy, Kumutha M; Kalaiselvam, Kaveena; Kang, Wen-Tyng; Al-Maleki, Anis R; Mariappan, Vanitha; Vadivelu, Jamuna

    2013-01-01

    The genus Burkholderia consists of diverse species which includes both "friends" and "foes." Some of the "friendly" Burkholderia spp. are extensively used in the biotechnological and agricultural industry for bioremediation and biocontrol. However, several members of the genus including B. pseudomallei, B. mallei, and B. cepacia, are known to cause fatal disease in both humans and animals. B. pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively, while B. cepacia infection is lethal to cystic fibrosis (CF) patients. Due to the high rate of infectivity and intrinsic resistance to many commonly used antibiotics, together with high mortality rate, B. mallei and B. pseudomallei are considered to be potential biological warfare agents. Treatments of the infections caused by these bacteria are often unsuccessful with frequent relapse of the infection. Thus, we are at a crucial stage of the need for Burkholderia vaccines. Although the search for a prophylactic therapy candidate continues, to date development of vaccines has not advanced beyond research to human clinical trials. In this article, we review the current research on development of safe vaccines with high efficacy against B. pseudomallei, B. mallei, and B. cepacia. It can be concluded that further research will enable elucidation of the potential benefits and risks of Burkholderia vaccines.

  2. Stress conditions triggering mucoid morphotype variation in Burkholderia species and effect on virulence in Galleria mellonella and biofilm formation in vitro.

    Directory of Open Access Journals (Sweden)

    Inês N Silva

    Full Text Available Burkholderia cepacia complex (Bcc bacteria are opportunistic pathogens causing chronic respiratory infections particularly among cystic fibrosis patients. During these chronic infections, mucoid-to-nonmucoid morphotype variation occurs, with the two morphotypes exhibiting different phenotypic properties. Here we show that in vitro, the mucoid clinical isolate Burkholderia multivorans D2095 gives rise to stable nonmucoid variants in response to prolonged stationary phase, presence of antibiotics, and osmotic and oxidative stresses. Furthermore, in vitro colony morphotype variation within other members of the Burkholderia genus occurred in Bcc and non-Bcc strains, irrespectively of their clinical or environmental origin. Survival to starvation and iron limitation was comparable for the mucoid parental isolate and the respective nonmucoid variant, while susceptibility to antibiotics and to oxidative stress was increased in the nonmucoid variants. Acute infection of Galleria mellonella larvae showed that, in general, the nonmucoid variants were less virulent than the respective parental mucoid isolate, suggesting a role for the exopolysaccharide in virulence. In addition, most of the tested nonmucoid variants produced more biofilm biomass than their respective mucoid parental isolate. As biofilms are often associated with increased persistence of pathogens in the CF lungs and are an indicative of different cell-to-cell interactions, it is possible that the nonmucoid variants are better adapted to persist in this host environment.

  3. Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate

    OpenAIRE

    Carlier, A; Agnoli, K; Pessi, G; Suppiger, A; Jenul, C; Schmid, N; Tummler, B.; Pinto-Carbo, M; Eberl, L

    2014-01-01

    The Burkholderia cepacia complex (BCC) is a group of related bacterial species that are commonly isolated from environmental samples. Members of the BCC can cause respiratory infections in cystic fibrosis patients and immunocompromised individuals. We report here the genome sequence of Burkholderia cenocepacia H111, a well-studied model strain of the BCC.

  4. Charakterisierung des Burkholderia cenocepacia Aquaglyceroporins

    OpenAIRE

    Wree, Dorothea

    2010-01-01

    In der vorliegenden Arbeit wurde ein Aquaglyceroporin des Krankenhausproblemkeims Burkholderia cenocepacia, BccGlpF, charakterisiert. Unter besonderer Beobachtung stand die Struktur-Funktionsbeziehung der eigentlich kochkonservierten NPA-Motive.

  5. Burkholderia in gladiool lastige bacterie

    NARCIS (Netherlands)

    Kok, B.J.; Aanholt, van J.T.M.

    2009-01-01

    In de bollen- en bloementeelt van gladiolen komt de laatste jaren de bacterieziekte Burkholderia gladiola voor die onder vochtige warme omstandigheden veel uitval veroorzaken. PPO onderzocht een aantal maatregelen om de ziekte in kralen, pitten en knollen te bestrijden

  6. Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods

    NARCIS (Netherlands)

    C. van Pelt (Cindy); C.M. Verduin (Cees); W.H.F. Goessens (Wil); M.C. Vos (Margreet); B. Tummler; C. Segonds; F. Reubsaet; A.F. van Belkum (Alex); H.A. Verbrugh (Henri)

    1999-01-01

    textabstractCystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situat

  7. Causal universe

    CERN Document Server

    Ellis, George FR; Pabjan, Tadeusz

    2013-01-01

    Written by philosophers, cosmologists, and physicists, this collection of essays deals with causality, which is a core issue for both science and philosophy. Readers will learn about different types of causality in complex systems and about new perspectives on this issue based on physical and cosmological considerations. In addition, the book includes essays pertaining to the problem of causality in ancient Greek philosophy, and to the problem of God's relation to the causal structures of nature viewed in the light of contemporary physics and cosmology.

  8. Symbiotic ß-proteobacteria beyond legumes: Burkholderia in Rubiaceae.

    Directory of Open Access Journals (Sweden)

    Brecht Verstraete

    Full Text Available Symbiotic ß-proteobacteria not only occur in root nodules of legumes but are also found in leaves of certain Rubiaceae. The discovery of bacteria in plants formerly not implicated in endosymbiosis suggests a wider occurrence of plant-microbe interactions. Several ß-proteobacteria of the genus Burkholderia are detected in close association with tropical plants. This interaction has occurred three times independently, which suggest a recent and open plant-bacteria association. The presence or absence of Burkholderia endophytes is consistent on genus level and therefore implies a predictive value for the discovery of bacteria. Only a single Burkholderia species is found in association with a given plant species. However, the endophyte species are promiscuous and can be found in association with several plant species. Most of the endophytes are part of the plant-associated beneficial and environmental group, but others are closely related to B. glathei. This soil bacteria, together with related nodulating and non-nodulating endophytes, is therefore transferred to a newly defined and larger PBE group within the genus Burkholderia.

  9. Development of a Selective Medium for the Fungal Pathogen Fusarium graminearum Using Toxoflavin Produced by the Bacterial Pathogen Burkholderia glumae

    Directory of Open Access Journals (Sweden)

    Boknam Jung

    2013-12-01

    Full Text Available The ascomycete fungus Fusarium graminearum is a major causal agent for Fusarium head blight in cereals and produces mycotoxins such as trichothecenes and zearalenone. Isolation of the fungal strains from air or cereals can be hampered by various other airborne fungal pathogens and saprophytic fungi. In this study, we developed a selective medium specific to F. graminearum using toxoflavin produced by the bacterial pathogen Burkholderia glumae. F. graminearum was resistant to toxoflavin, while other fungi were sensitive to this toxin. Supplementing toxoflavin into medium enhanced the isolation of F. graminearum from rice grains by suppressing the growth of saprophytic fungal species. In addition, a medium with or without toxoflavin exposed to wheat fields for 1 h had 84% or 25%, respectively, of colonies identified as F. graminearum. This selection medium provides an efficient tool for isolating F. graminearum, and can be adopted by research groups working on genetics and disease forecasting.

  10. Causal and causally separable processes

    Science.gov (United States)

    Oreshkov, Ognyan; Giarmatzi, Christina

    2016-09-01

    The idea that events are equipped with a partial causal order is central to our understanding of physics in the tested regimes: given two pointlike events A and B, either A is in the causal past of B, B is in the causal past of A, or A and B are space-like separated. Operationally, the meaning of these order relations corresponds to constraints on the possible correlations between experiments performed in the vicinities of the respective events: if A is in the causal past of B, an experimenter at A could signal to an experimenter at B but not the other way around, while if A and B are space-like separated, no signaling is possible in either direction. In the context of a concrete physical theory, the correlations compatible with a given causal configuration may obey further constraints. For instance, space-like correlations in quantum mechanics arise from local measurements on joint quantum states, while time-like correlations are established via quantum channels. Similarly to other variables, however, the causal order of a set of events could be random, and little is understood about the constraints that causality implies in this case. A main difficulty concerns the fact that the order of events can now generally depend on the operations performed at the locations of these events, since, for instance, an operation at A could influence the order in which B and C occur in A’s future. So far, no formal theory of causality compatible with such dynamical causal order has been developed. Apart from being of fundamental interest in the context of inferring causal relations, such a theory is imperative for understanding recent suggestions that the causal order of events in quantum mechanics can be indefinite. Here, we develop such a theory in the general multipartite case. Starting from a background-independent definition of causality, we derive an iteratively formulated canonical decomposition of multipartite causal correlations. For a fixed number of settings and

  11. The three-species consortium of genetically improved strains Cupriavidus necator RW112, Burkholderia xenovorans RW118, and Pseudomonas pseudoalcaligenes RW120, grows with technical polychlorobiphenyl, Aroclor 1242

    Directory of Open Access Journals (Sweden)

    Regina-Michaela eWittich

    2013-04-01

    Full Text Available Burkholderia xenovorans LB400, Cupriavidus necator H850, and Pseudomonas pseudoalcaligenes KF707 are bacterial strains able to mineralize biphenyl and to co-oxidize many of its halogenated derivatives (PCBs. Only strain LB400 also mineralizes a few mono- and dichlorobiphenyls, due to the presence of a functioning chlorocatechol pathway. Here, we used a Tn5-based minitransposon shuttle system to chromosomically introduce genes tcbRCDEF, encoding the chlorocatechol pathway into KF707, and genes cbdABC encoding a 2-chlorobenzoate 1,2-dioxygenase into KF707 and LB400, as well as transposon Tn4653 from the TOL plasmid providing genes xylXYZL, encoding a broad-range toluate (methylbenzoate dioxygenase and its dihydrodiol dehydrogenase, to extend the range for the mineralization of halogenated benzoates in LB400 and in KF707. The engineered derivatives of LB400, and KF707 thus gained the ability for the mineralization of all isomeric monochloro- and bromobenzoates of the so-called lower pathway which, consequently, also allowed the mineralization of all monochlorobiphenyls and a number of di- and trichlorobiphenyls, thus preventing the accumulation of halobenzoates and of catabolites thereof. LB400 and KF707 also grow with the two commercial PCB formulations, Aroclor 1221 and Aroclor 1232, as the sole carbon and energy sources, but not with higher halogenated PCB mixtures, similar to the already published strain RW112. Repeated exposition of the modified LB400 to short pulses of UV light, over a prolonged period of time, allowed the isolation of a derivative of LB400, termed RW118, capable of growth with Aroclor 1016 still containing only traces of biphenyl, and in co-culture with modified KF707 termed RW120, and modified H850 (RW112 with Aroclor 1242, the commercial mixture already void of biphenyl and monochlorobiphenyls.

  12. Causal mapping

    DEFF Research Database (Denmark)

    Rasmussen, Lauge Baungaard

    2006-01-01

    The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method......The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method...

  13. Actin-Based Motility of Burkholderia thailandensis Requires a Central Acidic Domain of BimA That Recruits and Activates the Cellular Arp2/3 Complex▿

    OpenAIRE

    Sitthidet, Chayada; Stevens, Joanne M; Field, Terence R.; Layton, Abigail N.; Korbsrisate, Sunee; Stevens, Mark P.

    2010-01-01

    Burkholderia species use BimA for intracellular actin-based motility. Uniquely, Burkholderia thailandensis BimA harbors a central and acidic (CA) domain. The CA domain was required for actin-based motility, binding to the cellular Arp2/3 complex, and Arp2/3-dependent polymerization of actin monomers. Our data reveal distinct strategies for actin-based motility among Burkholderia species.

  14. Ubiquity of Putative Type III Secretion Genes among Clinical and Environmental Burkholderia pseudomallei Isolates in Northern Australia

    OpenAIRE

    Smith-Vaughan, H C; Gal, D; Lawrie, P. M.; Winstanley, C.; Sriprakash, K S; Currie, B. J.

    2003-01-01

    Horseradish peroxidase-like type III secretion (TTS1) genes were present in all 116 Northern Australian Burkholderia pseudomallei isolates tested but were not detected in other common environmental Burkholderia species. PCR of TTS1 genes may prove valuable as a diagnostic test.

  15. Exploring the HME and HAE1 efflux systems in the genus Burkholderia

    Directory of Open Access Journals (Sweden)

    Pasca Maria

    2010-06-01

    Full Text Available Abstract Background The genus Burkholderia includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem. In this context a major role could be played by multidrug efflux pumps belonging to Resistance Nodulation Cell-Division (RND family, which allow bacterial cells to extrude a wide range of different substrates, including antibiotics. This study aims to i identify rnd genes in the 21 available completely sequenced Burkholderia genomes, ii analyze their phylogenetic distribution, iii define the putative function(s that RND proteins perform within the Burkholderia genus and iv try tracing the evolutionary history of some of these genes in Burkholderia. Results BLAST analysis of the 21 Burkholderia sequenced genomes, using experimentally characterized ceoB sequence (one of the RND family counterpart in the genus Burkholderia as probe, allowed the assembly of a dataset comprising 254 putative RND proteins. An extensive phylogenetic analysis revealed the occurrence of several independent events of gene loss and duplication across the different lineages of the genus Burkholderia, leading to notable differences in the number of paralogs between different genomes. A putative substrate [antibiotics (HAE1 proteins/heavy-metal (HME proteins] was also assigned to the majority of these proteins. No correlation was found between the ecological niche and the lifestyle of Burkholderia strains and the number/type of efflux pumps they possessed, while a relation can be found with genome size and taxonomy. Remarkably, we observed that only HAE1 proteins are mainly responsible for the different number of proteins observed in strains of the same species. Data concerning both the distribution and the phylogenetic analysis of the HAE1 and HME in the Burkholderia genus allowed depicting a likely evolutionary model accounting for the evolution and spreading of HME and HAE

  16. Efflux Pump-mediated Drug Resistance in Burkholderia

    Directory of Open Access Journals (Sweden)

    Nicole L Podnecky

    2015-04-01

    Full Text Available Several members of the genus Burkholderia are prominent pathogens. Infections caused by these bacteria are difficult to treat because of significant antibiotic resistance. Virtually all Burkholderia species are also resistant to polymyxin, prohibiting use of drugs like colistin that are available for treatment of infections caused by most other drug resistant Gram-negative bacteria. Despite clinical significance and antibiotic resistance of Burkholderia species, characterization of efflux pumps lags behind other non-enteric Gram-negative pathogens such as Acinetobacter baumannii and Pseudomonas aeruginosa. Although efflux pumps have been described in several Burkholderia species, they have been best studied in B. cenocepacia and B. pseudomallei. As in other non-enteric Gram-negatives, efflux pumps of the resistance nodulation cell division (RND family are the clinically most significant efflux systems in these two species. Several efflux pumps were described in B. cenocepacia, which when expressed confer resistance to clinically significant antibiotics, including aminoglycosides, chloramphenicol, fluoroquinolones, and tetracyclines. Three RND pumps have been characterized in B. pseudomallei, two of which confer either intrinsic or acquired resistance to aminoglycosides, macrolides, chloramphenicol, fluoroquinolones, tetracyclines, trimethoprim, and in some instances trimethoprim+sulfamethoxazole. Several strains of the host-adapted B. mallei, a clone of B. pseudomallei, lack AmrAB-OprA and are therefore aminoglycoside and macrolide susceptible. B. thailandensis is closely related to B. pseudomallei, but non-pathogenic to humans. Its pump repertoire and ensuing drug resistance profile parallels that of B. pseudomallei. An efflux pump in B. vietnamiensis plays a significant role in acquired aminoglycoside resistance. Summarily, efflux pumps are significant players in Burkholderia drug resistance.

  17. Characterization and Inference of Gene Gain/Loss Along Burkholderia Evolutionary History

    OpenAIRE

    Bo Zhu; Shengli Zhou; Miaomiao Lou; Jun Zhu; Bin Li; Guanlin Xie; GuLei Jin; René De Mot

    2011-01-01

    A comparative analysis of 60 complete Burkholderia genomes was conducted to obtain insight in the evolutionary history behind the diversity and pathogenicity at species level. A concatenated multiprotein phyletic pattern and a dataset with Burkholderia clusters of orthologous genes (BuCOGs) were constructed. The extent of horizontal gene transfer (HGT) was assessed using a Markov based probabilistic method. A reconstruction of the gene gains and losses history shows that more than half of the...

  18. Burkholderia ferrariae sp. nov., a novel bacterium isolated from an iron ore in Brazil.

    OpenAIRE

    Valverde, A; Delvasto, P.; Peix, A.; Velázquez, E; Santa Regina, I.; Ballester, A.; Rodríguez-Barrueco, C.; García-Balboa, C.; Igual, José Mariano

    2006-01-01

    A Gram-negative, non-spore-forming bacterial strain with the ability to solubilize highly insoluble phosphatic minerals was isolated from a high-phosphorous iron ore from Minas Gerais State, Brazil. This strain, designated FeGl01(T), was subjected to a polyphasic; taxonomic investigation. Comparative 16S rRNA gene sequence analysis indicated that it formed a distinct phylogenetic lineage within the genus Burkholderia together with several other species of the genus, e.g. Burkholderia sacchari...

  19. Protective response to subunit vaccination against intranasal Burkholderia mallei and B. pseudomallei challenge

    OpenAIRE

    Whitlock, Gregory C.; Deeraksa, Arpaporn; Qazi, Omar; Judy, Barbara M.; Taylor, Katherine; Propst, Katie L.; Duffy, Angie J.; Johnson, Kate; Kitto, G. Barrie; Brown, Katherine A.; Dow, Steven W.; Torres, Alfredo G.; Estes, D. Mark

    2010-01-01

    Burkholderia mallei and B. pseudomallei are Gram-negative pathogenic bacteria, responsible for the diseases glanders and melioidosis, respectively. Furthermore, there is currently no vaccine available against these Burkholderia species. In this study, we aimed to identify protective proteins against these pathogens. Immunization with recombinant B. mallei Hcp1 (type VI secreted/structural protein), BimA (autotransporter protein), BopA (type III secreted protein), and B. pseudomallei LolC (ABC...

  20. Epidemiological causality.

    Science.gov (United States)

    Morabia, Alfredo

    2005-01-01

    Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.

  1. Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Jaing, C

    2012-03-27

    The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.

  2. Molecular mechanisms underlying the close association between soil Burkholderia and fungi.

    Science.gov (United States)

    Stopnisek, Nejc; Zühlke, Daniela; Carlier, Aurélien; Barberán, Albert; Fierer, Noah; Becher, Dörte; Riedel, Katharina; Eberl, Leo; Weisskopf, Laure

    2016-01-01

    Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils. PMID:25989372

  3. Causality Principle

    OpenAIRE

    Chi, Do Minh

    2001-01-01

    We advance a famous principle - causality principle - but under a new view. This principle is a principium automatically leading to most fundamental laws of the nature. It is the inner origin of variation, rules evolutionary processes of things, and the answer of the quest for ultimate theories of the Universe.

  4. Genetic and phenotypic diversity in Burkholderia: contributions by prophage and phage-like elements

    Directory of Open Access Journals (Sweden)

    Ulrich Ricky L

    2010-07-01

    Full Text Available Abstract Background Burkholderia species exhibit enormous phenotypic diversity, ranging from the nonpathogenic, soil- and water-inhabiting Burkholderia thailandensis to the virulent, host-adapted mammalian pathogen B. mallei. Genomic diversity is evident within Burkholderia species as well. Individual isolates of Burkholderia pseudomallei and B. thailandensis, for example, carry a variety of strain-specific genomic islands (GIs, including putative pathogenicity and metabolic islands, prophage-like islands, and prophages. These GIs may provide some strains with a competitive advantage in the environment and/or in the host relative to other strains. Results Here we present the results of analysis of 37 prophages, putative prophages, and prophage-like elements from six different Burkholderia species. Five of these were spontaneously induced to form bacteriophage particles from B. pseudomallei and B. thailandensis strains and were isolated and fully sequenced; 24 were computationally predicted in sequenced Burkholderia genomes; and eight are previously characterized prophages or prophage-like elements. The results reveal numerous differences in both genome structure and gene content among elements derived from different species as well as from strains within species, due in part to the incorporation of additional DNA, or 'morons' into the prophage genomes. Implications for pathogenicity are also discussed. Lastly, RNAseq analysis of gene expression showed that many of the genes in ϕ1026b that appear to contribute to phage and lysogen fitness were expressed independently of the phage structural and replication genes. Conclusions This study provides the first estimate of the relative contribution of prophages to the vast phenotypic diversity found among the Burkholderiae.

  5. The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

    OpenAIRE

    Winsor, Geoffrey L.; Khaira, Bhavjinder; Van Rossum, Thea; Lo, Raymond; Whiteside, Matthew D.; Fiona S.L. Brinkman

    2008-01-01

    Summary: As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in ...

  6. Developing Peptide Mimotopes of Capsular Polysaccharides and Lipopolysaccharides Protective Antigens of Pathogenic Burkholderia Bacteria.

    Science.gov (United States)

    Guo, Pengfei; Zhang, Jing; Tsai, Shien; Li, Bingjie; Lo, Shyh-Ching

    2016-06-01

    Burkholderia pseudomallei (BP) and Burkholderia mallei (BM) are two species of pathogenic Burkholderia bacteria. Our laboratory previously identified four monoclonal antibodies (MAbs) that reacted against Burkholderia capsular polysaccharides (PS) and lipopolysaccharides (LPS) and effectively protected against a lethal dose of BP/BM infections in mice. In this study, we used phage display panning against three different phage peptide libraries to select phage clones specifically recognized by each of the four protective MAbs. After sequencing a total of 179 candidate phage clones, we examined in detail six selected phage clones carrying different peptide inserts for the specificity of binding by the respective target MAbs. Chemically synthesized peptides corresponding to those displayed by the six phage clones were conjugated to keyhole limpet hemocyanin carrier protein and tested for their binding specificity to the respective protective MAbs. The study revealed that four of the six peptides, all derived from the library displaying dodecapeptides, functioned well as "mimotopes" of Burkholderia PS and LPS as demonstrated by a high degree of specific competition against the binding of three protective MAbs to BP and BM. Our results suggest that the four selected peptide mimics corresponding to PS/LPS protective antigens of BP and BM could potentially be developed into peptide vaccines against pathogenic Burkholderia bacteria. PMID:27328059

  7. Draft genome sequence of Burkholderia sordidicola S170, a potential plant growth promoter isolated from coniferous forest soil in the Czech Republic

    DEFF Research Database (Denmark)

    Lladó, Salvador; Xu, Zhuofei; Sørensen, Søren Johannes;

    2014-01-01

    Burkholderia species are key players in the accumulation of carbon from cellulose decomposition in coniferous forest ecosystems. We report here the draft genome of Burkholderia sordidicola strain S170, containing features associated with known genes involved in plant growth promotion, the biologi...

  8. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR.

    Directory of Open Access Journals (Sweden)

    Erin P Price

    Full Text Available Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc, a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown's medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown's agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown's-positive colonies that are not B. pseudomallei.

  9. Comparison of Ashdown's Medium, Burkholderia cepacia Medium, and Burkholderia pseudomallei Selective Agar for Clinical Isolation of Burkholderia pseudomallei

    OpenAIRE

    Peacock, Sharon J.; Chieng, Grace; Cheng, Allen C.; Dance, David A. B.; Amornchai, Premjit; Wongsuvan, Gumphol; Teerawattanasook, Nittaya; Chierakul, Wirongrong; Day, Nicholas P J; Wuthiekanun, Vanaporn

    2005-01-01

    Ashdown's medium, Burkholderia pseudomallei selective agar (BPSA), and a commercial Burkholderia cepacia medium were compared for their abilities to grow B. pseudomallei from 155 clinical specimens that proved positive for this organism. The sensitivity of each was equivalent; the selectivity of BPSA was lower than that of Ashdown's or B. cepacia medium.

  10. The art of persistence-the secrets to Burkholderia chronic infections.

    Science.gov (United States)

    Lewis, Eric R G; Torres, Alfredo G

    2016-08-01

    The Gram-negative proteobacteria genus Burkholderia encompasses multiple bacterial species that are pathogenic to humans and other vertebrates. Two pathogenic species of interest within this genus are Burkholderia pseudomallei (Bpm) and the B. cepacia complex (Bcc); the former is the causative agent of melioidosis in humans and other mammals, and the latter is associated with pneumonia in immunocompromised patients. One understudied and shared characteristic of these two pathogenic groups is their ability to persist and establish chronic infection within the host. In this review, we will explore the depth of knowledge about chronic infections caused by persistent Bpm and Bcc. We examine the host risk factors and immune responses associated with more severe chronic infections. We also discuss host adaptation and phenotypes associated with persistent Burkholderia species. Lastly, we survey how other intracellular bacteria associated with chronic infections are combatted and explore possible future applications to target Burkholderia Our goal is to highlight understudied areas that should be addressed for a more thorough understanding of chronic Burkholderia infections and how to combat them. PMID:27440810

  11. Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis.

    Science.gov (United States)

    Deng, Peng; Wang, Xiaoqiang; Baird, Sonya M; Showmaker, Kurt C; Smith, Leif; Peterson, Daniel G; Lu, Shien

    2016-06-01

    Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The antifungal agent occidiofungin produced by MS14 has great potential for development of biopesticides and pharmaceutical drugs. However, the use of Burkholderia species as biocontrol agent in agriculture is restricted due to the difficulties in distinguishing between plant growth-promoting bacteria and the pathogenic bacteria. The complete MS14 genome was sequenced and analyzed to find what beneficial and virulence-related genes it harbors. The phylogenetic relatedness of B. contaminans MS14 and other 17 Burkholderia species was also analyzed. To research MS14's potential virulence, the gene regions related to the antibiotic production, antibiotic resistance, and virulence were compared between MS14 and other Burkholderia genomes. The genome of B. contaminans MS14 was sequenced and annotated. The genomic analyses reveal the presence of multiple gene sets for antimicrobial biosynthesis, which contribute to its antimicrobial activities. BLAST results indicate that the MS14 genome harbors a large number of unique regions. MS14 is closely related to another plant growth-promoting Burkholderia strain B. lata 383 according to the average nucleotide identity data. Moreover, according to the phylogenetic analysis, plant growth-promoting species isolated from soils and mammalian pathogenic species are clustered together, respectively. MS14 has multiple antimicrobial activity-related genes identified from the genome, but it lacks key virulence-related gene loci found in the pathogenic strains. Additionally, plant growth-promoting Burkholderia species have one or more antimicrobial biosynthesis genes in their genomes as compared with nonplant growth-promoting soil-isolated Burkholderia species. On the other hand, pathogenic species harbor multiple virulence-associated gene loci that are not present in nonpathogenic Burkholderia species. The MS14

  12. Characterization of integrons in Burkholderia cepacia clinical isolates

    Directory of Open Access Journals (Sweden)

    Linda Furlanis

    2010-03-01

    Full Text Available Burkholderia cepacia is an opportunistic pathogen able to colonize the airways of Cystic Fibrosis (CF patients, frequently developing chronic infections. In 20% of cases these infections cause severe and poorly controlled pathological situations because of the intrinsic antibiotic resistance expressed by the microorganism. CF patients are often subjected to antibiotic therapy: this facilitates the acquisition of antibiotic resistance determinants by the infecting bacteria. Integrons are mobile genetic elements that are widespread in bacterial populations and favor the acquisition of gene cassettes coding for these determinants.The presence of class 1 integrons was investigated by PCR with primers specific for the 5’ and 3’ ends in Burkholderia isolates recovered from patients in treatment at the CF center of Friuli Venezia Giulia. The same integron, carrying an uncommon allelic form (Ib of the aacA4 gene in its cassette array and conferring resistance to some aminoglycosides, was found in two independent isolates (different RAPD profiles infecting two different patients. In both isolates the integron was carried by plasmids and was still present 3 and 6 years later the first finding. Despite the exchange of integrons between bacterial pathogens is fully described, these items were not frequently found in Burkholderia isolates. Although the clinical relevance of the integron we identified is low (a single gene cassette encoding a widespread resistance,we feel concerned that these genetic elements begin to circulate in this bacterial species, as this could make more and more troublesome the treatment of infections notoriously difficult to eradicate.

  13. Phylogenetically Diverse Burkholderia Associated with Midgut Crypts of Spurge Bugs, Dicranocephalus spp. (Heteroptera: Stenocephalidae).

    Science.gov (United States)

    Kuechler, Stefan Martin; Matsuura, Yu; Dettner, Konrad; Kikuchi, Yoshitomo

    2016-06-25

    Diverse phytophagous heteropteran insects, commonly known as stinkbugs, are associated with specific gut symbiotic bacteria, which have been found in midgut cryptic spaces. Recent studies have revealed that members of the stinkbug families Coreidae and Alydidae of the superfamily Coreoidea are consistently associated with a specific group of the betaproteobacterial genus Burkholderia, called the "stinkbug-associated beneficial and environmental (SBE)" group, and horizontally acquire specific symbionts from the environment every generation. However, the symbiotic system of another coreoid family, Stenocephalidae remains undetermined. We herein investigated four species of the stenocephalid genus Dicranocephalus. Examinations via fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) revealed the typical arrangement and ultrastructures of midgut crypts and gut symbionts. Cloning and molecular phylogenetic analyses of bacterial genes showed that the midgut crypts of all species are colonized by Burkholderia strains, which were further assigned to different subgroups of the genus Burkholderia. In addition to the SBE-group Burkholderia, a number of stenocephalid symbionts belonged to a novel clade containing B. sordidicola and B. udeis, suggesting a specific symbiont clade for the Stenocephalidae. The symbiotic systems of stenocephalid bugs may provide a unique opportunity to study the ongoing evolution of symbiont associations in the stinkbug-Burkholderia interaction. PMID:27265344

  14. Isolation and Identification of Burkholderia glumae from Symptomless Rice Seeds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A survey on isolation and detection of the casual organism of bacterial grain rot of rice was conducted during 1997-2006.In 2006,six pathogenic bacterial strains were isolated from two symptomiess seed samples of rice (Oryza sativa L.) originally produced in Hainan Province and then planted in Zhejiang Province,China.They were identified as Burkholderia glumae which is the causal organism of bacterial grain rot of rice by physiological characteristics,colony morphology,pathogenicity test,Biolog,fatty acid methyl ester (FAME) analysis and RAPD-PCR compared with the four standard reference strains.It is confirmed that there is the infection of B.glumae in so-called 'health looking seeds'.

  15. In Vitro Susceptibilities of Burkholderia mallei in Comparison to Those of Other Pathogenic Burkholderia spp.

    OpenAIRE

    Kenny, D J; Russell, P; Rogers, D.; Eley, S M; Titball, R W

    1999-01-01

    The in vitro antimicrobial susceptibilities of isolates of Burkholderia mallei to 16 antibiotics were assessed and compared with the susceptibilities of Burkholderia pseudomallei and Burkholderia cepacia. The antibiotic susceptibility profile of B. mallei resembled that of B. pseudomallei more closely than that of B. cepacia, which corresponds to their similarities in terms of biochemistry, antigenicity, and pathogenicity. Ceftazidime, imipenem, doxycycline, and ciprofloxacin were active agai...

  16. Hymenoscyphus fraxineus vs. Hymenoscyphus albidus – A comparative light microscopic study on the causal agent of European ash dieback and related foliicolous, stroma-forming species

    Science.gov (United States)

    Baral, Hans-Otto; Bemmann, Martin

    2014-01-01

    Five species of Hymenoscyphus that fruit on black stromatized parts of dead leaves of deciduous trees are presented, giving details on their morphological and ecological characteristics. Several of these species have previously been misplaced in rutstroemiaceous genera because of the presence of a substratal stroma. However, the heteropolar, scutuloid ascospores with an often hook-like lateral protrusion at the rounded apex and the ascus apical ring of the Hymenoscyphus-type represent two reliable morphological characteristics that, together with molecular data, provide clear evidence for their placement in the genus Hymenoscyphus (Helotiaceae). Among the species treated is Hymenoscyphus fraxineus (=Hymenoscyphus pseudoalbidus), the causal agent of the European ash dieback disease. Since 1992 this species started within Europe to replace the rather uncommon Hymenoscyphus albidus, which is likewise confined to leaves of Fraxinus. Hy. fraxineus has been recorded already since 1990 in Eastern Asia (Japan, Korea, northeast of China), where it had been initially misidentified as Lambertella albida (≡Hy. albidus). In these regions, it occurs as a harmless saprotroph on Fraxinus mandshurica and Fraxinus rhynchophylla, suggesting that those populations are native while the European ash dieback disease has a recent Eastern Asiatic origin. The distinctly higher genetic diversity found in Japanese Hy. fraxineus in contrast to European Hy. fraxineus supports this view. Genetic similarities between Japanese Hy. fraxineus and European Hy. albidus suggest that also Hy. albidus might be a descendant of Asian Hy. fraxineus, though having invaded Europe much earlier. However, consistent genetic deviation between European and Asian Hy. fraxineus at two nucleotide positions of the ITS region indicates that the European ash disease originates from a region different from the presently known areas in Eastern Asia. Our results underline the importance of detailed morphological studies

  17. PPO zoekt naar mogelijkheden aanpak Burkholderia

    OpenAIRE

    Dwarswaard, A.; Van Dam

    2014-01-01

    In de bloemen- en knollenteelt van gladiool komt de afgelopen decennia met enige regelmaat de bacterieziekte Burkholderia voor. Vorig jaar startte PPO met een onderzoek naar de mogelijkheden om deze ziekte aan te pakken. Een tussenstand.

  18. An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

    Energy Technology Data Exchange (ETDEWEB)

    Davies, Douglas R.; Staker, Bart L.; Abendroth, Jan A.; Edwards, Thomas E.; Hartley, Robert; Leonard, Jess; Kim, Hidong; Rychel, Amanda L.; Hewitt, Stephen N.; Myler, Peter J.; Stewart, Lance J. (UWASH); (Emerald)

    2011-12-07

    Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.

  19. Role for the Burkholderia pseudomallei Type Three Secretion System Cluster 1 bpscN Gene in Virulence ▿

    OpenAIRE

    D'Cruze, Tanya; Gong, Lan; Treerat, Puthayalai; Ramm, Georg; John D Boyce; Prescott, Mark; Adler, Ben; Rodney J. Devenish

    2011-01-01

    Burkholderia pseudomallei, the causal agent of melioidosis, employs a number of virulence factors during its infection of mammalian cells. One such factor is the type three secretion system (TTSS), which is proposed to mediate the transport and secretion of bacterial effector molecules directly into host cells. The B. pseudomallei genome contains three TTSS gene clusters (designated TTSS1, TTSS2, and TTSS3). Previous research has indicated that neither TTSS1 nor TTSS2 is involved in B. pseudo...

  20. Molecular Procedure for Rapid Detection of Burkholderia mallei and Burkholderia pseudomallei

    OpenAIRE

    Bauernfeind, Adolf; Roller, Carsten; Meyer, Detlef; Jungwirth, Renate; Schneider, Ines

    1998-01-01

    A PCR procedure for the discrimination of Burkholderia mallei and Burkholderia pseudomallei was developed. It is based on the nucleotide difference T 2143 C (T versus C at position 2143) between B. mallei and B. pseudomallei detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel.

  1. Revised structures for the predominant O-polysaccharides expressed by Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    Heiss, Christian; Burtnick, Mary N.; Roberts, Rosemary A.; Black, Ian; Azadi, Parastoo; Brett, Paul J.

    2013-01-01

    O-Polysaccharides (OPS) were isolated from purified Burkholderia pseudomallei and Burkholderia mallei lipopolysaccharides by mild-acid hydrolysis and gel-permeation chromatography. 1-D and 2-D 1H and 13C NMR spectroscopy experiments revealed that the OPS antigens were unbranched heteropolymers with the following structures:

  2. Prevalence of Burkholderia pseudomallei in Guangxi, China.

    Science.gov (United States)

    Ma, G; Zheng, D; Cai, Q; Yuan, Z

    2010-01-01

    Melioidosis, an infectious disease caused by the Gram-negative bacterium Burkholderia pseudomallei, is now recognized as an important public health problem in Southeast Asia and tropical northern Australia. Although B. pseudomallei has been detected in various water and soil samples in southeast China, the enviromental distribution of B. pseudomallei in China is unclear. In the winter months of 2007, 154 and 130 soil and water samples, respectively, were collected from several locations in Guangxi, China. The samples were screened for B. pseudomallei by bacterial culture and identification and confirmed by PCR for species-specific 16S rDNA and flagellin genes. B. pseudomallei was detected in 8.4% of the soil samples but in none of the water samples. All positive samples were confined to a single low-lying region from rice paddy fields. Counts of B. pseudomallei ranged from 23 to 521 c.f.u./g soil. This is the first geographical distribution survey of B. pseudomallei in soil in Guangxi, China, and the data are of importance for further evaluating the impact of this pathogen on melioidosis in this region. PMID:19538822

  3. Strategies for Intracellular Survival of Burkholderia pseudomallei.

    Science.gov (United States)

    Allwood, Elizabeth M; Devenish, Rodney J; Prescott, Mark; Adler, Ben; Boyce, John D

    2011-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, a disease with high mortality that is prevalent in tropical regions of the world. A key component of the pathogenesis of melioidosis is the ability of B. pseudomallei to enter, survive, and replicate within mammalian host cells. For non-phagocytic cells, bacterial adhesins have been identified both on the bacterial surface and associated with Type 4 pili. Cell invasion involves components of one or more of the three Type 3 Secretion System clusters, which also mediate, at least in part, the escape of bacteria from the endosome into the cytoplasm, where bacteria move by actin-based motility. The mechanism of actin-based motility is not clearly understood, but appears to differ from characterized mechanisms in other bacterial species. A small proportion of intracellular bacteria is targeted by host cell autophagy, involving direct recruitment of LC3 to endosomes rather than through uptake by canonical autophagosomes. However, the majority of bacterial cells are able to circumvent autophagy and other intracellular defense mechanisms such as the induction of inducible nitric oxide synthase, and then replicate in the cytoplasm and spread to adjacent cells via membrane fusion, resulting in the formation of multi-nucleated giant cells. A potential role for host cell ubiquitin in the autophagic response to bacterial infection has recently been proposed. PMID:22007185

  4. Novel Selective Medium for Isolation of Burkholderia pseudomallei

    OpenAIRE

    Howard, K; Inglis, T. J. J.

    2003-01-01

    Isolation of Burkholderia pseudomallei currently relies on the use of Ashdown's selective agar (ASA). We designed a new selective agar (Burkholderia pseudomallei selective agar [BPSA]) to improve recovery of the more easily inhibited strains of B. pseudomallei. B. pseudomallei, Burkholderia cepacia, and Pseudomonas aeruginosa were used to determine the selectivity and sensitivity of BPSA. BPSA was more inhibitory to P. aeruginosa and B. cepacia and should make recognition of Burkholderia spec...

  5. 40 CFR 725.1075 - Burkholderia cepacia complex.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Burkholderia cepacia complex. 725.1075... Specific Microorganisms § 725.1075 Burkholderia cepacia complex. (a) Microorganism and significant new uses subject to reporting. (1) The microorganisms identified as the Burkholderia cepacia complex defined...

  6. Causal reasoning in physics

    CERN Document Server

    Frisch, Mathias

    2014-01-01

    Much has been written on the role of causal notions and causal reasoning in the so-called 'special sciences' and in common sense. But does causal reasoning also play a role in physics? Mathias Frisch argues that, contrary to what influential philosophical arguments purport to show, the answer is yes. Time-asymmetric causal structures are as integral a part of the representational toolkit of physics as a theory's dynamical equations. Frisch develops his argument partly through a critique of anti-causal arguments and partly through a detailed examination of actual examples of causal notions in physics, including causal principles invoked in linear response theory and in representations of radiation phenomena. Offering a new perspective on the nature of scientific theories and causal reasoning, this book will be of interest to professional philosophers, graduate students, and anyone interested in the role of causal thinking in science.

  7. Single amino acid substitution in homogentisate 1,2-dioxygenase is responsible for pigmentation in a subset of Burkholderia cepacia complex isolates

    OpenAIRE

    Gonyar, Laura A.; Fankhauser, Sarah C.; Joanna B Goldberg

    2014-01-01

    The Burkholderia cepacia complex (Bcc) is a group of Gram-negative bacilli that are ubiquitous in the environment and have emerged over the past 30 years as opportunistic pathogens in immunocompromised populations, specifically individuals with cystic fibrosis (CF) and chronic granulomatous disease. This complex of at least 18 distinct species is phenotypically and genetically diverse. One phenotype observed in a subset of Burkholderia cenocepacia (a prominent Bcc pathogen) isolates is the ab...

  8. Burkholderia novacaledonica sp. nov. and B. ultramafica sp. nov. isolated from roots of Costularia spp. pioneer plants of ultramafic soils in New Caledonia.

    Science.gov (United States)

    Guentas, Linda; Gensous, Simon; Cavaloc, Yvon; Ducousso, Marc; Amir, Hamid; De Georges de Ledenon, Benjamin; Moulin, Lionel; Jourand, Philippe

    2016-05-01

    The taxonomic status of eleven rhizospheric bacterial strains belonging to the genus Burkholderia and isolated from roots of Costularia (Cyperaceae), tropical herbaceous pioneer plants growing on ultramafic soils in New Caledonia, was investigated using a polyphasic taxonomic approach. The genetic analyses (16S rRNA genes, gyrB, recA, nreB and cnr) confirmed that all strains are Burkholderia and cluster into two separated groups. The DNA hybridization results showed low relatedness values to the closest relatives Burkholderia species. The phenotypic analyses confirmed that the two groups of strains could be differentiated from each other and from other known Burkholderia species. This polyphasic study revealed that these two groups of strains represent each a novel species of Burkholderia, for which the names Burkholderia novacaledonica sp. nov. (type strain STM10272(T)=LMG28615(T)=CIP110887(T)) and B. ultramafica sp. nov. (type strain STM10279(T)=LMG28614(T)=CIP110886(T)) are proposed, respectively. These strains of Burkholderia presented specific ecological traits such as the tolerance to the extreme edaphic constraints of ultramafic soils: they grew at pH between 4 and 8 and tolerate the strong unbalanced Ca/Mg ratio (1/19) and the high concentrations of heavy metals i.e. Co, Cr, Mn and Ni. Noteworthy B. ultramafica tolerated nickel until 10mM and B. novacaledonica up to 5mM. The presence of the nickel (nreB) and cobalt/nickel (cnr) resistance determinants encoding for protein involved in metal tolerance was found in all strains of both groups. Moreover, most of the strains were able to produce plant growth promoting molecules (ACC, IAA, NH3 and siderophores). Such ecological traits suggest that these new species of Burkholderia might be environmentally adaptable plant-associated bacteria and beneficial to plants. PMID:27049869

  9. Comparative genome‐wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis

    OpenAIRE

    Deng, Peng; Wang, Xiaoqiang; Baird, Sonya M.; Showmaker, Kurt C.; Smith, Leif; Peterson, Daniel G.; Lu, Shien

    2016-01-01

    Abstract Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The antifungal agent occidiofungin produced by MS14 has great potential for development of biopesticides and pharmaceutical drugs. However, the use of Burkholderia species as biocontrol agent in agriculture is restricted due to the difficulties in distinguishing between plant growth‐promoting bacteria and the pathogenic bacteria. The complete MS14 genome wa...

  10. Autotransporters and Their Role in the Virulence of Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    Adler, Natalie R. Lazar; Stevens, Joanne M; Stevens, Mark P.; Galyov, Edouard E.

    2011-01-01

    Burkholderia pseudomallei and Burkholderia mallei are closely related Gram-negative bacteria responsible for the infectious diseases melioidosis and glanders, respectively. Autotransporters (ATs) comprise a large and diverse family of secreted and outer membrane proteins that includes virulence-associated invasins, adhesins, proteases, and actin-nucleating factors. The B. pseudomallei K96243 genome contains 11 predicted ATs, eight of which share homologs in the B. mallei ATCC 23344 genome. Th...

  11. In Vitro Activity of Tigecycline against Burkholderia pseudomallei and Burkholderia thailandensis

    OpenAIRE

    Thamlikitkul, Visanu; Trakulsomboon, Suwanna

    2006-01-01

    Investigation of the in vitro activity of tigecycline against Burkholderia pseudomallei and Burkholderia thailandensis revealed that the inhibition zone diameters of tigecycline against all isolates were ≥20 mm and that the MIC50 values were 0.5 and 1 μg/ml and the MIC90 values were 2 and 1.5 μg/ml for B. pseudomallei and B. thailandensis, respectively.

  12. Autotransporters and their role in the virulence of Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    Lazar Adler, N.; Stevens, J; STEVENS, M.; Galyov, E

    2011-01-01

    Burkholderia pseudomallei and Burkholderia mallei are closely related Gram-negative bacteria responsible for the infectious diseases melioidosis and glanders, respectively. Autotransporters (ATs) comprise a large and diverse family of secreted and outer membrane proteins that includes virulence-associated invasins, adhesins, proteases and actin-nucleating factors. The B. pseudomallei K96243 genome contains eleven predicted ATs, eight of which share homologues in the B. mallei ATCC 23344 genom...

  13. The Equation of Causality

    OpenAIRE

    Chi, Do Minh

    1999-01-01

    We research the natural causality of the Universe. We find that the equation of causality provides very good results on physics. That is our first endeavour and success in describing a quantitative expression of the law of causality. Hence, our theoretical point suggests ideas to build other laws including the law of the Universe's evolution.

  14. GENOME ANALYSIS OF BURKHOLDERIA CEPACIA AC1100

    Science.gov (United States)

    Burkholderia cepacia is an important organism in bioremediation of environmental pollutants and it is also of increasing interest as a human pathogen. The genomic organization of B. cepacia is being studied in order to better understand its unusual adaptive capacity and genome pl...

  15. Natural Burkholderia mallei infection in Dromedary, Bahrain.

    Science.gov (United States)

    Wernery, Ulrich; Wernery, Renate; Joseph, Marina; Al-Salloom, Fajer; Johnson, Bobby; Kinne, Joerg; Jose, Shanti; Jose, Sherry; Tappendorf, Britta; Hornstra, Heidie; Scholz, Holger C

    2011-07-01

    We confirm a natural infection of dromedaries with glanders. Multilocus variable number tandem repeat analysis of a Burkholderia mallei strain isolated from a diseased dromedary in Bahrain revealed close genetic proximity to strain Dubai 7, which caused an outbreak of glanders in horses in the United Arab Emirates in 2004.

  16. Burkholderia pseudomallei Antibodies in Children, Cambodia

    OpenAIRE

    Wuthiekanun, Vanaporn; Pheaktra, Ngoun; Putchhat, Hor; Sin, Lina; Sen, Bun; Kumar, Varun; Langla, Sayan; Peacock, Sharon J.; Nicholas P. Day

    2008-01-01

    Antibodies to Burkholderia pseudomallei were detected in 16% of children in Siem Reap, Cambodia. This organism was isolated from 30% of rice paddies in the surrounding vicinity. Despite the lack of reported indigenous cases, melioidosis is likely to occur in Cambodia.

  17. Use of a Real-Time PCR TaqMan Assay for Rapid Identification and Differentiation of Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    U'Ren, Jana M.; Matthew N. Van Ert; James M Schupp; Easterday, W. Ryan; Simonson, Tatum S.; Okinaka, Richard T; Pearson, Talima; Keim, Paul

    2005-01-01

    A TaqMan allelic-discrimination assay designed around a synonymous single-nucleotide polymorphism was used to genotype Burkholderia pseudomallei and Burkholderia mallei isolates. The assay rapidly identifies and discriminates between these two highly pathogenic bacteria and does not cross-react with genetic near neighbors, such as Burkholderia thailandensis and Burkholderia cepacia.

  18. Recombinant Salmonella Expressing Burkholderia mallei LPS O Antigen Provides Protection in a Murine Model of Melioidosis and Glanders.

    Directory of Open Access Journals (Sweden)

    Dina A Moustafa

    Full Text Available Burkholderia pseudomallei and Burkholderia mallei are the etiologic agents of melioidosis and glanders, respectively. These bacteria are highly infectious via the respiratory route and can cause severe and often fatal diseases in humans and animals. Both species are considered potential agents of biological warfare; they are classified as category B priority pathogens. Currently there are no human or veterinary vaccines available against these pathogens. Consequently efforts are directed towards the development of an efficacious and safe vaccine. Lipopolysaccharide (LPS is an immunodominant antigen and potent stimulator of host immune responses. B. mallei express LPS that is structurally similar to that expressed by B. pseudomallei, suggesting the possibility of constructing a single protective vaccine against melioidosis and glanders. Previous studies of others have shown that antibodies against B. mallei or B. pseudomallei LPS partially protect mice against subsequent lethal virulent Burkholderia challenge. In this study, we evaluated the protective efficacy of recombinant Salmonella enterica serovar Typhimurium SL3261 expressing B. mallei O antigen against lethal intranasal infection with Burkholderia thailandensis, a surrogate for biothreat Burkholderia spp. in a murine model that mimics melioidosis and glanders. All vaccine-immunized mice developed a specific antibody response to B. mallei and B. pseudomallei O antigen and to B. thailandensis and were significantly protected against challenge with a lethal dose of B. thailandensis. These results suggest that live-attenuated SL3261 expressing B. mallei O antigen is a promising platform for developing a safe and effective vaccine.

  19. Recombinant Salmonella Expressing Burkholderia mallei LPS O Antigen Provides Protection in a Murine Model of Melioidosis and Glanders.

    Science.gov (United States)

    Moustafa, Dina A; Scarff, Jennifer M; Garcia, Preston P; Cassidy, Sara K B; DiGiandomenico, Antonio; Waag, David M; Inzana, Thomas J; Goldberg, Joanna B

    2015-01-01

    Burkholderia pseudomallei and Burkholderia mallei are the etiologic agents of melioidosis and glanders, respectively. These bacteria are highly infectious via the respiratory route and can cause severe and often fatal diseases in humans and animals. Both species are considered potential agents of biological warfare; they are classified as category B priority pathogens. Currently there are no human or veterinary vaccines available against these pathogens. Consequently efforts are directed towards the development of an efficacious and safe vaccine. Lipopolysaccharide (LPS) is an immunodominant antigen and potent stimulator of host immune responses. B. mallei express LPS that is structurally similar to that expressed by B. pseudomallei, suggesting the possibility of constructing a single protective vaccine against melioidosis and glanders. Previous studies of others have shown that antibodies against B. mallei or B. pseudomallei LPS partially protect mice against subsequent lethal virulent Burkholderia challenge. In this study, we evaluated the protective efficacy of recombinant Salmonella enterica serovar Typhimurium SL3261 expressing B. mallei O antigen against lethal intranasal infection with Burkholderia thailandensis, a surrogate for biothreat Burkholderia spp. in a murine model that mimics melioidosis and glanders. All vaccine-immunized mice developed a specific antibody response to B. mallei and B. pseudomallei O antigen and to B. thailandensis and were significantly protected against challenge with a lethal dose of B. thailandensis. These results suggest that live-attenuated SL3261 expressing B. mallei O antigen is a promising platform for developing a safe and effective vaccine.

  20. Sero-characterization of lipopolysaccharide from Burkholderia thailandensis

    OpenAIRE

    Qazi, Omar; Prior, Joann L.; Judy, Barbara M; Whitlock, Gregory C.; Kitto, G. Barrie; Torres, Alfredo G.; Estes, D. Mark; Brown, Katherine A

    2008-01-01

    We report the successful purification of lipopolysaccharide (LPS) from Burkholderia thailandesis, a Gram-negative bacterium, closely related to the highly pathogenic organisms Burkholderia pseudomallei and Burkholderia mallei. B. thailandensis LPS is shown to cross-react with rabbit and mouse sera obtained from inoculation with B. pseudomallei or B. mallei, respectively. These data suggest that B. thailandensis LPS shares similar structural features with LPS molecules from highly pathogenic B...

  1. Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex

    OpenAIRE

    Bartholdson, S. Josefin; Brown, Alan R.; Mewburn, Ben R.; Clarke, David J.; Fry, Stephen C; Campopiano, Dominic J.; Govan, John R. W.

    2008-01-01

    The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysa...

  2. Times and Causality

    OpenAIRE

    Davidson, Russell

    2013-01-01

    The understanding of causal chains and mechanisms is an essential part of any scientific activity that aims at better explanation of its subject matter, and better understanding of it. While any account of causality requires that a cause should precede its effect, accounts of causality inphysics are complicated by the fact that the role of time in current theoretical physics has evolved very substantially throughout the twentieth century. In this article, I review the status of time and causa...

  3. How to be causal

    CERN Document Server

    Kinsler, Paul

    2011-01-01

    I explain a simple definition of causality in widespread use, and indicate how it links to the Kramers Kronig relations. The specification of causality in terms of temporal differential eqations then shows us the way to write down dynamical models so that their causal nature in the sense used here should be obvious to all. In particular, I apply this reasoning to Maxwell's equations, which is an instructive example since their casual properties are sometimes debated.

  4. Combining functional and structural genomics to sample the essential Burkholderia structome.

    Directory of Open Access Journals (Sweden)

    Loren Baugh

    Full Text Available The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq. We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail.This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against

  5. Development of Burkholderia mallei and pseudomallei vaccines

    Directory of Open Access Journals (Sweden)

    Ediane Batista Silva

    2013-03-01

    Full Text Available B. mallei and B. pseudomallei are Gram-negative bacteria that cause glanders and melioidosis, respectively. Inhalational infection with either organism can result in severe and rapidly fatal pneumonia. Inoculation by the oral and cutaneous routes can also produce infection. chronic infection develops after recovery from acute infection with both agents, and control of infection with antibiotics requires prolonged treatment. Symptoms for both meliodosis and glanders are non-specific, making diagnosis difficult.B. pseudomallei can be located in the environment, but in the host, B. mallei and B. psedomallei are intracellular organisms. Thefection results in similar immune responses to both agents. Effective early innate immune responses are critical to controlling the early phase of the infection. Innate immune signaling molecules such as TLR, NOD, MyD88 and pro-inflammatory cytokines such as IFN- and TNF-α play key roles in regulating control of infection. Neutrophils and monocytes are critical cells in the early infection for these microorganisms. Both monocytes and macrophages are necessary for limiting dissemination of B. pseudomallei. In contrast, the role of adaptive immune responses in controlling Burkholderia infection is less well understood. However, T cell responses are critical for vaccine protection from Burkholderia infection. At present, effective vaccines for prevention of glanders or meliodosis have not been developed, although recently progress of Burkholderia vaccines has received renewed attention.This review will summarize current and past approaches to develop Burkholderia mallei and pseudomalllei vaccines, with emphasis on immune mechanisms of protection and the challenges facing the field. At present, immunization with live attenuated bacteria provides the most effective and durable immunity, and it is important therefore to understand the immune correlates of protection induced by live attenuated vaccines.

  6. Survival of Burkholderia pseudomallei on Environmental Surfaces.

    Science.gov (United States)

    Shams, Alicia M; Rose, Laura J; Hodges, Lisa; Arduino, Matthew J

    2007-12-01

    The survival of the biothreat agent Burkholderia pseudomallei on the surfaces of four materials was measured by culture and esterase activity analyses. The culture results demonstrated that this organism persisted for <24 h to <7 days depending on the material, bacterial isolate, and suspension medium. The persistence determined by analysis of esterase activity, as measured with a ScanRDI solid-phase cytometer, was always longer than the persistence determined by culture analysis.

  7. Causality in Classical Electrodynamics

    Science.gov (United States)

    Savage, Craig

    2012-01-01

    Causality in electrodynamics is a subject of some confusion, especially regarding the application of Faraday's law and the Ampere-Maxwell law. This has led to the suggestion that we should not teach students that electric and magnetic fields can cause each other, but rather focus on charges and currents as the causal agents. In this paper I argue…

  8. Burkholderia mallei and Burkholderia pseudomallei: the causative micro-organisms of glanders and melioidosis.

    Science.gov (United States)

    Gilad, Jacob

    2007-11-01

    Burkholderia mallei and Burkholderia pseudomallei are the causative micro-organisms of Glanders and Melioidosis, respectively. Although now rare in Western countries, both micro-organisms have recently gained much interest because of their unique potential as bioterrorism agents. This paper reviews the epidemiology, pathogenesis, diagnosis and treatment of Melioidosis and Glanders. Recent patents relating to these micro-organisms, especially potential vaccines, are presented. Continued research and development is urgently needed, especially in regard to rapid and accurate diagnosis of melioidosis and glanders, efficacious therapy and primary and secondary prevention.

  9. Causality and Composite Structure

    CERN Document Server

    Joglekar, Satish D

    2007-01-01

    We study the question of whether a composite structure of elementary particles, with a length scale $1/\\Lambda$, can leave observable effects of non-locality and causality violation at higher energies (but $\\lesssim \\Lambda$). We formulate a model-independent approach based on Bogoliubov-Shirkov formulation of causality. We analyze the relation between the fundamental theory (of finer constituents) and the derived theory (of composite particles). We assume that the fundamental theory is causal and formulate a condition which must be fulfilled for the derived theory to be causal. We analyze the condition and exhibit possibilities which fulfil and which violate the condition. We make comments on how causality violating amplitudes can arise.

  10. Causality in demand

    DEFF Research Database (Denmark)

    Nielsen, Max; Jensen, Frank; Setälä, Jari;

    2011-01-01

    to fish demand. On the German market for farmed trout and substitutes, it is found that supply sources, i.e. aquaculture and fishery, are not the only determinant of causality. Storing, tightness of management and aggregation level of integrated markets might also be important. The methodological......This article focuses on causality in demand. A methodology where causality is imposed and tested within an empirical co-integrated demand model, not prespecified, is suggested. The methodology allows different causality of different products within the same demand system. The methodology is applied...... implication is that more explicit focus on causality in demand analyses provides improved information. The results suggest that frozen trout forms part of a large European whitefish market, where prices of fresh trout are formed on a relatively separate market. Redfish is a substitute on both markets. The...

  11. Causality in Europeanization Research

    DEFF Research Database (Denmark)

    Lynggaard, Kennet

    2012-01-01

    Discourse analysis as a methodology is perhaps not readily associated with substantive causality claims. At the same time the study of discourses is very much the study of conceptions of causal relations among a set, or sets, of agents. Within Europeanization research we have seen endeavours...... to develop discursive institutional analytical frameworks and something that comes close to the formulation of hypothesis on the effects of European Union (EU) policies and institutions on domestic change. Even if these efforts so far do not necessarily amount to substantive theories or claims of causality......, it suggests that discourse analysis and the study of causality are by no means opposites. The study of Europeanization discourses may even be seen as an essential step in the move towards claims of causality in Europeanization research. This chapter deals with the question of how we may move from the study...

  12. Agency, time and causality

    Directory of Open Access Journals (Sweden)

    Thomas eWidlok

    2014-11-01

    Full Text Available Cognitive Scientists interested in causal cognition increasingly search for evidence from non-WEIRD people but find only very few cross-cultural studies that specifically target causal cognition. This article suggests how information about causality can be retrieved from ethnographic monographs, specifically from ethnographies that discuss agency and concepts of time. Many apparent cultural differences with regard to causal cognition dissolve when cultural extensions of agency and personhood to non-humans are taken into account. At the same time considerable variability remains when we include notions of time, linearity and sequence. The article focuses on ethnographic case studies from Africa but provides a more general perspective on the role of ethnography in research on the diversity and universality of causal cognition.

  13. Properties of Polyhydroxyalkanoate Granules and Bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates Growing on Glucose.

    Science.gov (United States)

    Sacco, Laís Postai; Castellane, Tereza Cristina Luque; Lopes, Erica Mendes; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

    2016-03-01

    A Burkholderia and Pseudomonas species designated as AB4 and AS1, respectively, were isolated from soil containing decomposing straw or sugar cane bagasse collected from Brazil. This study sought to evaluate the capacities of culture media, cell-free medium, and crude lysate preparations (containing PHB inclusion bodies) from bacterial cell cultures to stabilize emulsions with several hydrophobic compounds. Four conditions showed good production of bioemulsifiers (E24 ≥ 50 %), headed by substantially cell-free media from bacterial cell cultures in which bacterial isolates from Burkholderia sp. strain AB4 and Pseudomonas sp. strain AS1 were grown. Our results revealed that the both isolates (AB4 and AS1 strains) exhibited high emulsification indices (indicating usefulness in bioremediation) and good stabilities. PMID:26578147

  14. Study of class I integron in a Burkholderia cepacia complex strain isolated from blood colture

    Directory of Open Access Journals (Sweden)

    Linda Furlanis

    2011-06-01

    Full Text Available The Burkholderia cepacia complex (Bcc consists of several species that cause lung infections in patients with cystic fibrosis but are also capable to colonize immunocompromised patients. Once established, the infection is usually difficult to eradicate, as Bcc is intrinsically resistant to many antibiotics. Besides, the acquisition of additional resistance determinants by horizontal gene transfer makes very difficult the therapeutic approach to these infections. Among horizontally acquired DNAs, integrons have been frequently reported in many Gramnegative bacteria that affect human health, but they have not been found frequently in Burkholderia isolates until now. In the present work we report on a Bcc isolate, recovered from the blood of an immunocompromised patient, that carries a 2.3 kb class I integron already described in a Salmonella enterica isolate eight years ago, coding for aacA4, aadA1 and catB2 in its cassette array.

  15. Quorum Sensing Controls Swarming Motility of Burkholderia glumae through Regulation of Rhamnolipids.

    Directory of Open Access Journals (Sweden)

    Arvin Nickzad

    Full Text Available Burkholderia glumae is a plant pathogenic bacterium that uses an acyl-homoserine lactone-mediated quorum sensing system to regulate protein secretion, oxalate production and major virulence determinants such as toxoflavin and flagella. B. glumae also releases surface-active rhamnolipids. In Pseudomonas aeruginosa and Burkholderia thailandensis, rhamnolipids, along with flagella, are required for the social behavior called swarming motility. In the present study, we demonstrate that quorum sensing positively regulates the production of rhamnolipids in B. glumae and that rhamnolipids are necessary for swarming motility also in this species. We show that a rhlA- mutant, which is unable to produce rhamnolipids, loses its ability to swarm, and that this can be complemented by providing exogenous rhamnolipids. Impaired rhamnolipid production in a quorum sensing-deficient B. glumae mutant is the main factor responsible for its defective swarming motility behaviour.

  16. Quorum Sensing Controls Swarming Motility of Burkholderia glumae through Regulation of Rhamnolipids.

    Science.gov (United States)

    Nickzad, Arvin; Lépine, François; Déziel, Eric

    2015-01-01

    Burkholderia glumae is a plant pathogenic bacterium that uses an acyl-homoserine lactone-mediated quorum sensing system to regulate protein secretion, oxalate production and major virulence determinants such as toxoflavin and flagella. B. glumae also releases surface-active rhamnolipids. In Pseudomonas aeruginosa and Burkholderia thailandensis, rhamnolipids, along with flagella, are required for the social behavior called swarming motility. In the present study, we demonstrate that quorum sensing positively regulates the production of rhamnolipids in B. glumae and that rhamnolipids are necessary for swarming motility also in this species. We show that a rhlA- mutant, which is unable to produce rhamnolipids, loses its ability to swarm, and that this can be complemented by providing exogenous rhamnolipids. Impaired rhamnolipid production in a quorum sensing-deficient B. glumae mutant is the main factor responsible for its defective swarming motility behaviour. PMID:26047513

  17. Development of Burkholderia mallei and pseudomallei vaccines.

    Science.gov (United States)

    Silva, Ediane B; Dow, Steven W

    2013-01-01

    Burkholderia mallei and Burkholderia pseudomallei are Gram-negative bacteria that cause glanders and melioidosis, respectively. Inhalational infection with either organism can result in severe and rapidly fatal pneumonia. Inoculation by the oral and cutaneous routes can also produce infection. Chronic infection may develop after recovery from acute infection with both agents, and control of infection with antibiotics requires prolonged treatment. Symptoms for both meliodosis and glanders are non-specific, making diagnosis difficult. B. pseudomallei can be located in the environment, but in the host, B. mallei and B. psedomallei are intracellular organisms, and infection results in similar immune responses to both agents. Effective early innate immune responses are critical to controlling the early phase of the infection. Innate immune signaling molecules such as TLR, NOD, MyD88, and pro-inflammatory cytokines such as IFN-γ and TNF-α play key roles in regulating control of infection. Neutrophils and monocytes are critical cells in the early infection for both microorganisms. Both monocytes and macrophages are necessary for limiting dissemination of B. pseudomallei. In contrast, the role of adaptive immune responses in controlling Burkholderia infection is less well understood. However, T cell responses are critical for vaccine protection from Burkholderia infection. At present, effective vaccines for prevention of glanders or meliodosis have not been developed, although recently development of Burkholderia vaccines has received renewed attention. This review will summarize current and past approaches to develop B. mallei and B. pseudomalllei vaccines, with emphasis on immune mechanisms of protection and the challenges facing the field. At present, immunization with live attenuated bacteria provides the most effective and durable immunity, and it is important therefore to understand the immune correlates of protection induced by live attenuated vaccines. Subunit

  18. Actin-binding proteins from Burkholderia mallei and Burkholderia thailandensis can functionally compensate for the actin-based motility defect of a Burkholderia pseudomallei bimA mutant

    OpenAIRE

    Stevens, J. M.; Ulrich, R L; Taylor, L A; Wood, M W; DeShazer, D; M.P. Stevens; Galyov, E. E.

    2005-01-01

    Recently we identified a bacterial factor (BimA) required for actin-based motility of Burkholderia pseudomallei. Here we report that Burkholderia mallei and Burkholderia thailandensis are capable of actin-based motility in J774.2 cells and that BimA homologs of these bacteria can restore the actin-based motility defect of a B. pseudomallei bimA mutant. While the BimA homologs differ in their amino-terminal sequence, they interact directly with actin in vitro and vary in their ability to bind ...

  19. Actin-Binding Proteins from Burkholderia mallei and Burkholderia thailandensis Can Functionally Compensate for the Actin-Based Motility Defect of a Burkholderia pseudomallei bimA Mutant

    OpenAIRE

    Stevens, Joanne M; Ulrich, Ricky L.; Taylor, Lowrie A.; Wood, Michael W.; DeShazer, David; Stevens, Mark P.; Galyov, Edouard E.

    2005-01-01

    Recently we identified a bacterial factor (BimA) required for actin-based motility of Burkholderia pseudomallei. Here we report that Burkholderia mallei and Burkholderia thailandensis are capable of actin-based motility in J774.2 cells and that BimA homologs of these bacteria can restore the actin-based motility defect of a B. pseudomallei bimA mutant. While the BimA homologs differ in their amino-terminal sequence, they interact directly with actin in vitro and vary in their ability to bind ...

  20. Two Novel Clinical Presentations of Burkholderia cepacia Infection

    OpenAIRE

    Mukhopadhyay, Chiranjoy; Bhargava, Anudita; Ayyagari, Archana

    2004-01-01

    We report two cases of multidrug-resistant Burkholderia cepacia (B. cepacia genomovar I) and Burkholderia multivorans causing multiple liver abscesses in a patient with bronchial asthma (case 1) and peritonitis in a patient with cirrhosis and hepatitis C virus disease (case 2), respectively. Both patients were treated successfully.

  1. Draft Genomes for Eight Burkholderia mallei Isolates from Turkey

    Science.gov (United States)

    Daligault, H. E.; Davenport, K. W.; Minogue, T. D.; Bishop-Lilly, K. A.; Broomall, S. M.; Bruce, D. C.; Coyne, S. R.; Frey, K. G.; Gibbons, H. S.; Jaissle, J.; Koroleva, G. I.; Ladner, J. T.; Lo, C.-C.; Munk, C.; Wolcott, M. J.; Palacios, G. F.; Redden, C. L.; Rosenzweig, C. N.; Scholz, M. B.; Chain, P. S.

    2016-01-01

    Burkholderia mallei, the etiologic agent of glanders, is a Gram-negative, nonmotile, facultative intracellular pathogen. Although glanders has been eradicated from many parts of the world, the threat of B. mallei being used as a weapon is very real. Here we present draft genome assemblies of 8 Burkholderia mallei strains that were isolated in Turkey. PMID:26744368

  2. Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor

    OpenAIRE

    Johnson, S. L.; Bishop-Lilly, Kimberly A.; Ladner, Jason T.; Daligault, Hajnalka E.; Davenport, Karen W.; Jaissle, James; Frey, Kenneth G.; Koroleva, Galina I.; Bruce, David C.; Coyne, Susan R.; Broomall, Stacey M.; Li, Po-E; Teshima, Hazuki; Gibbons, Henry S.; Palacios, Gustavo F.

    2015-01-01

    The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention Category B listed), and nonpathogenic Gram-negative bacilli. Here we present full genome sequences for a panel of 59 Burkholderia strains, selected to aid in detection assay development.

  3. Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis.

    Science.gov (United States)

    Esmaeel, Qassim; Pupin, Maude; Kieu, Nam Phuong; Chataigné, Gabrielle; Béchet, Max; Deravel, Jovana; Krier, François; Höfte, Monica; Jacques, Philippe; Leclère, Valérie

    2016-06-01

    Burkholderia is an important genus encompassing a variety of species, including pathogenic strains as well as strains that promote plant growth. We have carried out a global strategy, which combined two complementary approaches. The first one is genome guided with deep analysis of genome sequences and the second one is assay guided with experiments to support the predictions obtained in silico. This efficient screening for new secondary metabolites, performed on 48 gapless genomes of Burkholderia species, revealed a total of 161 clusters containing nonribosomal peptide synthetases (NRPSs), with the potential to synthesize at least 11 novel products. Most of them are siderophores or lipopeptides, two classes of products with potential application in biocontrol. The strategy led to the identification, for the first time, of the cluster for cepaciachelin biosynthesis in the genome of Burkholderia ambifaria AMMD and a cluster corresponding to a new malleobactin-like siderophore, called phymabactin, was identified in Burkholderia phymatum STM815 genome. In both cases, the siderophore was produced when the strain was grown in iron-limited conditions. Elsewhere, the cluster for the antifungal burkholdin was detected in the genome of B. ambifaria AMMD and also Burkholderia sp. KJ006. Burkholderia pseudomallei strains harbor the genetic potential to produce a novel lipopeptide called burkhomycin, containing a peptidyl moiety of 12 monomers. A mixture of lipopeptides produced by Burkholderia rhizoxinica lowered the surface tension of the supernatant from 70 to 27 mN·m(-1) . The production of nonribosomal secondary metabolites seems related to the three phylogenetic groups obtained from 16S rRNA sequences. Moreover, the genome-mining approach gave new insights into the nonribosomal synthesis exemplified by the identification of dual C/E domains in lipopeptide NRPSs, up to now essentially found in Pseudomonas strains. PMID:27060604

  4. Genomic Sequence of Burkholderia multivorans NKI379, a Soil Bacterium That Inhibits the Growth of Burkholderia pseudomallei

    OpenAIRE

    Hsueh, Pei-Tan; Liu, Jong-Kang; Chen, Ya-Lei; Liu, Pei-Ju; Ni, Wen-Fan; Chen, Yao-Shen; Wu, Keh-Ming; Lin, Hsi-Hsun

    2015-01-01

    Burkholderia multivorans NKI379 is a soil bacterium that exhibits an antagonistic effect against the growth of Burkholderia pseudomallei, the causative agent of the infectious disease melioidosis. We report the draft genomic sequence of B. multivorans NKI379, which has a G+C content of 67% and 5,203 candidate protein-encoding genes.

  5. Causal Newton Gravity Law

    CERN Document Server

    Zinoviev, Yury M

    2012-01-01

    The equations of the relativistic causal Newton gravity law for the planets of the solar system are studied in the approximation when the Sun rests at the coordinates origin and the planets do not iteract between each other.

  6. Causal spin foams

    CERN Document Server

    Immirzi, Giorgio

    2016-01-01

    I discuss how to impose causality on spin-foam models, separating forward and backward propagation, turning a given triangulation to a 'causal set', and giving asymptotically the exponential of the Regge action, not a cosine. I show the equivalence of the prescriptions which have been proposed to achieve this. Essential to the argument is the closure condition for the 4-simplices, all made of space-like tetrahedra.

  7. Burkholderia thailandensis harbors two identical rhl gene clusters responsible for the biosynthesis of rhamnolipids

    Directory of Open Access Journals (Sweden)

    Woods Donald E

    2009-12-01

    Full Text Available Abstract Background Rhamnolipids are surface active molecules composed of rhamnose and β-hydroxydecanoic acid. These biosurfactants are produced mainly by Pseudomonas aeruginosa and have been thoroughly investigated since their early discovery. Recently, they have attracted renewed attention because of their involvement in various multicellular behaviors. Despite this high interest, only very few studies have focused on the production of rhamnolipids by Burkholderia species. Results Orthologs of rhlA, rhlB and rhlC, which are responsible for the biosynthesis of rhamnolipids in P. aeruginosa, have been found in the non-infectious Burkholderia thailandensis, as well as in the genetically similar important pathogen B. pseudomallei. In contrast to P. aeruginosa, both Burkholderia species contain these three genes necessary for rhamnolipid production within a single gene cluster. Furthermore, two identical, paralogous copies of this gene cluster are found on the second chromosome of these bacteria. Both Burkholderia spp. produce rhamnolipids containing 3-hydroxy fatty acid moieties with longer side chains than those described for P. aeruginosa. Additionally, the rhamnolipids produced by B. thailandensis contain a much larger proportion of dirhamnolipids versus monorhamnolipids when compared to P. aeruginosa. The rhamnolipids produced by B. thailandensis reduce the surface tension of water to 42 mN/m while displaying a critical micelle concentration value of 225 mg/L. Separate mutations in both rhlA alleles, which are responsible for the synthesis of the rhamnolipid precursor 3-(3-hydroxyalkanoyloxyalkanoic acid, prove that both copies of the rhl gene cluster are functional, but one contributes more to the total production than the other. Finally, a double ΔrhlA mutant that is completely devoid of rhamnolipid production is incapable of swarming motility, showing that both gene clusters contribute to this phenotype. Conclusions Collectively, these

  8. Quantum Causal Graph Dynamics

    CERN Document Server

    Arrighi, Pablo

    2016-01-01

    Consider a graph having quantum systems lying at each node. Suppose that the whole thing evolves in discrete time steps, according to a global, unitary causal operator. By causal we mean that information can only propagate at a bounded speed, with respect to the distance given by the graph. Suppose, moreover, that the graph itself is subject to the evolution, and may be driven to be in a quantum superposition of graphs---in accordance to the superposition principle. We show that these unitary causal operators must decompose as a finite-depth circuit of local unitary gates. This unifies a result on Quantum Cellular Automata with another on Reversible Causal Graph Dynamics. Along the way we formalize a notion of causality which is valid in the context of quantum superpositions of time-varying graphs, and has a number of good properties. Keywords: Quantum Lattice Gas Automata, Block-representation, Curtis-Hedlund-Lyndon, No-signalling, Localizability, Quantum Gravity, Quantum Graphity, Causal Dynamical Triangula...

  9. Brain abscess caused by Burkholderia pseudomallei

    International Nuclear Information System (INIS)

    Full text: Melioidosis, or infection with Burkholderia pseudomallei, is an important human disease in South East Asia and Northern Australia. Neurological manifestations are well recognized amongst its protean presentations, but direct focal central nervous system infection is infrequently described with only 9 adult and 5 paediatric cases reported in the English language literature. A case of brain abscess due to Burkholderia pseudomallei occurring in a 20 year old Dutch visitor to Australia which progressed despite antibiotic treatment is described. A review of the clinical manifestations, Magnetic Resonance (MR) appearance, diagnosis and treatment of melioidosis is presented, highlighting that: (i) physicians outside endernic areas should consider melioidosis in any patient with an appropriate travel history, (ii) MR imaging is more sensitive then CT in diagnosing early brain infection, especially of the brainstem; (iii) Bacterial culture, the mainstay of diagnosis, has many shortcomings; (iv)In vitro antibiotic sensitivity testing may not translate into clinical efficacy; and (v) Steroids appear to have little role, even in severe disease

  10. Assimetria causal: um estudo

    Directory of Open Access Journals (Sweden)

    Túlio Aguiar

    2003-12-01

    Full Text Available Neste artigo, examinamos o aspecto assimétrico da relação causal, confrontando-o com o ponto de vista humiano e neo-humiano. Seguindo Hausman e Ehring, favorecemos uma abordagem situacional para a assimetria causal. Nós exploramos a análise do famoso exemplo do mastro (Flagpole, esclarecendo as conexões entre causação e explicação. Nosso diagnóstico geral é que a tradição neo-humiana supõe, equivocadamente, que as relações nômicas, com exceção de pequenos detalhes, exaurem as relações causais.This paper examines the asymmetrical aspect of causal relation, confronting it to Humean and Neo-Humean's view. Following Hausman and Ehring, we favor a situational approach to causal asymmetry. We explore the Hausman's analysis of flagpole's example, clearing the connexions between causation and explanation. Our general diagnosis is that the Neo-humean tradition wrongly supposes that nomic relations, with the exception of minor details, exhaust the causal relations.

  11. Causality and the Doppler Peaks

    OpenAIRE

    Turok, Neil

    1996-01-01

    Could cosmic structure have formed by the action of causal physics within the standard hot big bang, or was a prior period of inflation required? Recently there has been some discussion of whether causal sources could reproduce the pattern of Doppler peaks of the standard scale-invariant adiabatic theory. This paper gives a rigorous definition of causality, and a causal decomposition of a general source. I present an example of a simple causal source which mimics the standard adiabatic theory...

  12. Versatility of the Burkholderia cepacia complex for the biosynthesis of exopolysaccharides: a comparative structural investigation.

    Directory of Open Access Journals (Sweden)

    Bruno Cuzzi

    Full Text Available The Burkholderia cepacia Complex assembles at least eighteen closely related species that are ubiquitous in nature. Some isolates show beneficial potential for biocontrol, bioremediation and plant growth promotion. On the contrary, other strains are pathogens for plants and immunocompromised individuals, like cystic fibrosis patients. In these subjects, they can cause respiratory tract infections sometimes characterised by fatal outcome. Most of the Burkholderia cepacia Complex species are mucoid when grown on a mannitol rich medium and they also form biofilms, two related characteristics, since polysaccharides are important component of biofilm matrices. Moreover, polysaccharides contribute to bacterial survival in a hostile environment by inhibiting both neutrophils chemotaxis and antimicrobial peptides activity, and by scavenging reactive oxygen species. The ability of these microorganisms to produce exopolysaccharides with different structures is testified by numerous articles in the literature. However, little is known about the type of polysaccharides produced in biofilms and their relationship with those obtained in non-biofilm conditions. The aim of this study was to define the type of exopolysaccharides produced by nine species of the Burkholderia cepacia Complex. Two isolates were then selected to compare the polysaccharides produced on agar plates with those formed in biofilms developed on cellulose membranes. The investigation was conducted using NMR spectroscopy, high performance size exclusion chromatography, and gas chromatography coupled to mass spectrometry. The results showed that the Complex is capable of producing a variety of exopolysaccharides, most often in mixture, and that the most common exopolysaccharide is always cepacian. In addition, two novel polysaccharide structures were determined: one composed of mannose and rhamnose and another containing galactose and glucuronic acid. Comparison of exopolysaccharides obtained

  13. Bacteria of the Burkholderia cepacia complex are cyanogenic under biofilm and colonial growth conditions

    Directory of Open Access Journals (Sweden)

    Hoshino Saiko

    2008-06-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (Bcc is a collection of nine genotypically distinct but phenotypically similar species. They show wide ecological diversity and include species that are used for promoting plant growth and bio-control as well species that are opportunistic pathogens of vulnerable patients. Over recent years the Bcc have emerged as problematic pathogens of the CF lung. Pseudomonas aeruginosa is another important CF pathogen. It is able to synthesise hydrogen cyanide (HCN, a potent inhibitor of cellular respiration. We have recently shown that HCN production by P. aeruginosa may have a role in CF pathogenesis. This paper describes an investigation of the ability of bacteria of the Bcc to make HCN. Results The genome of Burkholderia cenocepacia has 3 putative HCN synthase encoding (hcnABC gene clusters. B. cenocepacia and all 9 species of the Bcc complex tested were able to make cyanide at comparable levels to P. aeruginosa, but only when grown surface attached as colonies or during biofilm growth on glass beads. In contrast to P. aeruginosa and other cyanogenic bacteria, cyanide was not detected during planktonic growth of Bcc strains. Conclusion All species in the Bcc are cyanogenic when grown as surface attached colonies or as biofilms.

  14. Causal graph dynamics

    CERN Document Server

    Arrighi, Pablo

    2012-01-01

    We generalize the theory of Cellular Automata to arbitrary, time-varying graphs. In other words we formalize, and prove theorems about, the intuitive idea of a labelled graph which evolves in time - but under the natural constraint that information can only ever be transmitted at a bounded speed, with respect to the distance given by the graph. The notion of translation-invariance is also generalized. The definition we provide for these `causal graph dynamics' is simple and axiomatic. The theorems we provide also show that it is robust. For instance, causal graph dynamics are stable under composition and under restriction to radius one. In the finite case some fundamental facts of Cellular Automata theory carry through: causal graph dynamics admit a characterization as continuous functions and they are stable under inversion. The provided examples suggest a wide range of applications of this mathematical object, from complex systems science to theoretical physics. Keywords: Dynamical networks, Boolean network...

  15. Causal inference in econometrics

    CERN Document Server

    Kreinovich, Vladik; Sriboonchitta, Songsak

    2016-01-01

    This book is devoted to the analysis of causal inference which is one of the most difficult tasks in data analysis: when two phenomena are observed to be related, it is often difficult to decide whether one of them causally influences the other one, or whether these two phenomena have a common cause. This analysis is the main focus of this volume. To get a good understanding of the causal inference, it is important to have models of economic phenomena which are as accurate as possible. Because of this need, this volume also contains papers that use non-traditional economic models, such as fuzzy models and models obtained by using neural networks and data mining techniques. It also contains papers that apply different econometric models to analyze real-life economic dependencies.

  16. Complementarity, causality, and explanation

    CERN Document Server

    Losee, John

    2013-01-01

    Prior to the work of Niels Bohr, discussions on the relationship of cause and effect presupposed that successful causal attribution implies explanation. The success of quantum theory challenged this presupposition. In this succinct review of the history of these discussions, John Losee presents the philosophical background of debates over the cause-effect relation. He reviews the positions of Aristotle, René Descartes, Isaac Newton, David Hume, Immanuel Kant, and John Stuart Mill. He shows how nineteenth-century theories in physics and chemistry were informed by a dominant theory of causality

  17. Causal premise semantics.

    Science.gov (United States)

    Kaufmann, Stefan

    2013-08-01

    The rise of causality and the attendant graph-theoretic modeling tools in the study of counterfactual reasoning has had resounding effects in many areas of cognitive science, but it has thus far not permeated the mainstream in linguistic theory to a comparable degree. In this study I show that a version of the predominant framework for the formal semantic analysis of conditionals, Kratzer-style premise semantics, allows for a straightforward implementation of the crucial ideas and insights of Pearl-style causal networks. I spell out the details of such an implementation, focusing especially on the notions of intervention on a network and backtracking interpretations of counterfactuals.

  18. Use of a safe, reproducible, and rapid aerosol delivery method to study infection by Burkholderia pseudomallei and Burkholderia mallei in mice.

    Directory of Open Access Journals (Sweden)

    Eric R Lafontaine

    Full Text Available Burkholderia pseudomallei, the etiologic agent of melioidosis, is a saprophytic bacterium readily isolated from wet soils of countries bordering the equator. Burkholderia mallei is a host-adapted clone of B. pseudomallei that does not persist outside of its equine reservoir and causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by these organisms typically occurs via percutaneous inoculation or inhalation of aerosols, and the most common manifestation is severe pneumonia leading to fatal bacteremia. Glanders and melioidosis are difficult to diagnose and require prolonged antibiotic therapy with low success rates. There are no vaccines available to protect against either Burkholderia species, and there is concern regarding their use as biological warfare agents given that B. mallei has previously been utilized in this manner. Hence, experiments were performed to establish a mouse model of aerosol infection to study the organisms and develop countermeasures. Using a hand-held aerosolizer, BALB/c mice were inoculated intratracheally with strains B. pseudomallei 1026b and B. mallei ATCC23344 and growth of the agents in the lungs, as well as dissemination to the spleen, were examined. Mice infected with 10(2, 10(3 and 10(4 organisms were unable to control growth of B. mallei in the lungs and bacteria rapidly disseminated to the spleen. Though similar results were observed in mice inoculated with 10(3 and 10(4 B. pseudomallei cells, animals infected with 10(2 organisms controlled bacterial replication in the lungs, dissemination to the spleen, and the extent of bacteremia. Analysis of sera from mice surviving acute infection revealed that animals produced antibodies against antigens known to be targets of the immune response in humans. Taken together, these data show that small volume aerosol inoculation of mice results in acute disease, dose-dependent chronic infection, and immune responses

  19. Use of a safe, reproducible, and rapid aerosol delivery method to study infection by Burkholderia pseudomallei and Burkholderia mallei in mice.

    Science.gov (United States)

    Lafontaine, Eric R; Zimmerman, Shawn M; Shaffer, Teresa L; Michel, Frank; Gao, Xiudan; Hogan, Robert J

    2013-01-01

    Burkholderia pseudomallei, the etiologic agent of melioidosis, is a saprophytic bacterium readily isolated from wet soils of countries bordering the equator. Burkholderia mallei is a host-adapted clone of B. pseudomallei that does not persist outside of its equine reservoir and causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by these organisms typically occurs via percutaneous inoculation or inhalation of aerosols, and the most common manifestation is severe pneumonia leading to fatal bacteremia. Glanders and melioidosis are difficult to diagnose and require prolonged antibiotic therapy with low success rates. There are no vaccines available to protect against either Burkholderia species, and there is concern regarding their use as biological warfare agents given that B. mallei has previously been utilized in this manner. Hence, experiments were performed to establish a mouse model of aerosol infection to study the organisms and develop countermeasures. Using a hand-held aerosolizer, BALB/c mice were inoculated intratracheally with strains B. pseudomallei 1026b and B. mallei ATCC23344 and growth of the agents in the lungs, as well as dissemination to the spleen, were examined. Mice infected with 10(2), 10(3) and 10(4) organisms were unable to control growth of B. mallei in the lungs and bacteria rapidly disseminated to the spleen. Though similar results were observed in mice inoculated with 10(3) and 10(4) B. pseudomallei cells, animals infected with 10(2) organisms controlled bacterial replication in the lungs, dissemination to the spleen, and the extent of bacteremia. Analysis of sera from mice surviving acute infection revealed that animals produced antibodies against antigens known to be targets of the immune response in humans. Taken together, these data show that small volume aerosol inoculation of mice results in acute disease, dose-dependent chronic infection, and immune responses that correlate

  20. Use of a safe, reproducible, and rapid aerosol delivery method to study infection by Burkholderia pseudomallei and Burkholderia mallei in mice.

    Science.gov (United States)

    Lafontaine, Eric R; Zimmerman, Shawn M; Shaffer, Teresa L; Michel, Frank; Gao, Xiudan; Hogan, Robert J

    2013-01-01

    Burkholderia pseudomallei, the etiologic agent of melioidosis, is a saprophytic bacterium readily isolated from wet soils of countries bordering the equator. Burkholderia mallei is a host-adapted clone of B. pseudomallei that does not persist outside of its equine reservoir and causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by these organisms typically occurs via percutaneous inoculation or inhalation of aerosols, and the most common manifestation is severe pneumonia leading to fatal bacteremia. Glanders and melioidosis are difficult to diagnose and require prolonged antibiotic therapy with low success rates. There are no vaccines available to protect against either Burkholderia species, and there is concern regarding their use as biological warfare agents given that B. mallei has previously been utilized in this manner. Hence, experiments were performed to establish a mouse model of aerosol infection to study the organisms and develop countermeasures. Using a hand-held aerosolizer, BALB/c mice were inoculated intratracheally with strains B. pseudomallei 1026b and B. mallei ATCC23344 and growth of the agents in the lungs, as well as dissemination to the spleen, were examined. Mice infected with 10(2), 10(3) and 10(4) organisms were unable to control growth of B. mallei in the lungs and bacteria rapidly disseminated to the spleen. Though similar results were observed in mice inoculated with 10(3) and 10(4) B. pseudomallei cells, animals infected with 10(2) organisms controlled bacterial replication in the lungs, dissemination to the spleen, and the extent of bacteremia. Analysis of sera from mice surviving acute infection revealed that animals produced antibodies against antigens known to be targets of the immune response in humans. Taken together, these data show that small volume aerosol inoculation of mice results in acute disease, dose-dependent chronic infection, and immune responses that correlate

  1. Antibacterial activity of a lectin-like Burkholderia cenocepacia protein

    OpenAIRE

    Ghequire, Maarten; De Canck, Evelien; Wattiau, Pierre; Van Winge, Iris; Loris, Remy; Coenye, Tom; De Mot, René

    2013-01-01

    Abstract Bacteriocins of the LlpA family have previously been characterized in the γ-proteobacteria Pseudomonas and Xanthomonas. These proteins are composed of two MMBL (monocot mannose-binding lectin) domains, a module predominantly and abundantly found in lectins from monocot plants. Genes encoding four different types of LlpA-like proteins were identified in genomes from strains belonging to the Burkholderia cepacia complex (Bcc) and the Burkholderia pseudomallei group. A selected recombin...

  2. Understanding Causal Coherence Relations

    NARCIS (Netherlands)

    Mulder, G.

    2008-01-01

    The research reported in this dissertation focuses on the cognitive processes and representations involved in understanding causal coherence relations in text. Coherence relations are the meaning relations between the information units in the text, such as Cause-Consequence. These relations can be m

  3. Cyanide toxicity to Burkholderia cenocepacia is modulated by polymicrobial communities and environmental factors

    Directory of Open Access Journals (Sweden)

    Steve P. Bernier

    2016-05-01

    Full Text Available Microbes within polymicrobial communities can establish positive and negative interactions that have the potential to influence the overall behaviour of the community. Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc can co-exist in the lower airways, however several studies have shown that P. aeruginosa can effectively kill the Bcc in vitro, for which hydrogen cyanide was recently proposed to play a critical role. Here we show that modification of the environment (i.e. culture medium, long-term genetic adaptation of P. aeruginosa to the cystic fibrosis (CF lung, or the addition of another bacterial species to the community can alter the sensitivity of Burkholderia cenocepacia to P. aeruginosa toxins. We specifically demonstrate that undefined rich media leads to higher susceptibility of B. cenocepacia to P. aeruginosa toxins like cyanide as compared to a synthetic medium (SCFM, that mimics the CF lung nutritional content. Overall, our study shows that the polymicrobial environment can have profound effects on negative interactions mediated by P. aeruginosa against B. cenocepacia. In fact, evolved P. aeruginosa or the presence of other species such as Staphylococcus aureus can directly abolish the direct competition mediated by cyanide and consequently maintaining a higher level of species diversity within the community.

  4. Cyanide Toxicity to Burkholderia cenocepacia Is Modulated by Polymicrobial Communities and Environmental Factors.

    Science.gov (United States)

    Bernier, Steve P; Workentine, Matthew L; Li, Xiang; Magarvey, Nathan A; O'Toole, George A; Surette, Michael G

    2016-01-01

    Microbes within polymicrobial communities can establish positive and negative interactions that have the potential to influence the overall behavior of the community. Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc) can co-exist in the lower airways, however several studies have shown that P. aeruginosa can effectively kill the Bcc in vitro, for which hydrogen cyanide (HCN) was recently proposed to play a critical role. Here we show that modification of the environment (i.e., culture medium), long-term genetic adaptation of P. aeruginosa to the cystic fibrosis (CF) lung, or the addition of another bacterial species to the community can alter the sensitivity of Burkholderia cenocepacia to P. aeruginosa toxins. We specifically demonstrate that undefined rich media leads to higher susceptibility of B. cenocepacia to P. aeruginosa toxins like cyanide as compared to a synthetic medium (SCFM), that mimics the CF lung nutritional content. Overall, our study shows that the polymicrobial environment can have profound effects on negative interactions mediated by P. aeruginosa against B. cenocepacia. In fact, evolved P. aeruginosa or the presence of other species such as Staphylococcus aureus can directly abolish the direct competition mediated by cyanide and consequently maintaining a higher level of species diversity within the community. PMID:27242743

  5. Burkholderia dabaoshanensis sp. nov., a heavy-metal-tolerant bacteria isolated from Dabaoshan mining area soil in China.

    Directory of Open Access Journals (Sweden)

    Honghui Zhu

    Full Text Available Heavy-metal-tolerant bacteria, GIMN1.004(T, was isolated from mine soils of Dabaoshan in South China, which were acidic (pH 2-4 and polluted with heavy metals. The isolation was Gram-negative, aerobic, non-spore-forming, and rod-shaped bacteria having a cellular width of 0.5-0.6 µm and a length of 1.3-1.8 µm. They showed a normal growth pattern at pH 4.0-9.0 in a temperature ranging from 5 °C to 40 °C.The organism contained ubiquinone Q-8 as the predominant isoprenoid quinine, and C(16:0, summed feature 8 (C(18:1ω7c and C(18:1ω6c, C(18:0, summed feature 3 (C(16:1ω7c or iso-C(15:0 2-OH, C(17:0 cyclo, C(18:1ω9c, C(19:0 cyclo ω8c, C(14:0 as major fatty acid. These profiles were similar to those reported for Burkholderia species. The DNA G+C % of this strain was 61.6%. Based on the similarity to 16S rRNA gene sequence, GIMN1.004(T was considered to be in the genus Burkholderia. The similarities of 16S rRNA gene sequence between strain GIMN1.004(T and members of the genus Burkholderia were 96-99.4%, indicating that this novel strain was phylogenetically related to members of that genus. The novel strain showed the highest sequence similarities to Burkholderia soli DSM 18235(T (99.4%; Levels of DNA-DNA hybridization with DSM 18235(T was 25%. Physiological and biochemical tests including cell wall composition analysis, differentiated phenotype of this strain from that closely related Burkholderia species. The isolation had great tolerance to cadmium with MIC of 22 mmol/L, and adsorbability of 144.94 mg/g cadmium,and it was found to exhibit antibiotic resistance characteristics. The adsorptive mechanism of GIMN1.004(T for cadmium depended on the action of the amide,carboxy and phosphate of cell surface and producing low-molecular-weight (LMW organic acids to complex or chelated Cd(2+.Therefore, the strain GIMN1.004(T represented a new cadmium resistance species, which was tentatively named as Burkholderia dabaoshanensis sp. nov. The strain type

  6. Environmental Transmission of the Gut Symbiont Burkholderia to Phloem-Feeding Blissus insularis

    Science.gov (United States)

    Xu, Yao; Buss, Eileen A.; Boucias, Drion G.

    2016-01-01

    The plant-phloem-feeding Blissus insularis possesses specialized midgut crypts, which harbor a dense population of the exocellular bacterial symbiont Burkholderia. Most individual B. insularis harbor a single Burkholderia ribotype in their midgut crypts; however, a diverse Burkholderia community exists within a host population. To understand the mechanism underlying the consistent occurrence of various Burkholderia in B. insularis and their specific association, we investigated potential gut symbiont transmission routes. PCR amplification detected a low titer of Burkholderia in adult reproductive tracts; however, fluorescence in situ hybridization assays failed to produce detectable signals in these tracts. Furthermore, no Burkholderia-specific PCR signals were detected in eggs and neonates, suggesting that it is unlikely that B. insularis prenatally transmits gut symbionts via ovarioles. In rearing experiments, most nymphs reared on St. Augustinegrass treated with cultured Burkholderia harbored the cultured Burkholderia strains. Burkholderia was detected in the untreated host grass of B. insularis, and most nymphs reared on untreated grass harbored a Burkholderia ribotype that was closely related to a plant-associated Burkholderia strain. These findings revealed that B. insularis neonates acquired Burkholderia primarily from the environment (i.e., plants and soils), even though the possibility of acquisition via egg surface cannot be excluded. In addition, our study explains how the diverse Burkholderia symbiont community in B. insularis populations can be maintained. PMID:27548682

  7. Environmental Transmission of the Gut Symbiont Burkholderia to Phloem-Feeding Blissus insularis.

    Science.gov (United States)

    Xu, Yao; Buss, Eileen A; Boucias, Drion G

    2016-01-01

    The plant-phloem-feeding Blissus insularis possesses specialized midgut crypts, which harbor a dense population of the exocellular bacterial symbiont Burkholderia. Most individual B. insularis harbor a single Burkholderia ribotype in their midgut crypts; however, a diverse Burkholderia community exists within a host population. To understand the mechanism underlying the consistent occurrence of various Burkholderia in B. insularis and their specific association, we investigated potential gut symbiont transmission routes. PCR amplification detected a low titer of Burkholderia in adult reproductive tracts; however, fluorescence in situ hybridization assays failed to produce detectable signals in these tracts. Furthermore, no Burkholderia-specific PCR signals were detected in eggs and neonates, suggesting that it is unlikely that B. insularis prenatally transmits gut symbionts via ovarioles. In rearing experiments, most nymphs reared on St. Augustinegrass treated with cultured Burkholderia harbored the cultured Burkholderia strains. Burkholderia was detected in the untreated host grass of B. insularis, and most nymphs reared on untreated grass harbored a Burkholderia ribotype that was closely related to a plant-associated Burkholderia strain. These findings revealed that B. insularis neonates acquired Burkholderia primarily from the environment (i.e., plants and soils), even though the possibility of acquisition via egg surface cannot be excluded. In addition, our study explains how the diverse Burkholderia symbiont community in B. insularis populations can be maintained. PMID:27548682

  8. Exploitation of host cells by Burkholderia pseudomallei.

    Science.gov (United States)

    Stevens, Mark P; Galyov, Edouard E

    2004-04-01

    Intracellular bacterial pathogens have evolved mechanisms to enter and exit eukaryotic cells using the power of actin polymerisation and to subvert the activity of cellular enzymes and signal transduction pathways. The proteins deployed by bacteria to subvert cellular processes often mimic eukaryotic proteins in their structure or function. Studies on the exploitation of host cells by the facultative intracellular pathogen Burkholderia pseudomallei are providing novel insights into the pathogenesis of melioidosis, a serious invasive disease of animals and humans that is endemic in tropical and subtropical areas. B. pseudomallei can invade epithelial cells, survive and proliferate inside phagocytes, escape from endocytic vesicles, form actin-based membrane protrusions and induce host cell fusion. Here we review current understanding of the molecular mechanisms underlying these processes.

  9. Revisiting Causality in Markov Chains

    OpenAIRE

    Shojaee, Abbas

    2016-01-01

    Identifying causal relationships is a key premise of scientific research. The growth of observational data in different disciplines along with the availability of machine learning methods offers the possibility of using an empirical approach to identifying potential causal relationships, to deepen our understandings of causal behavior and to build theories accordingly. Conventional methods of causality inference from observational data require a considerable length of time series data to capt...

  10. Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex.

    Science.gov (United States)

    Bartholdson, S Josefin; Brown, Alan R; Mewburn, Ben R; Clarke, David J; Fry, Stephen C; Campopiano, Dominic J; Govan, John R W

    2008-08-01

    The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysaccharide (EPS) when onion tissue was provided as the sole nutrient. EPS production was not species-specific, was observed in isolates from both clinical and environmental sources, and did not correlate with the ability to cause maceration of onion tissue. Chemical analysis suggested that the onion components responsible for EPS induction were primarily the carbohydrates sucrose, fructose and fructans. Additional sugars were investigated, and all alcohol sugars tested were able to induce EPS production, in particular mannitol and glucitol. To investigate the molecular basis for EPS biosynthesis, we focused on the highly conserved bce gene cluster thought to be involved in cepacian biosynthesis. We demonstrated induction of the bce gene cluster by mannitol, and found a clear correlation between the inability of representatives of the Burkholderia cenocepacia ET12 lineage to produce EPS and the presence of an 11 bp deletion within the bceB gene, which encodes a glycosyltransferase. Insertional inactivation of bceB in Burkholderia ambifaria AMMD results in loss of EPS production on sugar alcohol media. These novel and surprising insights into EPS biosynthesis highlight the metabolic potential of the Bcc and show that a potential virulence factor may not be detected by routine laboratory culture. Our results also highlight a potential hazard in the use of inhaled mannitol as an osmolyte to improve mucociliary clearance in individuals with cystic fibrosis. PMID:18667584

  11. Context, causality, and appreciation.

    Science.gov (United States)

    Ross, Stephanie

    2013-04-01

    I applaud and elaborate on the contextualism at the heart of Bullot & Reber's (B&R's) theory, challenge two aspects of the appreciative structure they posit (the causal reasoning that allegedly underlies the design stance and the segregation of the component stages), suggest that expert and novice appreciators operate differently, and question the degree to which B&R's final theory is open to empirical investigation. PMID:23507111

  12. Causality between time series

    CERN Document Server

    Liang, X San

    2014-01-01

    Given two time series, can one tell, in a rigorous and quantitative way, the cause and effect between them? Based on a recently rigorized physical notion namely information flow, we arrive at a concise formula and give this challenging question, which is of wide concern in different disciplines, a positive answer. Here causality is measured by the time rate of change of information flowing from one series, say, X2, to another, X1. The measure is asymmetric between the two parties and, particularly, if the process underlying X1 does not depend on X2, then the resulting causality from X2 to X1 vanishes. The formula is tight in form, involving only the commonly used statistics, sample covariances. It has been validated with touchstone series purportedly generated with one-way causality. It has also been applied to the investigation of real world problems; an example presented here is the cause-effect relation between two climate modes, El Ni\\~no and Indian Ocean Dipole, which have been linked to the hazards in f...

  13. Tachyon Kinematics and causality

    International Nuclear Information System (INIS)

    The chronological order of the events along a space-like path is not invariant under Lorentz transformations, as wellknown. This led to an early conviction that tachyons would give rise to causal anomalies. A relativistic version of the Stuckelberg-Feynman switching procedure (SWP) has been invoked as the suitable tool to eliminate those anomalies. The application of the SWP does eliminate the motions backwards in time, but interchanges the roles of source and dector. This fact triggered the proposal of a host of causal paradoxes. Till now, however, it has not been recognized that such paradoxes can be sensibly discussed (and completely solved, at least in microphysics) only after having properly developed the tachyon relativistic mechanics. We start by showing how to apply the SWP, both in the case of ordiry Special Relativity, and in the case with tachyons. Then, we carefully exploit the kinematics of the tachyon-exchange between to (ordinary) bodies. Being finally able to tackle the tachyon-causality problem, we successively solve the paradoxes: (i) by Tolman-Regge; (ii) by Pirani; (iii) by Edmonds; (iv) by Bell. At last, we discuss a further, new paradox associated with the transmission of signals by modulated tachyon beams

  14. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Godoy, Daniel; Randle, Gaynor; Simpson, Andrew J; Aanensen, David M; Pitt, Tyrone L; Kinoshita, Reimi; Spratt, Brian G

    2003-05-01

    A collection of 147 isolates of Burkholderia pseudomallei, B. mallei, and B. thailandensis was characterized by multilocus sequence typing (MLST). The 128 isolates of B. pseudomallei, the causative agent of melioidosis, were obtained from diverse geographic locations, from humans and animals with disease, and from the environment and were resolved into 71 sequence types. The utility of the MLST scheme for epidemiological investigations was established by analyzing isolates from captive marine mammals and birds and from humans in Hong Kong with melioidosis. MLST gave a level of resolution similar to that given by pulsed-field gel electrophoresis and identified the same three clones causing disease in animals, each of which was also associated with disease in humans. The average divergence between the alleles of B. thailandensis and B. pseudomallei was 3.2%, and there was no sharing of alleles between these species. Trees constructed from differences in the allelic profiles of the isolates and from the concatenated sequences of the seven loci showed that the B. pseudomallei isolates formed a cluster of closely related lineages that were fully resolved from the cluster of B. thailandensis isolates, confirming their separate species status. However, isolates of B. mallei, the causative agent of glanders, recovered from three continents over a 30-year period had identical allelic profiles, and the B. mallei isolates clustered within the B. pseudomallei group of isolates. Alleles at six of the seven loci in B. mallei were also present within B. pseudomallei isolates, and B. mallei is a clone of B. pseudomallei that, on population genetics grounds, should not be given separate species status.

  15. Stable, Site-Specific Fluorescent Tagging Constructs Optimized for Burkholderia Species▿

    OpenAIRE

    Norris, Michael H.; Kang, Yun (Kenneth); Wilcox, Bruce; Hoang, Tung T.

    2010-01-01

    Several vectors that facilitate stable fluorescent labeling of Burkholderia pseudomallei and Burkholderia thailandensis were constructed. These vectors combined the effectiveness of the mini-Tn7 site-specific transposition system with fluorescent proteins optimized for Burkholderia spp., enabling bacterial tracking during cellular infection.

  16. Revisiting Causality in Markov Chains

    CERN Document Server

    Shojaee, Abbas

    2016-01-01

    Identifying causal relationships is a key premise of scientific research. The growth of observational data in different disciplines along with the availability of machine learning methods offers the possibility of using an empirical approach to identifying potential causal relationships, to deepen our understandings of causal behavior and to build theories accordingly. Conventional methods of causality inference from observational data require a considerable length of time series data to capture cause-effect relationship. We find that potential causal relationships can be inferred from the composition of one step transition rates to and from an event. Also known as Markov chain, one step transition rates are a commonly available resource in different scientific disciplines. Here we introduce a simple, effective and computationally efficient method that we termed 'Causality Inference using Composition of Transitions CICT' to reveal causal structure with high accuracy. We characterize the differences in causes,...

  17. Influence of neutrophil defects on Burkholderia cepacia complex pathogenesis

    Directory of Open Access Journals (Sweden)

    Laura A. Porter

    2011-11-01

    Full Text Available The Burkholderia cepacia complex (Bcc is a group of Gram-negative bacteria that are ubiquitous in the environment and have emerged as opportunistic pathogens in immunocompromised patients. The primary patient populations infected with Bcc include individuals with cystic fibrosis (CF, as well as those with chronic granulomatous disease (CGD. While Bcc infection in CF is better characterized than in CGD, these two genetic diseases are not obviously similar and it is currently unknown if there is any commonality in host immune defects that is responsible for the susceptibility to Bcc. CF is caused by mutations in the CF transmembrane conductance regulator, resulting in manifestations in various organ systems, however the major cause of morbidity and mortality is currently due to bacterial respiratory infections. CGD, on the other hand, is a genetic disorder that is caused by defects in phagocyte NADPH oxidase. Because of the defect in CGD, phagocytes in these patients are unable to produce reactive oxygen species, which results in increased susceptibility to bacterial and fungal infections. Despite this significant defect in microbial clearance, the spectrum of pathogens frequently implicated in infections in CGD is relatively narrow and includes some bacterial species that are considered almost pathognomonic for this disorder. Very little is known about the cause of the specific susceptibility to Bcc over other potential pathogens more prevalent in the environment, and a better understanding of specific mechanisms required for bacterial virulence has become a high priority. This review will summarize both the current knowledge and future directions related to Bcc virulence in immunocompromised individuals with a focus on the roles of bacterial factors and neutrophil defects in pathogenesis.

  18. Inhibition of Burkholderia multivorans Adhesion to Lung Epithelial Cells by Bivalent Lactosides

    Directory of Open Access Journals (Sweden)

    Trinidad Velasco-Torrijos

    2012-08-01

    Full Text Available Burkholderia cepacia complex (Bcc is an opportunistic pathogen in cystic fibrosis patients which is inherently resistant to antimicrobial agents. The mechanisms of attachment and pathogenesis of Bcc, a group of 17 species, are poorly understood. The most commonly identified Bcc species in newly colonised patients, Burkholderia multivorans, continues to be acquired from the environment. Development of therapies which can prevent or reduce the risk of colonization on exposure to Bcc in the environment would be a better alternative to antimicrobial agents. Previously, it has been shown that Bcc strains bound to many glycolipid receptors on lung epithelia. Using a real-time PCR method to quantify the levels of binding of B. multivorans to the lung epithelial cells, we have examined glycoconjugate derivatives for their potential to inhibit host cell attachment. Bivalent lactosides previously shown to inhibit galectin binding significantly reduced the attachment of B. multivorans to CF lung epithelial cells at micromolar concentrations. This was in contrast to monosaccharides and lactose, which were only effective in the millimolar range. Development of glycoconjugate therapies such as these, which inhibit attachment to lung epithelial cells, represent an alternative means of preventing infection with inherently antimicrobially resistant pathogens such as B. multivorans.

  19. Genomovars of Burkholderia cepacia Complex from Rice Rhizosphere and Clinic in China

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Burkholderia cepacia is regarded as a genetically distinct but phenotypically similar bacteria group referring to Burkholderia cepacia complex (Bcc), which is found not only in clinic but also in rice growing environment. It is very important in microbial safety of rice for us to understand the genomovar status of Bcc. Genomovar analysis was performed among 87 Bcc isolates by means of Hae Ⅲ-recA RFLP assays and species-specific PCR tests. Three genomovars were found from the rice rhizosphere including Ⅰ, ⅢB and Ⅴ, and genomovar Ⅴ was predominant. Genomovars Ⅰ, ⅢA and ⅢB existed in the clinical samples, and genomovar ⅢA was the most popular. It showed that genomovar composition was different between the Bcc strains from the rice rhizosphere and clinical environment. Simultaneously, the results revealed the genetic diversity of Bcc strains from the rice rhizosphere, and genomovar Ⅲ referred as virulent species in clinic also existed in the rice rhizosphere.

  20. Intraspecific variation in Burkholderia caledonica: Europe vs. Africa and soil vs. endophytic isolates.

    Science.gov (United States)

    Verstraete, Brecht; Peeters, Charlotte; van Wyk, Braam; Smets, Erik; Dessein, Steven; Vandamme, Peter

    2014-05-01

    The best-known interaction between bacteria and plants is the Rhizobium-legume symbiosis, but other bacteria-plant interactions exist, such as between Burkholderia and Rubiaceae (coffee family). A number of bacterial endophytes in Rubiaceae are closely related to the soil bacterium Burkholderia caledonica. This intriguing observation is explored by investigating isolates from different geographic regions (Western Europe vs. sub-Saharan Africa) and from different niches (free-living bacteria in soil vs. endophytic bacteria in host plants). The multilocus sequence analysis shows five clades, of which clade 1 with two basal isolates deviates from the rest and is therefore not considered further. All other isolates belong to the species B. caledonica, but two genetically different groups are identified. Group A holds only European isolates and group B holds isolates from Africa, with the exception of one European isolate. Although the European and African isolates are considered one species, some degree of genetic differentiation is evident. Endophytic isolates of B. caledonica are found in certain members of African Rubiaceae, but only in group B. Within this group, the endophytes cannot be distinguished from the soil isolates, which indicates a possible exchange of bacteria between soil and host plant. PMID:24433672

  1. Development and validation of Burkholderia pseudomallei-specific real-time PCR assays for clinical, environmental or forensic detection applications.

    Directory of Open Access Journals (Sweden)

    Erin P Price

    Full Text Available The bacterium Burkholderia pseudomallei causes melioidosis, a rare but serious illness that can be fatal if untreated or misdiagnosed. Species-specific PCR assays provide a technically simple method for differentiating B. pseudomallei from near-neighbor species. However, substantial genetic diversity and high levels of recombination within this species reduce the likelihood that molecular signatures will differentiate all B. pseudomallei from other Burkholderiaceae. Currently available molecular assays for B. pseudomallei detection lack rigorous validation across large in silico datasets and isolate collections to test for specificity, and none have been subjected to stringent quality control criteria (accuracy, precision, selectivity, limit of quantitation (LoQ, limit of detection (LoD, linearity, ruggedness and robustness to determine their suitability for environmental, clinical or forensic investigations. In this study, we developed two novel B. pseudomallei specific assays, 122018 and 266152, using a dual-probe approach to differentiate B. pseudomallei from B. thailandensis, B. oklahomensis and B. thailandensis-like species; other species failed to amplify. Species specificity was validated across a large DNA panel (>2,300 samples comprising Burkholderia spp. and non-Burkholderia bacterial and fungal species of clinical and environmental relevance. Comparison of assay specificity to two previously published B. pseudomallei-specific assays, BurkDiff and TTS1, demonstrated comparable performance of all assays, providing between 99.7 and 100% specificity against our isolate panel. Last, we subjected 122018 and 266152 to rigorous quality control analyses, thus providing quantitative limits of assay performance. Using B. pseudomallei as a model, our study provides a framework for comprehensive quantitative validation of molecular assays and provides additional, highly validated B. pseudomallei assays for the scientific research community.

  2. Entropy of Causal Horizons

    CERN Document Server

    Howard, Eric M

    2016-01-01

    We analyze spacetimes with horizons and study the thermodynamic aspects of causal horizons, suggesting that the resemblance between gravitational and thermodynamic systems has a deeper quantum mechanical origin. We find that the observer dependence of such horizons is a direct consequence of associating a temperature and entropy to a spacetime. The geometrical picture of a horizon acting as a one-way membrane for information flow can be accepted as a natural interpretation of assigning a quantum field theory to a spacetime with boundary, ultimately leading to a close connection with thermodynamics.

  3. Quantum information causality.

    Science.gov (United States)

    Pitalúa-García, Damián

    2013-05-24

    How much information can a transmitted physical system fundamentally communicate? We introduce the principle of quantum information causality, which states the maximum amount of quantum information that a quantum system can communicate as a function of its dimension, independently of any previously shared quantum physical resources. We present a new quantum information task, whose success probability is upper bounded by the new principle, and show that an optimal strategy to perform it combines the quantum teleportation and superdense coding protocols with a task that has classical inputs. PMID:23745844

  4. Inferring deterministic causal relations

    OpenAIRE

    Daniusis, Povilas; Janzing, Dominik; Mooij, Joris; Zscheischler, Jakob; Steudel, Bastian; Zhang, Kun; Schoelkopf, Bernhard

    2012-01-01

    We consider two variables that are related to each other by an invertible function. While it has previously been shown that the dependence structure of the noise can provide hints to determine which of the two variables is the cause, we presently show that even in the deterministic (noise-free) case, there are asymmetries that can be exploited for causal inference. Our method is based on the idea that if the function and the probability density of the cause are chosen independently, then the ...

  5. Oropharyngeal aspiration of Burkholderia mallei and Burkholderia pseudomallei in BALB/c mice.

    Directory of Open Access Journals (Sweden)

    Kevin L Schully

    Full Text Available Burkholderia mallei and Burkholderia pseudomallei are potentially lethal pathogens categorized as biothreat agents due, in part, to their ability to be disseminated via aerosol. There are no protective vaccines against these pathogens and treatment options are limited and cumbersome. Since disease severity is greatest when these agents are inhaled, efforts to develop pre- or post-exposure prophylaxis focus largely on inhalation models of infection. Here, we demonstrate a non-invasive and technically simple method for affecting the inhalational challenge of BALB/c mice with B. pseudomallei and B. mallei. In this model, two investigators utilized common laboratory tools such as forceps and a micropipette to conduct and characterize an effective and reproducible inhalational challenge of BALB/c mice with B. mallei and B. pseudomallei. Challenge by oropharyngeal aspiration resulted in acute disease. Additionally, 50% endpoints for B. pseudomallei K96243 and B. mallei ATCC 23344 were nearly identical to published aerosol challenge methods. Furthermore, the pathogens disseminated to all major organs typically targeted by these agents where they proliferated. The pro-inflammatory cytokine production in the proximal and peripheral fluids demonstrated a rapid and robust immune response comparable to previously described murine and human studies. These observations demonstrate that OA is a viable alternative to aerosol exposure.

  6. Experimental Phage Therapy for Burkholderia pseudomallei Infection.

    Science.gov (United States)

    Guang-Han, Ong; Leang-Chung, Choh; Vellasamy, Kumutha Malar; Mariappan, Vanitha; Li-Yen, Chang; Vadivelu, Jamuna

    2016-01-01

    Burkholderia pseudomallei is an intracellular Gram-negative bacterial pathogen intrinsically resistant to a variety of antibiotics. Phages have been developed for use as an alternative treatment therapy, particularly for bacterial infections that do not respond to conventional antibiotics. In this study, we investigated the use of phages to treat cells infected with B. pseudomallei. Phage C34 isolated from seawater was purified and characterised on the basis of its host range and morphology using transmission electron microscopy (TEM). Phage C34 was able to lyse 39.5% of B. pseudomallei clinical strains. Due to the presence of contractile tail, phage C34 is classified as a member of the family Myoviridae, a tailed double-stranded DNA virus. When 2 × 105 A549 cells were exposed to 2 × 107 PFU of phage C34, 24 hours prior to infection with 2 × 106 CFU of B. pseudomallei, it was found that the survivability of the cells increased to 41.6 ± 6.8% as compared to 22.8 ± 6.0% in untreated control. Additionally, application of phage successfully rescued 33.3% of mice infected with B. pseudomallei and significantly reduced the bacterial load in the spleen of the phage-treated mice. These findings indicate that phage can be a potential antimicrobial agent for B. pseudomallei infections. PMID:27387381

  7. Burkholderia pseudomallei transcriptional adaptation in macrophages

    Directory of Open Access Journals (Sweden)

    Chieng Sylvia

    2012-07-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a facultative intracellular pathogen of phagocytic and non-phagocytic cells. How the bacterium interacts with host macrophage cells is still not well understood and is critical to appreciate the strategies used by this bacterium to survive and how intracellular survival leads to disease manifestation. Results Here we report the expression profile of intracellular B. pseudomallei following infection of human macrophage-like U937 cells. During intracellular growth over the 6 h infection period, approximately 22 % of the B. pseudomallei genome showed significant transcriptional adaptation. B. pseudomallei adapted rapidly to the intracellular environment by down-regulating numerous genes involved in metabolism, cell envelope, motility, replication, amino acid and ion transport system and regulatory function pathways. Reduced expression in catabolic and housekeeping genes suggested lower energy requirement and growth arrest during macrophage infection, while expression of genes encoding anaerobic metabolism functions were up regulated. However, whilst the type VI secretion system was up regulated, expression of many known virulence factors was not significantly modulated over the 6hours of infection. Conclusions The transcriptome profile described here provides the first comprehensive view of how B. pseudomallei survives within host cells and will help identify potential virulence factors and proteins that are important for the survival and growth of B. pseudomallei within human cells.

  8. Burkholderia pseudomallei musculoskeletal infections (melioidosis in India

    Directory of Open Access Journals (Sweden)

    Pandey Vivek

    2010-01-01

    Full Text Available Melioidosis, an infection due to gram negative Burkholderia pseudomallei, is an important cause of sepsis in east Asia especially Thailand and northern Australia. It usually causes abscesses in lung, liver, spleen, skeletal muscle and parotids especially in patients with diabetes, chronic renal failure and thalassemia. Musculoskeletal melioidosis is not common in India even though sporadic cases have been reported mostly involving soft tissues. During a two-year-period, we had five patients with musculoskeletal melioidosis. All patients presented with multifocal osteomyelitis, recurrent osteomyelitis or septic arthritis. One patient died early because of septicemia and multi-organ failure. All patients were diagnosed on the basis of positive pus culture. All patients were treated by surgical debridement followed by a combination of antibiotics; (ceftazidime, amoxy-clavulanic acid, co-trimoxazole and doxycycline for six months except for one who died due to fulminant septicemia. All other patients recovered completely with no recurrences. With increasing awareness and better diagnostic facilities, probably musculoskeletal melioidosis will be increasingly diagnosed in future.

  9. Recent Advances in Burkholderia mallei and B. pseudomallei Research

    Science.gov (United States)

    Hatcher, Christopher L.; Muruato, Laura A.

    2015-01-01

    Burkholderia mallei and Burkholderia pseudomallei are Gram-negative organisms, which are etiological agents of glanders and melioidosis, respectively. Although only B. pseudomallei is responsible for a significant number of human cases, both organisms are classified as Tier 1 Select Agents and their diseases lack effective diagnosis and treatment. Despite a recent resurgence in research pertaining to these organisms, there are still a number of knowledge gaps. This article summarizes the latest research progress in the fields of B. mallei and B. pseudomallei pathogenesis, vaccines, and diagnostics. PMID:25932379

  10. Experimental test of nonlocal causality.

    Science.gov (United States)

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G; Fedrizzi, Alessandro

    2016-08-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell's local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect.

  11. Causal inference based on counterfactuals

    Directory of Open Access Journals (Sweden)

    Höfler M

    2005-09-01

    Full Text Available Abstract Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept.

  12. Experimental test of nonlocal causality.

    Science.gov (United States)

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G; Fedrizzi, Alessandro

    2016-08-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell's local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect. PMID:27532045

  13. 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.

  14. Experimental test of nonlocal causality

    OpenAIRE

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G.; Fedrizzi, Alessandro

    2016-01-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell’s local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data fro...

  15. Causal evolution of wave packets

    CERN Document Server

    Eckstein, Michał

    2016-01-01

    Drawing from the optimal transport theory adapted to the relativistic setting we formulate the principle of a causal flow of probability and apply it in the wave packet formalism. We demonstrate that whereas the Dirac system is causal, the relativistic-Schr\\"odinger Hamiltonian impels a superluminal evolution of probabilities. We quantify the causality breakdown in the latter system and argue that, in contrast to the popular viewpoint, it is not related to the localisation properties of the states.

  16. Relativistic hydrodynamics - causality and stability

    OpenAIRE

    Ván, P.; Biró, T. S.

    2007-01-01

    Causality and stability in relativistic dissipative hydrodynamics are important conceptual issues. We argue that causality is not restricted to hyperbolic set of differential equations. E.g. heat conduction equation can be causal considering the physical validity of the theory. Furthermore we propose a new concept of relativistic internal energy that clearly separates the dissipative and non-dissipative effects. We prove that with this choice we remove all known instabilities of the linear re...

  17. Relationship of causal effects in a causal chain and related inference

    Institute of Scientific and Technical Information of China (English)

    GENG; Zhi; HE; Yangbo; WANG; Xueli

    2004-01-01

    This paper discusses the relationship among the total causal effect and local causal effects in a causal chain and identifiability of causal effects. We show a transmission relationship of causal effects in a causal chain. According to the relationship, we give an approach to eliminating confounding bias through controlling for intermediate variables in a causal chain.

  18. Causality Statistical Perspectives and Applications

    CERN Document Server

    Berzuini, Carlo; Bernardinell, Luisa

    2012-01-01

    A state of the art volume on statistical causality Causality: Statistical Perspectives and Applications presents a wide-ranging collection of seminal contributions by renowned experts in the field, providing a thorough treatment of all aspects of statistical causality. It covers the various formalisms in current use, methods for applying them to specific problems, and the special requirements of a range of examples from medicine, biology and economics to political science. This book:Provides a clear account and comparison of formal languages, concepts and models for statistical causality. Addr

  19. A new bacterial disease of carnation in Portugal caused by Burkholderia andropogonis

    Directory of Open Access Journals (Sweden)

    Madalena Eloy

    2008-12-01

    Full Text Available The occurrence of a leaf spot disease of carnation caused by Burkholderia andropogonis is recorded for the first time in Portugal. Symptoms consisted of ‘eyespot’ lesions on all aerial plant parts, often bordered by water-soaked halos on the leaves. As the disease progressed lesions became dark brown and affected areas dried out. Phenotypic studies and Polymerase Chain Reaction using specific primers Pf/Pr targeted to 16S rDNA of B. andropogonis were used to identify the pathogen. Pathogenicity tests on china pink plants, re-isolation of the pathogen from inoculated plants and further PCR testing confirmed the identification of the bacterium. Infected plants came from an open air nursery and the whole production was destroyed to avoid dissemination of the pathogen.A ocorrência da mancha bacteriana do craveiro causada por Burkholderia andropogonis é pela primeira vez assinalada em Portugal. Os sintomas observados consistiam em manchas em forma de olho-de-perdiz em todos os órgãos aéreos das plantas afectadas, frequentemente circundadas por halos hidrópicos nas folhas. À medida que a doença progredia, as lesões adquiriam uma coloração castanha escura, acabando os órgãos afectados por secar. A identificação do agente causal da doença baseou-se no estudo dos seus caracteres fenotípicos e na Reacção em Cadeia da Polimerase (PCR, utilizando os iniciadores específicos Pf/Pr dirigidos à região 16S rDNA de B. andropogonis. A identificação foi confirmada por ensaios de patogenicidade em cravinas, reisolamento do agente causal da doença a partir das plantas inoculadas e novos ensaios PCR. As plantas infectadas provinham de um viveiro ao ar livre e toda a produção foi destruída a fim de evitar a disseminação do patogéneo.

  20. Identifiability of causal effect for a simple causal model

    Institute of Scientific and Technical Information of China (English)

    郑忠国; 张艳艳; 童行伟

    2002-01-01

    Counterfactual model is put forward to discuss the causal inference in the directed acyclic graph and its corresponding identifiability is thus studied with the ancillary information based on conditional independence. It is shown that the assumption of ignorability can be expanded to the assumption of replaceability,under which the causal efiects are identifiable.

  1. Structural Equations and Causal Explanations: Some Challenges for Causal SEM

    Science.gov (United States)

    Markus, Keith A.

    2010-01-01

    One common application of structural equation modeling (SEM) involves expressing and empirically investigating causal explanations. Nonetheless, several aspects of causal explanation that have an impact on behavioral science methodology remain poorly understood. It remains unclear whether applications of SEM should attempt to provide complete…

  2. Research Status and Prospect ofBurkholderia glumae, the Pathogen Causing Bacterial Panicle Blight

    Institute of Scientific and Technical Information of China (English)

    CUI Zhou-qi; ZHU Bo; XIE Guan-lin; LI Bin; HUANG Shi-wen

    2016-01-01

    Bacterial panicle blight caused by Burkholderia glumae is one of the most severe seed-borne bacterial diseases of rice in the world. Currently, this disease has affected many countries of Asia, Africa, South and North America. It is a typical example of the shifting from minor plant disease to major disease due to the changes of environmental conditions. Some virulent factors of B. glumae have been identified, including toxoflavins and lipases, whose productions are dependent on the TofI/TofR quorum-sensing system, and type III effectors. In spite of its economic significance, neither effective control measure for this disease nor resistant rice variety is currently available. In recent years, genomics, transcriptomics and other molecular methods have provided useful information for better understanding the molecular mechanisms underlyingB. glumaevirulence and the rice defence mechanisms against pathogens. For the prevention of this pathogen, our laboratory has developed a rapid and sensitive multiplex PCR assay for detecting and distinguishingB. glumae from otherBurkholderia species. This improved understanding ofB. glumae will shed new light on bacterial panicle blight disease management.

  3. Inferring deterministic causal relations

    CERN Document Server

    Daniusis, Povilas; Mooij, Joris; Zscheischler, Jakob; Steudel, Bastian; Zhang, Kun; Schoelkopf, Bernhard

    2012-01-01

    We consider two variables that are related to each other by an invertible function. While it has previously been shown that the dependence structure of the noise can provide hints to determine which of the two variables is the cause, we presently show that even in the deterministic (noise-free) case, there are asymmetries that can be exploited for causal inference. Our method is based on the idea that if the function and the probability density of the cause are chosen independently, then the distribution of the effect will, in a certain sense, depend on the function. We provide a theoretical analysis of this method, showing that it also works in the low noise regime, and link it to information geometry. We report strong empirical results on various real-world data sets from different domains.

  4. Survival of Burkholderia pseudomallei in Water

    Directory of Open Access Journals (Sweden)

    Woods Donald E

    2008-05-01

    Full Text Available Abstract Background The ability of Burkholderia pseudomallei to survive in water likely contributes to its environmental persistence in endemic regions. To determine the physiological adaptations which allow B. pseudomallei to survive in aqueous environments, we performed microarray analyses of B. pseudomallei cultures transferred from Luria broth (LB to distilled water. Findings Increased expression of a gene encoding for a putative membrane protein (BPSL0721 was confirmed using a lux-based transcriptional reporter system, and maximal expression was noted at approximately 6 hrs after shifting cells from LB to water. A BPSL0721 deficient mutant of B. pseudomallei was able to survive in water for at least 90 days indicating that although involved, BPSL0721 was not essential for survival. BPSL2961, a gene encoding a putative phosphatidylglycerol phosphatase (PGP, was also induced when cells were shifted to water. This gene is likely involved in cell membrane biosynthesis. We were unable to construct a PGP mutant suggesting that the gene is not only involved in survival in water but is essential for cell viability. We also examined mutants of polyhydroxybutyrate synthase (phbC, lipopolysaccharide (LPS oligosaccharide and capsule synthesis, and these mutations did not affect survival in water. LPS mutants lacking outer core were found to lose viability in water by 200 days indicating that an intact LPS core provides an outer membrane architecture which allows prolonged survival in water. Conclusion The results from these studies suggest that B. pseudomallei survival in water is a complex process that requires an LPS molecule which contains an intact core region.

  5. Characterization of the papilionoid-Burkholderia interaction in the Fynbos biome: The diversity and distribution of beta-rhizobia nodulating Podalyria calyptrata (Fabaceae, Podalyrieae).

    Science.gov (United States)

    Lemaire, Benny; Van Cauwenberghe, Jannick; Verstraete, Brecht; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Sprent, Janet; James, Euan K; Muasya, A Muthama

    2016-02-01

    The South African Fynbos soils are renowned for nitrogen-fixing Burkholderia associated with diverse papilionoid legumes of the tribes Crotalarieae, Hypocalypteae, Indigofereae, Phaseoleae and Podalyrieae. However, despite numerous rhizobial studies in the region, the symbiotic diversity of Burkholderia has not been investigated in relation to a specific host legume and its geographical provenance. This study analyzed the diversity of nodulating strains of Burkholderia from the legume species Podalyria calyptrata. Diverse lineages were detected that proved to be closely related to Burkholderia taxa, originating from hosts in other legume tribes. By analyzing the genetic variation of chromosomal (recA) and nodulation (nodA) sequence data in relation to the sampling sites we assessed the geographical distribution patterns of the P. calyptrata symbionts. Although we found a degree of genetically differentiated rhizobial populations, a correlation between genetic (recA and nodA) and geographic distances among populations was not observed, suggesting high rates of dispersal and rhizobial colonization within Fynbos soils. PMID:26689612

  6. Production and characterization of chimeric monoclonal antibodies against Burkholderia pseudomallei and B. mallei using the DHFR expression system.

    Directory of Open Access Journals (Sweden)

    Hyung-Yong Kim

    Full Text Available Burkholderia pseudomallei (BP and B. mallei (BM are closely related gram-negative, facultative anaerobic bacteria which cause life-threatening melioidosis in human and glanders in horse, respectively. Our laboratory has previously generated and characterized more than 100 mouse monoclonal antibodies (MAbs against BP and BM, according to in vitro and in vivo assay. In this study, 3 MAbs (BP7 10B11, BP7 2C6, and BP1 7F7 were selected to develop into chimeric mouse-human monoclonal antibodies (cMAbs against BP and/or BM. For the stable production of cMAbs, we constructed 4 major different vector systems with a dihydrofolate reductase (DHFR amplification marker, and optimized transfection/selection conditions in mammalian host cells with the single-gene and/or double-gene expression system. These 3 cMAbs were stably produced by the DHFR double mutant Chinese hamster ovarian (CHO-DG44 cells. By ELISA and Western blot analysis using whole bacterial antigens treated by heat (65°C/90 min, sodium periodate, and proteinase K, the cMAb BP7 10B11 (cMAb CK1 reacted with glycoproteins (34, 38, 48 kDa in BP; 28, 38, 48 kDa in BM. The cMAb BP7 2C6 (cMAb CK2 recognized surface-capsule antigens with molecular sizes of 38 to 52 kDa, and 200 kDa in BM. The cMAb CK2 was weakly reactive to 14∼28, 200 kDa antigens in BP. The cMAb BP1 7F7 (cMAb CK3 reacted with lipopolysaccharides (38∼52 kDa in BP; 38∼60 kDa in B. thailandensis. Western blot results with the outer surface antigens of the 3 Burkholderia species were consistent with results with the whole Burkholderia cell antigens, suggesting that these immunodominant antigens reacting with the 3 cMAbs were primarily present on the outer surface of the Burkholderia species. These 3 cMAbs would be useful for analyzing the role of the major outer surface antigens in Burkholderia infection.

  7. The Madagascar hissing cockroach as a novel surrogate host for Burkholderia pseudomallei, B. mallei and B. thailandensis

    Directory of Open Access Journals (Sweden)

    Fisher Nathan A

    2012-06-01

    Full Text Available Abstract Background Burkholderia pseudomallei and Burkholderia mallei are gram-negative pathogens responsible for the diseases melioidosis and glanders, respectively. Both species cause disease in humans and animals and have been designated as category B select agents by the Centers for Disease Control and Prevention (CDC. Burkholderia thailandensis is a closely related bacterium that is generally considered avirulent for humans. While it can cause disease in rodents, the B. thailandensis 50% lethal dose (LD50 is typically ≥ 104-fold higher than the B. pseudomallei and B. mallei LD50 in mammalian models of infection. Here we describe an alternative to mammalian hosts in the study of virulence and host-pathogen interactions of these Burkholderia species. Results Madagascar hissing cockroaches (MH cockroaches possess a number of qualities that make them desirable for use as a surrogate host, including ease of breeding, ease of handling, a competent innate immune system, and the ability to survive at 37°C. MH cockroaches were highly susceptible to infection with B. pseudomallei, B. mallei and B. thailandensis and the LD50 was 50 for Escherichia coli in MH cockroaches was >105 cfu. B. pseudomallei, B. mallei, and B. thailandensis cluster 1 type VI secretion system (T6SS-1 mutants were all attenuated in MH cockroaches, which is consistent with previous virulence studies conducted in rodents. B. pseudomallei mutants deficient in the other five T6SS gene clusters, T6SS-2 through T6SS-6, were virulent in both MH cockroaches and hamsters. Hemocytes obtained from MH cockroaches infected with B. pseudomallei harbored numerous intracellular bacteria, suggesting that this facultative intracellular pathogen can survive and replicate inside of MH cockroach phagocytic cells. The hemolymph extracted from these MH cockroaches also contained multinuclear giant cells (MNGCs with intracellular B. pseudomallei, which indicates that infected hemocytes can

  8. Understanding the Pathogenicity of Burkholderia contaminans, an Emerging Pathogen in Cystic Fibrosis

    Science.gov (United States)

    Nunvar, Jaroslav; Kalferstova, Lucie; Bloodworth, Ruhi A. M.; Kolar, Michal; Degrossi, Jose; Lubovich, Silvina; Cardona, Silvia T.; Drevinek, Pavel

    2016-01-01

    Several bacterial species from the Burkholderia cepacia complex (Bcc) are feared opportunistic pathogens that lead to debilitating lung infections with a high risk of developing fatal septicemia in cystic fibrosis (CF) patients. However, the pathogenic potential of other Bcc species is yet unknown. To elucidate clinical relevance of Burkholderia contaminans, a species frequently isolated from CF respiratory samples in Ibero-American countries, we aimed to identify its key virulence factors possibly linked with an unfavorable clinical outcome. We performed a genome-wide comparative analysis of two isolates of B. contaminans ST872 from sputum and blood culture of a female CF patient in Argentina. RNA-seq data showed significant changes in expression for quorum sensing-regulated virulence factors and motility and chemotaxis. Furthermore, we detected expression changes in a recently described low-oxygen-activated (lxa) locus which encodes stress-related proteins, and for two clusters responsible for the biosynthesis of antifungal and hemolytic compounds pyrrolnitrin and occidiofungin. Based on phenotypic assays that confirmed changes in motility and in proteolytic, hemolytic and antifungal activities, we were able to distinguish two phenotypes of B. contaminans that coexisted in the host and entered her bloodstream. Whole genome sequencing revealed that the sputum and bloodstream isolates (each representing a distinct phenotype) differed by over 1,400 mutations as a result of a mismatch repair-deficient hypermutable state of the sputum isolate. The inferred lack of purifying selection against nonsynonymous mutations and the high rate of pseudogenization in the derived isolate indicated limited evolutionary pressure during evolution in the nutrient-rich, stable CF sputum environment. The present study is the first to examine the genomic and transcriptomic differences between longitudinal isolates of B. contaminans. Detected activity of a number of putative virulence

  9. Novel lytic bacteriophages from soil that lyse Burkholderia pseudomallei.

    Science.gov (United States)

    Yordpratum, Umaporn; Tattawasart, Unchalee; Wongratanacheewin, Surasakdi; Sermswan, Rasana W

    2011-01-01

    Burkholderia pseudomallei is a Gram-negative saprophytic bacterium that causes severe sepsis with a high mortality rate in humans and a vaccine is not available. Bacteriophages are viruses of bacteria that are ubiquitous in nature. Several lysogenic phages of Burkholderia spp. have been found but information is scarce for lytic phages. Six phages, ST2, ST7, ST70, ST79, ST88 and ST96, which lyse B. pseudomallei, were isolated from soil in an endemic area. The phages belong to the Myoviridae family. The range of estimated genome sizes is 24.0-54.6 kb. Phages ST79 and ST96 lysed 71% and 67% of tested B. pseudomallei isolates and formed plaques on Burkholderia mallei but not other tested bacteria, with the exception of closely related Burkholderia thailandensis which was lysed by ST2 and ST96 only. ST79 and ST96 were observed to clear a mid-log culture by lysis within 6 h when infected at a multiplicity of infection of 0.1. As ST79 and ST96 phages effectively lysed B. pseudomallei, their potential use as a biocontrol of B. pseudomallei in the environment or alternative treatment in infected hosts could lead to benefits from phages that are available in nature. PMID:21091532

  10. Expert Causal Reasoning and Explanation.

    Science.gov (United States)

    Kuipers, Benjamin

    The relationship between cognitive psychologists and researchers in artificial intelligence carries substantial benefits for both. An ongoing investigation in causal reasoning in medical problem solving systems illustrates this interaction. This paper traces a dialectic of sorts in which three different types of causal resaoning for medical…

  11. Introduction to causal dynamical triangulations

    DEFF Research Database (Denmark)

    Görlich, Andrzej

    2013-01-01

    The method of causal dynamical triangulations is a non-perturbative and background-independent approach to quantum theory of gravity. In this review we present recent results obtained within the four dimensional model of causal dynamical triangulations. We describe the phase structure of the model...

  12. Re-thinking local causality

    NARCIS (Netherlands)

    Friederich, Simon

    2015-01-01

    There is widespread belief in a tension between quantum theory and special relativity, motivated by the idea that quantum theory violates J. S. Bell's criterion of local causality, which is meant to implement the causal structure of relativistic space-time. This paper argues that if one takes the es

  13. Causal Inference and Developmental Psychology

    Science.gov (United States)

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  14. Neural Correlates of Causal Power Judgments

    Directory of Open Access Journals (Sweden)

    Denise Dellarosa Cummins

    2014-12-01

    Full Text Available Causal inference is a fundamental component of cognition and perception. Probabilistic theories of causal judgment (most notably causal Bayes networks derive causal judgments using metrics that integrate contingency information. But human estimates typically diverge from these normative predictions. This is because human causal power judgments are typically strongly influenced by beliefs concerning underlying causal mechanisms, and because of the way knowledge is retrieved from human memory during the judgment process. Neuroimaging studies indicate that the brain distinguishes causal events from mere covariation, and between perceived and inferred causality. Areas involved in error prediction are also activated, implying automatic activation of possible exception cases during causal decision-making.

  15. The Visual Causality Analyst: An Interactive Interface for Causal Reasoning.

    Science.gov (United States)

    Wang, Jun; Mueller, Klaus

    2016-01-01

    Uncovering the causal relations that exist among variables in multivariate datasets is one of the ultimate goals in data analytics. Causation is related to correlation but correlation does not imply causation. While a number of casual discovery algorithms have been devised that eliminate spurious correlations from a network, there are no guarantees that all of the inferred causations are indeed true. Hence, bringing a domain expert into the casual reasoning loop can be of great benefit in identifying erroneous casual relationships suggested by the discovery algorithm. To address this need we present the Visual Causal Analyst-a novel visual causal reasoning framework that allows users to apply their expertise, verify and edit causal links, and collaborate with the causal discovery algorithm to identify a valid causal network. Its interface consists of both an interactive 2D graph view and a numerical presentation of salient statistical parameters, such as regression coefficients, p-values, and others. Both help users in gaining a good understanding of the landscape of causal structures particularly when the number of variables is large. Our framework is also novel in that it can handle both numerical and categorical variables within one unified model and return plausible results. We demonstrate its use via a set of case studies using multiple practical datasets. PMID:26529703

  16. Removal of Burkholderia cepacia biofilms with oxidants

    Science.gov (United States)

    Koenig, D. W.; Mishra, S. K.; Pierson, D. L.

    1995-01-01

    Iodine is used to disinfect the water system aboard US space shuttles and is the anticipated biocide for the international space station. Water quality on spacecraft must be maintained at the highest possible levels for the safety of the crew. Furthermore, the treatment process used to maintain the quality of water on research must be robust and operate for long periods with minimal crew intervention. Biofilms are recalcitrant and pose a major threat with regard to chronic contamination of spacecraft water systems. We measured the effectiveness of oxidizing biocides on the removal and regrowth of Burkholderia (Pseudomonas) cepacia biofilms. B. cepacia, isolated from the water distribution system of the space shuttle Discovery, was grown in continuous culture to produce a bacterial contamination source for biofilm formation and removal studies. A 10(7) CFU ml-1 B. cepacia suspension, in distilled water, was used to form biofilms on 3000 micrometers2 glass surfaces. Rates of attachment were measured directly with image analysis and were found to be 7.8, 15.2, and 22.8 attachment events h-1 for flow rates of 20.7, 15.2, and 9.8 ml min-1, respectively. After 18 h of formation, the B. cepacia biofilms were challenged with oxidants (ozone, chlorine, and iodine) and the rates of biofilm removal determined by image analysis. Fifty percent of the biofilm material was removed in the first hour of continous treatment with 24 mg l-1 chlorine or 2 mg l-1 ozone. Iodine (48 mg l-1) did not remove any measurable cellular material after 6 h continuous contact. After this first removal of biofilms by the oxidants, the surface was allowed to refoul and was again treated with the biocide. Iodine was the only compound that was unable to remove cellular debris from either primary or secondary biofilms. Moreover, treating primary biofilms with iodine increased the rate of formation of secondary biofilms, from 4.4 to 5.8 attachment events h-1. All the oxidants tested inactivated the B

  17. ["Karoshi" and causal relationships].

    Science.gov (United States)

    Hamajima, N

    1992-08-01

    This paper aims to introduce a measure for use by physicians for stating the degree of probable causal relationship for "Karoshi", ie, a sudden death from cerebrovascular diseases or ischemic heart diseases under occupational stresses, as well as to give a brief description for legal procedures associated with worker's compensation and civil trial in Japan. It is a well-used measure in epidemiology, "attributable risk percent (AR%)", which can be applied to describe the extent of contribution to "Karoshi" of the excess occupational burdens the deceased worker was forced to bear. Although several standards such as average occupational burdens for the worker, average occupational burdens for an ordinary worker, burdens in a nonoccupational life, and a complete rest, might be considered for the AR% estimation, the average occupational burdens for an ordinary worker should normally be utilized as a standard for worker's compensation. The adoption of AR% could be helpful for courts to make a consistent judgement whether "Karoshi" cases are compensatable or not. PMID:1392028

  18. Screening a mushroom extract library for activity against Acinetobacter baumannii and Burkholderia cepacia and the identification of a compound with anti-Burkholderia activity

    Directory of Open Access Journals (Sweden)

    Rott Marc

    2010-01-01

    Full Text Available Abstract Background Acinetobacter baumannii and species within the Burkholderia cepacia complex (BCC are significant opportunistic bacterial pathogens of humans. These species exhibit a high degree of antibiotic resistance, and some clinical isolates are resistant to all currently available antimicrobial drugs used for treatment. Thus, new drugs are needed to treat infections by these species. Mushrooms could be a potential source for new drugs to treat A. baumannii and BCC infections. Methods The aim of this study was to screen a library of crude extracts from 330 wild mushrooms by disk diffusion assays for antibacterial activity against A. baumannii and Burkholderia cepacia in the hope of identifying a novel natural drug that could be used to treat infections caused by these species. Once positive hits were identified, the extracts were subjected to bioassay-guided separations to isolate and identify the active drug molecules. MICs were performed to gauge the in vitro activity of the purified compounds. Results Only three crude extracts (0.9% had activity against A. baumannii and B. cepacia. Compounds from two of these extracts had MICs greater than 128 μg/ml, and further analyses were not performed. From the third extract, prepared from Leucopaxillus albissimus, 2-aminoquinoline (2-AQ was isolated. This compound exhibited a modest MIC in vitro against strains from nine different BCC species, including multi-drug resistant clinical isolates (MIC = 8-64 μg/ml, and a weak MIC (128 μg/ml against A baumannii. The IC50 against a murine monocyte line was 1.5 mg/ml. Conclusion The small number of positive hits in this study suggests that finding a new drug from mushrooms to treat Gram-negative bacterial infections may be difficult. Although 2-AQ was identified in one mushroom, and it was shown to inhibit the growth of multi-drug resistant BCC isolates, the relatively high MICs (8-128 μg/ml for both A. baumannii and BCC strains suggests that 2-AQ

  19. Classical planning and causal implicatures

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Benotti, Luciana

    to generate clarification requests"; as a result we can model task-oriented dialogue as an interactive process locally structured by negotiation of the underlying task. We give several examples of Frolog-human dialog, discuss the limitations imposed by the classical planning paradigm, and indicate......In this paper we motivate and describe a dialogue manager (called Frolog) which uses classical planning to infer causal implicatures. A causal implicature is a type of Gricean relation implicature, a highly context dependent form of inference. As we shall see, causal implicatures are important...

  20. Burkholderia pseudomallei Type III Secretion System Cluster 3 ATPase BsaS, a Chemotherapeutic Target for Small-Molecule ATPase Inhibitors

    OpenAIRE

    Gong, Lan; Lai, Shu-Chin; Treerat, Puthayalai; Prescott, Mark; Adler, Ben; John D Boyce; Rodney J. Devenish

    2015-01-01

    Melioidosis is an infectious disease of high mortality for humans and other animal species; it is prevalent in tropical regions worldwide. The pathogenesis of melioidosis depends on the ability of its causative agent, the Gram-negative bacterium Burkholderia pseudomallei, to enter and survive in host cells. B. pseudomallei can escape from the phagosome into the cytosol of phagocytic cells where it replicates and acquires actin-mediated motility, avoiding killing by the autophagy-dependent pro...

  1. Identification of Burkholderia mallei and Burkholderia pseudomallei adhesins for human respiratory epithelial cells

    Directory of Open Access Journals (Sweden)

    Hogan Robert J

    2010-09-01

    Full Text Available Abstract Background Burkholderia pseudomallei and Burkholderia mallei cause the diseases melioidosis and glanders, respectively. A well-studied aspect of pathogenesis by these closely-related bacteria is their ability to invade and multiply within eukaryotic cells. In contrast, the means by which B. pseudomallei and B. mallei adhere to cells are poorly defined. The purpose of this study was to identify adherence factors expressed by these organisms. Results Comparative sequence analyses identified a gene product in the published genome of B. mallei strain ATCC23344 (locus # BMAA0649 that resembles the well-characterized Yersinia enterocolitica autotransporter adhesin YadA. The gene encoding this B. mallei protein, designated boaA, was expressed in Escherichia coli and shown to significantly increase adherence to human epithelial cell lines, specifically HEp2 (laryngeal cells and A549 (type II pneumocytes, as well as to cultures of normal human bronchial epithelium (NHBE. Consistent with these findings, disruption of the boaA gene in B. mallei ATCC23344 reduced adherence to all three cell types by ~50%. The genomes of the B. pseudomallei strains K96243 and DD503 were also found to contain boaA and inactivation of the gene in DD503 considerably decreased binding to monolayers of HEp2 and A549 cells and to NHBE cultures. A second YadA-like gene product highly similar to BoaA (65% identity was identified in the published genomic sequence of B. pseudomallei strain K96243 (locus # BPSL1705. The gene specifying this protein, termed boaB, appears to be B. pseudomallei-specific. Quantitative attachment assays demonstrated that recombinant E. coli expressing BoaB displayed greater binding to A549 pneumocytes, HEp2 cells and NHBE cultures. Moreover, a boaB mutant of B. pseudomallei DD503 showed decreased adherence to these respiratory cells. Additionally, a B. pseudomallei strain lacking expression of both boaA and boaB was impaired in its ability to

  2. On causality of extreme events

    CERN Document Server

    Zanin, Massimiliano

    2016-01-01

    Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect both linear and non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task.

  3. Causal Structure and Spacetime Singularities

    CERN Document Server

    Stoica, Ovidiu Cristinel

    2015-01-01

    In General Relativity the metric can be recovered from the structure of the lightcones and a measure giving the volume element. Since the causal structure seems to be simpler than the Lorentzian manifold structure, this suggests that it is more fundamental. But there are cases when seemingly healthy causal structure and measure determine a singular metric. Here it is shown that this is not a bug, but a feature, because big-bang and black hole singularities are instances of this situation. But while the metric is special at singularities, being singular, the causal structure and the measure are not special in an explicit way at singularities. Therefore, considering the causal structure more fundamental than the metric provides a more natural framework to deal with spacetime singularities.

  4. Causal reasoning with mental models

    OpenAIRE

    Khemlani, Sangeet S.; Barbey, Aron K.; Johnson-Laird, Philip N

    2014-01-01

    This paper outlines the model-based theory of causal reasoning. It postulates that the core meanings of causal assertions are deterministic and refer to temporally-ordered sets of possibilities: A causes B to occur means that given A, B occurs, whereas A enables B to occur means that given A, it is possible for B to occur. The paper shows how mental models represent such assertions, and how these models underlie deductive, inductive, and abductive reasoning yielding explanations. It reviews e...

  5. Consciousness and the "Causal Paradox"

    OpenAIRE

    Velmans, Max

    1996-01-01

    Viewed from a first-person perspective consciousness appears to be necessary for complex, novel human activity - but viewed from a third-person perspective consciousness appears to play no role in the activity of brains, producing a "causal paradox". To resolve this paradox one needs to distinguish consciousness of processing from consciousness accompanying processing or causing processing. Accounts of consciousness/brain causal interactions switch between first- and third-person perspectives...

  6. Realist Magic : Objects, Ontology, Causality

    OpenAIRE

    Morton, Timothy

    2013-01-01

    Object-oriented ontology offers a startlingly fresh way to think about causality that takes into account developments in physics since 1900. Causality, argues, Object Oriented Ontology (OOO), is aesthetic. In this book, Timothy Morton explores what it means to say that a thing has come into being, that it is persisting, and that it has ended. Drawing from examples in physics, biology, ecology, art, literature and music, Morton demonstrates the counterintuitive yet elegant explanatory power of...

  7. Correlation Measure Equivalence in Dynamic Causal Structures

    CERN Document Server

    Gyongyosi, Laszlo

    2016-01-01

    We prove an equivalence transformation between the correlation measure functions of the causally-unbiased quantum gravity space and the causally-biased standard space. The theory of quantum gravity fuses the dynamic (nonfixed) causal structure of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity space, the events are causally nonseparable and all time bias vanishes, which makes it no possible to use the standard causally-biased entropy and the correlation measure functions. Since a corrected causally-unbiased entropy function leads to an undefined, obscure mathematical structure, in our approach the correction is made in the data representation of the causally-unbiased space. We prove that the standard causally-biased entropy function with a data correction can be used to identify correlations in dynamic causal structures. As a corollary, all mathematical properties of the causally-biased correlation measure functions are preserved in the causally-unbiased space. The eq...

  8. Cytotoxicity Associated with Trichloroethylene Oxidation in Burkholderia cepacia G4

    OpenAIRE

    Yeager, Chris M.; Bottomley, Peter J; Arp, Daniel J.

    2001-01-01

    The effects of trichloroethylene (TCE) oxidation on toluene 2-monooxygenase activity, general respiratory activity, and cell culturability were examined in the toluene-oxidizing bacterium Burkholderia cepacia G4. Nonspecific damage outpaced inactivation of toluene 2-monooxygenase in B. cepacia G4 cells. Cells that had degraded approximately 0.5 μmol of TCE (mg of cells−1) lost 95% of their acetate-dependent O2 uptake activity (a measure of general respiratory activity), yet toluene-dependent ...

  9. Burkholderia pseudomallei Capsular Polysaccharide Conjugates Provide Protection against Acute Melioidosis

    OpenAIRE

    Scott, Andrew E.; Mary N Burtnick; Stokes, Margaret G. M.; Whelan, Adam O.; Williamson, E. Diane; Atkins, Timothy P.; Prior, Joann L.; Brett, Paul J

    2014-01-01

    Burkholderia pseudomallei, the etiologic agent of melioidosis, is a CDC tier 1 select agent that causes severe disease in both humans and animals. Diagnosis and treatment of melioidosis can be challenging, and in the absence of optimal chemotherapeutic intervention, acute disease is frequently fatal. Melioidosis is an emerging infectious disease for which there are currently no licensed vaccines. Due to the potential malicious use of B. pseudomallei as well as its impact on public health in r...

  10. Dissecting novel virulent determinants in the Burkholderia cepacia complex

    OpenAIRE

    George P Tegos; Haynes, Mark K.; Schweizer, Herbert P.

    2012-01-01

    Prevention and control of infectious diseases remains a major public health challenge and a number of highly virulent pathogens are emerging both in and beyond the hospital setting. Despite beneficial aspects such as use in biocontrol and bioremediation exhibited by members of the Burkholderia cepacia complex (Bcc) some members of this group have recently gained attention as significant bacterial pathogens due to their high levels of intrinsic antibiotic resistance, transmissibility in nosoco...

  11. Burkholderia Pseudomallei Causing Bone and Joint Infections: A Clinical Update

    OpenAIRE

    Raja, Nadeem Sajjad; Scarsbrook, Christine

    2016-01-01

    Burkholderia pseudomallei (B. pseudomallei), a causative agent of an emerging infectious disease melioidosis, is endemic in the tropical regions of the world. Due to increased international travel, the infection is now also seen outside of the tropics. The majority of patients with identified risk factors such as diabetes mellitus, heavy alcohol use, malignancy, chronic lung and kidney disease, corticosteroid use, thalassemia, rheumatic heart disease, systemic lupus erythematosus and cardiac ...

  12. Symbiotic ß-Proteobacteria beyond Legumes: Burkholderia in Rubiaceae

    OpenAIRE

    Brecht Verstraete; Steven Janssens; Erik Smets; Steven Dessein

    2013-01-01

    Symbiotic ß-proteobacteria not only occur in root nodules of legumes but are also found in leaves of certain Rubiaceae. The discovery of bacteria in plants formerly not implicated in endosymbiosis suggests a wider occurrence of plant-microbe interactions. Several ß-proteobacteria of the genus Burkholderia are detected in close association with tropical plants. This interaction has occurred three times independently, which suggest a recent and open plant-bacteria association. The presence or a...

  13. Burkholderia pseudomallei: Its Detection in Soil and Seroprevalence in Bangladesh

    OpenAIRE

    Jilani, Md. Shariful Alam; Robayet, Jamshedul Alam Mohammad; Mohiuddin, Md.; Hasan, Md. Rokib; Ahsan, Chowdhury Rafiqul; Haq, Jalaluddin Ashraful

    2016-01-01

    Background Melioidosis, caused by Burkholderia pseudomallei, is an endemic disease in Bangladesh. No systematic study has yet been done to detect the environmental source of the organism and its true extent in Bangladesh. The present study attempted to isolate B. pseudomallei in soil samples and to determine its seroprevalence in several districts in Bangladesh. Methodology and Results Soil samples were collected from rural areas of four districts of Bangladesh from where culture confirmed me...

  14. Causality, causality, causality: the view of education inputs and outputs from economics

    OpenAIRE

    Lisa Barrow; Cecilia Elena Rouse

    2005-01-01

    Educators and policy makers are increasingly intent on using scientifically-based evidence when making decisions about education policy. Thus, education research today must necessarily be focused on identifying the causal relationships between education inputs and student outcomes. In this paper we discuss methodologies for estimating the causal effect of resources on education outcomes; we also review what we believe to be the best evidence from economics on a few important inputs: spending,...

  15. Causality in physiological signals.

    Science.gov (United States)

    Müller, Andreas; Kraemer, Jan F; Penzel, Thomas; Bonnemeier, Hendrik; Kurths, Jürgen; Wessel, Niels

    2016-05-01

    Health is one of the most important non-material assets and thus also has an enormous influence on material values, since treating and preventing diseases is expensive. The number one cause of death worldwide today originates in cardiovascular diseases. For these reasons the aim of understanding the functions and the interactions of the cardiovascular system is and has been a major research topic throughout various disciplines for more than a hundred years. The purpose of most of today's research is to get as much information as possible with the lowest possible effort and the least discomfort for the subject or patient, e.g. via non-invasive measurements. A family of tools whose importance has been growing during the last years is known under the headline of coupling measures. The rationale for this kind of analysis is to identify the structure of interactions in a system of multiple components. Important information lies for example in the coupling direction, the coupling strength, and occurring time lags. In this work, we will, after a brief general introduction covering the development of cardiovascular time series analysis, introduce, explain and review some of the most important coupling measures and classify them according to their origin and capabilities in the light of physiological analyses. We will begin with classical correlation measures, go via Granger-causality-based tools, entropy-based techniques (e.g. momentary information transfer), nonlinear prediction measures (e.g. mutual prediction) to symbolic dynamics (e.g. symbolic coupling traces). All these methods have contributed important insights into physiological interactions like cardiorespiratory coupling, neuro-cardio-coupling and many more. Furthermore, we will cover tools to detect and analyze synchronization and coordination (e.g. synchrogram and coordigram). As a last point we will address time dependent couplings as identified using a recent approach employing ensembles of time series. The

  16. Uniform infinite and Gibbs causal triangulations

    NARCIS (Netherlands)

    Zohren, Stefan

    2012-01-01

    We discuss uniform infinite causal triangulations (UICT) and Gibbs causal triangulations which are probabilistic models for the causal dynamical triangulations (CDT) approach to quantum gravity. Since there is a bijection between causal triangulations and planar rooted trees we first discuss some as

  17. Causality and Tense - two temporal structure builders

    NARCIS (Netherlands)

    Oversteegen, E.

    2005-01-01

    By force of causes precede effects, causality contributes to the temporal meaning of discourse. In case of semantic causal relations, this contribution is straightforward, but in case of epistemic causal relations, it is not. In order to gain insight into the semantics of epistemic causal relations,

  18. Draft Genome Sequence of Burkholderia dolosa PC543 Isolated from Cystic Fibrosis Airways

    OpenAIRE

    Workentine, Matthew L; Michael G Surette; Bernier, Steve P

    2014-01-01

    Burkholderia dolosa is a member of the Burkholderia cepacia complex, a group of opportunistic bacterial pathogens often associated with fatal chronic infections in the lungs of patients suffering from cystic fibrosis (CF). Here, we announce the draft genome sequence of B. dolosa PC543 (LMG 19468), a CF airway isolate.

  19. Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria.

    Science.gov (United States)

    DiSalvo, Susanne; Haselkorn, Tamara S; Bashir, Usman; Jimenez, Daniela; Brock, Debra A; Queller, David C; Strassmann, Joan E

    2015-09-01

    Symbiotic associations can allow an organism to acquire novel traits by accessing the genetic repertoire of its partner. In the Dictyostelium discoideum farming symbiosis, certain amoebas (termed "farmers") stably associate with bacterial partners. Farmers can suffer a reproductive cost but also gain beneficial capabilities, such as carriage of bacterial food (proto-farming) and defense against competitors. Farming status previously has been attributed to amoeba genotype, but the role of bacterial partners in its induction has not been examined. Here, we explore the role of bacterial associates in the initiation, maintenance, and phenotypic effects of the farming symbiosis. We demonstrate that two clades of farmer-associated Burkholderia isolates colonize D. discoideum nonfarmers and infectiously endow them with farmer-like characteristics, indicating that Burkholderia symbionts are a major driver of the farming phenomenon. Under food-rich conditions, Burkholderia-colonized amoebas produce fewer spores than uncolonized counterparts, with the severity of this reduction being dependent on the Burkholderia colonizer. However, the induction of food carriage by Burkholderia colonization may be considered a conditionally adaptive trait because it can confer an advantage to the amoeba host when grown in food-limiting conditions. We observed Burkholderia inside and outside colonized D. discoideum spores after fruiting body formation; this observation, together with the ability of Burkholderia to colonize new amoebas, suggests a mixed mode of symbiont transmission. These results change our understanding of the D. discoideum farming symbiosis by establishing that the bacterial partner, Burkholderia, is an important causative agent of the farming phenomenon.

  20. Antimicrobial and antibiofilm activity of LL-37 and its truncated variants against Burkholderia pseudomallei

    NARCIS (Netherlands)

    S. Kanthawong; J.G.M. Bolscher; E.C.I. Veerman; J. van Marle; H.J.J. de Soet; K. Nazmi; S. Wongratanacheewin; S. Taweechaisupapong

    2012-01-01

    The Gram-negative bacterium Burkholderia pseudomallei is the aetiological agent of melioidosis, which is an endemic disease in tropical areas of Southeast Asia and Northern Australia. Burkholderia pseudomallei has intrinsic resistance to a number of commonly used antibiotics and has also been report

  1. Using multispectral imaging flow cytometry to assess an in vitro intracellular Burkholderia thailandensis infection model.

    Science.gov (United States)

    Jenner, Dominic; Ducker, Catherine; Clark, Graeme; Prior, Jo; Rowland, Caroline A

    2016-04-01

    The use of in vitro models to understand the interaction of bacteria with host cells is well established. In vitro bacterial infection models are often used to quantify intracellular bacterial load by lysing cell populations and subsequently enumerating the bacteria. Modern established techniques employ the use of fluorescence technologies such as flow cytometry, fluorescent microscopy, and/or confocal microscopy. However, these techniques often lack either the quantification of large data sets (microscopy) or use of gross fluorescence signal which lacks the visual confirmation that can provide additional confidence in data sets. Multispectral imaging flow cytometry (MIFC) is a novel emerging field of technology. This technology captures a bright field and fluorescence image of cells in a flow using a charged coupled device camera. It allows the analysis of tens of thousands of single cell images, making it an extremely powerful technology. Here MIFC was used as an alternative method of analyzing intracellular bacterial infection using Burkholderia thailandensis E555 as a model organism. It has been demonstrated that the data produced using traditional enumeration is comparable to data analyzed using MIFC. It has also been shown that by using MIFC it is possible to generate other data on the dynamics of the infection model rather than viable counts alone. It has been demonstrated that it is possible to inhibit the uptake of bacteria into mammalian cells and identify differences between treated and untreated cell populations. The authors believe this to be the first use of MIFC to analyze a Burkholderia bacterial species during intracellular infection. © 2016 Crown copyright. Published by Wiley Periodicals Inc. on behalf of ISAC. PMID:26841315

  2. Characterization of the Burkholderia thailandensis SOS response by using whole-transcriptome shotgun sequencing.

    Science.gov (United States)

    Ulrich, Ricky L; Deshazer, David; Kenny, Tara A; Ulrich, Melanie P; Moravusova, Anna; Opperman, Timothy; Bavari, Sina; Bowlin, Terry L; Moir, Donald T; Panchal, Rekha G

    2013-10-01

    The bacterial SOS response is a well-characterized regulatory network encoded by most prokaryotic bacterial species and is involved in DNA repair. In addition to nucleic acid repair, the SOS response is involved in pathogenicity, stress-induced mutagenesis, and the emergence and dissemination of antibiotic resistance. Using high-throughput sequencing technology (SOLiD RNA-Seq), we analyzed the Burkholderia thailandensis global SOS response to the fluoroquinolone antibiotic, ciprofloxacin (CIP), and the DNA-damaging chemical, mitomycin C (MMC). We demonstrate that a B. thailandensis recA mutant (RU0643) is ∼4-fold more sensitive to CIP in contrast to the parental strain B. thailandensis DW503. Our RNA-Seq results show that CIP and MMC treatment (P SOS response were induced and include lexA, uvrA, dnaE, dinB, recX, and recA. At the genome-wide level, we found an overall decrease in gene expression, especially for genes involved in amino acid and carbohydrate transport and metabolism, following both CIP and MMC exposure. Interestingly, we observed the upregulation of several genes involved in bacterial motility and enhanced transcription of a B. thailandensis genomic island encoding a Siphoviridae bacteriophage designated E264. Using B. thailandensis plaque assays and PCR with B. mallei ATCC 23344 as the host, we demonstrate that CIP and MMC exposure in B. thailandensis DW503 induces the transcription and translation of viable bacteriophage in a RecA-dependent manner. This is the first report of the SOS response in Burkholderia spp. to DNA-damaging agents. We have identified both common and unique adaptive responses of B. thailandensis to chemical stress and DNA damage.

  3. Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex

    Directory of Open Access Journals (Sweden)

    Shrivastava Savita

    2008-12-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (BCC is a versatile group of Gram negative organisms that can be found throughout the environment in sources such as soil, water, and plants. While BCC bacteria can be involved in beneficial interactions with plants, they are also considered opportunistic pathogens, specifically in patients with cystic fibrosis and chronic granulomatous disease. These organisms also exhibit resistance to many antibiotics, making conventional treatment often unsuccessful. KS10 was isolated as a prophage of B. cenocepacia K56-2, a clinically relevant strain of the BCC. Our objective was to sequence the genome of this phage and also determine if this prophage encoded any virulence determinants. Results KS10 is a 37,635 base pairs (bp transposable phage of the opportunistic pathogen Burkholderia cenocepacia. Genome sequence analysis and annotation of this phage reveals that KS10 shows the closest sequence homology to Mu and BcepMu. KS10 was found to be a prophage in three different strains of B. cenocepacia, including strains K56-2, J2315, and C5424, and seven tested clinical isolates of B. cenocepacia, but no other BCC species. A survey of 23 strains and 20 clinical isolates of the BCC revealed that KS10 is able to form plaques on lawns of B. ambifaria LMG 19467, B. cenocepacia PC184, and B. stabilis LMG 18870. Conclusion KS10 is a novel phage with a genomic organization that differs from most phages in that its capsid genes are not aligned into one module but rather separated by approximately 11 kb, giving evidence of one or more prior genetic rearrangements. There were no potential virulence factors identified in KS10, though many hypothetical proteins were identified with no known function.

  4. Snake Cathelicidin NA-CATH and Smaller Helical Antimicrobial Peptides Are Effective against Burkholderia thailandensis.

    Directory of Open Access Journals (Sweden)

    Ryan J Blower

    Full Text Available Burkholderia thailandensis is a Gram-negative soil bacterium used as a model organism for B. pseudomallei, the causative agent of melioidosis and an organism classified category B priority pathogen and a Tier 1 select agent for its potential use as a biological weapon. Burkholderia species are reportedly "highly resistant" to antimicrobial agents, including cyclic peptide antibiotics, due to multiple resistance systems, a hypothesis we decided to test using antimicrobial (host defense peptides. In this study, a number of cationic antimicrobial peptides (CAMPs were tested in vitro against B. thailandensis for both antimicrobial activity and inhibition of biofilm formation. Here, we report that the Chinese cobra (Naja atra cathelicidin NA-CATH was significantly antimicrobial against B. thailandensis. Additional cathelicidins, including the human cathelicidin LL-37, a sheep cathelicidin SMAP-29, and some smaller ATRA peptide derivatives of NA-CATH were also effective. The D-enantiomer of one small peptide (ATRA-1A was found to be antimicrobial as well, with EC50 in the range of the L-enantiomer. Our results also demonstrate that human alpha-defensins (HNP-1 & -2 and a short beta-defensin-derived peptide (Peptide 4 of hBD-3 were not bactericidal against B. thailandensis. We also found that the cathelicidin peptides, including LL-37, NA-CATH, and SMAP-29, possessed significant ability to prevent biofilm formation of B. thailandensis. Additionally, we show that LL-37 and its D-enantiomer D-LL-37 can disperse pre-formed biofilms. These results demonstrate that although B. thailandensis is highly resistant to many antibiotics, cyclic peptide antibiotics such as polymyxin B, and defensing peptides, some antimicrobial peptides including the elapid snake cathelicidin NA-CATH exert significant antimicrobial and antibiofilm activity towards B. thailandensis.

  5. Snake Cathelicidin NA-CATH and Smaller Helical Antimicrobial Peptides Are Effective against Burkholderia thailandensis.

    Science.gov (United States)

    Blower, Ryan J; Barksdale, Stephanie M; van Hoek, Monique L

    2015-01-01

    Burkholderia thailandensis is a Gram-negative soil bacterium used as a model organism for B. pseudomallei, the causative agent of melioidosis and an organism classified category B priority pathogen and a Tier 1 select agent for its potential use as a biological weapon. Burkholderia species are reportedly "highly resistant" to antimicrobial agents, including cyclic peptide antibiotics, due to multiple resistance systems, a hypothesis we decided to test using antimicrobial (host defense) peptides. In this study, a number of cationic antimicrobial peptides (CAMPs) were tested in vitro against B. thailandensis for both antimicrobial activity and inhibition of biofilm formation. Here, we report that the Chinese cobra (Naja atra) cathelicidin NA-CATH was significantly antimicrobial against B. thailandensis. Additional cathelicidins, including the human cathelicidin LL-37, a sheep cathelicidin SMAP-29, and some smaller ATRA peptide derivatives of NA-CATH were also effective. The D-enantiomer of one small peptide (ATRA-1A) was found to be antimicrobial as well, with EC50 in the range of the L-enantiomer. Our results also demonstrate that human alpha-defensins (HNP-1 & -2) and a short beta-defensin-derived peptide (Peptide 4 of hBD-3) were not bactericidal against B. thailandensis. We also found that the cathelicidin peptides, including LL-37, NA-CATH, and SMAP-29, possessed significant ability to prevent biofilm formation of B. thailandensis. Additionally, we show that LL-37 and its D-enantiomer D-LL-37 can disperse pre-formed biofilms. These results demonstrate that although B. thailandensis is highly resistant to many antibiotics, cyclic peptide antibiotics such as polymyxin B, and defensing peptides, some antimicrobial peptides including the elapid snake cathelicidin NA-CATH exert significant antimicrobial and antibiofilm activity towards B. thailandensis. PMID:26196513

  6. Burkholderia cenocepacia Differential Gene Expression during Host–Pathogen Interactions and Adaptation to the Host Environment

    Science.gov (United States)

    O’Grady, Eoin P.; Sokol, Pamela A.

    2011-01-01

    Members of the Burkholderia cepacia complex (Bcc) are important in medical, biotechnological, and agricultural disciplines. These bacteria naturally occur in soil and water environments and have adapted to survive in association with plants and animals including humans. All Bcc species are opportunistic pathogens including Burkholderia cenocepacia that causes infections in cystic fibrosis and chronic granulomatous disease patients. The adaptation of B. cenocepacia to the host environment was assessed in a rat chronic respiratory infection model and compared to that of high cell-density in vitro grown cultures using transcriptomics. The distribution of genes differentially expressed on chromosomes 1, 2, and 3 was relatively proportional to the size of each genomic element, whereas the proportion of plasmid-encoded genes differentially expressed was much higher relative to its size and most genes were induced in vivo. The majority of genes encoding known virulence factors, components of types II and III secretion systems and chromosome 2-encoded type IV secretion system were similarly expressed between in vitro and in vivo environments. Lower expression in vivo was detected for genes encoding N-acyl-homoserine lactone synthase CepI, orphan LuxR homolog CepR2, zinc metalloproteases ZmpA and ZmpB, LysR-type transcriptional regulator ShvR, nematocidal protein AidA, and genes associated with flagellar motility, Flp type pilus formation, and type VI secretion. Plasmid-encoded type IV secretion genes were markedly induced in vivo. Additional genes induced in vivo included genes predicted to be involved in osmotic stress adaptation or intracellular survival, metal ion, and nutrient transport, as well as those encoding outer membrane proteins. Genes identified in this study are potentially important for virulence during host–pathogen interactions and may be associated with survival and adaptation to the host environment during chronic lung infections. PMID:22919581

  7. Draft Genome Sequence of Burkholderia cenocepacia Strain CEIB S5-2, a Methyl Parathion- and p-Nitrophenol-Degrading Bacterium, Isolated from Agricultural Soils in Morelos, Mexico

    OpenAIRE

    Martínez-Ocampo, Fernando; Fernández López, Maikel Gilberto; Lozano-Aguirre Beltrán, Luis Fernando; Popoca-Ursino, Elida Carolina; Ortiz-Hernández, M. Laura; Sánchez-Salinas, Enrique; Ramos Quintana, Fernando; Villalobos-López, Miguel A.; Dantán-González, Edgar

    2016-01-01

    Burkholderia cenocepacia is an opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC). Burkholderia cenocepacia strain CEIB S5-2 was isolated from agricultural soils in Morelos, Mexico, and previously has shown its abilities for bioremediation. In this study, we report the draft genome sequence of Burkholderia cenocepacia strain CEIB S5-2.

  8. Draft Genome Sequence of Burkholderia cenocepacia Strain CEIB S5-2, a Methyl Parathion- and p-Nitrophenol-Degrading Bacterium, Isolated from Agricultural Soils in Morelos, Mexico

    Science.gov (United States)

    Martínez-Ocampo, Fernando; Fernández López, Maikel Gilberto; Lozano-Aguirre Beltrán, Luis Fernando; Popoca-Ursino, Elida Carolina; Ortiz-Hernández, M. Laura; Sánchez-Salinas, Enrique; Ramos Quintana, Fernando; Villalobos-López, Miguel A.

    2016-01-01

    Burkholderia cenocepacia is an opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC). Burkholderia cenocepacia strain CEIB S5-2 was isolated from agricultural soils in Morelos, Mexico, and previously has shown its abilities for bioremediation. In this study, we report the draft genome sequence of Burkholderia cenocepacia strain CEIB S5-2. PMID:27125479

  9. Statistics, Causality and Bell's theorem

    CERN Document Server

    Gill, Richard D

    2012-01-01

    Bell's (1964) theorem is popularly supposed to establish the non-locality of quantum physics as a mathematical-physical theory. Building from this, observed violation of Bell's inequality in experiments such as that of Aspect and coworkers (1982) is popularly supposed to provide empirical proof of non-locality in the real world. This paper reviews recent work on Bell's theorem, linking it to issues in causality as understood by statisticians. The paper starts with a new proof of a strong (finite sample) version of Bell's theorem which relies only on elementary arithmetic and (counting) probability. This proof underscores the fact that Bell's theorem tells us that quantum theory is incompatible with the conjunction of three cherished and formerly uncontroversial physical principles, nicknamed here locality, realism, and freedom. The first, locality, is obviously connected to causality: causal influences need time to propagate spatially. Less obviously, the other two principles, realism and freedom, are also fo...

  10. Introductive remarks on causal inference

    Directory of Open Access Journals (Sweden)

    Silvana A. Romio

    2013-05-01

    Full Text Available One of the more challenging issues in epidemiological research is being able to provide an unbiased estimate of the causal exposure-disease effect, to assess the possible etiological mechanisms and the implication for public health. A major source of bias is confounding, which can spuriously create or mask the causal relationship. In the last ten years, methodological research has been developed to better de_ne the concept of causation in epidemiology and some important achievements have resulted in new statistical models. In this review, we aim to show how a technique the well known by statisticians, i.e. standardization, can be seen as a method to estimate causal e_ects, equivalent under certain conditions to the inverse probability treatment weight procedure.

  11. Causal reasoning with mental models.

    Science.gov (United States)

    Khemlani, Sangeet S; Barbey, Aron K; Johnson-Laird, Philip N

    2014-01-01

    This paper outlines the model-based theory of causal reasoning. It postulates that the core meanings of causal assertions are deterministic and refer to temporally-ordered sets of possibilities: A causes B to occur means that given A, B occurs, whereas A enables B to occur means that given A, it is possible for B to occur. The paper shows how mental models represent such assertions, and how these models underlie deductive, inductive, and abductive reasoning yielding explanations. It reviews evidence both to corroborate the theory and to account for phenomena sometimes taken to be incompatible with it. Finally, it reviews neuroscience evidence indicating that mental models for causal inference are implemented within lateral prefrontal cortex. PMID:25389398

  12. Causal reasoning with mental models

    Directory of Open Access Journals (Sweden)

    Sangeet eKhemlani

    2014-10-01

    Full Text Available This paper outlines the model-based theory of causal reasoning. It postulates that the core meanings of causal assertions are deterministic and refer to temporally-ordered sets of possibilities: A causes B to occur means that given A, B occurs, whereas A enables B to occur means that given A, it is possible for B to occur. The paper shows how mental models represent such assertions, and how these models underlie deductive, inductive, and abductive reasoning yielding explanations. It reviews evidence both to corroborate the theory and to account for phenomena sometimes taken to be incompatible with it. Finally, it reviews neuroscience evidence indicating that mental models for causal inference are implemented within lateral prefrontal cortex.

  13. Gravitation, Causality, and Quantum Consistency

    CERN Document Server

    Hertzberg, Mark P

    2016-01-01

    We examine the role of consistency with causality and quantum mechanics in determining the properties of gravitation. We begin by constructing two different classes of interacting theories of massless spin 2 particles -- gravitons. One involves coupling the graviton with the lowest number of derivatives to matter, the other involves coupling the graviton with higher derivatives to matter, making use of the linearized Riemann tensor. The first class requires an infinite tower of terms for consistency, which is known to lead uniquely to general relativity. The second class only requires a finite number of terms for consistency, which appears as a new class of theories of massless spin 2. We recap the causal consistency of general relativity and show how this fails in the second class for the special case of coupling to photons, exploiting related calculations in the literature. In an upcoming publication [1] this result is generalized to a much broader set of theories. Then, as a causal modification of general ...

  14. Causality and Primordial Tensor Modes

    CERN Document Server

    Baumann, Daniel

    2009-01-01

    We introduce the real space correlation function of $B$-mode polarization of the cosmic microwave background (CMB) as a probe of superhorizon tensor perturbations created by inflation. By causality, any non-inflationary mechanism for gravitational wave production after reheating, like global phase transitions or cosmic strings, must have vanishing correlations for angular separations greater than the angle subtended by the particle horizon at recombination, i.e. $\\theta \\gtrsim 2^\\circ$. Since ordinary $B$-modes are defined non-locally in terms of the Stokes parameters $Q$ and $U$ and therefore don't have to respect causality, special care is taken to define `causal $\\tilde B$-modes' for the analysis. We compute the real space $\\tilde B$-mode correlation function for inflation and discuss its detectability on superhorizon scales where it provides an unambiguous test of inflationary gravitational waves. The correct identification of inflationary tensor modes is crucial since it relates directly to the energy s...

  15. Causal Models for Risk Management

    Directory of Open Access Journals (Sweden)

    Neysis Hernández Díaz

    2013-12-01

    Full Text Available In this work a study about the process of risk management in major schools in the world. The project management tools worldwide highlights the need to redefine risk management processes. From the information obtained it is proposed the use of causal models for risk analysis based on information from the project or company, say risks and the influence thereof on the costs, human capital and project requirements and detect the damages of a number of tasks without tribute to the development of the project. A study on the use of causal models as knowledge representation techniques causal, among which are the Fuzzy Cognitive Maps (DCM and Bayesian networks, with the most favorable MCD technique to use because it allows modeling the risk information witho ut having a knowledge base either itemize.

  16. Discrimination of Burkholderia mallei/pseudomallei from Burkholderia thailandensis by sequence comparison of a fragment of the ribosomal protein S21 (rpsU) gene

    OpenAIRE

    Frickmann, H.; Chantratita, N.; Gauthier, Y. P.; Neubauer, H.; Hagen, R. M.

    2012-01-01

    Discrimination of Burkholderia (B.) pseudomallei and B. mallei from environmental B. thailandensis is challenging. We describe a discrimination method based on sequence comparison of the ribosomal protein S21 (rpsU) gene.

  17. Temperature has a causal effect on avian timing of reproduction

    NARCIS (Netherlands)

    Visser, M.E.; Holleman, L.J.M.; Caro, S.P.

    2009-01-01

    Many bird species reproduce earlier in years with high spring temperatures, but little is known about the causal effect of temperature. Temperature may have a direct effect on timing of reproduction but the correlation may also be indirect, for instance via food phenology. As climate change has led

  18. Use of a Safe, Reproducible, and Rapid Aerosol Delivery Method to Study Infection by Burkholderia pseudomallei and Burkholderia mallei in Mice

    OpenAIRE

    Eric R Lafontaine; Zimmerman, Shawn M.; Teresa L Shaffer; Frank Michel; Xiudan Gao; Hogan, Robert J.

    2013-01-01

    Burkholderia pseudomallei, the etiologic agent of melioidosis, is a saprophytic bacterium readily isolated from wet soils of countries bordering the equator. Burkholderia mallei is a host-adapted clone of B. pseudomallei that does not persist outside of its equine reservoir and causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by these organisms typically occurs via percutaneous inoculation or inhalation of aerosols, and the most comm...

  19. On the Axioms of Causal Set Theory

    CERN Document Server

    Dribus, Benjamin F

    2013-01-01

    This paper offers suggested improvements to the causal sets program in discrete gravity, which treats spacetime geometry as an emergent manifestation of causal structure at the fundamental scale. This viewpoint, which I refer to as the causal metric hypothesis, is summarized by Rafael Sorkin's phrase, "order plus number equals geometry." Proposed improvements include recognition of a generally nontransitive causal relation more fundamental than the causal order, an improved local picture of causal structure, development and use of relation space methods, and a new background-independent version of the histories approach to quantum theory. Besides causal set theory, \\`a la Bombelli, Lee, Meyer, and Sorkin, this effort draws on Isham's topos-theoretic framework for physics, Sorkin's quantum measure theory, Finkelstein's causal nets, and Grothendieck's structural principles. This approach circumvents undesirable structural features in causal set theory, such as the permeability of maximal antichains, studied by ...

  20. Causality problem in Economic Science

    Directory of Open Access Journals (Sweden)

    JOSÉ LUIS RETOLAZA

    2007-12-01

    Full Text Available The main point of the paper is the problem of the economy to be consider like a science in the most strict term of the concept. In the first step we are going to tackle a presentation about what we understand by science to subsequently present some of the fallacies which have bring certain scepticism about the scientific character of the investigation in economy, to know: 1 The differences between hard and weak sciences -physics and social; 2 The differences between paradigm, —positivist and phenomenological— 3 The differences between physic causalityand historic causality. In the second step we are going to talk about two fundamental problems which are questioned: 1 the confusion between ontology and gnoseology and, 2 the erroneous concept of causality that commonly is used. In the last step of the paper we are going over the recent models of «causal explanation» and we suggest the probabilistic casualty development next with a more elaborated models of causal explanation, like a way to conjugate the scientific severity with the possibility to tackle complex economic realities.

  1. Causal Behaviour on Carter spacetime

    CERN Document Server

    Blanco, Oihane F

    2015-01-01

    In this work we will focus on the causal character of Carter Spacetime (see B. Carter, Causal structure in space-time, Gen. Rel. Grav. 1 4 337-406, 1971). The importance of this spacetime is the following: for the causally best well behaved spacetimes (the globally hyperbolic ones), there are several characterizations or alternative definitions. In some cases, it has been shown that some of the causal properties required in these characterizations can be weakened. But Carter spacetime provides a counterexample for an impossible relaxation in one of them. We studied the possibility of Carter spacetime to be a counterexample for impossible lessening in another characterization, based on the previous results. In particular, we will prove that the time-separation or Lorentzian distance between two chosen points in Carter spacetime is infinite. Although this spacetime turned out not to be the counterexample we were looking for, the found result is interesting per se and provides ideas for alternate approaches to t...

  2. Causal feedbacks in climate change

    NARCIS (Netherlands)

    Nes, van E.H.; Scheffer, M.; Brovkin, V.; Lenton, T.M.; Ye, H.; Deyle, E.; Sugihara, G.

    2015-01-01

    The statistical association between temperature and greenhouse gases over glacial cycles is well documented1, but causality behind this correlation remains difficult to extract directly from the data. A time lag of CO2 behind Antarctic temperature—originally thought to hint at a driving role for tem

  3. Granger Causality and Unit Roots

    DEFF Research Database (Denmark)

    Rodríguez-Caballero, Carlos Vladimir; Ventosa-Santaulària, Daniel

    2014-01-01

    The asymptotic behavior of the Granger-causality test under stochastic nonstationarity is studied. Our results confirm that the inference drawn from the test is not reliable when the series are integrated to the first order. In the presence of deterministic components, the test statistic diverges...

  4. Free Fermions on causal sets

    CERN Document Server

    Noldus, Johan

    2013-01-01

    We construct a Dirac theory on causal sets; a key element in the construction being that the causet must be regarded as emergent in an appropriate sense too. We further notice that mixed norm spaces appear in the construction allowing for negative norm particles and "ghosts".

  5. Entanglement, holography and causal diamonds

    Science.gov (United States)

    de Boer, Jan; Haehl, Felix M.; Heller, Michal P.; Myers, Robert C.

    2016-08-01

    We argue that the degrees of freedom in a d-dimensional CFT can be reorganized in an insightful way by studying observables on the moduli space of causal diamonds (or equivalently, the space of pairs of timelike separated points). This 2 d-dimensional space naturally captures some of the fundamental nonlocality and causal structure inherent in the entanglement of CFT states. For any primary CFT operator, we construct an observable on this space, which is defined by smearing the associated one-point function over causal diamonds. Known examples of such quantities are the entanglement entropy of vacuum excitations and its higher spin generalizations. We show that in holographic CFTs, these observables are given by suitably defined integrals of dual bulk fields over the corresponding Ryu-Takayanagi minimal surfaces. Furthermore, we explain connections to the operator product expansion and the first law of entanglemententropy from this unifying point of view. We demonstrate that for small perturbations of the vacuum, our observables obey linear two-derivative equations of motion on the space of causal diamonds. In two dimensions, the latter is given by a product of two copies of a two-dimensional de Sitter space. For a class of universal states, we show that the entanglement entropy and its spin-three generalization obey nonlinear equations of motion with local interactions on this moduli space, which can be identified with Liouville and Toda equations, respectively. This suggests the possibility of extending the definition of our new observables beyond the linear level more generally and in such a way that they give rise to new dynamically interacting theories on the moduli space of causal diamonds. Various challenges one has to face in order to implement this idea are discussed.

  6. Burkholderia glumae EN EL CULTIVO DE ARROZ EN COSTA RICA

    Directory of Open Access Journals (Sweden)

    Andrea Quesada-Gonz\\u00E1lez

    2014-01-01

    Full Text Available Burkholderia glumae en el cultivo de arroz en Costa Rica. El objetivo de este trabajo fue determinar la presencia de Burkholderia glumae en arroz en Costa Rica. La bacteria Burkholderia glumae está asociada al cultivo del arroz en el que provoca la enfermedad llamada añublo bacterial. Bajo condiciones ambientales favorables, la densidad bacteriana aumenta, lo que provoca que, bajo un sistema de regulación denominado quorum sensing, se expresen sus mecanismos de virulencia mediante la activación de genes responsables para la síntesis de la toxoflavina, que bloquea el flujo de nutrientes, para la biogénesis de flagelos y la respuesta quimiotáctica, y la producción de la enzima catalasa. Las plantas desarrollan la sintomatología que finalmente conlleva a un vaneamiento del grano provocando pérdidas económicas importantes. Se investigó la situación referente a la contaminación del grano de arroz causado por esta bacteria en Costa Rica durante los años 2009 y 2010, mediante un convenio entre la Corporación Nacional Arrocera y el Laboratorio de Fitopatología del Centro de Investigación en Protección de Cultivos de la Universidad de Costa Rica. Se usó la metodología de PCR de punto final recomendada por investigadores del Centro Internacional de Agricultura Tropical en Colombia y se reforzó la identificación, por medio de técnicas de microbiología convencional. Se obtuvieron resultados que indican la presencia de la bacteria en Costa Rica, la primera información sobre la prevalencia de un fitopatógeno bacteriano de gran importancia para el sector arrocero.

  7. Genome Sequencing and Transposon Mutagenesis of Burkholderia seminalis TC3.4.2R3 Identify Genes Contributing to Suppression of Orchid Necrosis Caused by B. gladioli.

    Science.gov (United States)

    Araújo, Welington L; Creason, Allison L; Mano, Emy T; Camargo-Neves, Aline A; Minami, Sonia N; Chang, Jeff H; Loper, Joyce E

    2016-06-01

    From a screen of 36 plant-associated strains of Burkholderia spp., we identified 24 strains that suppressed leaf and pseudobulb necrosis of orchid caused by B. gladioli. To gain insights into the mechanisms of disease suppression, we generated a draft genome sequence from one suppressive strain, TC3.4.2R3. The genome is an estimated 7.67 megabases in size, with three replicons, two chromosomes, and the plasmid pC3. Using a combination of multilocus sequence analysis and phylogenomics, we identified TC3.4.2R3 as B. seminalis, a species within the Burkholderia cepacia complex that includes opportunistic human pathogens and environmental strains. We generated and screened a library of 3,840 transposon mutants of strain TC3.4.2R3 on orchid leaves to identify genes contributing to plant disease suppression. Twelve mutants deficient in suppression of leaf necrosis were selected and the transposon insertions were mapped to eight loci. One gene is in a wcb cluster that is related to synthesis of extracellular polysaccharide, a key determinant in bacterial-host interactions in other systems, and the other seven are highly conserved among Burkholderia spp. The fundamental information developed in this study will serve as a resource for future research aiming to identify mechanisms contributing to biological control. PMID:26959838

  8. Burkholderia Hep_Hag autotransporter (BuHA proteins elicit a strong antibody response during experimental glanders but not human melioidosis

    Directory of Open Access Journals (Sweden)

    Foster Simon J

    2007-03-01

    Full Text Available Abstract Background The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei. Results Using bacteriophage-mediated immunoscreening we identified genes expressed in vivo during experimental equine glanders infection. A family of immunodominant antigens were identified that share protein domain architectures with hemagglutinins and invasins. These have been designated Burkholderia Hep_Hag autotransporter (BuHA proteins. A total of 110/207 positive clones (53% of a B. mallei expression library screened with sera from two infected horses belonged to this family. This contrasted with 6/189 positive clones (3% of a B. pseudomallei expression library screened with serum from 21 patients with culture-proven melioidosis. Conclusion Members of the BuHA proteins are found in other Gram-negative bacteria and have been shown to have important roles related to virulence. Compared with other bacterial species, the genomes of both B. mallei and B. pseudomallei contain a relative abundance of this family of proteins. The domain structures of these proteins suggest that they function as multimeric surface proteins that modulate interactions of the cell with the host and environment. Their effect on the cellular immune response to B. mallei and their potential as diagnostics for glanders requires further study.

  9. The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis.

    Science.gov (United States)

    Carlier, Aurelien; Fehr, Linda; Pinto-Carbó, Marta; Schäberle, Till; Reher, Raphael; Dessein, Steven; König, Gabriele; Eberl, Leo

    2016-09-01

    A majority of Ardisia species harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted hereditarily and have not yet been cultured outside of their host. Because the plants cannot develop beyond the seedling stage without their symbionts, the symbiosis is considered obligatory. We sequenced for the first time the genome of Candidatus Burkholderia crenata (Ca. B. crenata), the leaf nodule symbiont of Ardisia crenata. The genome of Ca. B. crenata is the smallest Burkholderia genome to date. It contains a large amount of insertion sequences and pseudogenes and displays features consistent with reductive genome evolution. The genome does not encode functions commonly associated with plant symbioses such as nitrogen fixation and plant hormone metabolism. However, we identified unique genes with a predicted role in secondary metabolism in the genome of Ca. B. crenata. Specifically, we provide evidence that the bacterial symbionts are responsible for the synthesis of compound FR900359, a cyclic depsipeptide with biomedical properties previously isolated from leaves of A. crenata. PMID:26663534

  10. Anticipation of physical causality guides eye movements

    OpenAIRE

    Wende, Kim; Theunissen, Laetitia; Missal, Marcus

    2016-01-01

    Causality is a unique feature of human perception. We present here a behavioral investigation of the influence of physical causality during visual pursuit of object collisions. Pursuit and saccadic eye movements of human subjects were recorded during ocular pursuit of two concurrently launched targets, one that moved according to the laws of Newtonian mechanics (the causal target) and the other one that moved in a physically implausible direction (the non-causal target). We found that anticip...

  11. Estimating causal structure using conditional DAG models

    OpenAIRE

    Oates, Chris J.; Smith, Jim Q.; Mukherjee, Sach

    2014-01-01

    This paper considers inference of causal structure in a class of graphical models called "conditional DAGs". These are directed acyclic graph (DAG) models with two kinds of variables, primary and secondary. The secondary variables are used to aid in estimation of causal relationships between the primary variables. We give causal semantics for this model class and prove that, under certain assumptions, the direction of causal influence is identifiable from the joint observational distribution ...

  12. Designing Effective Supports for Causal Reasoning

    Science.gov (United States)

    Jonassen, David H.; Ionas, Ioan Gelu

    2008-01-01

    Causal reasoning represents one of the most basic and important cognitive processes that underpin all higher-order activities, such as conceptual understanding and problem solving. Hume called causality the "cement of the universe" [Hume (1739/2000). Causal reasoning is required for making predictions, drawing implications and inferences, and…

  13. Representing Personal Determinants in Causal Structures.

    Science.gov (United States)

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  14. Exploring Individual Differences in Preschoolers' Causal Stance

    Science.gov (United States)

    Alvarez, Aubry; Booth, Amy E.

    2016-01-01

    Preschoolers, as a group, are highly attuned to causality, and this attunement is known to facilitate memory, learning, and problem solving. However, recent work reveals substantial individual variability in the strength of children's "causal stance," as demonstrated by their curiosity about and preference for new causal information. In…

  15. Expectations and Interpretations during Causal Learning

    Science.gov (United States)

    Luhmann, Christian C.; Ahn, Woo-kyoung

    2011-01-01

    In existing models of causal induction, 4 types of covariation information (i.e., presence/absence of an event followed by presence/absence of another event) always exert identical influences on causal strength judgments (e.g., joint presence of events always suggests a generative causal relationship). In contrast, we suggest that, due to…

  16. Painless causality in defect calculations

    CERN Document Server

    Cheung, C; Cheung, Charlotte; Magueijo, Joao

    1997-01-01

    Topological defects must respect causality, a statement leading to restrictive constraints on the power spectrum of the total cosmological perturbations they induce. Causality constraints have for long been known to require the presence of an under-density in the surrounding matter compensating the defect network on large scales. This so-called compensation can never be neglected and significantly complicates calculations in defect scenarios, eg. computing cosmic microwave background fluctuations. A quick and dirty way to implement the compensation are the so-called compensation fudge factors. Here we derive the complete photon-baryon-CDM backreaction effects in defect scenarios. The fudge factor comes out as an algebraic identity and so we drop the negative qualifier ``fudge''. The compensation scale is computed and physically interpreted. Secondary backreaction effects exist, and neglecting them constitutes the well-defined approximation scheme within which one should consider compensation factor calculatio...

  17. Velocity requirements for causality violation

    CERN Document Server

    Modanese, Giovanni

    2013-01-01

    It is known that the hypothetical existence of superluminal signals would imply the logical possibility of active causal violation: an observer in relative motion with respect to a primary source could in principle emit secondary superluminal signals (triggered by the primary ones) which go back in time and deactivate the primary source before the initial emission. This is a direct consequence of the structure of the Lorentz transformations, sometimes called "Regge-Tolman paradox". It is straightforward to find a formula for the velocity of the moving observer required to produce the causality violation. When applied to some recent claims of slight superluminal propagation, this formula yields a required velocity very close to the speed of light; this raises some doubts about the real physical observability of such violations. We re-compute this velocity requirement introducing a realistic delay between the reception of the primary signal and the emission of the secondary. It turns out that for -any- delay it...

  18. Recurrent urinary tract infection by burkholderia cepacia in a live related renal transplant recipient

    International Nuclear Information System (INIS)

    Burkholderia cepacia is high virulent organism usually causing lower respiratory tract infections especially in Cystic fibrosis (CF) patients and post lung transplant. Urinary tract infections with Burkholderia cepacia have been associated after bladder irrigation or use of contaminated hospital objects. Post renal transplant urinary tract infection (UTI) is the most common infectious complications. Recurrent urinary tract infection with Burkholderia cepacia is a rare finding. Complete anatomical evaluation is essential in case recurrent urinary tract infections (UTI) after renal transplant. Vesico-ureteric reflux (VUR) and neurogenic urinary bladder was found to be important risk factors. (author)

  19. A case of native valve endocarditis caused by Burkholderia cepacia without predisposing factors

    Directory of Open Access Journals (Sweden)

    Han Seong

    2011-05-01

    Full Text Available Abstract Background Infective endocarditis is rarely caused by Burkholderia cepacia. This infection is known to occur particularly in immunocompromised hosts, intravenous heroin users, and in patients with prosthetic valve replacement. Most patients with Burkholderia cepacia endocarditis usually need surgical treatment in addition to antimicrobial treatment. Case Presentation Here, we report the case of a patient who developed Burkholderia cepacia-induced native valve endocarditis with consequent cerebral involvement without any predisposing factors; she was successfully treated by antimicrobial agents only. Conclusion In this report, we also present literature review of relevant cases.

  20. Burkholderia cepacia lipase is a promising biocatalyst for biofuel production.

    Science.gov (United States)

    Sasso, Francesco; Natalello, Antonino; Castoldi, Simone; Lotti, Marina; Santambrogio, Carlo; Grandori, Rita

    2016-07-01

    Lipases resistant to inhibition and denaturation by methanol are valuable tools for biotechnological applications, in particular for biofuel production. Microbial lipases have attracted a great deal of interest because of their stability at high concentrations of organic solvents. Burkholderia cepacia lipase (BCL) is tested here for robustness towards methanol in terms of conformational stability and catalytic activity in transesterification assays. This lipase turns out to be even more tolerant than the homologous and better characterized enzyme from Burkholderia glumae. BCL unfolding transition, as monitored by far-UV circular dichroism (CD) and intrinsic fluorescence, displays a Tm above 60°C in the presence of 50% methanol. The protein unfolds at low pH, and the organic solvent affects the nature of the denatured state under acidic conditions. The protein performs well in transesterification assays upon prolonged incubations at high methanol concentrations. BCL is highly tolerant to methanol and displays particularly high conformational stability under conditions employed for transesterification reactions. These features depict BCL as a promising enzyme for biofuel industry. PMID:27067648

  1. Phenomenology of Causal Dynamical Triangulations

    CERN Document Server

    Mielczarek, Jakub

    2015-01-01

    The four dimensional Causal Dynamical Triangulations (CDT) approach to quantum gravity is already more than ten years old theory with numerous unprecedented predictions such as non-trivial phase structure of gravitational field and dimensional running. Here, we discuss possible empirical consequences of CDT derived based on the two features of the approach mentioned above. A possibility of using both astrophysical and cosmological observations to test CDT is discussed. We show that scenarios which can be ruled out at the empirical level exist.

  2. Velocity Requirements for Causality Violation

    Science.gov (United States)

    Modanese, Giovanni

    We re-examine the "Regge-Tolman paradox" with reference to some recent experimental results. It is straightforward to find a formula for the velocity v of the moving system required to produce causality violation. This formula typically yields a velocity very close to the speed of light (for instance, v/c > 0.97 for X-shaped microwaves), which raises some doubts about the real physical observability of the violations. We then compute the velocity requirement introducing a delay between the reception of the primary signal and the emission of the secondary. It turns out that in principle for any delay it is possible to find moving observers able to produce active causal violation. This is mathematically due to the singularity of the Lorentz transformations for β →1. For a realistic delay due to the propagation of a luminal precursor, we find that causality violations in the reported experiments are still more unlikely (v/c > 0.989), and even in the hypothesis that the superluminal propagation velocity goes to infinity, the velocity requirement is bounded by v/c > 0.62. We also prove that if two oscopic bodies exchange energy and momentum through superluminal signals, then the swap of signal source and target is incompatible with the Lorentz transformations; therefore it is not possible to distinguish between source and target, even with reference to a definite reference frame.

  3. Entanglement, Holography and Causal Diamonds

    CERN Document Server

    de Boer, Jan; Heller, Michal P; Myers, Robert C

    2016-01-01

    We argue that the degrees of freedom in a d-dimensional CFT can be re-organized in an insightful way by studying observables on the moduli space of causal diamonds (or equivalently, the space of pairs of timelike separated points). This 2d-dimensional space naturally captures some of the fundamental nonlocality and causal structure inherent in the entanglement of CFT states. For any primary CFT operator, we construct an observable on this space, which is defined by smearing the associated one-point function over causal diamonds. Known examples of such quantities are the entanglement entropy of vacuum excitations and its higher spin generalizations. We show that in holographic CFTs, these observables are given by suitably defined integrals of dual bulk fields over the corresponding Ryu-Takayanagi minimal surfaces. Furthermore, we explain connections to the operator product expansion and the first law of entanglement entropy from this unifying point of view. We demonstrate that for small perturbations of the va...

  4. A family history of deoxyribonuclease II: surprises from Trichinella spiralis and Burkholderia pseudomallei.

    Science.gov (United States)

    MacLea, Kyle S; Krieser, Ronald J; Eastman, Alan

    2003-02-13

    Deoxyribonuclease IIalpha (DNase IIalpha) is an acidic endonuclease found in lysosomes and nuclei, and it is also secreted. Though its Caenorhabditis elegans homolog, NUC-1, is required for digesting DNA of apoptotic cell corpses and dietary DNA, it is not required for viability. However, DNase IIalpha is required in mice for correct development and viability, because undigested cell corpses lead to lesions throughout the body. Recently, we showed that, in contrast to previous reports, active DNase IIalpha consists of one contiguous polypeptide. To better analyze DNase II protein structure and determine residues important for activity, extensive database searches were conducted to find distantly related family members. We report 29 new partial or complete homologs from 21 species. Four homologs with differences at the purported active site histidine residue were detected in the parasitic nematodes Trichinella spiralis and Trichinella pseudospiralis. When these mutations were reconstructed in human DNase IIalpha, the expressed proteins were inactive. DNase II homologs were also identified in non-metazoan species. In particular, the slime-mold Dictyostelium, the protozoan Trichomonas vaginalis, and the bacterium Burkholderia pseudomallei all contain sequences with significant similarity and identity to previously cloned DNase II family members. We report an analysis of their sequences and implications for DNase II protein structure and evolution. PMID:12594037

  5. TRACKING THE RESPONSE OF BURKHOLDERIA CEPACIA G4 5223-PR1 IN AQUIFER MICROCOSMS

    Science.gov (United States)

    The introduction of bacteria into the environment for bioremediation purposes (bioaugmentation) requires analysis and monitoring of microbial population dynamics to define persistence and activity from both efficacy and risk assessment perspectives, Burkholderia cepacia G4 5223-P...

  6. AQUIFER PROTIST RESPONSE AND THE POTENTIAL FOR TCE BIOREMEDIATION WITH BURKHOLDERIA CEPACIA G4 PR1

    Science.gov (United States)

    The introduction of bacteria into the environment for bioremediation purposes (bioaugmentation) requires analysis and monitoring of the persistence and activity of microbial population for efficacy and risk assessment purposes. Burkholderia cepacia G4 PR123 and PR131 constitutive...

  7. BIOAUGMENTATION WITH BURKHOLDERIA CEPACIA PR1301 FOR IN SITU BIOREMEDIATION OF TRICHLOROETHYLENE CONTAMINATED GROUNDWATER (RESEARCH BRIEF)

    Science.gov (United States)

    A pilot field study was conducted at the Moffett Federal Airfield, Mountain View, California, to determine whether effective in-situ aerobic cometabolic biodegradation of TCE could be accomplished through bioaugmentation with a genetically modified strain of Burkholderia cepacia ...

  8. Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976

    OpenAIRE

    Song, Lihua; Yu, Yonghui; Feng, Le; He, Jun; WANG, Tao; Zhu, Hong; Duan, Qing

    2015-01-01

    Burkholderia pseudomallei is the etiological agent of the potentially fatal disease melioidosis. Here, we report the draft genome sequence of a virulent water isolate obtained from the Hainan Province of China in 1976, B. pseudomallei strain 350105.

  9. Powder formulation of Burkholderia cepacia for control of rape seed damping-off caused by Rhizoctonia solani.

    Science.gov (United States)

    Sharifi-Tehrani, A; Ahmadzadeh, M; Sarani, S; Farzaneh, M

    2007-01-01

    Talc-based formulation of Burkholderia cepaci strain Bu1 was tested as seed and soil drenchs separately for its ability to control Rhizoctonia soloni the causal agent of rape seed damping-off in greenhouse and field trials. In general, the formulated bacteria was more effective to suppress the disease than the suspension of bacteria cells in carboxymethylcellulose solution (1% w/v), in both greenhouse and field trials. The formulation of strain Bul as soil and seed treatments had the greatest effect on reducing the rape seed damping-off in greenhouse and field trials (66.7, 53.3, 64.4 and 40% respectively). The formulation of strain Bu1 as soil and seed treatments were the most effective treatments to increase the root dry weights in the infected soil in greenhouse. The formulation of strain Bul as soil drench had the greatest effect on enhancement of the fresh weight of roots and stem fresh and dry weights. The formulation of strain Bu1 stored at 4 degrees C exhibited better shelf Life and efficacy in vitro than it's counterpart stored at 25 degrees C. PMID:18399433

  10. Vertical transmission explains the specific Burkholderia pattern in Sphagnum mosses at multi-geographic scale

    OpenAIRE

    AnastasiaBragina; ChristianBerg

    2013-01-01

    The betaproteobacterial genus Burkholderia is known for its versatile interactions with its hosts that can range from beneficial to pathogenic. A plant-beneficial-environmental (PBE) Burkholderia cluster was recently separated from the pathogen cluster, yet still little is known about burkholderial diversity, distribution, colonization, and transmission patterns on plants. In our study, we applied a combination of high-throughput molecular and microscopic methods to examine the aforementioned...

  11. Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

    OpenAIRE

    Nandi, Tannistha; Holden, Matthew; Didelot, Xavier; Mehershahi, Kurosh; Boddey, Justin A; Beacham, Ifor; Peak, Ian; Harting, John; Baybayan, Primo; Guo, Yan; Wang, Susana; How, Lee Chee; Sim, Bernice; Essex-Lopresti, Angela; Sarkar-Tyson, Mitali

    2015-01-01

    This study was supported by a core grant to P.T. from the GIS, an A-STAR research institute. The sequencing of the Burkholderia pseudomallei strains was supported by Wellcome Trust grant 098051 to J.P. Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental ...

  12. Breaking the arrows of causality

    DEFF Research Database (Denmark)

    Valsiner, Jaan

    2014-01-01

    Theoretical models of catalysis have proven to bring with them major breakthroughs in chemistry and biology, from the 1830s onward. It can be argued that the scientific status of chemistry has become established through the move from causal to catalytic models. Likewise, the central explanatory...... role of cyclical models in biology has made it possible to move from the idea of genetic determination to that of epigenetic negotiation as the core of biological theory. In psychology, catalytic thinking has been outside of the realm of accepted scientific schemes, as the axiomatic dependence upon the...

  13. The Impossibility of Causality Testing

    OpenAIRE

    Conway, Roger K.; P. A. V. B. Swamy; Yanagida, John F.; Muehlen, Peter von zur

    1984-01-01

    Causality tests developed by Sims and Granger are fatally flawed for several reasons First, when two variables, X and Y, are uncorrelated, X has no linear predictive value for Y, but X,and Y may be nonlinearly related unless they are statistically Independent, In which case X and Y are not related at all The light-hand side variables In a regression equation are exogenous If they are mean Independent of the disturbance term Mean Independence IS stronger than uncorrelatedness The proofs for de...

  14. Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp.

    OpenAIRE

    Ong, Hui San; Mohamed, Rahmah; Firdaus-Raih, Mohd

    2012-01-01

    Members of the Burkholderia family occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of available Burkholderia genomes has revealed a core set of 178 glycan-associated proteins shared by all Burkholderia of which 68 are homologous to known essential genes. The genome sequence compari...

  15. Probing the Cultural Constitution of Causal Cognition - A Research Program.

    Science.gov (United States)

    Bender, Andrea; Beller, Sieghard

    2016-01-01

    To what extent is the way people perceive, represent, and reason about causal relationships dependent on culture? While there have been sporadic attempts to explore this question, a systematic investigation is still lacking. Here, we propose that human causal cognition is not only superficially affected by cultural background, but that it is co-constituted by the cultural nature of the human species. To this end, we take stock of on-going research, with a particular focus on the methodological approaches taken: cross-species comparisons, archeological accounts, developmental studies, cross-cultural, and cross-linguistic experiments, as well as in-depth within-culture analyses of cognitive concepts, processes, and changes over time. We argue that only a combination of these approaches will allow us to integrate different components of cognition, levels of analysis, and points of view-the key requirements for a comprehensive, interdisciplinary research program to advance this field. PMID:26941695

  16. Space and time in perceptual causality.

    Science.gov (United States)

    Straube, Benjamin; Chatterjee, Anjan

    2010-01-01

    Inferring causality is a fundamental feature of human cognition that allows us to theorize about and predict future states of the world. Michotte suggested that humans automatically perceive causality based on certain perceptual features of events. However, individual differences in judgments of perceptual causality cast doubt on Michotte's view. To gain insights in the neural basis of individual difference in the perception of causality, our participants judged causal relationships in animations of a blue ball colliding with a red ball (a launching event) while fMRI-data were acquired. Spatial continuity and temporal contiguity were varied parametrically in these stimuli. We did not find consistent brain activation differences between trials judged as caused and those judged as non-caused, making it unlikely that humans have universal instantiation of perceptual causality in the brain. However, participants were slower to respond to and showed greater neural activity for violations of causality, suggesting that humans are biased to expect causal relationships when moving objects appear to interact. Our participants demonstrated considerable individual differences in their sensitivity to spatial and temporal characteristics in perceiving causality. These qualitative differences in sensitivity to time or space in perceiving causality were instantiated in individual differences in activation of the left basal ganglia or right parietal lobe, respectively. Thus, the perception that the movement of one object causes the movement of another is triggered by elemental spatial and temporal sensitivities, which themselves are instantiated in specific distinct neural networks. PMID:20463866

  17. Space and time in perceptual causality

    Directory of Open Access Journals (Sweden)

    Benjamin Straube

    2010-04-01

    Full Text Available Inferring causality is a fundamental feature of human cognition that allows us to theorize about and predict future states of the world. Michotte suggested that humans automatically perceive causality based on certain perceptual features of events. However, individual differences in judgments of perceptual causality cast doubt on Michotte’s view. To gain insights in the neural basis of individual difference in the perception of causality, our participants judged causal relationships in animations of a blue ball colliding with a red ball (a launching event while fMRI-data were acquired. Spatial continuity and temporal contiguity were varied parametrically in these stimuli. We did not find consistent brain activation differences between trials judged as caused and those judged as non-caused, making it unlikely that humans have universal instantiation of perceptual causality in the brain. However, participants were slower to respond to and showed greater neural activity for violations of causality, suggesting that humans are biased to expect causal relationships when moving objects appear to interact. Our participants demonstrated considerable individual differences in their sensitivity to spatial and temporal characteristics in perceiving causality. These qualitative differences in sensitivity to time or space in perceiving causality were instantiated in individual differences in activation of the left basal ganglia or right parietal lobe, respectively. Thus, the perception that the movement of one object causes the movement of another is triggered by elemental spatial and temporal sensitivities, which themselves are instantiated in specific distinct neural networks.

  18. The Functions of Danish Causal Conjunctions

    Directory of Open Access Journals (Sweden)

    Rita Therkelsen

    2004-01-01

    Full Text Available In the article I propose an analysis of the Danish causal conjunctions fordi, siden and for based on the framework of Danish Functional Grammar. As conjunctions they relate two clauses, and their semantics have in common that it indicates a causal relationship between the clauses. The causal conjunctions are different as far as their distribution is concerned; siden conjoins a subordinate clause and a main clause, for conjoins two main clauses, and fordi is able to do both. Methodologically I have based my analysis on these distributional properties comparing siden and fordi conjoining a subordinate and a main clause, and comparing for and fordi conjoining two main clauses, following the thesis that they would establish a causal relationship between different kinds of content. My main findings are that fordi establishes a causal relationship between the events referred to by the two clauses, and the whole utterance functions as a statement of this causal relationship. Siden presupposes such a general causal relationship between the two events and puts forward the causing event as a reason for assuming or wishing or ordering the caused event, siden thus establishes a causal relationship between an event and a speech act. For equally presupposes a general causal relationship between two events and it establishes a causal relationship between speech acts, and fordi conjoining two main clauses is able to do this too, but in this position it also maintains its event-relating ability, the interpretation depending on contextual factors.

  19. Glanders: off to the races with Burkholderia mallei.

    Science.gov (United States)

    Whitlock, Gregory C; Estes, D Mark; Torres, Alfredo G

    2007-12-01

    Burkholderia mallei, the etiologic agent of the disease known as glanders, is primarily a disease affecting horses and is transmitted to humans by direct contact with infected animals. The use of B. mallei as a biological weapon has been reported and currently, there is no vaccine available for either humans or animals. Despite the history and highly infective nature of B. mallei, as well as its potential use as a bio-weapon, B. mallei research to understand the pathogenesis and the host responses to infection remains limited. Therefore, this minireview will focus on current efforts to elucidate B. mallei virulence, the associated host immune responses elicited during infection and discuss the feasibility of vaccine development.

  20. Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts

    OpenAIRE

    Bontemps, C.; Rogel, M. A.; Wiechmann, A.; Mussabekova, A.; Moody, S.; Simon, M F; Moulin, Lionel; Elliott, G. N.; Lacercat-Didier, L.; Dasilva, C.; Grether, R; Camargo-Ricalde, S. L.; Chen, W.M.; SPRENT, J. I.; Martinez-Romero, E.

    2016-01-01

    The legume genus Mimosa has > 500 species, with two major centres of diversity, Brazil (c. 350 spp.) and Mexico (c. 100 spp.). In Brazil most species are nodulated by Burkholderia. Here we asked whether this is also true of native and endemic Mexican species. We have tested this apparent affinity for betaproteobacteria by examining the symbionts of native and endemic species of Mimosa in Mexico, especially from the central highlands where Mimosa spp. have diversified. Nodules were tested for ...

  1. Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

    Directory of Open Access Journals (Sweden)

    Dennis Jonathan J

    2010-10-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (BCC is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616, KS14 (vB_BceM-KS14 and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511. Results KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E' translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The lysBC genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an ISBmu2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations. Conclusions KS5, KS14 and KL3 are the

  2. Development of ceftazidime resistance in an acute Burkholderia pseudomallei infection

    Directory of Open Access Journals (Sweden)

    Sarovich DS

    2012-08-01

    Full Text Available Derek S Sarovich,1,2,* Erin P Price,1,2,* Direk Limmathurotsakul,3 James M Cook,1 Alex T Von Schulze,1 Spenser R Wolken,1 Paul Keim,1 Sharon J Peacock,3,4 Talima Pearson1 1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; 2Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Darwin, Australia; 3Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; 4Department of Medicine, University of Cambridge, Cambridge, United Kingdom*These authors contributed equally to this workAbstract: Burkholderia pseudomallei, a bacterium that causes the disease melioidosis, is intrinsically resistant to many antibiotics. First-line antibiotic therapy for treating melioidosis is usually the synthetic β-lactam, ceftazidime (CAZ, as almost all B. pseudomallei strains are susceptible to this drug. However, acquired CAZ resistance can develop in vivo during treatment with CAZ, which can lead to mortality if therapy is not switched to a different drug in a timely manner. Serial B. pseudomallei isolates obtained from an acute Thai melioidosis patient infected by a CAZ susceptible strain, who ultimately succumbed to infection despite being on CAZ therapy for the duration of their infection, were analyzed. Isolates that developed CAZ resistance due to a proline to serine change at position 167 in the β-lactamase PenA were identified. Importantly, these CAZ resistant isolates remained sensitive to the alternative melioidosis treatments; namely, amoxicillin-clavulanate, imipenem, and meropenem. Lastly, real-time polymerase chain reaction-based assays capable of rapidly identifying CAZ resistance in B. pseudomallei isolates at the position 167 mutation site were developed. The ability to rapidly identify the emergence of CAZ resistant B. pseudomallei populations in melioidosis patients will allow timely alterations in treatment strategies

  3. Use of the common marmoset to study Burkholderia mallei infection.

    Directory of Open Access Journals (Sweden)

    Tomislav Jelesijevic

    Full Text Available Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4 to 2.5 X 10(5 bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3 bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3 organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B

  4. Use of the common marmoset to study Burkholderia mallei infection.

    Science.gov (United States)

    Jelesijevic, Tomislav; Zimmerman, Shawn M; Harvey, Stephen B; Mead, Daniel G; Shaffer, Teresa L; Estes, D Mark; Michel, Frank; Quinn, Frederick D; Hogan, Robert J; Lafontaine, Eric R

    2015-01-01

    Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus) were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4) to 2.5 X 10(5) bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3) bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3) organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B. mallei.

  5. Rapid Antimicrobial Susceptibility Testing of Bacillus anthracis, Yersinia pestis, and Burkholderia pseudomallei by Use of Laser Light Scattering Technology.

    Science.gov (United States)

    Bugrysheva, Julia V; Lascols, Christine; Sue, David; Weigel, Linda M

    2016-06-01

    Rapid methods to determine antimicrobial susceptibility would assist in the timely distribution of effective treatment or postexposure prophylaxis in the aftermath of the release of bacterial biothreat agents such as Bacillus anthracis, Yersinia pestis, or Burkholderia pseudomallei Conventional susceptibility tests require 16 to 48 h of incubation, depending on the bacterial species. We evaluated a method that is based on laser light scattering technology that measures cell density in real time. We determined that it has the ability to rapidly differentiate between growth (resistant) and no growth (susceptible) of several bacterial threat agents in the presence of clinically relevant antimicrobials. Results were available in 10 h of incubation. Use of laser scattering technology decreased the time required to determine antimicrobial susceptibility by 50% to 75% for B. anthracis, Y. pestis, and B. pseudomallei compared to conventional methods. PMID:26984973

  6. Probabilistic causality and radiogenic cancers

    International Nuclear Information System (INIS)

    A review and scrutiny of the literature on probability and probabilistic causality shows that it is possible under certain assumptions to estimate the probability that a certain type of cancer diagnosed in an individual exposed to radiation prior to diagnosis was caused by this exposure. Diagnosis of this causal relationship like diagnosis of any disease - malignant or not - requires always some subjective judgments by the diagnostician. It is, therefore, illusory to believe that tables based on actuarial data can provide objective estimates of the chance that a cancer diagnosed in an individual is radiogenic. It is argued that such tables can only provide a base from which the diagnostician(s) deviate in one direction or the other according to his (their) individual (consensual) judgment. Acceptance of a physician's diagnostic judgment by patients is commonplace. Similar widespread acceptance of expert judgment by claimants in radiation compensation cases does presently not exist. Judicious use of the present radioepidemiological tables prepared by the Working Group of the National Institutes of Health or of updated future versions of similar tables may improve the situation. 20 references

  7. Antioxidant enzymes activities of Burkholderia spp. strains-oxidative responses to Ni toxicity.

    Science.gov (United States)

    Dourado, M N; Franco, M R; Peters, L P; Martins, P F; Souza, L A; Piotto, F A; Azevedo, R A

    2015-12-01

    Increased agriculture production associated with intense application of herbicides, pesticides, and fungicides leads to soil contamination worldwide. Nickel (Ni), due to its high mobility in soils and groundwater, constitutes one of the greatest problems in terms of environmental pollution. Metals, including Ni, in high concentrations are toxic to cells by imposing a condition of oxidative stress due to the induction of reactive oxygen species (ROS), which damage lipids, proteins, and DNA. This study aimed to characterize the Ni antioxidant response of two tolerant Burkholderia strains (one isolated from noncontaminated soil, SNMS32, and the other from contaminated soil, SCMS54), by measuring superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione S-transferase (GST) activities. Ni accumulation and bacterial growth in the presence of the metal were also analyzed. The results showed that both strains exhibited different trends of Ni accumulation and distinct antioxidant enzymes responses. The strain from contaminated soil (SCMS54) exhibited a higher Ni biosorption and exhibited an increase in SOD and GST activities after 5 and 12 h of Ni exposure. The analysis of SOD, CAT, and GR by nondenaturing PAGE revealed the appearance of an extra isoenzyme in strain SCMS54 for each enzyme. The results suggest that the strain SCMS54 isolated from contaminated soil present more plasticity with potential to be used in soil and water bioremediation. PMID:26289332

  8. Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing

    Directory of Open Access Journals (Sweden)

    Karger Axel

    2012-10-01

    Full Text Available Abstract Background Burkholderia (B. pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. Results A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343 was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Conclusions Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS

  9. Linear causal modeling with structural equations

    CERN Document Server

    Mulaik, Stanley A

    2009-01-01

    Emphasizing causation as a functional relationship between variables that describe objects, Linear Causal Modeling with Structural Equations integrates a general philosophical theory of causation with structural equation modeling (SEM) that concerns the special case of linear causal relations. In addition to describing how the functional relation concept may be generalized to treat probabilistic causation, the book reviews historical treatments of causation and explores recent developments in experimental psychology on studies of the perception of causation. It looks at how to perceive causal

  10. The problem of causality in cultivation research

    OpenAIRE

    Rossmann, Constanze; Brosius, Hans-Bernd

    2004-01-01

    This paper offers an up-to-date review of problems in determining causal relationships in cultivation research, and considers the research rationales of various approaches with special reference to causal interpretation. It describes in turn a number of methodologies for addressing the problem and resolving it as far as this is possible. The issue of causal inference arises not only in cultivation research, however, but is basic to all media effects theories and approaches primarily at the ma...

  11. Identifying Causal Effects with Computer Algebra

    CERN Document Server

    García-Puente, Luis David; Sullivant, Seth

    2010-01-01

    The long-standing identification problem for causal effects in graphical models has many partial results but lacks a systematic study. We show how computer algebra can be used to either prove that a causal effect can be identified, generically identified, or show that the effect is not generically identifiable. We report on the results of our computations for linear structural equation models, where we determine precisely which causal effects are generically identifiable for all graphs on three and four vertices.

  12. Causal inference in economics and marketing.

    Science.gov (United States)

    Varian, Hal R

    2016-07-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  13. Causal inference in economics and marketing

    Science.gov (United States)

    Varian, Hal R.

    2016-01-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual—a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  14. Burkholderia mallei and Burkholderia pseudomallei stimulate differential inflammatory responses from human alveolar type II cells (ATII and macrophages.

    Directory of Open Access Journals (Sweden)

    Richard eLu

    2012-12-01

    Full Text Available Alveolar type II pneumocytes (ATII and alveolar macrophages (AM play a crucial role in the lung’s innate immune response. Burkholderia pseudomallei (BP and Burkholderia mallei (BM are facultative Gram-negative bacilli that cause melioidosis and glanders, respectively. The inhalation of these pathogens can cause lethal disease and death in humans. We sought to compare the pathogenesis of and host responses to BP and BM through contact with human primary ATII cells and monocytes-derived macrophages (MDM. We hypothesized that because BP and BM induce different disease outcomes, each pathogen would induce distinct, unique host immune responses from resident pulmonary cells. Our findings showed that BP adhered readily to ATII cells compared to BM. BP, but not BM, was rapidly internalized by macrophages where it replicated to high numbers. Further, BP induced significantly higher levels of pro-inflammatory cytokine secretion from ATII cells (IL-6, IL-8 and macrophages (IL-6, TNFα at 6h post-infection compared to BM (p<0.05. Interestingly, BM induced the anti-inflammatory cytokine, IL-10, in ATII cells and macrophages at 6h post-infection, with delayed induction of inflammatory cytokines at 24h post-infection. Because BP is flagellated and produces LPS, we confirmed that it stimulated both Toll-like receptor (TLR 4 and TLR5 via NF-κb activation while the non-flagellated BM stimulated only TLR4. These data show the differences in BP and BM pathogenicity in the lung when infecting human ATII cells and macrophages and demonstrate the ability of these pathogens to elicit distinct immune responses from resident lung cells which may open new targets for therapeutic intervention to fight against these pathogens.

  15. Heterogeneous Causal Effects and Sample Selection Bias

    DEFF Research Database (Denmark)

    Breen, Richard; Choi, Seongsoo; Holm, Anders

    2015-01-01

    The role of education in the process of socioeconomic attainment is a topic of long standing interest to sociologists and economists. Recently there has been growing interest not only in estimating the average causal effect of education on outcomes such as earnings, but also in estimating how...... causal effects might vary over individuals or groups. In this paper we point out one of the under-appreciated hazards of seeking to estimate heterogeneous causal effects: conventional selection bias (that is, selection on baseline differences) can easily be mistaken for heterogeneity of causal effects...

  16. 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.

  17. Comparison theorems for causal diamonds

    CERN Document Server

    Berthiere, Clement; Solodukhin, Sergey N

    2015-01-01

    We formulate certain inequalities for the geometric quantities characterizing causal diamonds in curved and Minkowski spacetimes. These inequalities involve the red-shift factor which, as we show explicitly in the spherically symmetric case, is monotonic in the radial direction and it takes its maximal value at the centre. As a byproduct of our discussion we re-derive Bishop's inequality without assuming the positivity of the spatial Ricci tensor. We then generalize our considerations to arbitrary, static and not necessarily spherically symmetric, asymptotically flat spacetimes. In the case of spacetimes with a horizon our generalization involves the so-called {\\it domain of dependence}. The respective volume, expressed in terms of the duration measured by a distant observer compared with the volume of the domain in Minkowski spacetime, exhibits behaviours which differ if $d=4$ or $d>4$. This peculiarity of four dimensions is due to the logarithmic subleading term in the asymptotic expansion of the metric nea...

  18. 广西金花茶炭疽病的病原鉴定及其寄主抗性评价%Identification of causal organism of yellow camellia anthracnose in Guangxi and evaluation of camellia species for host resistance

    Institute of Scientific and Technical Information of China (English)

    谢玲; 黄思良; 岑贞陆; 黄连冬; 刘宇宁; ManojKumarSrivastavar; 李杨瑞

    2009-01-01

    于2003年首次在广西防城金花茶国家级自然保护区发现金花茶炭疽病,并从病叶上分离出金花茶炭疽菌;根据致病性测定和病原菌株形态观察结果,将其鉴定为Colletotrichum camelliae Mass.,由该菌引起的金花茶炭疽腐在广西属首次报道.为了寻找炭疽病的抗源,通过测定13种金花茶和3种山茶对金花茶炭疽病菌的抗性,结果表明:防城金花茶(C.chrysantha var.phaeopubisperma S.Y.Liang et Z.H.Tang)、东兴金花茶(C.tunghinensis Chang)、多瓣金花茶(C.multipetala S.Y.Liang et C.Z.Deng)、小花金花茶(C.micrantha S.Y.Liang et C.Y.Zhong)、顶生平果金花茶(C.pingguoensis var.teminalis(Liang et su)S.Y.Liang)5个种或变种表现抗病反应;博白大果油茶(Camellia gigantocarpa Hu et T.c.Huang)、红山茶(Camellia japonica Linn)的红露珍品种、金花茶(Camellia chrysantha(Hu)Tuyama)以及显脉金花茶(Camellia euphlebia Merr.ex Sealy)对Colletotrichum camelliae表现为免疫反应,这些抗性材料将为金花茶的种质改良提供优质抗源.%The vellow camellia anthracnose disease was observed for the first time in 2003 in Fangcheng Yellow Camellia National Natural Reserve,Fangchenggang city,Guangxi,China.The isolates from the affected leaves were obtained and their pathogenecity to yellow camellia leaves were confirmed.The pathogen was identified as Colletotrichum camelliae Mass.,based on the morphological and cultural characteristics as well as pathogenecity of the isolates.To evaluate the yellow camellia resistance to the pathogen,13 yellow camellia species and 3 camellia species have been evaluated for host resistance identification.The restilts showed that five moderately resistant species were confirmed,including Camellia chrysantha var.phaeopubisperma S.Y.Liang et Z.H.Tang,Camella tunghinensis Chang,Camellia multipetala S.Y.Liang et C.Z.Deng.Camellia mierantha S.Y.Liang et C.Y.Zhong and Camellia pingguoensis var.teminalis(Liang et su

  19. The Power of Causal Beliefs and Conflicting Evidence on Causal Judgments and Decision Making

    Science.gov (United States)

    Garcia-Retamero, Rocio; Muller, Stephanie M.; Catena, Andres; Maldonado, Antonio

    2009-01-01

    In two experiments, we investigated the relative impact of causal beliefs and empirical evidence on both decision making and causal judgments, and whether this relative impact could be altered by previous experience. 2. Selected groups of participants in both experiments received pre-training with either causal or neutral cues, or no pre-training…

  20. Unpacking the causal chain of financial literacy

    OpenAIRE

    Carpena, Fenella; Cole, Shawn; Shapiro, Jeremy; Zia, Bilal

    2011-01-01

    A growing body of literature examines the causal impact of financial literacy on individual, household, and firm level outcomes. This paper unpacks the mechanism of impact by focusing on the first link in the causal chain. Specifically, it studies the experimental impact of financial literacy on three distinct dimensions of financial knowledge. The analysis finds that financial literacy do...

  1. Causal Indicator Models: Identification, Estimation, and Testing

    Science.gov (United States)

    Bollen, Kenneth A.; Davis, Walter R.

    2009-01-01

    We discuss the identification, estimation, and testing of structural equation models that have causal indicators. We first provide 2 rules of identification that are particularly helpful in models with causal indicators--the 2C emitted paths rule and the exogenous X rule. We demonstrate how these rules can help us distinguish identified from…

  2. Causal Moderation Analysis Using Propensity Score Methods

    Science.gov (United States)

    Dong, Nianbo

    2012-01-01

    This paper is based on previous studies in applying propensity score methods to study multiple treatment variables to examine the causal moderator effect. The propensity score methods will be demonstrated in a case study to examine the causal moderator effect, where the moderators are categorical and continuous variables. Moderation analysis is an…

  3. Controlling for causally relevant third variables.

    Science.gov (United States)

    Goodie, Adam S; Williams, Cristina C; Crooks, C L

    2003-10-01

    In 3 experiments, the authors tested the conditions under which 3rd variables are controlled for in making causal judgments. The authors hypothesized that 3rd variables are controlled for when the 3rd variables are themselves perceived as causal. In Experiment 1, the participants predicted test performance after seeing information about wearing a lucky garment, taking a test-preparation course, and staying up late. The course (perceived as more causally relevant) was controlled for more than was the garment (perceived as less causally relevant) in assessing the effectiveness of staying up late. In Experiments 2 and 3, to obviate the many alternative accounts that arise from the realistic cover story of Experiment 1, participants predicted flowers' blooming after the presentation or nonpresentation of liquids. When one liquid was trained as causal, it was controlled for more in judging another liquid than when it was trained as neutral. Overall, stimuli perceived as causal were controlled for more when judging other stimuli. The authors concluded that the effect of perceived causal relevance on causal conditionalizing is real and normatively reasonable. PMID:14672103

  4. On the spectral formulation of Granger causality.

    Science.gov (United States)

    Chicharro, D

    2011-12-01

    Spectral measures of causality are used to explore the role of different rhythms in the causal connectivity between brain regions. We study several spectral measures related to Granger causality, comprising the bivariate and conditional Geweke measures, the directed transfer function, and the partial directed coherence. We derive the formulation of dependence and causality in the spectral domain from the more general formulation in the information-theory framework. We argue that the transfer entropy, the most general measure derived from the concept of Granger causality, lacks a spectral representation in terms of only the processes associated with the recorded signals. For all the spectral measures we show how they are related to mutual information rates when explicitly considering the parametric autoregressive representation of the processes. In this way we express the conditional Geweke spectral measure in terms of a multiple coherence involving innovation variables inherent to the autoregressive representation. We also link partial directed coherence with Sims' criterion of causality. Given our results, we discuss the causal interpretation of the spectral measures related to Granger causality and stress the necessity to explicitly consider their specific formulation based on modeling the signals as linear Gaussian stationary autoregressive processes.

  5. mediation: R Package for Causal Mediation Analysis

    Directory of Open Access Journals (Sweden)

    Dustin Tingley

    2014-09-01

    Full Text Available In this paper, we describe the R package mediation for conducting causal mediation analysis in applied empirical research. In many scientific disciplines, the goal of researchers is not only estimating causal effects of a treatment but also understanding the process in which the treatment causally affects the outcome. Causal mediation analysis is frequently used to assess potential causal mechanisms. The mediation package implements a comprehensive suite of statistical tools for conducting such an analysis. The package is organized into two distinct approaches. Using the model-based approach, researchers can estimate causal mediation effects and conduct sensitivity analysis under the standard research design. Furthermore, the design-based approach provides several analysis tools that are applicable under different experimental designs. This approach requires weaker assumptions than the model-based approach. We also implement a statistical method for dealing with multiple (causally dependent mediators, which are often encountered in practice. Finally, the package also offers a methodology for assessing causal mediation in the presence of treatment noncompliance, a common problem in randomized trials.

  6. Causally pathological spacetimes are physically relevant

    CERN Document Server

    Hubeny, V E; Ross, S F; Hubeny, Veronika E.; Rangamani, Mukund; Ross, Simon F.

    2005-01-01

    We argue that in the context of string theory, the usual restriction to globally hyperbolic spacetimes should be considerably relaxed. We exhibit an example of a spacetime which only satisfies the causal condition, and so is arbitrarily close to admitting closed causal curves, but which has a well-behaved dual description, free of paradoxes.

  7. Structural intervention distance for evaluating causal graphs

    DEFF Research Database (Denmark)

    Peters, Jonas; Bühlmann, Peter

    2015-01-01

    Causal inference relies on the structure of a graph, often a directed acyclic graph (DAG). Different graphs may result in different causal inference statements and different intervention distributions. To quantify such differences, we propose a (pre-)metric between DAGs, the structural interventi...... implementation with software code available on the first author's home page....

  8. Campbell's and Rubin's Perspectives on Causal Inference

    Science.gov (United States)

    West, Stephen G.; Thoemmes, Felix

    2010-01-01

    Donald Campbell's approach to causal inference (D. T. Campbell, 1957; W. R. Shadish, T. D. Cook, & D. T. Campbell, 2002) is widely used in psychology and education, whereas Donald Rubin's causal model (P. W. Holland, 1986; D. B. Rubin, 1974, 2005) is widely used in economics, statistics, medicine, and public health. Campbell's approach focuses on…

  9. Causalities of the Taiwan Stock Market

    OpenAIRE

    Juhi-Lian Julian Ting

    2003-01-01

    Volatility, fitting with first order Landau expansion, stationarity, and causality of the Taiwan stock market (TAIEX) are investigated based on daily records. Instead of consensuses that consider stock market index change as a random time series we propose the market change as a dual time series consists of the index and the corresponding volume. Therefore, causalities between these two time series are investigated.

  10. Causal random geometry from stochastic quantization

    DEFF Research Database (Denmark)

    Ambjørn, Jan; Loll, R.; Westra, W.;

    2010-01-01

     in this short note we review a recently found formulation of two-dimensional causal quantum gravity defined through Causal Dynamical Triangulations and stochastic quantization. This procedure enables one to extract the nonperturbative quantum Hamiltonian of the random surface model including the...... the sum over topologies. Interestingly, the generally fictitious stochastic time corresponds to proper time on the geometries...

  11. Survey of Bartonella spp. in U.S. bed bugs detects Burkholderia multivorans but not Bartonella.

    Directory of Open Access Journals (Sweden)

    Virna L Saenz

    Full Text Available Bed bugs (Cimex lectularius L. have resurged in the United States and globally. Bed bugs are hematophagous ectoparasites of humans and other animals, including domestic pets, chickens, and bats, and their blood feeding habits contribute to their potential as disease vectors. Several species of Bartonella are re-emergent bacterial pathogens that also affect humans, domestic pets, bats and a number of other wildlife species. Because reports of both bed bugs and Bartonella have been increasing in the U.S., and because their host ranges can overlap, we investigated whether the resurgences of these medically important pathogens and their potential vector might be linked, by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent and from bed bugs that have been in culture in the laboratory for several years. We screened a total of 331 bed bugs: 316 bed bugs from 36 unique collections in 29 geographic locations in 13 states, 10 bed bugs from two colonies maintained in the laboratory for 3 yr, and 5 bed bugs from a colony that has been in culture since before the recent resurgence of bed bugs. Bartonella spp. DNA was screened using a polymerase chain reaction assay targeting the 16S-23S rRNA intergenic transcribed spacer region. Bartonella DNA was not amplified from any bed bug, but five bed bugs from four different apartments of an elderly housing building in North Carolina contained DNA sequences that corresponded to Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector.

  12. Causality, Bell's theorem, and Ontic Definiteness

    CERN Document Server

    Henson, Joe

    2011-01-01

    Bell's theorem shows that the reasonable relativistic causal principle known as "local causality" is not compatible with the predictions of quantum mechanics. It is not possible maintain a satisfying causal principle of this type while dropping any of the better-known assumptions of Bell's theorem. However, another assumption of Bell's theorem is the use of classical logic. One part of this assumption is the principle of "ontic definiteness", that is, that it must in principle be possible to assign definite truth values to all propositions treated in the theory. Once the logical setting is clarified somewhat, it can be seen that rejecting this principle does not in any way undermine the type of causal principle used by Bell. Without ontic definiteness, the deterministic causal condition known as Einstein Locality succeeds in banning superluminal influence (including signalling) whilst allowing correlations that violate Bell's inequalities. Objections to altering logic, and the consequences for operational and...

  13. Granger causality in wall-bounded turbulence

    International Nuclear Information System (INIS)

    Granger causality is based on the idea that if a variable helps to predict another one, then they are probably involved in a causality relationship. This technique is based on the identification of a predictive model for causality detection. The aim of this paper is to use Granger causality to study the dynamics and the energy redistribution between scales and components in wall-bounded turbulent flows. In order to apply it on flows, Granger causality is generalized for snapshot-based observations of large size using linear-model identification methods coming from model reduction. Optimized DMD, a variant of the Dynamic Mode Decomposition, is considered for building a linear model based on snapshots. This method is used to link physical events and extract physical mechanisms associated to the bursting process in the logarithmic layer of a turbulent channel flow.

  14. Quantum-coherent mixtures of causal relations

    CERN Document Server

    MacLean, Jean-Philippe W; Spekkens, Robert W; Resch, Kevin J

    2016-01-01

    Understanding the causal influences that hold among the parts of a system is critical both to explaining that system's natural behaviour and to controlling it through targeted interventions. In a quantum world, understanding causal relations is equally important, but the set of possibilities is far richer. The two basic ways in which a pair of time-ordered quantum systems may be causally related are by a cause-effect mechanism or by a common cause acting on both. Here, we show that it is possible to have a coherent mixture of these two possibilities. We realize such a nonclassical causal relation in a quantum optics experiment and derive a set of criteria for witnessing the coherence based on a quantum version of Berkson's paradox. The interplay of causality and quantum theory lies at the heart of challenging foundational puzzles, such as Bell's theorem and the search for quantum gravity, but could also provide a resource for novel quantum technologies.

  15. On the spectral dimension of causal triangulations

    CERN Document Server

    Durhuus, Bergfinnur; Wheater, John F

    2009-01-01

    We introduce an ensemble of infinite causal triangulations, called the uniform infinite causal triangulation, and show that it is equivalent to an ensemble of infinite trees, the uniform infinite planar tree. It is proved that in both cases the Hausdorff dimension almost surely equals 2. The infinite causal triangulations are shown to be almost surely recurrent or, equivalently, their spectral dimension is almost surely less than or equal to 2. We also establish that for certain reduced versions of the infinite causal triangulations the spectral dimension equals 2 both for the ensemble average and almost surely. The triangulation ensemble we consider is equivalent to the causal dynamical triangulation model of two-dimensional quantum gravity and therefore our results apply to that model.

  16. φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity

    Directory of Open Access Journals (Sweden)

    Kvitko Brian H

    2012-12-01

    Full Text Available Abstract Background Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237. Results We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains. Conclusions The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.

  17. A Possible Link between Infection with Burkholderia Bacteria and Systemic Lupus Erythematosus Based on Epitope Mimicry

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2008-01-01

    Full Text Available We previously demonstrated that purified polyclonal and monoclonal anti-dsDNA antibodies bind a 15-mer peptide ASPVTARVLWKASHV in ELISA and Dot blot. This 15-mer peptide partial sequence ARVLWKASH shares similarity with burkholderia bacterial cytochrome B 561 partial sequence ARVLWRATH. In this study, we show that purified anti-dsDNA antibodies react with burkholderia fungorum bacterial cell lysates in Western blot. We used anti-dsDNA antibodies to make an anti-dsDNA antibodies affinity column and used this column to purify the burkholderia fungorum bacterial protein. Purified anti-dsDNA antibodies bind specifically to purified bacterial antigen and purified bacterial antigen blocked the anti-dsDNA antibodies binding to dsDNA antigen. Sera with anti-dsDNA antibodies bind specifically to purified bacterial antigen. We obtained protein partial sequence of RAGTDEGFG which is shared with burkholderia bacterial transcription regulator protein sequence. Sera with anti-dsDNA antibodies bind to RAGTDEGFG peptide better than control groups. These data support our hypothesis that the origin of anti-dsDNA antibodies in SLE may be associated with burkholderia bacterial infection.

  18. 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

  19. ALIEN SPECIES: THEIR ROLE IN AMPHIBIAN POPULATION DECLINES AND RESTORATION

    Science.gov (United States)

    Alien species (also referred to as exotic, invasive, introduced, or normative species) have been implicated as causal agents in population declines of many amphibian species. Herein, we evaluate the relative contributions of alien species and other factors in adversely affecting ...

  20. Causal systems categories: differences in novice and expert categorization of causal phenomena.

    Science.gov (United States)

    Rottman, Benjamin M; Gentner, Dedre; Goldwater, Micah B

    2012-07-01

    We investigated the understanding of causal systems categories--categories defined by common causal structure rather than by common domain content--among college students. We asked students who were either novices or experts in the physical sciences to sort descriptions of real-world phenomena that varied in their causal structure (e.g., negative feedback vs. causal chain) and in their content domain (e.g., economics vs. biology). Our hypothesis was that there would be a shift from domain-based sorting to causal sorting with increasing expertise in the relevant domains. This prediction was borne out: the novice groups sorted primarily by domain and the expert group sorted by causal category. These results suggest that science training facilitates insight about causal structures.

  1. Spread of entanglement and causality

    Science.gov (United States)

    Casini, Horacio; Liu, Hong; Mezei, Márk

    2016-07-01

    We investigate causality constraints on the time evolution of entanglement entropy after a global quench in relativistic theories. We first provide a general proof that the so-called tsunami velocity is bounded by the speed of light. We then generalize the free particle streaming model of [1] to general dimensions and to an arbitrary entanglement pattern of the initial state. In more than two spacetime dimensions the spread of entanglement in these models is highly sensitive to the initial entanglement pattern, but we are able to prove an upper bound on the normalized rate of growth of entanglement entropy, and hence the tsunami velocity. The bound is smaller than what one gets for quenches in holographic theories, which highlights the importance of interactions in the spread of entanglement in many-body systems. We propose an interacting model which we believe provides an upper bound on the spread of entanglement for interacting relativistic theories. In two spacetime dimensions with multiple intervals, this model and its variations are able to reproduce intricate results exhibited by holographic theories for a significant part of the parameter space. For higher dimensions, the model bounds the tsunami velocity at the speed of light. Finally, we construct a geometric model for entanglement propagation based on a tensor network construction for global quenches.

  2. Spread of entanglement and causality

    CERN Document Server

    Casini, Horacio; Mezei, Márk

    2015-01-01

    We investigate causality constraints on the time evolution of entanglement entropy after a global quench in relativistic theories. We first provide a general proof that the so-called tsunami velocity is bounded by the speed of light. We then generalize the free particle streaming model of arXiv:cond-mat/0503393 to general dimensions and to an arbitrary entanglement pattern of the initial state. In more than two spacetime dimensions the spread of entanglement in these models is highly sensitive to the initial entanglement pattern, but we are able to prove an upper bound on the normalized rate of growth of entanglement entropy, and hence the tsunami velocity. The bound is smaller than what one gets for quenches in holographic theories, which highlights the importance of interactions in the spread of entanglement in many-body systems. We propose an interacting model which we believe provides an upper bound on the spread of entanglement for interacting relativistic theories. In two spacetime dimensions with multi...

  3. Burkholderia pseudomallei induces IL-23 production in primary human monocytes.

    Science.gov (United States)

    Kulsantiwong, Panthong; Pudla, Matsayapan; Boondit, Jitrada; Wikraiphat, Chanthiwa; Dunachie, Susanna J; Chantratita, Narisara; Utaisincharoen, Pongsak

    2016-06-01

    Burkholderia pseudomallei, a gram-negative intracellular bacterium, is a causative agent of melioidosis. The bacterium has been shown to induce the innate immune response, particularly pro-inflammatory cytokine production in several of both mouse and human cell types. In the present study, we investigate host immune response in B. pseudomallei-infected primary human monocytes. We discover that wild-type B. pseudomallei is able to survive and multiply inside the primary human monocytes. In contrast, B. pseudomallei LPS mutant, a less virulent strain, is susceptible to host killing during bacterial infection. Moreover, microarray result showed that wild-type B. pseudomallei but not B. pseudomallei LPS mutant is able to activate gene expression of IL-23 as demonstrated by the up-regulation of p19 and p40 subunit expression. Consistent with gene expression analysis, the secretion of IL-23 analyzed by ELISA also showed that wild-type B. pseudomallei induces a significantly higher level of IL-23 secretion than that of B. pseudomallei LPS mutant. These results implied that IL-23 may be an important cytokine for the innate immune response during B. pseudomallei infection. The regulation of IL-23 production may drive the different host innate immune responses between patients and may relate to the severity of melioidosis. PMID:26563410

  4. [Pharyngitis due to Burkholderia cepacia. Person-to-person transmission].

    Science.gov (United States)

    Fajardo Olivares, M; Cordero Carrasco, J L; Beteta López, A; Escobar Izquierdo, A B; Sacristán Enciso, B

    2004-06-01

    Burkholderia cepacia is a Gram-negative bacillus that is widely distributed in nature; it is isolated from the ground, water, plants and vegetables. Generally, it produces nosocomial infection due to contamination of disinfectants, medical equipment, prosthetic material and drugs, such as anesthetics or liquids used in urological irrigation. The most probable mechanism of transmission is through hospital material or through fomites among people after contact for several weeks or months. Recently, it has been considered as an important pathogen in immunocompromised patients, or in those with significant underlying diseases, such as chronic granulomastosis or cystic fibrosis. We present a case of pharyngitis due to B. cepacia and its transmission within a few days in two immunocompetent twin siblings without previous underlying diseases. The infection disappeared after specific treatment for this microorganism was started. We believe that samples should be taken from the pharynx and nasal pits in patients with acute upper respiratory tract processes that do not respond to empiric antibiotic treatment, before classifying them as viral infection without etiologic diagnosis.

  5. Molecular Characterization of Putative Virulence Determinants in Burkholderia pseudomallei

    Directory of Open Access Journals (Sweden)

    Suat Moi Puah

    2014-01-01

    Full Text Available The Gram-negative saprophyte Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease which is endemic in Southeast Asia and northern Australia. This bacterium possesses many virulence factors which are thought to contribute to its survival and pathogenicity. Using a virulent clinical isolate of B. pseudomallei and an attenuated strain of the same B. pseudomallei isolate, 6 genes BPSL2033, BP1026B_I2784, BP1026B_I2780, BURPS1106A_A0094, BURPS1106A_1131, and BURPS1710A_1419 were identified earlier by PCR-based subtractive hybridization. These genes were extensively characterized at the molecular level, together with an additional gene BPSL3147 that had been identified by other investigators. Through a reverse genetic approach, single-gene knockout mutants were successfully constructed by using site-specific insertion mutagenesis and were confirmed by PCR. BPSL2033::Km and BURPS1710A_1419::Km mutants showed reduced rates of survival inside macrophage RAW 264.7 cells and also low levels of virulence in the nematode infection model. BPSL2033::Km demonstrated weak statistical significance (P=0.049 at 8 hours after infection in macrophage infection study but this was not seen in BURPS1710A_1419::Km. Nevertheless, complemented strains of both genes were able to partially restore the gene defects in both in vitro and in vivo studies, thus suggesting that they individually play a minor role in the virulence of B. pseudomallei.

  6. Mouse model of sublethal and lethal intraperitoneal glanders (Burkholderia mallei).

    Science.gov (United States)

    Fritz, D L; Vogel, P; Brown, D R; Deshazer, D; Waag, D M

    2000-11-01

    Sixty male BALB/c mice were inoculated intraperitoneally with either a sublethal or a lethal dose of Burkholderia mallei China 7 strain, then killed at multiple time points postinoculation. Histopathologic changes were qualitatively similar in both groups and consisted of pyogranulomatous inflammation. In sublethal study mice, changes were first seen at 6 hours in mediastinal lymph nodes, then in spleen, liver, peripheral lymph nodes, and bone marrow at day 3. These changes generally reached maximal incidence and severity by day 4 but decreased by comparison in all tissues except the liver. Changes were first seen in lethal study mice also at 6 hours in mediastinal lymph nodes and in spleens. At day 1, changes were present in liver, peripheral lymph nodes, and bone marrow. The incidence and severity of these changes were maximal at day 2. In contrast to sublethal study mice, the incidence and severity of the changes did not decrease through the remainder of the study. The most significant difference between the two groups was the rapid involvement of the spleen in the lethal study mice. Changes indicative of impaired vascular perfusion were more frequently seen in the sublethal study mice. Our findings indicate that mice are susceptible to B. mallei infection and may serve as an appropriate model for glanders infection in a resistant host such as human beings. Additionally, by immunoelectron microscopy, we showed the presence of type I O-antigenic polysaccharide (capsular) antigen surrounding B. mallei.

  7. Incidence of Burkholderia mallei infection among indigenous equines in India

    Science.gov (United States)

    Malik, Praveen; Singha, Harisankar; Goyal, Sachin K; Khurana, Sandip K; Tripathi, Badri Naryan; Dutt, Abha; Singh, Dabal; Sharma, Neeraj; Jain, Sanjay

    2015-01-01

    Burkholderia mallei is the causative agent of glanders which is a highly contagious and fatal disease of equines. Considering the nature and severity of the disease in equines, and potential of transmission to human beings, glanders is recognised as a ‘notifiable’ disease in many countries. An increasing number of glanders outbreaks throughout the Asian continents, including India, have been noticed recently. In view of the recent re-emergence of the disease, the present study was undertaken to estimate the prevalence of glanders among indigenous equines from different parts of India. Serum samples were analysed by complement fixation test (CFT) and ELISA for the detection of B mallei specific antibodies. A total of 7794 equines, which included 4720 horses, 1881 donkeys and 1193 mules were sampled from April 2011 to December 2014 from 10 states of India. Serologically, 36 equines (pony=7, mules=10, horses=19) were found to be positive for glanders by CFT and indirect-ELISA. The highest number of cases were detected in Uttar Pradesh (n=31) followed by Himachal Pradesh (n=4) and Chhattisgarh (n=1). Isolation of B mallei was attempted from nasal and abscess swabs collected from seropositive equines. Four isolates of B mallei were cultured from nasal swabs of two mules and two ponies. Identity of the isolates was confirmed by PCR and sequencing of fliP gene fragment. The study revealed circulation of B mallei in northern India and the need for continued surveillance to support the eradication. PMID:26457190

  8. Monitoring Therapeutic Treatments against Burkholderia Infections Using Imaging Techniques

    Directory of Open Access Journals (Sweden)

    Tiffany M. Mott

    2013-05-01

    Full Text Available Burkholderia mallei, the etiologic agent of glanders, are Category B select agents with biothreat potential, and yet effective therapeutic treatments are lacking. In this study, we showed that CpG administration increased survival, demonstrating protection in the murine glanders model. Bacterial recovery from infected lungs, liver and spleen was significantly reduced in CpG-treated animals as compared with non-treated mice. Reciprocally, lungs of CpG-treated infected animals were infiltrated with higher levels of neutrophils and inflammatory monocytes, as compared to control animals. Employing the B. mallei bioluminescent strain CSM001 and the Neutrophil-Specific Fluorescent Imaging Agent, bacterial dissemination and neutrophil trafficking were monitored in real-time using multimodal in vivo whole body imaging techniques. CpG-treatment increased recruitment of neutrophils to the lungs and reduced bioluminescent bacteria, correlating with decreased bacterial burden and increased protection against acute murine glanders. Our results indicate that protection of CpG-treated animals was associated with recruitment of neutrophils prior to infection and demonstrated, for the first time, simultaneous real time in vivo imaging of neutrophils and bacteria. This study provides experimental evidence supporting the importance of incorporating optimized in vivo imaging methods to monitor disease progression and to evaluate the efficacy of therapeutic treatment during bacterial infections.

  9. Burkholderia Pseudomallei Causing Bone and Joint Infections: A Clinical Update.

    Science.gov (United States)

    Raja, Nadeem Sajjad; Scarsbrook, Christine

    2016-03-01

    Burkholderia pseudomallei (B. pseudomallei), a causative agent of an emerging infectious disease melioidosis, is endemic in the tropical regions of the world. Due to increased international travel, the infection is now also seen outside of the tropics. The majority of patients with identified risk factors such as diabetes mellitus, heavy alcohol use, malignancy, chronic lung and kidney disease, corticosteroid use, thalassemia, rheumatic heart disease, systemic lupus erythematosus and cardiac failure acquire this organism through percutaneous inoculation or inhalation. The clinical manifestations are variable, ranging from localized abscess formation to septicemia. Melioidotic bone and joint infections are rarely reported but are an established entity. The knee joint is the most commonly affected joint in melioidosis, followed by the ankle, hip and shoulder joints. Melioidosis should be in the differential diagnosis of bone and joint infections in residents or returning travelers from the endemic area. Melioidosis diagnosis is missed in many parts of the world due to the lack of awareness of this infection and limited laboratory training and diagnostic techniques. It also mimics other diseases such as tuberculosis. Delay in the diagnosis, or the initiation of appropriate and effective treatment against melioidosis, could worsen the outcome. Initial therapy with ceftazidime, or carbapenem with or without cotrimoxazole is recommended, followed by the oral eradication therapy (based on the antimicrobial susceptibility) with amoxicillin/clavulanic acid or cotrimoxazole. Surgical intervention remains important. This paper reviews current literature on the epidemiology, clinical features, diagnosis, and management of melioidotic bone and joint infections. PMID:26728713

  10. Burkholderia cenocepacia zinc metalloproteases influence resistance to antimicrobial peptides.

    Science.gov (United States)

    Kooi, Cora; Sokol, Pamela A

    2009-09-01

    Burkholderia cenocepacia secretes two zinc-dependent metalloproteases, designated ZmpA and ZmpB. Previously, ZmpA and ZmpB have been shown to cleave several proteins important in host defence. In this study, the ability of ZmpA and ZmpB to digest and inactivate antimicrobial peptides involved in innate immunity was examined. ZmpB but not ZmpA cleaved beta-defensin-1. ZmpA but not ZmpB cleaved the cathelicidin LL-37. Both enzymes cleaved elafin and secretory leukocyte inhibitor, which are antimicrobial peptides as well as neutrophil elastase inhibitors. Both ZmpA and ZmpB cleaved protamine, a fish antimicrobial peptide, and a zmpA zmpB mutant was more sensitive to protamine killing than the parental strain. ZmpA or ZmpB cleavage of elafin inactivated its anti-protease activity. The effect of ZmpA and ZmpB on the neutrophil proteases elastase and cathepsin G was also examined but neither enzyme was active against these host proteases. These studies suggest that ZmpA and ZmpB may influence the resistance of B. cenocepacia to host antimicrobial peptides as well as alter the host protease/anti-protease balance in chronic respiratory infections.

  11. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis.

    Science.gov (United States)

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-01-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

  12. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

    Science.gov (United States)

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-09-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

  13. Mining Causality for Explanation Knowledge from Text

    Institute of Scientific and Technical Information of China (English)

    Chaveevan Pechsiri; Asanee Kawtrakul

    2007-01-01

    Mining causality is essential to provide a diagnosis. This research aims at extracting the causality existing within multiple sentences or EDUs (Elementary Discourse Unit). The research emphasizes the use of causality verbs because they make explicit in a certain way the consequent events of a cause, e.g., "Aphids suck the sap from rice leaves. Then leaves will shrink. Later, they will become yellow and dry.". A verb can also be the causal-verb link between cause and effect within EDU(s), e.g., "Aphids suck the sap from rice leaves causing leaves to be shrunk" ("causing" is equivalent to a causal-verb link in Thai). The research confronts two main problems: identifying the interesting causality events from documents and identifying their boundaries. Then, we propose mining on verbs by using two different machine learning techniques, Naive Bayes classifier and Support Vector Machine. The resulted mining rules will be used for the identification and the causality extraction of the multiple EDUs from text. Our multiple EDUs extraction shows 0.88 precision with 0.75 recall from Na'ive Bayes classifier and 0.89 precision with 0.76 recall from Support Vector Machine.

  14. Causal localizations in relativistic quantum mechanics

    International Nuclear Information System (INIS)

    Causal localizations describe the position of quantum systems moving not faster than light. They are constructed for the systems with finite spinor dimension. At the center of interest are the massive relativistic systems. For every positive mass, there is the sequence of Dirac tensor-localizations, which provides a complete set of inequivalent irreducible causal localizations. They obey the principle of special relativity and are fully Poincaré covariant. The boosters are determined by the causal position operator and the other Poincaré generators. The localization with minimal spinor dimension is the Dirac localization. Thus, the Dirac equation is derived here as a mere consequence of the principle of causality. Moreover, the higher tensor-localizations, not known so far, follow from Dirac’s localization by a simple construction. The probability of localization for positive energy states results to be described by causal positive operator valued (PO-) localizations, which are the traces of the causal localizations on the subspaces of positive energy. These causal Poincaré covariant PO-localizations for every irreducible massive relativistic system were, all the more, not known before. They are shown to be separated. Hence, the positive energy systems can be localized within every open region by a suitable preparation as accurately as desired. Finally, the attempt is made to provide an interpretation of the PO-localization operators within the frame of conventional quantum mechanics attributing an important role to the negative energy states

  15. Causal localizations in relativistic quantum mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Castrigiano, Domenico P. L., E-mail: castrig@ma.tum.de; Leiseifer, Andreas D., E-mail: andreas.leiseifer@tum.de [Fakultät für Mathematik, TU München, Boltzmannstraße 3, 85747 Garching (Germany)

    2015-07-15

    Causal localizations describe the position of quantum systems moving not faster than light. They are constructed for the systems with finite spinor dimension. At the center of interest are the massive relativistic systems. For every positive mass, there is the sequence of Dirac tensor-localizations, which provides a complete set of inequivalent irreducible causal localizations. They obey the principle of special relativity and are fully Poincaré covariant. The boosters are determined by the causal position operator and the other Poincaré generators. The localization with minimal spinor dimension is the Dirac localization. Thus, the Dirac equation is derived here as a mere consequence of the principle of causality. Moreover, the higher tensor-localizations, not known so far, follow from Dirac’s localization by a simple construction. The probability of localization for positive energy states results to be described by causal positive operator valued (PO-) localizations, which are the traces of the causal localizations on the subspaces of positive energy. These causal Poincaré covariant PO-localizations for every irreducible massive relativistic system were, all the more, not known before. They are shown to be separated. Hence, the positive energy systems can be localized within every open region by a suitable preparation as accurately as desired. Finally, the attempt is made to provide an interpretation of the PO-localization operators within the frame of conventional quantum mechanics attributing an important role to the negative energy states.

  16. Perception of causality in schizophrenia spectrum disorder.

    Science.gov (United States)

    Tschacher, Wolfgang; Kupper, Zeno

    2006-10-01

    Patients with schizophrenia spectrum disorders often maintain deviating views on cause-effect relationships, especially when positive and disorganization symptoms are manifest. Altered perceived causality is prominent in delusional ideation, in ideas of reference, and in the mentalizing ability (theory of mind [ToM]) of patients. Perceiving causal relationships may be understood either as higher order cognitive reasoning or as low-level information processing. In the present study, perception of causality was investigated as a low-level, preattentional capability similar to gestalt-like perceptual organization. Thirty-one patients (24 men and 7 women with mean age 27.7 years) and the same number of healthy control subjects matched to patients with respect to age and sex were tested. A visual paradigm was used in which 2 identical discs move, from opposite sides of a monitor, steadily toward and then past one another. Their coincidence generates an ambiguous, bistable percept (discs either "stream through" or "bounce off" one another). The bouncing perception, ie, perceived causality, is enhanced when auditory stimuli are presented at the time of coincidence. Psychopathology was measured using the Positive and Negative Syndrome Scale. It was found that positive symptoms were strongly associated with increased perceived causality and disorganization with attenuated perceived causality. Patients in general were not significantly different from controls, but symptom subgroups showed specifically altered perceived causality. Perceived causality as a basic preattentional process may contribute to higher order cognitive alterations and ToM deficiencies. It is suggested that cognitive remediation therapy should address both increased and reduced perception of causality. PMID:16896057

  17. On the origin of Hill's causal criteria.

    Science.gov (United States)

    Morabia, A

    1991-09-01

    The rules to assess causation formulated by the eighteenth century Scottish philosopher David Hume are compared to Sir Austin Bradford Hill's causal criteria. The strength of the analogy between Hume's rules and Hill's causal criteria suggests that, irrespective of whether Hume's work was known to Hill or Hill's predecessors, Hume's thinking expresses a point of view still widely shared by contemporary epidemiologists. The lack of systematic experimental proof to causal inferences in epidemiology may explain the analogy of Hume's and Hill's, as opposed to Popper's, logic.

  18. Causal localizations in relativistic quantum mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Leiseifer, Andreas David

    2014-06-30

    Sufficient and necessary conditions for causal localizations of massive relativistic systems are developed. It is proven that the Dirac- and the Dirac tensor-system are up to unitary equivalence the only irreducible causal localizations with finite spinor dimension which have a massive relativistic extension. A formula for this extension is given. The existence of arbitrarily good localized states of positive energy is shown. In the context of the causality condition a Paley-Wiener theorem for bounded measurable matrix-valued functions is proven.

  19. Causality and momentum conservation from relative locality

    Science.gov (United States)

    Amelino-Camelia, Giovanni; Bianco, Stefano; Brighenti, Francesco; Buonocore, Riccardo Junior

    2015-04-01

    Theories involving curved momentum space, which recently became a topic of interest in the quantum-gravity literature, can, in general, violate many apparently robust aspects of our current description of the laws of physics, including relativistic invariance, locality, causality, and global momentum conservation. Here, we explore some aspects of the pathologies arising in generic theories involving curved momentum space for what concerns causality and momentum conservation. However, we also report results suggesting that when momentum space is maximally symmetric, and the theory is formulated relativistically, most notably including translational invariance with the associated relativity of spacetime locality, momentum is globally conserved and there is no violation of causality.

  20. Causal structures of pp-waves

    CERN Document Server

    Hubeny, V E; Hubeny, Veronika E.; Rangamani, Mukund

    2002-01-01

    We discuss the causal structure of pp-wave spacetimes using the ideal point construction outlined by Geroch, Kronheimer, and Penrose. This generalizes the recent work of Marolf and Ross, who considered similar issues for plane wave spacetimes. We address the question regarding the dimension of the causal boundary for certain specific pp-wave backgrounds. In particular, we demonstrate that the pp-wave spacetime which gives rise to the N = 2 sine-Gordon string world-sheet theory is geodesically complete and has a one-dimensional causal boundary.

  1. The CMB in a Causal Set Universe

    CERN Document Server

    Zuntz, Joe

    2007-01-01

    We discuss Cosmic Microwave Background constraints on the causal set theory of quantum gravity, which has made testable predictions about the nature of dark energy. We flesh out previously discussed heuristic constraints by showing how the power spectrum of causal set dark energy fluctuations can be found from the overlap volumes of past light cones of points in the universe. Using a modified Boltzmann code we put constraints on the single parameter of the theory that are somewhat stronger than previous ones. We conclude that causal set theory cannot explain late-time acceleration without radical alterations to General Relativity.

  2. Intrinsic Universality of Causal Graph Dynamics

    Directory of Open Access Journals (Sweden)

    Simon Martiel

    2013-09-01

    Full Text Available Causal graph dynamics are transformations over graphs that capture two important symmetries of physics, namely causality and homogeneity. They can be equivalently defined as continuous and translation invariant transformations or functions induced by a local rule applied simultaneously on every vertex of the graph. Intrinsic universality is the ability of an instance of a model to simulate every other instance of the model while preserving the structure of the computation at every step of the simulation. In this work we present the construction of a family of intrinsically universal instances of causal graphs dynamics, each instance being able to simulate a subset of instances.

  3. Burkholderia cepacia complex in Serbian patients with cystic fibrosis: prevalence and molecular epidemiology.

    Science.gov (United States)

    Vasiljevic, Z V; Novovic, K; Kojic, M; Minic, P; Sovtic, A; Djukic, S; Jovcic, B

    2016-08-01

    The Burkholderia cepacia complex (Bcc) organisms remain significant pathogens in patients with cystic fibrosis (CF). This study was performed to evaluate the prevalence, epidemiological characteristics, and presence of molecular markers associated with virulence and transmissibility of the Bcc strains in the National CF Centre in Belgrade, Serbia. The Bcc isolates collected during the four-year study period (2010-2013) were further examined by 16 s rRNA gene, pulsed-field gel electrophoresis of genomic DNA, multilocus sequence typing analysis, and phylogenetic analysis based on concatenated sequence of seven alleles. Fifty out of 184 patients (27.2 %) were colonized with two Bcc species, B. cenocepacia (n = 49) and B. stabilis (n = 1). Thirty-four patients (18.5 %) had chronic colonization. Typing methods revealed a high level of similarity among Bcc isolates, indicating a person-to-person transmission or acquisition from a common source. New sequence types (STs) were identified, and none of the STs with an international distribution were found. One centre-specific ST, B. cenocepacia ST856, was highly dominant and shared by 48/50 (96 %) patients colonized by Bcc. This clone was characterized by PCR positivity for both the B. cepacia epidemic strain marker and cable pilin, and showed close genetic relatedness to the epidemic strain CZ1 (ST32). These results indicate that the impact of Bcc on airway colonization in the Serbian CF population is high and virtually exclusively limited to a single clone of B. cenocepacia. The presence of a highly transmissible clone and probable patient-to-patient spread was observed. PMID:27177755

  4. Selecting appropriate cases when tracing causal mechanisms

    DEFF Research Database (Denmark)

    Beach, Derek; Pedersen, Rasmus Brun

    2016-01-01

    , ontological determinism, causal asymmetry and causal homogeneity and the importance of context. We then develop a set of case selection guidelines that are in methodological alignment with these underlying assumptions. Section 4 develops guidelines for research where the mechanism is the primary focus......The last decade has witnessed resurgence in the interest in studying the causal mechanisms linking causes and outcomes in the social sciences. This article explores the overlooked implications for case selection when tracing mechanisms using in-depth case studies. Our argument is that existing case...... selection guidelines are appropriate for research aimed at making cross-case claims about causal relationships, where case selection is primarily used to control for other causes. However, existing guidelines are not in alignment with case-based research that aims to trace mechanisms, where the goal is to...

  5. A Causal Model for Diagnostic Reasoning

    Institute of Scientific and Technical Information of China (English)

    PENG Guoqiang; CHENG Hu

    2000-01-01

    Up to now, there have been many methods for knowledge representation and reasoning in causal networks, but few of them include the research on the coactions of nodes. In practice, ignoring these coactions may influence the accuracy of reasoning and even give rise to incorrect reasoning. In this paper, based on multilayer causal networks, the definitions on coaction nodes are given to construct a new causal network called Coaction Causal Network, which serves to construct a model of neural network for diagnosis followed by fuzzy reasoning, and then the activation rules are given and neural computing methods are used to finish the diagnostic reasoning. These methods are proved in theory and a method of computing the number of solutions for the diagnostic reasoning is given. Finally, the experiments and the conclusions are presented.

  6. The Gravity Dual of Boundary Causality

    CERN Document Server

    Engelhardt, Netta

    2016-01-01

    In gauge/gravity duality, points which are not causally related on the boundary cannot be causally related through the bulk; this is the statement of boundary causality. By the Gao-Wald theorem, the averaged null energy condition in the bulk is sufficient to ensure this property. Here we proceed in the converse direction: we derive a necessary as well as sufficient condition for the preservation of boundary causality under perturbative (quantum or stringy) corrections to the bulk. The condition that we find is a (background-dependent) constraint on the amount by which light cones can "open" over all null bulk geodesics. We show that this constraint is weaker than the averaged null energy condition.

  7. The Temporal Logic of Causal Structures

    CERN Document Server

    Kleinberg, Samantha

    2012-01-01

    Computational analysis of time-course data with an underlying causal structure is needed in a variety of domains, including neural spike trains, stock price movements, and gene expression levels. However, it can be challenging to determine from just the numerical time course data alone what is coordinating the visible processes, to separate the underlying prima facie causes into genuine and spurious causes and to do so with a feasible computational complexity. For this purpose, we have been developing a novel algorithm based on a framework that combines notions of causality in philosophy with algorithmic approaches built on model checking and statistical techniques for multiple hypotheses testing. The causal relationships are described in terms of temporal logic formulae, reframing the inference problem in terms of model checking. The logic used, PCTL, allows description of both the time between cause and effect and the probability of this relationship being observed. We show that equipped with these causal f...

  8. What becomes of a causal set

    CERN Document Server

    Wuthrich, Christian

    2015-01-01

    Unlike the relativity theory it seeks to replace, causal set theory has been interpreted to leave space for a substantive, though perhaps 'localized', form of 'becoming'. The possibility of fundamental becoming is nourished by the fact that the analogue of Stein's theorem from special relativity does not hold in causal set theory. Despite this, we find that in many ways, the debate concerning becoming parallels the well-rehearsed lines it follows in the domain of relativity. We present, however, some new twists and challenges. In particular, we show that a novel and exotic notion of becoming is compatible with causal sets. In contrast to the 'localized' becoming considered compatible with the dynamics of causal set theory by its advocates, our novel kind of becoming, while not answering to the typical A-theoretic demands, is 'global' and objective.

  9. Ten simple rules for dynamic causal modeling.

    NARCIS (Netherlands)

    Stephan, K.E.; Penny, W.D.; Moran, R.J.; Ouden, H.E.M. den; Daunizeau, J.; Friston, K.J.

    2010-01-01

    Dynamic causal modeling (DCM) is a generic Bayesian framework for inferring hidden neuronal states from measurements of brain activity. It provides posterior estimates of neurobiologically interpretable quantities such as the effective strength of synaptic connections among neuronal populations and

  10. Causality Between Urban Concentration and Environmental Quality

    Directory of Open Access Journals (Sweden)

    Amin Pujiati

    2015-08-01

    Full Text Available Population is concentrated in urban areas can cause the external diseconomies on environment if it exceeds the carrying capacity of the space and the urban economy. Otherwise the quality of the environment is getting better, led to the concentration of population in urban areas are increasingly high. This study aims to analyze the relationship of causality between the urban concentration and environmental quality in urban agglomeration areas. The data used in the study of secondary data obtained from the Central Bureau of statistics and the City Government from 2000 to 2013. The analytical method used is the Granger causality and descriptive. Granger causality study results showed no pattern of reciprocal causality, between urban concentration and the quality of the environment, but there unidirectional relationship between the urban concentration and environmental quality. This means that increasing urban concentration led to decreased environmental quality.

  11. Causal Structure and Birefringence in Nonlinear Electrodynamics

    OpenAIRE

    de Melo, C. A. M.; Medeiros, L. G.; Pompeia, P. J.(Instituto de Fomento e Coordenação Industrial, Departamento de Ciência e Tecnologia Aeroespacial, Praça Mal. Eduardo Gomes 50, 12228-901, São José dos Campos, SP , Brazil)

    2014-01-01

    We investigate the causal structure of general nonlinear electrodynamics and determine which Lagrangians generate an effective metric conformal to Minkowski. We also proof that there is only one analytic nonlinear electrodynamics presenting no birefringence.

  12. The Causal Effects of Father Absence

    OpenAIRE

    McLanahan, Sara; TACH, LAURA; Schneider, Daniel

    2013-01-01

    The literature on father absence is frequently criticized for its use of cross-sectional data and methods that fail to take account of possible omitted variable bias and reverse causality. We review studies that have responded to this critique by employing a variety of innovative research designs to identify the causal effect of father absence, including studies using lagged dependent variable models, growth curve models, individual fixed effects models, sibling fixed effects models, natural ...

  13. Locally Causal Dynamical Triangulations in Two Dimensions

    CERN Document Server

    Loll, Renate

    2015-01-01

    We analyze the universal properties of a new two-dimensional quantum gravity model defined in terms of Locally Causal Dynamical Triangulations (LCDT). Measuring the Hausdorff and spectral dimensions of the dynamical geometrical ensemble, we find numerical evidence that the continuum limit of the model lies in a new universality class of two-dimensional quantum gravity theories, inequivalent to both Euclidean and Causal Dynamical Triangulations.

  14. Inter-causal Independence and Heterogeneous Factorization

    OpenAIRE

    Zhang, Nevin Lianwen; Poole, David L

    2013-01-01

    It is well known that conditional independence can be used to factorize a joint probability into a multiplication of conditional probabilities. This paper proposes a constructive definition of inter-causal independence, which can be used to further factorize a conditional probability. An inference algorithm is developed, which makes use of both conditional independence and inter-causal independence to reduce inference complexity in Bayesian networks.

  15. Causal Inference in Urban and Regional Economics

    OpenAIRE

    Nathaniel Baum-Snow; Fernando Ferreira

    2014-01-01

    Recovery of causal relationships in data is an essential part of scholarly inquiry in the social sciences. This chapter discusses strategies that have been successfully used in urban and regional economics for recovering such causal relationships. Essential to any successful empirical inquiry is careful consideration of the sources of variation in the data that identify parameters of interest. Interpretation of such parameters should take into account the potential for their heterogeneity as ...

  16. Causal transmission in reduced-form models

    OpenAIRE

    Vassili Bazinas; Bent Nielsen

    2015-01-01

    We propose a method to explore the causal transmission of a catalyst variable through two endogenous variables of interest. The method is based on the reduced-form system formed from the conditional distribution of the two endogenous variables given the catalyst. The method combines elements from instru- mental variable analysis and Cholesky decomposition of structural vector autoregressions. We give conditions for uniqueness of the causal transmission.

  17. Causales de ausencia de responsabilidad penal

    Directory of Open Access Journals (Sweden)

    Jaime Sandoval Fernández

    2003-01-01

    Full Text Available Este trabajo se ocupa de las causales de ausencia de responsabilidad penal, especialmente de aquellas que tienen efecto en el injusto. Como subtemas se delimita el concepto de responsabilidad penal y su ausencia. Se estudian las principales teorias a cerca de la relación tipicidad-antijuridicidad y su incidencia en el derecho penal colombiano. Por último contiene una propuesta acerca de cómo deberian agruparse las causales del arto 32 C. PlOO.

  18. Associative foundation of causal learning in rats.

    Science.gov (United States)

    Polack, Cody W; McConnell, Bridget L; Miller, Ralph R

    2013-03-01

    Are humans unique in their ability to interpret exogenous events as causes? We addressed this question by observing the behavior of rats for indications of causal learning. Within an operant motor-sensory preconditioning paradigm, associative surgical techniques revealed that rats attempted to control an outcome (i.e., a potential effect) by manipulating a potential exogenous cause (i.e., an intervention). Rats were able to generate an innocuous auditory stimulus. This stimulus was then paired with an aversive stimulus. The animals subsequently avoided potential generation of the predictive cue, but not if the aversive stimulus was subsequently devalued or the predictive cue was extinguished (Exp. 1). In Experiment 2, we demonstrated that the aversive stimulus we used was in fact aversive, that it was subject to devaluation, that the cue-aversive stimulus pairings did make the cue a conditioned stimulus, and that the cue was subject to extinction. In Experiments 3 and 4, we established that the decrease in leverpressing observed in Experiment 1 was goal-directed instrumental behavior rather than purely a product of Pavlovian conditioning. To the extent that interventions suggest causal reasoning, it appears that causal reasoning can be based on associations between contiguous exogenous events. Thus, contiguity appears capable of establishing causal relationships between exogenous events. Our results challenge the widely held view that causal learning is uniquely human, and suggest that causal learning is explicable in an associative framework. PMID:22562460

  19. Effect of gamma irradiation on Burkholderia thailandensis (Burkholderia pseudomallei surrogate) survival under combinations of pH and NaCl

    International Nuclear Information System (INIS)

    This study evaluated the effect of gamma irradiation on Burkholderia thailandensis (Burkholderia pseudomallei surrogate; potential bioterrorism agent) survival under different levels of NaCl and pH. B. thailandensis in Luria Bertani broth supplemented with NaCl (0-3%), and pH-adjusted to 4-7 was treated with gamma irradiation (0-0.5 kGy). Surviving cell counts of bacteria were then enumerated on tryptic soy agar. Data for the cell counts were also used to calculate D10 values (the dose required to reduce 1 log CFU/mL of B. thailandensis). Cell counts of B. thailandensis were decreased (P10 values ranged from 0.04 to 0.07 kGy, regardless of NaCl and pH level. These results indicate that low doses of gamma irradiation should be a useful treatment in decreasing the potential bioterrorism bacteria, which may possibly infect humans through foods.

  20. Polar lipids of Burkholderia pseudomallei induce different host immune responses.

    Directory of Open Access Journals (Sweden)

    Mercedes Gonzalez-Juarrero

    Full Text Available Melioidosis is a disease in tropical and subtropical regions of the world that is caused by Burkholderia pseudomallei. In endemic regions the disease occurs primarily in humans and goats. In the present study, we used the goat as a model to dissect the polar lipids of B. pseudomallei to identify lipid molecules that could be used for adjuvants/vaccines or as diagnostic tools. We showed that the lipidome of B. pseudomallei and its fractions contain several polar lipids with the capacity to elicit different immune responses in goats, namely rhamnolipids and ornithine lipids which induced IFN-γ, whereas phospholipids and an undefined polar lipid induced strong IL-10 secretion in CD4(+ T cells. Autologous T cells co-cultured with caprine dendritic cells (cDCs and polar lipids of B. pseudomallei proliferated and up-regulated the expression of CD25 (IL-2 receptor molecules. Furthermore, we demonstrated that polar lipids were able to up-regulate CD1w2 antigen expression in cDCs derived from peripheral blood monocytes. Interestingly, the same polar lipids had only little effect on the expression of MHC class II DR antigens in the same caprine dendritic cells. Finally, antibody blocking of the CD1w2 molecules on cDCs resulted in decreased expression for IFN-γ by CD4(+ T cells. Altogether, these results showed that polar lipids of B. pseudomallei are recognized by the caprine immune system and that their recognition is primarily mediated by the CD1 antigen cluster.

  1. Recovery efficiencies for Burkholderia thailandensis from various aerosol sampling media

    Directory of Open Access Journals (Sweden)

    Paul eDabisch

    2012-06-01

    Full Text Available Burkholderia thailandensis is used in the laboratory as a surrogate of the more virulent B. pseudomallei. Since inhalation is believed to be a natural route of infection for B. pseudomallei, many animal studies with B. pseudomallei and B. thailandensis utilize the inhalation route of exposure. The aim of the present study was to quantify the recovery efficiency of culturable B. thailandensis from several common aerosol sampling devices to ensure that collected microorganisms could be reliably recovered post-collection. The sampling devices tested included 25-mm gelatin filters, 25-mm stainless steel disks used in Mercer cascade impactors, and two types of glass impingers. The results demonstrate that while several processing methods tested resulted in significantly lower physical recovery efficiencies than other methods, it was possible to obtain culturable recovery efficiencies for B. thailandensis and physical recovery efficiencies for 1 μm fluorescent spheres of at least 0.95 from all of the sampling media tested given an appropriate sample processing procedure. The results of the present study also demonstrated that the bubbling action of liquid media in all-glass impingers (AGIs can result in physical loss of material from the collection medium, although additional studies are needed to verify the exact mechanisms involved. Overall, the results of this study demonstrate that the collection mechanism as well as the post-collection processing method can significantly affect the recovery from and retention of culturable microorganisms in sampling media, potentially affecting the calculated airborne concentration and any subsequent estimations of risk or dose derived from such data.

  2. Deciphering the role of RND efflux transporters in Burkholderia cenocepacia.

    Directory of Open Access Journals (Sweden)

    Silvia Bazzini

    Full Text Available Burkholderia cenocepacia J2315 is representative of a highly problematic group of cystic fibrosis (CF pathogens. Eradication of B. cenocepacia is very difficult with the antimicrobial therapy being ineffective due to its high resistance to clinically relevant antimicrobial agents and disinfectants. RND (Resistance-Nodulation-Cell Division efflux pumps are known to be among the mediators of multidrug resistance in gram-negative bacteria. Since the significance of the 16 RND efflux systems present in B. cenocepacia (named RND-1 to -16 has been only partially determined, the aim of this work was to analyze mutants of B. cenocepacia strain J2315 impaired in RND-4 and RND-9 efflux systems, and assess their role in the efflux of toxic compounds. The transcriptomes of mutants deleted individually in RND-4 and RND-9 (named D4 and D9, and a double-mutant in both efflux pumps (named D4-D9, were compared to that of the wild-type B. cenocepacia using microarray analysis. Microarray data were confirmed by qRT-PCR, phenotypic experiments, and by Phenotype MicroArray analysis. The data revealed that RND-4 made a significant contribution to the antibiotic resistance of B. cenocepacia, whereas RND-9 was only marginally involved in this process. Moreover, the double mutant D4-D9 showed a phenotype and an expression profile similar to D4. The microarray data showed that motility and chemotaxis-related genes appeared to be up-regulated in both D4 and D4-D9 strains. In contrast, these gene sets were down-regulated or expressed at levels similar to J2315 in the D9 mutant. Biofilm production was enhanced in all mutants. Overall, these results indicate that in B. cenocepacia RND pumps play a wider role than just in drug resistance, influencing additional phenotypic traits important for pathogenesis.

  3. Proof that Burkholderia Strains Form Effective Symbioses with Legumes: a Study of Novel Mimosa-Nodulating Strains from South America

    OpenAIRE

    Chen, Wen-Ming; de Faria, Sergio M.; Straliotto, Rosângela; Pitard, Rosa M.; Simões-Araùjo, Jean L.; Chou, Jui-Hsing; Chou, Yi-Ju; Barrios, Edmundo; Prescott, Alan R; Geoffrey N Elliott; Sprent, Janet I.; J. Peter W. Young; James, Euan K.

    2005-01-01

    Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other β-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known β-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to t...

  4. The relationship of biofilm production to biocontrol activity of Burkholderia pyrrocinia FP62

    Science.gov (United States)

    Foliar biocontrol agent (BCA) efficacy is often inconsistent due to poor colonization and survival on plant surfaces. Burkholderia pyrrocinia FP62, a superior leaf colonist and BCA of Botrytis cinerea, forms unsaturated biofilms on plant surfaces. To determine the relationship between biocontrol act...

  5. N-acylhomoserine-lactone-mediated communication between Pseudomonas aeruginosa and Burkholderia cepacia in mixed biofilms

    DEFF Research Database (Denmark)

    Riedel, K.; Hentzer, Morten; Geisenberger, O.;

    2001-01-01

    Pseudomonas aeruginosa and Burkholderia cepacia are capable of forming mixed biofilms in the lungs of cystic fibrosis patients. Both bacteria employ quorum-sensing systems, which rely on N-acylhomoserine lactone (AHL) signal molecules, to co- ordinate expression of virulence factors with the...

  6. Interaction of insulin with Burkholderia pseudomallei may be caused by a preservative

    OpenAIRE

    Simpson, A; Wuthiekanun, V

    2000-01-01

    Aim—To re-examine the previously reported in vitro interaction of insulin with Burkholderia pseudomallei, in the light of a suggestion that the interaction may have resulted from the presence of the preservative m-cresol in commercial preparations.

  7. Antimicrobial Properties of an Oxidizer Produced by Burkholderia cenocepacia P525

    Science.gov (United States)

    A compound with both oxidizing properties and antibiotic properties was extracted and purified from broth cultures of Burkholderia cenocepacia strain P525. A four step purification procedure was used to increase its specific activity ~ 400 fold and to yield a HPLC- UV chromatogram containing a sing...

  8. Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6.

    Science.gov (United States)

    D'haeseleer, Patrik; Johnson, Shannon L; Davenport, Karen W; Chain, Patrick S; Schoeniger, Joe; Ray, Debjit; Sinha, Anupama; Williams, Kelly P; Peña, José; Branda, Steven S; El-Etr, Sahar

    2016-01-01

    Here, we present the draft genome sequence of Burkholderia pseudomallei PHLS 6, a virulent clinical strain isolated from a melioidosis patient in Bangladesh in 1960. The draft genome consists of 39 contigs and is 7,322,181 bp long. PMID:27365360

  9. Burkholderia pseudomallei infection in a cystic fibrosis patient from the Caribbean: A case report

    OpenAIRE

    Dimas Mateos Corral; Allan L Coates; Yvonne CW Yau; Raymond Tellier; Mindy Glass; Jones, Steven M.; Waters, Valerie J.

    2008-01-01

    Burkholderia pseudomallei is a pathogen identified with increasing frequency in the respiratory tracts of cystic fibrosis (CF) patients from endemic areas such as Southeast Asia and northern Australia. The following report describes the first known reported case in a CF patient from the Caribbean attending a North American CF clinic.

  10. NOVEL ORGANIZATION OF THE GENES FOR PHTHALATE DEGRADATION FROM BURKHOLDERIA CEPACIA DBO1

    Science.gov (United States)

    Burkholderia cepacia DBO1 is able to utilize phthalate as the sole source of carbon and energy for growth. Two overlapping cosmid clones containing the genes for phthalate degradation were isolated from this strain. Subcloning and activity analysis localized the genes for phthala...

  11. Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria)

    OpenAIRE

    Ettinger, CL; Shehata, HR; Johnston-Monje, D; Raizada, MN; Eisen, JA

    2015-01-01

    Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds.

  12. Draft Genome Sequence of the Haloacid-Degrading Burkholderia caribensis Strain MBA4

    OpenAIRE

    Pan, Yanling; Kong, Ka Fai; Tsang, Jimmy S. H.

    2014-01-01

    Burkholderia caribensis MBA4 was isolated from soil for its ability to utilize 2-haloacid. An inducible haloacid operon, encoding for a dehalogenase and a permease, is mainly responsible for the biotransformation. Here, we report the draft genome sequence of this strain.

  13. Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria)

    Science.gov (United States)

    Ettinger, Cassandra L.; Shehata, Hanan R.; Johnston-Monje, David; Raizada, Manish N.

    2015-01-01

    Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds. PMID:25614570

  14. Susceptibility of Caenorhabditis elegans to Burkholderia infection depends on prior diet and secreted bacterial attractants.

    Directory of Open Access Journals (Sweden)

    Vaughn S Cooper

    Full Text Available The nematode Caenorhabditis elegans may be killed by certain pathogenic bacteria and thus is a model organism for studying interactions between bacteria and animal hosts. However, growing nematodes on prey bacteria may influence their susceptibility to potential pathogens. A method of axenic nematode culture was developed to isolate and quantify interactions between C. elegans and potentially pathogenic strains of the Burkholderia cepacia complex. Studying these dynamics in liquid solution rather than on agar surfaces minimized nematode avoidance behavior and resolved more differences among isolates. Most isolates of B. cenocepacia, B. ambifaria and B. cepacia caused 60-80% mortality of nematodes after 7 days, whereas isolates of B. multivorans caused less mortality (<25% and supported nematode reproduction. However, some B. cenocepacia isolates recovered from chronic infections were much less virulent (5-28% mortality. As predicted, prior diet altered the outcome of interactions between nematodes and bacteria. When given the choice between Burkholderia and E. coli as prey on agar, axenically raised nematodes initially preferred most lethal Burkholderia isolates to E. coli as a food source, but this was not the case for nematodes fed E. coli, which avoided toxic Burkholderia. This food preference was associated with the cell-free supernatant and thus secreted compounds likely mediated bacterial-nematode interactions. This model, which isolates interactions between bacteria and nematodes from the effects of prior feeding, demonstrates that bacteria can influence nematode behavior and their susceptibility to pathogens.

  15. Study of the mode of action of a polygalacturonase from the phytopathogen Burkholderia cepacia

    DEFF Research Database (Denmark)

    Massa, C.; Clausen, Mads Hartvig; Stojan, J.;

    2007-01-01

    We have recently isolated and heterologously expressed BcPeh28A, an endopolygalacturonase from the phytopathogenic Gram-negative bacterium Burkholderia cepacia. Endopolygalacturonases belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions...

  16. The symbiotic role of O-antigen of Burkholderia symbiont in association with host Riptortus pedestris.

    Science.gov (United States)

    Kim, Jiyeun Kate; Park, Ha Young; Lee, Bok Luel

    2016-07-01

    Riptortus pedestris harboring Burkholderia symbiont is a useful symbiosis model to study the molecular interactions between insects and bacteria. We recently reported that the lipopolysaccharide O-antigen is absent in the Burkholderia symbionts isolated from Riptortus guts. Here, we investigated the symbiotic role of O-antigen comprehensively in the Riptortus-Burkholderia model. Firstly, Burkholderia mutant strains deficient of O-antigen biosynthesis genes were generated and confirmed for their different patterns of the lipopolysaccharide by electrophoretic analysis. The O-antigen-deficient mutant strains initially exhibited a reduction of infectivity, having significantly lower level of symbiont population at the second-instar stage. However, both the wild-type and O-antigen mutant symbionts exhibited a similar level of symbiont population from the third-instar stage, indicating that the O-antigen deficiency did not affect the bacterial persistence in the host midgut. Taken together, we showed that the lipopolysaccharide O-antigen of gut symbiont plays an exclusive role in the initial symbiotic association. PMID:26875632

  17. Concomitant Cryptococcosis and Burkholderia Infection in an Asymptomatic Lung Transplant Patient with Cystic Fibrosis

    OpenAIRE

    2010-01-01

    Concomitant pulmonary infections with Cryptococcus neoformans and Burkholderia cepacia in lung transplant recipients are very rare and create unique diagnostic and therapeutic dilemmas. Herein, we present a double lung transplant patient with cystic fibrosis who was found to have coinfection with these two rare organisms, though he was completely asymptomatic.

  18. The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

    DEFF Research Database (Denmark)

    Holden, Matthew T G; Seth-Smith, Helena M B; Crossman, Lisa C;

    2009-01-01

    Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradica...

  19. Distribution of Melioidosis Cases and Viable Burkholderia pseudomallei in Soil: Evidence for Emerging Melioidosis in Taiwan▿

    OpenAIRE

    Chen, Yao-Shen; Lin, Hsi-Hsun; Mu, Jung-Jung; Chiang, Chuen-Sheue; Chen, Chang-Hsun; Buu, Leh-Mia; Lin, Yusen E.; Chen, Ya-Lei

    2010-01-01

    A survey for the prevalence if Burkholderia pseudomallei in soil in Taiwan found that its incidence is comparable to that in other regions of the world where melioidosis is endemic. The presence of identical genetic patterns among the clinical and environmental isolates evaluated suggested a link between the pathogens present in contaminated soil and the emergence of indigenous melioidosis.

  20. Burkholderia mallei and Burkholderia pseudomallei cluster 1 type VI secretion system gene expression is negatively regulated by iron and zinc.

    Directory of Open Access Journals (Sweden)

    Mary N Burtnick

    Full Text Available Burkholderia mallei is a facultative intracellular pathogen that causes glanders in humans and animals. Previous studies have demonstrated that the cluster 1 type VI secretion system (T6SS-1 expressed by this organism is essential for virulence in hamsters and is positively regulated by the VirAG two-component system. Recently, we have shown that T6SS-1 gene expression is up-regulated following internalization of this pathogen into phagocytic cells and that this system promotes multinucleated giant cell formation in infected tissue culture monolayers. In the present study, we further investigated the complex regulation of this important virulence factor. To assess T6SS-1 expression, B. mallei strains were cultured in various media conditions and Hcp1 production was analyzed by Western immunoblotting. Transcript levels of several VirAG-regulated genes (bimA, tssA, hcp1 and tssM were also determined using quantitative real time PCR. Consistent with previous observations, T6SS-1 was not expressed during growth of B. mallei in rich media. Curiously, growth of the organism in minimal media (M9G or minimal media plus casamino acids (M9CG facilitated robust expression of T6SS-1 genes whereas growth in minimal media plus tryptone (M9TG did not. Investigation of this phenomenon confirmed a regulatory role for VirAG in this process. Additionally, T6SS-1 gene expression was significantly down-regulated by the addition of iron and zinc to M9CG. Other genes under the control of VirAG did not appear to be as tightly regulated by these divalent metals. Similar results were observed for B. pseudomallei, but not for B. thailandensis. Collectively, our findings indicate that in addition to being positively regulated by VirAG, B. mallei and B. pseudomallei T6SS-1 gene expression is negatively regulated by iron and zinc.

  1. Linear structures, causal sets and topology

    Science.gov (United States)

    Hudetz, Laurenz

    2015-11-01

    Causal set theory and the theory of linear structures (which has recently been developed by Tim Maudlin as an alternative to standard topology) share some of their main motivations. In view of that, I raise and answer the question how these two theories are related to each other and to standard topology. I show that causal set theory can be embedded into Maudlin's more general framework and I characterise what Maudlin's topological concepts boil down to when applied to discrete linear structures that correspond to causal sets. Moreover, I show that all topological aspects of causal sets that can be described in Maudlin's theory can also be described in the framework of standard topology. Finally, I discuss why these results are relevant for evaluating Maudlin's theory. The value of this theory depends crucially on whether it is true that (a) its conceptual framework is as expressive as that of standard topology when it comes to describing well-known continuous as well as discrete models of spacetime and (b) it is even more expressive or fruitful when it comes to analysing topological aspects of discrete structures that are intended as models of spacetime. On one hand, my theorems support (a). The theory is rich enough to incorporate causal set theory and its definitions of topological notions yield a plausible outcome in the case of causal sets. On the other hand, the results undermine (b). Standard topology, too, has the conceptual resources to capture those topological aspects of causal sets that are analysable within Maudlin's framework. This fact poses a challenge for the proponents of Maudlin's theory to prove it fruitful.

  2. POLYCLONAL OUTBREAK OF BLOODSTREAM INFECTIONS CAUSED BY Burkholderia cepacia COMPLEX IN HEMATOLOGY AND BONE MARROW TRANSPLANT OUTPATIENT UNITS

    Directory of Open Access Journals (Sweden)

    Icaro Boszczowski

    2014-01-01

    Full Text Available Aim: The objective was to describe an outbreak of bloodstream infections by Burkholderia cepacia complex (Bcc in bone marrow transplant and hematology outpatients. Methods: On February 15, 2008 a Bcc outbreak was suspected. 24 cases were identified. Demographic and clinical data were evaluated. Environment and healthcare workers' (HCW hands were cultured. Species were determined and typed. Reinforcement of hand hygiene, central venous catheter (CVC care, infusion therapy, and maintenance of laminar flow cabinet were undertaken. 16 different HCWs had cared for the CVCs. Multi-dose heparin and saline were prepared on counter common to both units. Findings: 14 patients had B. multivorans (one patient had also B. cenopacia, six non-multivorans Bcc and one did not belong to Bcc. Clone A B. multivorans occurred in 12 patients (from Hematology; in 10 their CVC had been used on February 11/12. Environmental and HCW cultures were negative. All patients were treated with meropenem, and ceftazidime lock-therapy. Eight patients (30% were hospitalized. No deaths occurred. After control measures (multidose vial for single patient; CVC lock with ceftazidime; cleaning of laminar flow cabinet; hand hygiene improvement; use of cabinet to store prepared medication, no new cases occurred. Conclusions: This polyclonal outbreak may be explained by a common source containing multiple species of Bcc, maybe the laminar flow cabinet common to both units. There may have been contamination by B. multivorans (clone A of multi-dose vials.

  3. Cellular senescence as the causal nexus of aging

    Directory of Open Access Journals (Sweden)

    Naina eBhatia-Dey

    2016-02-01

    Full Text Available We present cellular senescence as the ultimate driver of the aging process, as a causal nexus that bridges microscopic subcellular damage with the phenotypic, macroscopic effect of aging. It is important to understand how the various types of subcellular damage correlated with the aging process lead to the larger, visible effects of anatomical aging. While it has always been assumed that subcellular damage (cause results in macroscopic aging (effect, the bridging link between the two has been hard to define. Here, we propose that this bridge, which we term the causal nexus, is in fact cellular senescence. The subcellular damage itself does not directly cause the visible signs of aging, but rather, as the damage accumulates and reaches a critical mass, cells cease to proliferate and acquire the deleterious senescence-associated secretory phenotype (SASP which then leads to the macroscopic consequences of tissue breakdown to create the physiologically aged phenotype. Thus senescence is a precondition for anatomical aging, and this explains why aging is a gradual process that remains largely invisible during most of its progression. The subcellular damage includes shortening of telomeres, damage to mitochondria, aneuploidy and DNA double-strand breaks triggered by various genetic, epigenetic, and environmental factors. Damage pathways acting in isolation or in concert converge at the causal nexus of cellular senescence. In each species some types of damage can be more causative than in others and operate at a variable pace; for example, telomere erosion appears to be a primary cause in human cells, whereas activation of tumor suppressor genes is more causative in rodents. Such species-specific mechanisms indicate that despite different initial causes, most of aging is traced to a single convergent causal nexus: senescence. The exception is in some invertebrate species that escape senescence, and in nondividing cells such as neurons, where

  4. The Cradle of Causal Reasoning: Newborns' Preference for Physical Causality

    Science.gov (United States)

    Mascalzoni, Elena; Regolin, Lucia; Vallortigara, Giorgio; Simion, Francesca

    2013-01-01

    Perception of mechanical (i.e. physical) causality, in terms of a cause-effect relationship between two motion events, appears to be a powerful mechanism in our daily experience. In spite of a growing interest in the earliest causal representations, the role of experience in the origin of this sensitivity is still a matter of dispute. Here, we…

  5. Causal impressions: predicting when, not just whether.

    Science.gov (United States)

    Young, Michael E; Rogers, Ester T; Beckmann, Joshua S

    2005-03-01

    In 1739, David Hume established the so-called cues to causality--environmental cues that are important to the inference of causality. Although this descriptive account has been corroborated experimentally, it has not been established why these cues are useful, except that they may reflect statistical regularities in the environment. One of the cues to causality, covariation, helps predict whether an effect will occur, but not its time of occurrence. In the present study, evidence is provided that spatial and temporal contiguity improve an observer's ability to predict when an effect will occur, thus complementing the utility of covariation as a predictor of whether an effect will occur. While observing Michotte's (1946/1963) launching effect, participants showed greater accuracy and precision in their predictions of the onset of movement by the launched object when there was spatial and temporal contiguity. Furthermore, when auditory cues that bridged a delayed launch were included, causal ratings and predictability were similarly affected. These results suggest that the everyday inference of causality relies on our ability to predict whether and when an effect will occur.

  6. Preschoolers prefer to learn causal information

    Directory of Open Access Journals (Sweden)

    Aubry eAlvarez

    2015-02-01

    Full Text Available Young children, in general, appear to have a strong drive to explore the environment in ways that reveal its underlying causal structure. But are they really attuned specifically to casual information in this quest for understanding, or do they show equal interest in other types of non-obvious information about the world? To answer this question, we introduced 20 three-year-old children to two puppets who were anxious to tell the child about a set of novel artifacts and animals. One puppet consistently described causal properties of the items while the other puppet consistently described carefully matched non-causal properties of the same items. After a familiarization period in which children learned which type of information to expect from each informant, children were given the opportunity to choose which they wanted to hear describe each of eight pictured test items. On average, children chose to hear from the informant that provided causal descriptions on 72% of the trials. This preference for causal information has important implications for explaining the role of conceptual information in supporting early learning and may suggest means for maximizing interest and motivation in young children.

  7. Burkholderia pseudomallei genome plasticity associated with genomic island variation

    Directory of Open Access Journals (Sweden)

    Currie Bart J

    2008-04-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. Results Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9, to 76% for a metabolic island (GI 16. The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands. The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3. The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27. The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing; these were ST 70 (n = 15 isolates, ST 54 (n = 11, and ST 167 (n = 9. The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained

  8. Causal binding of actions to their effects.

    Science.gov (United States)

    Buehner, Marc J; Humphreys, Gruffydd R

    2009-10-01

    According to widely held views in cognitive science harking back to David Hume, causality cannot be perceived directly, but instead is inferred from patterns of sensory experience, and the quality of these inferences is determined by perceivable quantities such as contingency and contiguity. We report results that suggest a reversal of Hume's conjecture: People's sense of time is warped by the experience of causality. In a stimulus-anticipation task, participants' response behavior reflected a shortened experience of time in the case of target stimuli participants themselves had generated, relative to equidistant, equally predictable stimuli they had not caused. These findings suggest that causality in the mind leads to temporal binding of cause and effect, and extend and generalize beyond earlier claims of intentional binding between action and outcome.

  9. Causal inheritence in plane wave quotients

    Energy Technology Data Exchange (ETDEWEB)

    Hubeny, Veronika E.; Rangamani, Mukund; Ross, Simon F.

    2003-11-24

    We investigate the appearance of closed timelike curves in quotients of plane waves along spacelike isometries. First we formulate a necessary and sufficient condition for a quotient of a general spacetime to preserve stable causality. We explicitly show that the plane waves are stably causal; in passing, we observe that some pp-waves are not even distinguishing. We then consider the classification of all quotients of the maximally supersymmetric ten-dimensional plane wave under a spacelike isometry, and show that the quotient will lead to closed timelike curves iff the isometry involves a translation along the u direction. The appearance of these closed timelike curves is thus connected to the special properties of the light cones in plane wave spacetimes. We show that all other quotients preserve stable causality.

  10. The causal meaning of Hamilton's rule.

    Science.gov (United States)

    Okasha, Samir; Martens, Johannes

    2016-03-01

    Hamilton's original derivation of his rule for the spread of an altruistic gene (rb>c) assumed additivity of costs and benefits. Recently, it has been argued that an exact version of the rule holds under non-additive pay-offs, so long as the cost and benefit terms are suitably defined, as partial regression coefficients. However, critics have questioned both the biological significance and the causal meaning of the resulting rule. This paper examines the causal meaning of the generalized Hamilton's rule in a simple model, by computing the effect of a hypothetical experiment to assess the cost of a social action and comparing it to the partial regression definition. The two do not agree. A possible way of salvaging the causal meaning of Hamilton's rule is explored, by appeal to R. A. Fisher's 'average effect of a gene substitution'. PMID:27069669

  11. Causality, initial conditions and inflationary magnetogenesis

    CERN Document Server

    Tsagas, Christos G

    2016-01-01

    The post-inflationary evolution of inflation-produced magnetic fields, conventional or not, can change dramatically when two fundamental issues are accounted for. The first is causality, which demands that local physical processes can never affect superhorizon perturbations. The second is the nature of the transition from inflation to reheating and then to the radiation era, which determine the initial conditions at the start of these epochs. Technically, the latter issue can be addressed by appealing to Israel's junction conditions. Causality implies that inflationary magnetic fields dot not freeze into the matter until they have re-entered the causal horizon. The nature of cosmological transitions and the associated initial conditions, on the other hand, determine the large-scale magnetic evolution after inflation. Put together, the two can slow down the adiabatic decay of superhorizon-sized magnetic fields throughout their post-inflationary life and thus lead to considerably stronger residual strengths. Th...

  12. Normalizing the causality between time series

    Science.gov (United States)

    Liang, X. San

    2015-08-01

    Recently, a rigorous yet concise formula was derived to evaluate information flow, and hence the causality in a quantitative sense, between time series. To assess the importance of a resulting causality, it needs to be normalized. The normalization is achieved through distinguishing a Lyapunov exponent-like, one-dimensional phase-space stretching rate and a noise-to-signal ratio from the rate of information flow in the balance of the marginal entropy evolution of the flow recipient. It is verified with autoregressive models and applied to a real financial analysis problem. An unusually strong one-way causality is identified from IBM (International Business Machines Corporation) to GE (General Electric Company) in their early era, revealing to us an old story, which has almost faded into oblivion, about "Seven Dwarfs" competing with a giant for the mainframe computer market.

  13. Complete genome sequence of Burkholderia sp. strain PAMC28687, a potential octopine-utilizing bacterium isolated from Antarctica lichen.

    Science.gov (United States)

    Han, So-Ra; Yu, Sang-Cheol; Ahn, Do-Hwan; Park, Hyun; Oh, Tae-Jin

    2016-05-20

    We report the complete genome sequence of Burkholderia sp. PAMC28687, which was isolated from the Antarctica lichen Useea sp., for better understanding of its catabolic traits in utilizing octopine as a source of carbon/nitrogen between Burkholderia and lichen. The genome consists of three circular chromosomes with five circular plasmids for the total 6,881,273bp sized genome with a G+C content of 58.14%. PMID:27034021

  14. A causally connected superluminal Warp Drive spacetime

    CERN Document Server

    Loup, F; Waite, D; Halerewicz, E F; Stabno, M; Kuntzman, M; Sims, R

    2002-01-01

    It will be shown that while horizons do not exist for warp drive spacetimes traveling at subluminal velocities horizons begin to develop when a warp drive spacetime reaches luminal velocities. However it will be shown that the control region of a warp drive ship lie within the portion of the warped region that is still causally connected to the ship even at superluminal velocities, therefore allowing a ship to slow to subluminal velocities. Further it is shown that the warped regions which are causally disconnected from a warp ship have no correlation to the ship velocity.

  15. Causal interpretation of stochastic differential equations

    DEFF Research Database (Denmark)

    Sokol, Alexander; Hansen, Niels Richard

    2014-01-01

    We give a causal interpretation of stochastic differential equations (SDEs) by defining the postintervention SDE resulting from an intervention in an SDE. We show that under Lipschitz conditions, the solution to the postintervention SDE is equal to a uniform limit in probability of postintervention...... structural equation models based on the Euler scheme of the original SDE, thus relating our definition to mainstream causal concepts. We prove that when the driving noise in the SDE is a Lévy process, the postintervention distribution is identifiable from the generator of the SDE....

  16. Inferring causality from noisy time series data

    DEFF Research Database (Denmark)

    Mønster, Dan; Fusaroli, Riccardo; Tylén, Kristian;

    2016-01-01

    Convergent Cross-Mapping (CCM) has shown high potential to perform causal inference in the absence of models. We assess the strengths and weaknesses of the method by varying coupling strength and noise levels in coupled logistic maps. We find that CCM fails to infer accurate coupling strength...... injections in intermediate-to-strongly coupled systems could enable more accurate causal inferences. Given the inherent noisy nature of real-world systems, our findings enable a more accurate evaluation of CCM applicability and advance suggestions on how to overcome its weaknesses....

  17. Transcriptional response of Burkholderia cenocepacia J2315 sessile cells to treatments with high doses of hydrogen peroxide and sodium hypochlorite

    Directory of Open Access Journals (Sweden)

    Nelis Hans

    2010-02-01

    Full Text Available Abstract Background Burkholderia cepacia complex bacteria are opportunistic pathogens, which can cause severe respiratory tract infections in patients with cystic fibrosis (CF. As treatment of infected CF patients is problematic, multiple preventive measures are taken to reduce the infection risk. Besides a stringent segregation policy to prevent patient-to-patient transmission, clinicians also advise patients to clean and disinfect their respiratory equipment on a regular basis. However, problems regarding the efficacy of several disinfection procedures for the removal and/or killing of B. cepacia complex bacteria have been reported. In order to unravel the molecular mechanisms involved in the resistance of biofilm-grown Burkholderia cenocepacia cells against high concentrations of reactive oxygen species (ROS, the present study focussed on the transcriptional response in sessile B. cenocepacia J2315 cells following exposure to high levels of H2O2 or NaOCl. Results The exposure to H2O2 and NaOCl resulted in an upregulation of the transcription of 315 (4.4% and 386 (5.4% genes, respectively. Transcription of 185 (2.6% and 331 (4.6% genes was decreased in response to the respective treatments. Many of the upregulated genes in the NaOCl- and H2O2-treated biofilms are involved in oxidative stress as well as general stress response, emphasizing the importance of the efficient neutralization and scavenging of ROS. In addition, multiple upregulated genes encode proteins that are necessary to repair ROS-induced cellular damage. Unexpectedly, a prolonged treatment with H2O2 also resulted in an increased transcription of multiple phage-related genes. A closer inspection of hybridisation signals obtained with probes targeting intergenic regions led to the identification of a putative 6S RNA. Conclusion Our results reveal that the transcription of a large fraction of B. cenocepacia J2315 genes is altered upon exposure of sessile cells to ROS. These

  18. Introducing Mechanics by Tapping Core Causal Knowledge

    Science.gov (United States)

    Klaassen, Kees; Westra, Axel; Emmett, Katrina; Eijkelhof, Harrie; Lijnse, Piet

    2008-01-01

    This article concerns an outline of an introductory mechanics course. It is based on the argument that various uses of the concept of force (e.g. from Kepler, Newton and everyday life) share an explanatory strategy based on core causal knowledge. The strategy consists of (a) the idea that a force causes a deviation from how an object would move of…

  19. Linear Response Laws and Causality in Electrodynamics

    Science.gov (United States)

    Yuffa, Alex J.; Scales, John A.

    2012-01-01

    Linear response laws and causality (the effect cannot precede the cause) are of fundamental importance in physics. In the context of classical electrodynamics, students often have a difficult time grasping these concepts because the physics is obscured by the intermingling of the time and frequency domains. In this paper, we analyse the linear…

  20. A Causal Construction of Diffusion Processes

    OpenAIRE

    Banek, Tadeusz

    2010-01-01

    A simple nonlinear integral equation for Ito's map is obtained. Although, it does not include stochastic integrals, it does give causal construction of diffusion processes which can be easily implemented by iteration systems. Applications in financial modelling and extension to fBm are discussed.

  1. The metagenomic approach and causality in virology

    Directory of Open Access Journals (Sweden)

    Silvana Beres Castrignano

    2015-01-01

    Full Text Available Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.

  2. Causality and Time in Historical Institutionalism

    DEFF Research Database (Denmark)

    Mahoney, James; Mohamedali, Khairunnisa; Nguyen, Christoph

    2016-01-01

    This chapter explores the dual concern with causality and time in historical institutionalism using a graphical approach. The analysis focuses on three concepts that are central to this field: critical junctures, gradual change, and path dependence. The analysis makes explicit and formal the logic...

  3. Escaping Myopia: Teaching Students about Historical Causality

    Science.gov (United States)

    Waring, Scott M.

    2010-01-01

    There are so many aspects to teaching history that are vital to creating well-rounded historical thinkers, but one of the most fundamental and most overlooked elements is the idea of causality. Far too many students do not understand the idea of causation, that there are multiple reasons for why historical events occurred and transpired in the way…

  4. Exploring Torus Universes in Causal Dynamical Triangulations

    DEFF Research Database (Denmark)

    Budd, Timothy George; Loll, R.

    2013-01-01

    Motivated by the search for new observables in nonperturbative quantum gravity, we consider Causal Dynamical Triangulations (CDT) in 2+1 dimensions with the spatial topology of a torus. This system is of particular interest, because one can study not only the global scale factor, but also global...

  5. Marriage and Anomie: A Causal Argument

    Science.gov (United States)

    Lee, Gary R.

    1974-01-01

    A sample of 394 married couples is employed to test the possibility of an association between marital satisfaction and personal (attitudinal) anomie. The hypothesis is supported. Conclusions are offered relevant to anomie theory, and to utilization of marital and family phenomena as independent variables in causal explanations of nonfamily events.…

  6. Manipulation and the causal Markov condition

    OpenAIRE

    Hausman, Daniel; Woodward, James

    2004-01-01

    This paper explores the relationship between a manipulability conception of causation and the causal Markov condition (CM). We argue that violations of CM also violate widely shared expectations—implicit in the manipulability conception—having to do with the absence of spontaneous correlations. They also violate expectations concerning the connection between independence or dependence relationships in the presence and absence of interventions.

  7. Causality and Teleology in High School Biology.

    Science.gov (United States)

    Tamir, Pinchas

    1985-01-01

    Ability to distinguish between causal (cause-effect) and teleological (means-ends) explanations was measured in 1905 twelfth-grade biology students and found to be dependent on student knowledge. Although the inability to make these distinctions contributes to misconceptions in biology, appropriate instruction can easily remedy the problem. Sample…

  8. Causal and Teleological Explanations in Biology

    Science.gov (United States)

    Yip, Cheng-Wai

    2009-01-01

    A causal explanation in biology focuses on the mechanism by which a biological process is brought about, whereas a teleological explanation considers the end result, in the context of the survival of the organism, as a reason for certain biological processes or structures. There is a tendency among students to offer a teleological explanation…

  9. Causality and analyticity in quantum fields theory

    International Nuclear Information System (INIS)

    This is a presentation of results on the causal and analytical structure of Green functions and on the collision amplitudes in fields theories, for massive particles of one type, with a positive mass and a zero spin value. (A.B.)

  10. Comments: Causal Interpretations of Mediation Effects

    Science.gov (United States)

    Jo, Booil; Stuart, Elizabeth A.

    2012-01-01

    The authors thank Dr. Lindsay Page for providing a nice illustration of the use of the principal stratification framework to define causal effects, and a Bayesian model for effect estimation. They hope that her well-written article will help expose education researchers to these concepts and methods, and move the field of mediation analysis in…

  11. Sequential causal learning in humans and rats

    NARCIS (Netherlands)

    H. Lu; R.R. Rojas; T. Beckers; A. Yuille

    2008-01-01

    Recent experiments (Beckers, De Houwer, Pineño, & Miller, 2005;Beckers, Miller, De Houwer, & Urushihara, 2006) have shown that pretraining with unrelated cues can dramatically influence the performance of humans in a causal learning paradigm and rats in a standard Pavlovian conditioning paradigm. Su

  12. Detection of Burkholderia pseudomallei toxin-mediated inhibition of protein synthesis using a Caenorhabditis elegans ugt-29 biosensor.

    Science.gov (United States)

    Wong, Rui-Rui; Kong, Cin; Lee, Song-Hua; Nathan, Sheila

    2016-01-01

    Toxins are believed to play a crucial role in Burkholderia pseudomallei pathogenicity, however to date, only a few have been identified. The discovery of additional toxic molecules is limited by the lack of a sensitive indicator of B. pseudomallei toxicity. Previously, from a whole genome transcriptome analysis of B. pseudomallei-infected Caenorhabditis elegans, we noted significant overexpression of a number of worm genes encoding detoxification enzymes, indicating the host's attempt to clear bacterial toxic molecules. One of these genes, ugt-29, a family member of UDP-glucuronosyltransferases, was the most robustly induced phase II detoxification gene. In this study, we show that strong induction of ugt-29 is restricted to infections by the most virulent species among the pathogens tested. We also noted that ugt-29 is activated upon disruption of host protein synthesis. Hence, we propose that UGT-29 could be a promising biosensor to detect B. pseudomallei toxins that compromise host protein synthesis. The identification of bactobolin, a polyketide-peptide hybrid molecule, as a toxic molecule of B. pseudomallei further verifies the utilization of this surveillance system to search for bacterial toxins. Hence, a ugt-29 based reporter should be useful in screening for other molecules that inhibit host protein synthesis. PMID:27273550

  13. Detection of Burkholderia pseudomallei toxin-mediated inhibition of protein synthesis using a Caenorhabditis elegans ugt–29 biosensor

    Science.gov (United States)

    Wong, Rui-Rui; Kong, Cin; Lee, Song-Hua; Nathan, Sheila

    2016-01-01

    Toxins are believed to play a crucial role in Burkholderia pseudomallei pathogenicity, however to date, only a few have been identified. The discovery of additional toxic molecules is limited by the lack of a sensitive indicator of B. pseudomallei toxicity. Previously, from a whole genome transcriptome analysis of B. pseudomallei-infected Caenorhabditis elegans, we noted significant overexpression of a number of worm genes encoding detoxification enzymes, indicating the host’s attempt to clear bacterial toxic molecules. One of these genes, ugt–29, a family member of UDP-glucuronosyltransferases, was the most robustly induced phase II detoxification gene. In this study, we show that strong induction of ugt–29 is restricted to infections by the most virulent species among the pathogens tested. We also noted that ugt–29 is activated upon disruption of host protein synthesis. Hence, we propose that UGT–29 could be a promising biosensor to detect B. pseudomallei toxins that compromise host protein synthesis. The identification of bactobolin, a polyketide-peptide hybrid molecule, as a toxic molecule of B. pseudomallei further verifies the utilization of this surveillance system to search for bacterial toxins. Hence, a ugt–29 based reporter should be useful in screening for other molecules that inhibit host protein synthesis. PMID:27273550

  14. Trimeric autotransporter adhesins in members of the Burkholderia cepacia complex: a multifunctional family of proteins implicated in virulence

    Directory of Open Access Journals (Sweden)

    Arsénio Mendes Fialho

    2011-12-01

    Full Text Available Trimeric autotransporter adhesins (TAAs are multimeric surface proteins, involved in various biological traits of pathogenic Gram-negative bacteria including adherence, biofilm formation, invasion, survival within eukaryotic cells, serum resistance and cytotoxicity. TAAs have a modular architecture composed by a conserved membrane-anchored C-terminal domain and a variable number of stalk and head domains. In this study, a bioinformatic approach has been used to analyze the distribution and architecture of TAAs among Burkholderia cepacia complex (Bcc genomes. Fifteen genomes were probed revealing a total of 74 encoding sequences. Compared with other bacterial species, the Bcc genomes contain a disproportionately large number of TAAs (two genes to up to 8 genes, such as in B.cenocepacia. Phylogenetic analysis showed that the TAAs grouped into at least eight distinct clusters. TAAs with serine-rich repeats are clearly well separated from others, thereby representing a different evolutionary lineage. Comparative gene mapping across Bcc genomes reveals that TAA genes are inserted within conserved synteny blocks. We further focused our analysis on the epidemic strain B. cenocepacia J2315 in which 7 TAAs were annotated. Among these, 3 TAA-encoding genes (BCAM019, BCAM0223 and BCAM0224 are organized into a cluster and are candidates for multifunctional virulence factors. Here we review the current insights into the functional role of BCAM0224 as a model locus.

  15. Early growth promotion and leaf level physiology changes in Burkholderia phytofirmans strain PsJN inoculated switchgrass.

    Science.gov (United States)

    Wang, Bingxue; Mei, Chuansheng; Seiler, John R

    2015-01-01

    Switchgrass (SG) is one of the most promising next generation biofuel crops in North America. Inoculation with bacterial endophytes has improved growth of several plant species. Our study demonstrated that Burkholderia phytofirmans strain PsJN, a well-studied plant growth promoting rhizo-bacterium (PGPR) significantly increased both aboveground and belowground biomass (DW) and promoted elongation of root, stem and leaf within 17 days following inoculation. Furthermore, the enhanced root growth in PsJN inoculated plants lagged behind the shoot response, resulting in greater allocation to aboveground growth (p = 0.0041). Lower specific root length (SRL, p = 0.0158) and higher specific leaf weight (SLW, p = 0.0029) were also observed in PsJN inoculated seedlings, indicating changes in development. Photosynthetic rates (Ps) were also significantly higher in PsJN inoculated seedlings after 17 days (54%, p = 0.0016), and this occurred initially without increases in stomatal conductance resulting in significantly greater water use efficiency (WUE, 37.7%, p = 0.0467) and lower non-stomatal limitation (LNS, 29.6%, p = 0.0222). These rapid changes in leaf level physiology are at least partially responsible for the growth enhancement due to PsJN. PMID:25461696

  16. Reassessment of Phomopsis species on grapevines

    NARCIS (Netherlands)

    Niekerk, van J.M.; Groenewald, J.Z.; Farr, D.F.; Fourie, P.H.; Halleen, F.; Crous, P.W.

    2005-01-01

    Ten species of Phomopsis have previously been identified from grapevines. Of these, P. viticola, the causal agent of Phomopsis cane and leaf spot, and P. vitimegaspora, the causal agent of swelling arm of grapevines, have been confirmed as severe pathogens of this host. Earlier taxonomic treatments

  17. Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions.

    Directory of Open Access Journals (Sweden)

    Sandra Schwarz

    Full Text Available Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs of Burkholderia thailandensis (B. thai in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans-leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections.

  18. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

    Directory of Open Access Journals (Sweden)

    Harvey Steven P

    2007-03-01

    Full Text Available Abstract Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were

  19. Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315.

    Science.gov (United States)

    Du, Wen-Li; Dubarry, Nelly; Passot, Fanny M; Kamgoué, Alain; Murray, Heath; Lane, David; Pasta, Franck

    2016-07-01

    Bacterial genomes typically consist of a single chromosome and, optionally, one or more plasmids. But whole-genome sequencing reveals about ten per-cent of them to be multipartite, with additional replicons which by size and indispensability are considered secondary chromosomes. This raises the questions of how their replication and partition is managed without compromising genome stability and of how such genomes arose. Vibrio cholerae, with a 1 Mb replicon in addition to its 3 Mb chromosome, is the only species for which maintenance of a multipartite genome has been investigated. In this study we have explored the more complex genome of Burkholderia cenocepacia (strain J2315). It comprises an extra replicon (c2) of 3.21 Mb, comparable in size to the3.87Mb main chromosome (c1), another extra replicon(c3) of 0.87 Mb and a plasmid of 0.09 Mb. The replication origin of c1 is typically chromosomal and those of c2 and c3 are plasmid-like; all are replicated bidirectionally. Fluorescence microscopy of tagged origins indicates that all initiate replication at mid-cell and segregate towards the cell quarter positions sequentially, c1-c2-p1/c3. c2 segregation is as well-phased with the cell cycle as c1, implying that this plasmid-like origin has become subject to regulation not typical of plasmids; in contrast, c3 segregates more randomly through the cycle. Disruption of individual Par systems by deletion of parAB or by addition of parS sites showed each Par system to govern the positioning of its own replicon only. Inactivation of c1, c2 and c3 Par systems not only reduced growth rate, generated anucleate cells and compromised viability but influenced processes beyond replicon partition, notably regulation of replication, chromosome condensation and cell size determination. In particular, the absence of the c1 ParA protein altered replication of all three chromosomes, suggesting that the partition system of the main chromosome is a major participant in the choreography of

  20. Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315.

    Directory of Open Access Journals (Sweden)

    Wen-Li Du

    2016-07-01

    Full Text Available Bacterial genomes typically consist of a single chromosome and, optionally, one or more plasmids. But whole-genome sequencing reveals about ten per-cent of them to be multipartite, with additional replicons which by size and indispensability are considered secondary chromosomes. This raises the questions of how their replication and partition is managed without compromising genome stability and of how such genomes arose. Vibrio cholerae, with a 1 Mb replicon in addition to its 3 Mb chromosome, is the only species for which maintenance of a multipartite genome has been investigated. In this study we have explored the more complex genome of Burkholderia cenocepacia (strain J2315. It comprises an extra replicon (c2 of 3.21 Mb, comparable in size to the3.87Mb main chromosome (c1, another extra replicon(c3 of 0.87 Mb and a plasmid of 0.09 Mb. The replication origin of c1 is typically chromosomal and those of c2 and c3 are plasmid-like; all are replicated bidirectionally. Fluorescence microscopy of tagged origins indicates that all initiate replication at mid-cell and segregate towards the cell quarter positions sequentially, c1-c2-p1/c3. c2 segregation is as well-phased with the cell cycle as c1, implying that this plasmid-like origin has become subject to regulation not typical of plasmids; in contrast, c3 segregates more randomly through the cycle. Disruption of individual Par systems by deletion of parAB or by addition of parS sites showed each Par system to govern the positioning of its own replicon only. Inactivation of c1, c2 and c3 Par systems not only reduced growth rate, generated anucleate cells and compromised viability but influenced processes beyond replicon partition, notably regulation of replication, chromosome condensation and cell size determination. In particular, the absence of the c1 ParA protein altered replication of all three chromosomes, suggesting that the partition system of the main chromosome is a major participant in the

  1. Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations.

    Science.gov (United States)

    Menard, Aymeric; Monnez, Claire; Estrada de Los Santos, Paulina; Segonds, Christine; Caballero-Mellado, Jesus; Lipuma, John J; Chabanon, Gerard; Cournoyer, Benoit

    2007-05-01

    Burkholderia vietnamiensis is the third most prevalent species of the Burkholderia cepacia complex (Bcc) found in cystic fibrosis (CF) patients. Its ability at fixing nitrogen makes it one of the main Bcc species showing strong filiations with environmental reservoirs. In this study, 83% (29 over 35) of the B. vietnamiensis CF isolates and 100% of the environmental ones (over 29) were found expressing the dinitrogenase complex (encoded by the nif cluster) which is essential in N(2) fixation. Among the deficient strains, two were found growing with ammonium chloride suggesting that they were defective in N(2) fixation, and four with amino acids supplements suggesting that they were harbouring auxotrophic mutations. To get insights about the genetic events that led to the emergence of the N(2)-fixing defective strains, a genetic analysis of B. vietnamiensis nitrogen-fixing property was undertaken. A 40-kb-long nif cluster and nif regulatory genes were identified within the B. vietnamiensis strain G4 genome sequence, and analysed. Transposon mutagenesis and nifH genetic marker exchanges showed the nif cluster and several other genes like gltB (encoding a subunit of the glutamate synthase) to play a key role in B. vietnamiensis ability at growing in nitrogen-free media. nif cluster DNA probings of restricted genomic DNA blots showed a full deletion of the nif cluster for one of the N(2)-fixing defective strain while the other one showed a genetic organization similar to the one of the G4 strain. For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N(2)-fixing deficiencies.

  2. Burkholderia Species Are Major Inhabitants of White Lupin Cluster Roots▿†

    OpenAIRE

    Weisskopf, Laure; Heller, Stefanie; Eberl, Leo

    2011-01-01

    The formation of cluster roots by plants represents a highly efficient strategy for acquisition of sparingly available phosphate. This particular root type is characterized by a densely branched structure and high exudation of organic acids and protons, which are likely to influence the resident bacterial community. Until now, the identity of the bacterial populations living in cluster roots has not been investigated. We applied cultivation-dependent and cultivation-independent methods to cha...

  3. Distinct human antibody response to the biological warfare agent Burkholderia mallei.

    Science.gov (United States)

    Varga, John J; Vigil, Adam; DeShazer, David; Waag, David M; Felgner, Philip; Goldberg, Joanna B

    2012-10-01

    The genetic similarity between Burkholderia mallei (glanders) and Burkholderia pseudomallei (melioidosis) had led to the general assumption that pathogenesis of each bacterium would be similar. In 2000, the first human case of glanders in North America since 1945 was reported in a microbiology laboratory worker. Leveraging the availability of pre-exposure sera for this individual and employing the same well-characterized protein array platform that has been previously used to study a large cohort of melioidosis patients in southeast Asia, we describe the antibody response in a human with glanders. Analysis of 156 peptides present on the array revealed antibodies against 17 peptides with a > 2-fold increase in this infection. Unexpectedly, when the glanders data were compared with a previous data set from B. pseudomallei infections, there were only two highly increased antibodies shared between these two infections. These findings have implications in the diagnosis and treatment of B. mallei and B. pseudomallei infections.

  4. Workshop on treatment of and postexposure prophylaxis for Burkholderia pseudomallei and B. mallei Infection, 2010.

    Science.gov (United States)

    Lipsitz, Rebecca; Garges, Susan; Aurigemma, Rosemarie; Baccam, Prasith; Blaney, David D; Cheng, Allen C; Currie, Bart J; Dance, David; Gee, Jay E; Larsen, Joseph; Limmathurotsakul, Direk; Morrow, Meredith G; Norton, Robert; O'Mara, Elizabeth; Peacock, Sharon J; Pesik, Nicki; Rogers, L Paige; Schweizer, Herbert P; Steinmetz, Ivo; Tan, Gladys; Tan, Patrick; Wiersinga, W Joost; Wuthiekanun, Vanaporn; Smith, Theresa L

    2012-12-01

    The US Public Health Emergency Medical Countermeasures Enterprise convened subject matter experts at the 2010 HHS Burkholderia Workshop to develop consensus recommendations for postexposure prophylaxis against and treatment for Burkholderia pseudomallei and B. mallei infections, which cause melioidosis and glanders, respectively. Drugs recommended by consensus of the participants are ceftazidime or meropenem for initial intensive therapy, and trimethoprim/sulfamethoxazole or amoxicillin/clavulanic acid for eradication therapy. For postexposure prophylaxis, recommended drugs are trimethoprim/sulfamethoxazole or co-amoxiclav. To improve the timely diagnosis of melioidosis and glanders, further development and wide distribution of rapid diagnostic assays were also recommended. Standardized animal models and B. pseudomallei strains are needed for further development of therapeutic options. Training for laboratory technicians and physicians would facilitate better diagnosis and treatment options.

  5. Enhanced bioconversion of ethylene glycol to glycolic acid by a newly isolated Burkholderia sp. EG13.

    Science.gov (United States)

    Gao, Xiaoxin; Ma, Zhengfei; Yang, Limin; Ma, Jiangquan

    2014-10-01

    Burkholderia sp. EG13 with high ethylene glycol-oxidizing activity was isolated from soil, which could be used for the synthesis of glycolic acid from the oxidation of ethylene glycol. Using the resting cells of Burkholderia sp. EG13 as biocatalysts, the optimum reaction temperature and pH were 30 °C and 6.0, respectively. After 24 h of biotransformation, the yield of glycolic acid from 200 mM ethylene glycol was 98.8 %. Furthermore, an integrated bioprocess for the production of glycolic acid which involved in situ product removal (ISPR) was investigated. Using fed-batch method with ISPR, a total of 793 mM glycolic acid has been accumulated in the reaction mixture after the 4th feed.

  6. Temperature has a causal effect on avian timing of reproduction.

    Science.gov (United States)

    Visser, Marcel E; Holleman, Leonard J M; Caro, Samuel P

    2009-06-22

    Many bird species reproduce earlier in years with high spring temperatures, but little is known about the causal effect of temperature. Temperature may have a direct effect on timing of reproduction but the correlation may also be indirect, for instance via food phenology. As climate change has led to substantial shifts in timing, it is essential to understand this causal relationship to predict future impacts of climate change. We tested the direct effect of temperature on laying dates in great tits (Parus major) using climatized aviaries in a 6-year experiment. We mimicked the temperature patterns from two specific years in which our wild population laid either early ('warm' treatment) or late ('cold' treatment). Laying dates were affected by temperature directly. As the relevant temperature period started three weeks prior to the mean laying date, with a range of just 4 degrees C between the warm and the cold treatments, and as the birds were fed ad libitum, it is likely that temperature acted as a cue rather than lifting an energetic constraint on the onset of egg production. We furthermore show a high correlation between the laying dates of individuals reproducing both in aviaries and in the wild, validating investigations of reproduction of wild birds in captivity. Our results demonstrate that temperature has a direct effect on timing of breeding, an important step towards assessing the implication of climate change on seasonal timing. PMID:19324731

  7. Purification and characterization of chlorophenol 4-monooxygenase from Burkholderia cepacia AC1100.

    OpenAIRE

    Xun, L

    1996-01-01

    Burkholderia (formerly Pseudomonas) cepacia AC1100 mineralizes the herbicide 2,4,5-trichlorophenoxyacetate (2,4,5-T), and the first intermediate of 2,4,5-T degradation is 2,4,5-trichlorophenol. Chlorophenol 4-monooxygenase activity responsible for 2,4,5-trichlorophenol degradation was detected in the cell extract. The enzyme consisted of two components separated during purification, and both were purified to more than 95% homogeneity. The reconstituted enzyme catalyzed the hydroxylation of se...

  8. Isolation and characterization of Burkholderia sp. strain CCA53 exhibiting ligninolytic potential

    OpenAIRE

    Akita, Hironaga; Kimura, Zen-ichiro; Mohd Yusoff, Mohd Zulkhairi; Nakashima, Nobutaka; Hoshino, Tamotsu

    2016-01-01

    Microbial degradation of lignin releases fermentable sugars, effective utilization of which could support biofuel production from lignocellulosic biomass. In the present study, a lignin-degrading bacterium was isolated from leaf soil and identified as Burkholderia sp. based on 16S rRNA gene sequencing. This strain was named CCA53, and its lignin-degrading capability was assessed by observing its growth on medium containing alkali lignin or lignin-associated aromatic monomers as the sole carbo...

  9. An objective approach for Burkholderia pseudomallei strain selection as challenge material for medical countermeasures efficacy testing

    OpenAIRE

    Kristopher E Van Zandt; Apichai eTuanyok; Paul eKeim; Warren, Richard L.; H. Carl eGelhaus

    2012-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, a rare disease of biodefense concern with high mortality and extreme difficulty in treatment. No human vaccines are available that protect against B. pseudomallei infection, and with the current limitations of antibiotic treatment, the development of new preventative and therapeutic interventions is crucial. Although clinical trials could be used to test the efficacy of new medical countermeasures (MCMs), the high mortality rate...

  10. An Objective Approach for Burkholderia pseudomallei Strain Selection as Challenge Material for Medical Countermeasures Efficacy Testing

    OpenAIRE

    Kristopher E Van Zandt; Tuanyok, Apichai; Paul S Keim; Warren, Richard L.; Gelhaus, H. Carl

    2012-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, a rare disease of biodefense concern with high mortality and extreme difficulty in treatment. No human vaccines are available that protect against B. pseudomallei infection, and with the current limitations of antibiotic treatment, the development of new preventative and therapeutic interventions is crucial. Although clinical trials could be used to test the efficacy of new medical countermeasures (MCMs), the high mortality rate...

  11. Comparison of different PCR approaches for characterization of Burkholderia (Pseudomonas) cepacia isolates.

    OpenAIRE

    Liu, P. Y.; Shi, Z Y; Lau, Y J; HU, B S; Shyr, J M; Tsai, W S; Lin, Y. H.; Tseng, C Y

    1995-01-01

    In this study, we evaluated three PCR methods for epidemiological typing of Burkholderia (Pseudomonas) cepacia--PCR-ribotyping, arbitrarily primed PCR (AP-PCR) and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR)--and compared them with pulsed-field gel electrophoresis. The analysis was performed with 31 isolates of B. cepacia, comprising 23 epidemiologically unrelated isolates and 8 isolates collected from the same patient during two episodes of bacteremia. Pulsed-fiel...

  12. In Vitro Antifungal Activity of Burkholderia gladioli pv. agaricicola against Some Phytopathogenic Fungi

    OpenAIRE

    Elshafie, Hazem S.; Ippolito Camele; Rocco Racioppi; Laura Scrano; Iacobellis, Nicola S.; Bufo, Sabino A.

    2012-01-01

    The trend to search novel microbial natural biocides has recently been increasing in order to avoid the environmental pollution from use of synthetic pesticides. Among these novel natural biocides are the bioactive secondary metabolites of Burkholderia gladioli pv. agaricicola (Bga). The aim of this study is to determine antifungal activity of Bga strains against some phytopathogenic fungi. The fungicidal tests were carried out using cultures and cell-free culture filtrates against Botrytis c...

  13. A Burkholderia pseudomallei Toxin Inhibits Helicase Activity of Translation Factor eIF4A

    OpenAIRE

    Cruz, Abimael; Hautbergue, Guillaume M.; Artymiuk, Peter J.; Baker, Patrick J.; Bokori-Brown, Monika; Chang, Chung-Te; Dickman, Mark J.; Essex-Lopresti, Angela; Harding, Sarah V.; Mahadi, Nor Muhammad; Marshall, Laura E.; Mobbs, George W.; Mohamed, Rahmah; Nathan, Sheila; Ngugi, Sarah A.

    2011-01-01

    The structure of BPSL1549, a protein of unknown function from Burkholderia pseudomallei reveals a similarity to E. coli cytotoxic necrotizing factor 1. We found that BPSL1549 acted as a potent cytotoxin against eukaryotic cells and was lethal when administered to mice. Expression levels of bpsl1549 correlate with conditions expected to promote or suppress pathogenicity. BPSL1549 promotes deamidation of Gln339 of the translation initiation factor eIF4A, abolishing its helicase activity and inh...

  14. Purification and sequence analysis of 4-methyl-5-nitrocatechol oxygenase from Burkholderia sp. strain DNT.

    OpenAIRE

    Haigler, B E; Suen, W C; Spain, J C

    1996-01-01

    4-Methyl-5-nitrocatechol (MNC) is an intermediate in the degradation of 2,4-dinitrotoluene by Burkholderia sp. strain DNT. In the presence of NADPH and oxygen, MNC monooxygenase catalyzes the removal of the nitro group from MNC to form 2-hydroxy-5-methylquinone. The gene (dntB) encoding MNC monooxygenase has been previously cloned and characterized. In order to examine the properties of MNC monooxygenase and to compare it with other enzymes, we sequenced the gene encoding the MNC monooxygenas...

  15. Hexadecane and Tween 80 Stimulate Lipase Production in Burkholderia glumae by Different Mechanisms▿

    OpenAIRE

    Boekema, Bouke K. H. L.; Beselin, Anke; Breuer, Michael; Hauer, Bernhard; Koster, Margot; Rosenau, Frank; Jaeger, Karl-Erich; Tommassen, Jan

    2007-01-01

    Burkholderia glumae strain PG1 produces a lipase of biotechnological relevance. Lipase production by this strain and its derivative LU8093, which was obtained through classical strain improvement, was investigated under different conditions. When 10% hexadecane was included in the growth medium, lipolytic activity in both strains could be increased ∼7-fold after 24 h of growth. Hexadecane also stimulated lipase production in a strain containing the lipase gene fused to the tac promoter, indic...

  16. CD4+ T cell immunity to the Burkholderia pseudomallei ABC transporter LolC in melioidosis

    OpenAIRE

    Chu, Karen K.; Tippayawat, Patcharaporn; Walker, Nicola J.; Harding, Sarah V.; Atkins, Helen S.; Maillere, Bernard; Bancroft, Gregory J; Lertmemongkolchai, Ganjana; Altmann, Daniel M

    2010-01-01

    Burkholderia pseudomallei (Bp) causes melioidosis, a disease with a wide range of possible outcomes, from seroconversion and dormancy to sepsis and death. This spectrum of host-pathogen interactions poses challenging questions about heterogeneity in immunity to Bp. Models show protection to be dependent on CD4+ cells and IFNγ, but little is known about specific target antigens. Having previously implicated the ABC transporter, LolC, in protective immunity, we here use epitope prediction, HLA ...

  17. Identification of a LolC Homologue in Burkholderia pseudomallei, a Novel Protective Antigen for Melioidosis▿

    OpenAIRE

    Harland, David N; Chu, Karen; Haque, Ashraful; Nelson, Michelle; Walker, Nicola J.; Sarkar-Tyson, Mitali; Atkins, Timothy P.; Moore, Benjamin; Brown, Katherine A.; Bancroft, Gregory; Titball, Richard W.; Atkins, Helen S.

    2007-01-01

    Melioidosis is an emerging disease of humans in Southeast Asia and tropical Australia. The bacterium causing this disease, Burkholderia pseudomallei, is also considered a bioterrorism agent, and as yet there is no licensed vaccine for preventing B. pseudomallei infection. In this study, we evaluated selected proteins (LolC, PotF, and OppA) of the ATP-binding cassette systems of B. pseudomallei as candidate vaccine antigens. Nonmembrane regions of the B. pseudomallei proteins were expressed an...

  18. Outbreak of Subclinical Mastitis in a Flock of Dairy Sheep Associated with Burkholderia cepacia Complex Infection

    OpenAIRE

    Berriatua, E.; Ziluaga, I.; Miguel-Virto, C.; Uribarren, P.; Juste, R.; Laevens, S.; Vandamme, P.; Govan, J. R. W.

    2001-01-01

    An outbreak of subclinical mastitis in a flock of 620 milking sheep was investigated. Microbiological and epidemiological analyses identified the causative agent as belonging to the Burkholderia cepacia complex (formerly Pseudomonas cepacia). Every ewe in the milking flock was individually tested for subclinical mastitis on two separate occasions, 6 weeks apart, by the California (rapid) mastitis test (CMT). The proportion of CMT-positive ewes was 69 of 393 (17.6%) on the first sampling and 2...

  19. Burkholderia cepacia and cystic fibrosis: do natural environments present a potential hazard?

    OpenAIRE

    Butler, S. L.; DOHERTY, C.J; Hughes, J. E.; Nelson, J W; Govan, J R

    1995-01-01

    An environmental survey of 55 sites yielded only 12 Burkholderia cepacia isolates, none of which displayed the phenotypic properties of a multiresistant epidemic strain associated with pulmonary colonization in patients with cystic fibrosis. Although the environment probably poses a low risk for patients with cystic fibrosis as a source of B. cepacia, the pathogenic potential of individual environmental strains remains unclear. We advise caution in the development of B. cepacia as a biocontro...

  20. Evaluation of six commercial DNA extraction kits for recovery of Burkholderia pseudomallei DNA.

    Science.gov (United States)

    Marques, Maria Angela de Mello; Zimmermann, Pia; Messelhäußer, Ute; Sing, Andreas

    2012-12-01

    Six commercially available DNA extraction kits, as well as thermal lysis and proteinase K DNA extraction were evaluated regarding bacterial inactivation, DNA yield and purity, and their use in a Burkholderia pseudomallei real-time PCR. While all methods successfully inactivated the bacteria, by measuring DNA purity and the level of detection by real-time PCR, the proteinase K method was the most sensitive.

  1. Bioremediation of refinery wastewater using immobilised Burkholderia cepacia and Corynebacterium sp and their transconjugants

    OpenAIRE

    Abdullahi T. Ajao; Sabo E. Yakubu; Veronica J. Umoh; Joseph B. Ameh

    2013-01-01

    When oil spill occurs, it poses serious toxic hazards to all forms of life. Mixed culture of Burkholderia cepacia and Corynebacterium sp isolated from refinery sludge using selective enrichment technique was used for bioremediation of refinery wastewater in a laboratoryscale bioreactor. Physicochemical parameters of both raw and treated water were as determined and compared with Federal Environ - mental Protection Agency (FEPA-limit, Abuja, Nigeria) to asses the efficiency of the bioremediati...

  2. An Effect of Biofield Treatment on Multidrug-resistant Burkholderia cepacia: A Multihost Pathogen

    OpenAIRE

    Trivedi, Mahendra Kumar

    2015-01-01

    Burkholderia cepacia (B. cepacia) is an opportunistic, Gram negative pathogen which causes infection mainly in immunocompromised population and associated with high rate of morbidity and mortality in cystic fibrosis patients. Aim of the present study was to analyze the impact of biofield treatment on multidrug resistant B. cepacia. Clinical sample of B. cepacia was divided into two groups i.e. control and biofield treated. The analysis was done after 10 days of treatment and compared with con...

  3. Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil

    Science.gov (United States)

    Kimura, Zen-ichiro; Yusoff, Mohd Zulkhairi Mohd; Nakashima, Nobutaka; Hoshino, Tamotsu

    2016-01-01

    Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain, which consists of a total of 4 contigs containing 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding sequences. PMID:27389268

  4. Antimicrobial Drug–Selection Markers for Burkholderia pseudomallei and B. mallei

    OpenAIRE

    Schweizer, Herbert P.; Peacock, Sharon J.

    2008-01-01

    Genetic research into the select agents Burkholderia pseudomallei and B. mallei is currently hampered by a paucity of approved antimicrobial drug–selection markers. The strict regulations imposed on researchers in the United States but not in other parts of the world lead to discrepancies in practice, hinder distribution of genetically modified strains, and impede progress in the field. Deliberation and decisions regarding alternative selection markers (antimicrobial and nonantimicrobial drug...

  5. Survival, Sublethal Injury, and Recovery of Environmental Burkholderia pseudomallei in Soil Subjected to Desiccation

    OpenAIRE

    Larsen, Eloise; Smith, James J.; Norton, Robert; Corkeron, Maree

    2013-01-01

    Environmental Burkholderia pseudomallei isolated from sandy soil at Castle Hill, Townsville, in the dry tropic region of Queensland, Australia, was inoculated into sterile-soil laboratory microcosms subjected to variable soil moisture. Survival and sublethal injury of the B. pseudomallei strain were monitored by recovery using culture-based methods. Soil extraction buffer yielded higher recoveries as an extraction agent than sterile distilled water. B. pseudomallei was not recoverable when in...

  6. The causal link between energy and output growth: Evidence from Markov switching Granger causality

    International Nuclear Information System (INIS)

    In this paper we empirically investigate the causal link between energy consumption and economic growth employing a Markov switching Granger causality analysis. We carry out our investigation using annual U.S. real GDP, total final energy consumption and total primary energy consumption data which cover the period between 1968 and 2010. We find that there are significant changes in the causal relation between energy consumption and economic growth over the sample period under investigation. Our results show that total final energy consumption and total primary energy consumption have significant predictive content for real economic activity in the U.S. economy. Furthermore, the causality running from energy consumption to output growth seems to be strongly apparent particularly during the periods of economic downturn and energy crisis. We also document that output growth has predictive power in explaining total energy consumption. Furthermore, the power of output growth in predicting total energy consumption is found to diminish after the mid of 1980s. - Highlights: • Total energy consumption has predictive content for real economic activity. • The causality from energy to output growth is apparent in the periods of recession. • The causality from energy to output growth is strong in the periods of energy crisis. • Output growth has predictive power in explaining total energy consumption. • The power of output growth in explaining energy diminishes after the mid of 1980s

  7. Biodegradation of PAHs by Burkholderia sp. VITRSB1 Isolated from Marine Sediments

    Directory of Open Access Journals (Sweden)

    T. Revathy

    2015-01-01

    Full Text Available The polycyclic aromatic hydrocarbons (PAHs pollution to the environment is a major threat to the living organisms, and hence the degradation of these PAHs is necessary. Studies on PAHs degrading bacteria have focussed on terrestrial microbes and the potential of marine derived microbes is undermined. Herein we report the isolation and characterization of PAHs degrading Burkholderia sp. from lagoon sediments collected at the Southern coast of India. The strain was Gram negative, rod-shaped, motile, and ∼2–5 μm in length. Based on the phylogenetic data the strain was identified as Burkholderia and designated as VITRSB1. Initial PAHs degradation ability of the strain was assessed using basal salt medium supplemented with diesel, kerosene, toluene, aniline, naphthalene, and phenol. The strain was found to be effectively degrading kerosene, diesel, toluene, and aniline even at higher concentration (1%. However, naphthalene and aniline were degraded only at lower concentration (0.1% and phenol, camphor, and DAP inhibited the growth of the strain. Furthermore, the degraded end products of the PAHs were determined using FTIR. Notably, none of the end products were found to be toxic to the biosphere. Our results indicate that the isolated Burkholderia sp. could be a prospective candidate for the effective degradation of selective PAHs.

  8. Biodegradation of PAHs by Burkholderia sp. VITRSB1 Isolated from Marine Sediments.

    Science.gov (United States)

    Revathy, T; Jayasri, M A; Suthindhiran, K

    2015-01-01

    The polycyclic aromatic hydrocarbons (PAHs) pollution to the environment is a major threat to the living organisms, and hence the degradation of these PAHs is necessary. Studies on PAHs degrading bacteria have focussed on terrestrial microbes and the potential of marine derived microbes is undermined. Herein we report the isolation and characterization of PAHs degrading Burkholderia sp. from lagoon sediments collected at the Southern coast of India. The strain was Gram negative, rod-shaped, motile, and ∼2-5 μm in length. Based on the phylogenetic data the strain was identified as Burkholderia and designated as VITRSB1. Initial PAHs degradation ability of the strain was assessed using basal salt medium supplemented with diesel, kerosene, toluene, aniline, naphthalene, and phenol. The strain was found to be effectively degrading kerosene, diesel, toluene, and aniline even at higher concentration (1%). However, naphthalene and aniline were degraded only at lower concentration (0.1%) and phenol, camphor, and DAP inhibited the growth of the strain. Furthermore, the degraded end products of the PAHs were determined using FTIR. Notably, none of the end products were found to be toxic to the biosphere. Our results indicate that the isolated Burkholderia sp. could be a prospective candidate for the effective degradation of selective PAHs. PMID:26605106

  9. Assessing statistical significance in causal graphs

    Directory of Open Access Journals (Sweden)

    Chindelevitch Leonid

    2012-02-01

    Full Text Available Abstract Background Causal graphs are an increasingly popular tool for the analysis of biological datasets. In particular, signed causal graphs--directed graphs whose edges additionally have a sign denoting upregulation or downregulation--can be used to model regulatory networks within a cell. Such models allow prediction of downstream effects of regulation of biological entities; conversely, they also enable inference of causative agents behind observed expression changes. However, due to their complex nature, signed causal graph models present special challenges with respect to assessing statistical significance. In this paper we frame and solve two fundamental computational problems that arise in practice when computing appropriate null distributions for hypothesis testing. Results First, we show how to compute a p-value for agreement between observed and model-predicted classifications of gene transcripts as upregulated, downregulated, or neither. Specifically, how likely are the classifications to agree to the same extent under the null distribution of the observed classification being randomized? This problem, which we call "Ternary Dot Product Distribution" owing to its mathematical form, can be viewed as a generalization of Fisher's exact test to ternary variables. We present two computationally efficient algorithms for computing the Ternary Dot Product Distribution and investigate its combinatorial structure analytically and numerically to establish computational complexity bounds. Second, we develop an algorithm for efficiently performing random sampling of causal graphs. This enables p-value computation under a different, equally important null distribution obtained by randomizing the graph topology but keeping fixed its basic structure: connectedness and the positive and negative in- and out-degrees of each vertex. We provide an algorithm for sampling a graph from this distribution uniformly at random. We also highlight theoretical

  10. Trimmed Granger causality between two groups of time series

    OpenAIRE

    Hung, Ying-Chao; Tseng, Neng-Fang; Balakrishnan, Narayanaswamy

    2014-01-01

    The identification of causal effects between two groups of time series has been an important topic in a wide range of applications such as economics, engineering, medicine, neuroscience, and biology. In this paper, a simplified causal relationship (called trimmed Granger causality) based on the context of Granger causality and vector autoregressive (VAR) model is introduced. The idea is to characterize a subset of “important variables” for both groups of time series so that the underlying cau...

  11. Institutional Investors and Stock Market Development: A Causality Study

    OpenAIRE

    Guler Aras; Alovsat Muslumov

    2008-01-01

    This article examines causality relationships between institutional investors and stock market development based on the panel data compiled from 23 OECD countries for the years 1982 through 2000. In order to test causality relationship, Sims’ causality test based on Granger definition of causality was used in our study. Our empirical results provide evidence that there are statistically significant positive relationship between institutional investors and stock market development. The develop...

  12. Effect of gamma irradiation on Burkholderia thailandensis (Burkholderia pseudomallei surrogate) survival under combinations of pH and NaCl

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Yohan; Kim, Jae-Hun; Byun, Myung-Woo [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk 580-185 (Korea, Republic of); Choi, Kyoung-Hee [Department of Oral Microbiology, College of Dentistry, Wonkwang University, Iksan, Jeollabuk 570-749 (Korea, Republic of); Lee, Ju-Woon, E-mail: sjwlee@kaeri.re.k [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk 580-185 (Korea, Republic of)

    2010-04-15

    This study evaluated the effect of gamma irradiation on Burkholderia thailandensis (Burkholderia pseudomallei surrogate; potential bioterrorism agent) survival under different levels of NaCl and pH. B. thailandensis in Luria Bertani broth supplemented with NaCl (0-3%), and pH-adjusted to 4-7 was treated with gamma irradiation (0-0.5 kGy). Surviving cell counts of bacteria were then enumerated on tryptic soy agar. Data for the cell counts were also used to calculate D{sub 10} values (the dose required to reduce 1 log CFU/mL of B. thailandensis). Cell counts of B. thailandensis were decreased (P<0.05) as irradiation dose increased, and no differences (P>=0.05) in cell counts of the bacteria were observed among different levels of NaCl and pH. D{sub 10} values ranged from 0.04 to 0.07 kGy, regardless of NaCl and pH level. These results indicate that low doses of gamma irradiation should be a useful treatment in decreasing the potential bioterrorism bacteria, which may possibly infect humans through foods.

  13. Effect of gamma irradiation on Burkholderia thailandensis ( Burkholderia pseudomallei surrogate) survival under combinations of pH and NaCl

    Science.gov (United States)

    Yoon, Yohan; Kim, Jae-Hun; Byun, Myung-Woo; Choi, Kyoung-Hee; Lee, Ju-Woon

    2010-04-01

    This study evaluated the effect of gamma irradiation on Burkholderia thailandensis ( Burkholderia pseudomallei surrogate; potential bioterrorism agent) survival under different levels of NaCl and pH. B. thailandensis in Luria Bertani broth supplemented with NaCl (0-3%), and pH-adjusted to 4-7 was treated with gamma irradiation (0-0.5 kGy). Surviving cell counts of bacteria were then enumerated on tryptic soy agar. Data for the cell counts were also used to calculate D10 values (the dose required to reduce 1 log CFU/mL of B. thailandensis). Cell counts of B. thailandensis were decreased ( Pbacteria were observed among different levels of NaCl and pH. D10 values ranged from 0.04 to 0.07 kGy, regardless of NaCl and pH level. These results indicate that low doses of gamma irradiation should be a useful treatment in decreasing the potential bioterrorism bacteria, which may possibly infect humans through foods.

  14. Interpretational Confounding or Confounded Interpretations of Causal Indicators?

    Science.gov (United States)

    Bainter, Sierra A.; Bollen, Kenneth A.

    2014-01-01

    In measurement theory, causal indicators are controversial and little understood. Methodological disagreement concerning causal indicators has centered on the question of whether causal indicators are inherently sensitive to interpretational confounding, which occurs when the empirical meaning of a latent construct departs from the meaning…

  15. Rationales in Children's Causal Learning from Others' Actions

    Science.gov (United States)

    Sobel, David M.; Sommerville, Jessica A.

    2009-01-01

    Shown commensurate actions and information by an adult, preschoolers' causal learning was influenced by the pedagogical context in which these actions occurred. Four-year-olds who were provided with a reason for an experimenter's action relevant to learning causal structure showed more accurate causal learning than children exposed to the same…

  16. Mind and Meaning: Piaget and Vygotsky on Causal Explanation.

    Science.gov (United States)

    Beilin, Harry

    1996-01-01

    Piaget's theory has been characterized as descriptive and not explanatory, not qualifying as causal explanation. Piaget was consistent in showing how his theory was both explanatory and causal. Vygotsky also endorsed causal-genetic explanation but, on the basis of knowledge of only Piaget's earliest works, he claimed that Piaget's theory was not…

  17. A Bayesian Theory of Sequential Causal Learning and Abstract Transfer

    Science.gov (United States)

    Lu, Hongjing; Rojas, Randall R.; Beckers, Tom; Yuille, Alan L.

    2016-01-01

    Two key research issues in the field of causal learning are how people acquire causal knowledge when observing data that are presented sequentially, and the level of abstraction at which learning takes place. Does sequential causal learning solely involve the acquisition of specific cause-effect links, or do learners also acquire knowledge about…

  18. How to Be Causal: Time, Spacetime and Spectra

    Science.gov (United States)

    Kinsler, Paul

    2011-01-01

    I explain a simple definition of causality in widespread use, and indicate how it links to the Kramers-Kronig relations. The specification of causality in terms of temporal differential equations then shows us the way to write down dynamical models so that their causal nature "in the sense used here" should be obvious to all. To extend existing…

  19. Causality and Nonlocality as Axioms for Quantum Mechanics

    OpenAIRE

    Popescu, Sandu; Rohrlich, Daniel

    1997-01-01

    Quantum mechanics permits nonlocality - both nonlocal correlations and nonlocal equations of motion - while respecting relativistic causality. Is quantum mechanics the unique theory that reconciles nonlocality and causality? We consider two models, going beyond quantum mechanics, of nonlocality: "superquantum" correlations, and nonlocal "jamming" of correlations. These models are consistent with some definitions of nonlocality and causality.

  20. Normalizing the causality between time series

    CERN Document Server

    Liang, X San

    2015-01-01

    Recently, a rigorous yet concise formula has been derived to evaluate the information flow, and hence the causality in a quantitative sense, between time series. To assess the importance of a resulting causality, it needs to be normalized. The normalization is achieved through distinguishing three types of fundamental mechanisms that govern the marginal entropy change of the flow recipient. A normalized or relative flow measures its importance relative to other mechanisms. In analyzing realistic series, both absolute and relative information flows need to be taken into account, since the normalizers for a pair of reverse flows belong to two different entropy balances; it is quite normal that two identical flows may differ a lot in relative importance in their respective balances. We have reproduced these results with several autoregressive models. We have also shown applications to a climate change problem and a financial analysis problem. For the former, reconfirmed is the role of the Indian Ocean Dipole as ...

  1. Sentencing goals, causal attributions, ideology, and personality.

    Science.gov (United States)

    Carroll, J S; Perkowitz, W T; Lurigio, A J; Weaver, F M

    1987-01-01

    Disparity in sentencing of criminals has been related to a variety of individual difference variables. We propose a framework establishing resonances or coherent patterns among sentencing goals, causal attributions, ideology, and personality. Two studies are described, one with law and criminology students, the other with probation officers. Relations among the different types of variables reveal two resonances among both students and officers. One comprises various conservative and moralistic elements: a tough, punitive stance toward crime; belief in individual causality for crime; high scores on authoritarianism, dogmatism, and internal locus of control; lower moral stage; and political conservatism. The second comprises various liberal elements: rehabilitation, belief in economic and other external determinants of crime, higher moral stage, and belief in the powers and responsibilities of government to correct social problems. Implications of these results are discussed for individual differences in sentencing, attribution theory, and attempts to reduce disparity. PMID:3820064

  2. A New Spin on Causality Constraints

    CERN Document Server

    Hartman, Thomas; Kundu, Sandipan

    2016-01-01

    Causality in a shockwave state is related to the analytic properties of a four-point correlation function. Extending recent results for scalar probes, we show that this constrains the couplings of the stress tensor to light spinning operators in conformal field theory, and interpret these constraints in terms of the interaction with null energy. For spin-1 and spin-2 conserved currents in four dimensions, the resulting inequalities are a subset of the Hofman-Maldacena conditions for positive energy deposition. It is well known that energy conditions in holographic theories are related to causality on the gravity side; our results make a connection on the CFT side, and extend it to non-holographic theories.

  3. Consistence beats causality in recommender systems

    CERN Document Server

    Zhu, Xuzhen; Hu, Zheng; Zhang, Ping; Zhou, Tao

    2015-01-01

    The explosive growth of information challenges people's capability in finding out items fitting to their own interests. Recommender systems provide an efficient solution by automatically push possibly relevant items to users according to their past preferences. Recommendation algorithms usually embody the causality from what having been collected to what should be recommended. In this article, we argue that in many cases, a user's interests are stable, and thus the previous and future preferences are highly consistent. The temporal order of collections then does not necessarily imply a causality relationship. We further propose a consistence-based algorithm that outperforms the state-of-the-art recommendation algorithms in disparate real data sets, including \\textit{Netflix}, \\textit{MovieLens}, \\textit{Amazon} and \\textit{Rate Your Music}.

  4. An insider's guide to quantum causal histories

    CERN Document Server

    Markopoulou, F

    2000-01-01

    A review is given of recent work aimed at constructing a quantum theory of cosmology in which all observables refer to information measurable by observers inside the universe. At the classical level the algebra of observables should be modified to take into account the fact that observers can only give truth values to observables that have to do with their backwards light cone. The resulting algebra is a Heyting rather than a Boolean algebra. The complement is non-trivial and contains information about horizons and topology change. Representation of such observables quantum mechanically requires a many-Hilbert space formalism, in which different observers make measurements in different Hilbert spaces. I describe such a formalism, called "quantum causal histories"; examples include causally evolving spin networks and quantum computers.

  5. Consistence beats causality in recommender systems

    OpenAIRE

    Zhu, Xuzhen; Tian, Hui; Hu, Zheng; Zhang, Ping; Zhou, Tao

    2015-01-01

    The explosive growth of information challenges people's capability in finding out items fitting to their own interests. Recommender systems provide an efficient solution by automatically push possibly relevant items to users according to their past preferences. Recommendation algorithms usually embody the causality from what having been collected to what should be recommended. In this article, we argue that in many cases, a user's interests are stable, and thus the previous and future prefere...

  6. Gauge theory origins of supergravity causal structure

    CERN Document Server

    Kabat, D; Kabat, Daniel; Lifschytz, Gilad

    1999-01-01

    We discuss the gauge theory mechanisms which are responsible for the causal structure of the dual supergravity. For D-brane probes we show that the light cone structure and Killing horizons of supergravity emerge dynamically. They are associated with the appearance of new light degrees of freedom in the gauge theory, which we explicitly identify. This provides a picture of physics at the horizon of a black hole as seen by a D-brane probe.

  7. Imposing causality on a matrix model

    International Nuclear Information System (INIS)

    We introduce a new matrix model that describes Causal Dynamical Triangulations (CDT) in two dimensions. In order to do so, we introduce a new, simpler definition of 2D CDT and show it to be equivalent to the old one. The model makes use of ideas from dually weighted matrix models, combined with multi-matrix models, and can be studied by the method of character expansion.

  8. Isocausal spacetimes may have different causal boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Flores, J L; Herrera, J [Departamento de Algebra, Geometria y Topologia, Facultad de Ciencias, Universidad de Malaga, Campus Teatinos, 29071 Malaga (Spain); Sanchez, M, E-mail: floresj@agt.cie.uma.es, E-mail: jherrera@uma.es, E-mail: sanchezm@ugr.es [Departamento de Geometria y Topologia, Facultad de Ciencias, Universidad de Granada, Avenida Fuentenueva s/n, 18071 Granada (Spain)

    2011-09-07

    We construct an example which shows that two isocausal spacetimes, in the sense introduced recently in GarcIa-Parrado and Senovilla (2003 Class. Quantum Grav. 20 625-64), may have c-boundaries which are not equal (more precisely, not equivalent, as no bijection between the completions can preserve all the binary relations induced by causality). This example also suggests that isocausality can be useful for the understanding and computation of the c-boundary.

  9. A causally connected superluminal Warp Drive spacetime

    OpenAIRE

    Loup, F.; Held, R.; Waite, D; Halerewicz, Jr., E.; Stabno, M.; Kuntzman, M.; Sims, R.

    2002-01-01

    It will be shown that while horizons do not exist for warp drive spacetimes traveling at subluminal velocities horizons begin to develop when a warp drive spacetime reaches luminal velocities. However it will be shown that the control region of a warp drive ship lie within the portion of the warped region that is still causally connected to the ship even at superluminal velocities, therefore allowing a ship to slow to subluminal velocities. Further it is shown that the warped regions which ar...

  10. Relativistic causality and position space renormalization

    CERN Document Server

    Todorov, Ivan

    2016-01-01

    We survey the causal position space renormalization with a special attention to the role of Raymond Stora in the development of the subject. Renormalization is effected by subtracting pole terms in analytically regularized amplitudes. Residues are identified with periods whose relation to recent development in number theory is emphasized. We demonstrate the possibility of integration over internal vertices in the case of a (massless) conformal theory and display the dilation and the conformal anomaly.

  11. Extending Temporal Causal Graph For Diagnosis Problems

    OpenAIRE

    Belouaer, Lamia; Bouzid, Maroua; Mouhoub, Malek

    2009-01-01

    Poster International audience Abductive diagnosis (Brusoni et al. 1998) consists in finding explanations for given observations by using rules of inference based on the causal dependences of the system. Time is important for abductive diagnosis (Hamscher and Davis 1984), (Hamscher, Console, and Kleer 1992). There are few works in litterature handling temporal diagnosis (Kautz 1999). They differ in the expressiveness of the temporal knowledge. We propose a new approach for Temporal Diagn...

  12. Ten simple rules for dynamic causal modeling

    OpenAIRE

    Stephan, K E; Penny, W.D.; Moran, R. J.; den Ouden, H.E.M.; Daunizeau, J.; Friston, K J

    2010-01-01

    Dynamic causal modeling (DCM) is a generic Bayesian framework for inferring hidden neuronal states from measurements of brain activity. It provides posterior estimates of neurobiologically interpretable quantities such as the effective strength of synaptic connections among neuronal populations and their context-dependent modulation. DCM is increasingly used in the analysis of a wide range of neuroimaging and electrophysiological data. Given the relative complexity of DCM, compared to convent...

  13. Bayesian Discovery of Linear Acyclic Causal Models

    CERN Document Server

    Hoyer, Patrik O

    2012-01-01

    Methods for automated discovery of causal relationships from non-interventional data have received much attention recently. A widely used and well understood model family is given by linear acyclic causal models (recursive structural equation models). For Gaussian data both constraint-based methods (Spirtes et al., 1993; Pearl, 2000) (which output a single equivalence class) and Bayesian score-based methods (Geiger and Heckerman, 1994) (which assign relative scores to the equivalence classes) are available. On the contrary, all current methods able to utilize non-Gaussianity in the data (Shimizu et al., 2006; Hoyer et al., 2008) always return only a single graph or a single equivalence class, and so are fundamentally unable to express the degree of certainty attached to that output. In this paper we develop a Bayesian score-based approach able to take advantage of non-Gaussianity when estimating linear acyclic causal models, and we empirically demonstrate that, at least on very modest size networks, its accur...

  14. A causal dispositional account of fitness.

    Science.gov (United States)

    Triviño, Vanessa; Nuño de la Rosa, Laura

    2016-09-01

    The notion of fitness is usually equated to reproductive success. However, this actualist approach presents some difficulties, mainly the explanatory circularity problem, which have lead philosophers of biology to offer alternative definitions in which fitness and reproductive success are distinguished. In this paper, we argue  that none of these alternatives is satisfactory and, inspired by Mumford and Anjum's dispositional theory of causation, we offer a definition of fitness as a causal dispositional property. We argue that, under this framework, the distinctiveness that biologists usually attribute to fitness-namely, the fact that fitness is something different from both the physical traits of an organism and the number of offspring it leaves-can be explained, and the main problems associated with the concept of fitness can be solved. Firstly, we introduce Mumford and Anjum's dispositional theory of causation and present our definition of fitness as a causal disposition. We explain in detail each of the elements involved in our definition, namely: the relationship between fitness and the functional dispositions that compose it, the emergent character of fitness, and the context-sensitivity of fitness. Finally, we explain how fitness and realized fitness, as well as expected and realized fitness are distinguished in our approach to fitness as a causal disposition. PMID:27338570

  15. [Causality in cardiology: concepts in evolution].

    Science.gov (United States)

    Méndez, Gustavo F

    2005-01-01

    This paper describes several concepts about causality from Empedocles, Aristoteles and Galeno, to Koch and Hill and the evolution of these concepts related to cardiovascular diseases. Also defines cause and risk, and the philosophical theories about scientific knowledge: inductive versus refutation analysis. On these basis, the study of cardiovascular disease's causality, especially coronary heart disease, allows us the identification of several risk factors involved in its development. However, even with the presently coronary heart disease risk charts (from Framingham and European studies) the higher probability for the development of a cardiovascular ischemic event is around 40%, establishing an important degree of uncertainty. With the improvement in molecular biology techniques, genetics have attempted to analyse several genetic polymorphisms in search of the origin of coronary heart disease. Unfortunately, less than 10% of these polymorphisms have had a positive correlation with coronary heart disease being of minor risk that those obtained for having the diagnosis of type 2 diabetes mellitus or hypercholesterolemia. On these basis, the requirement of new population research projects in which clinical and genetic risk factors are to be studied for the appropriate understanding of the causality process of cardiovascular diseases must be a worldwide priority.

  16. Causality, initial conditions, and inflationary magnetogenesis

    Science.gov (United States)

    Tsagas, Christos G.

    2016-05-01

    The post-inflationary evolution of inflation-produced magnetic fields, conventional or not, can change dramatically when two fundamental issues are accounted for. The first is causality, which demands that local physical processes can never affect superhorizon perturbations. The second is the nature of the transition from inflation to reheating and then to the radiation era, which determine the initial conditions at the start of these epochs. Causality implies that inflationary magnetic fields do not freeze into the matter until they have re-entered the causal horizon. The nature of the cosmological transitions and the associated initial conditions, on the other hand, determine the large-scale magnetic evolution after inflation. Put together, the two can slow down the adiabatic magnetic decay on superhorizon scales throughout the Universe's post-inflationary evolution and thus lead to considerably stronger residual magnetic fields. This is "good news" for both the conventional and the nonconventional scenarios of cosmic magnetogenesis. Mechanisms operating outside standard electromagnetism, in particular, do not need to enhance their fields too much during inflation in order to produce seeds that can feed the galactic dynamo today. In fact, even conventionally produced inflationary magnetic fields might be able to sustain the dynamo.

  17. A causal dispositional account of fitness.

    Science.gov (United States)

    Triviño, Vanessa; Nuño de la Rosa, Laura

    2016-09-01

    The notion of fitness is usually equated to reproductive success. However, this actualist approach presents some difficulties, mainly the explanatory circularity problem, which have lead philosophers of biology to offer alternative definitions in which fitness and reproductive success are distinguished. In this paper, we argue  that none of these alternatives is satisfactory and, inspired by Mumford and Anjum's dispositional theory of causation, we offer a definition of fitness as a causal dispositional property. We argue that, under this framework, the distinctiveness that biologists usually attribute to fitness-namely, the fact that fitness is something different from both the physical traits of an organism and the number of offspring it leaves-can be explained, and the main problems associated with the concept of fitness can be solved. Firstly, we introduce Mumford and Anjum's dispositional theory of causation and present our definition of fitness as a causal disposition. We explain in detail each of the elements involved in our definition, namely: the relationship between fitness and the functional dispositions that compose it, the emergent character of fitness, and the context-sensitivity of fitness. Finally, we explain how fitness and realized fitness, as well as expected and realized fitness are distinguished in our approach to fitness as a causal disposition.

  18. Causal beliefs about depression in different cultural groups – What do cognitive psychological theories of causal learning and reasoning predict?

    OpenAIRE

    York eHagmayer; Neele eEngelmann

    2014-01-01

    Cognitive psychological research focusses on causal learning and reasoning while cognitive anthropological and social science research tend to focus on systems of beliefs. Our aim was to explore how these two types of research can inform each other. Cognitive psychological theories (causal model theory and causal Bayes nets) were used to derive predictions for systems of causal beliefs. These predictions were then applied to lay theories of depression as a specific test case. A systematic...

  19. Causal beliefs about depression in different cultural groups—what do cognitive psychological theories of causal learning and reasoning predict?

    OpenAIRE

    Hagmayer, York; Engelmann, Neele

    2014-01-01

    Cognitive psychological research focuses on causal learning and reasoning while cognitive anthropological and social science research tend to focus on systems of beliefs. Our aim was to explore how these two types of research can inform each other. Cognitive psychological theories (causal model theory and causal Bayes nets) were used to derive predictions for systems of causal beliefs. These predictions were then applied to lay theories of depression as a specific test case. A systematic lite...

  20. Burkholderia ambifaria and B. caribensis promote growth and increase yield in grain amaranth (Amaranthus cruentus and A. hypochondriacus) by improving plant nitrogen uptake.

    Science.gov (United States)

    Parra-Cota, Fannie I; Peña-Cabriales, Juan J; de Los Santos-Villalobos, Sergio; Martínez-Gallardo, Norma A; Délano-Frier, John P

    2014-01-01

    Grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. However, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. In this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in Amaranthus hypochondriacus cv. Nutrisol and A. cruentus cv. Candil, two commercially important grain amaranth cultivars. The plants were grown in a rich substrate, high in organic matter, nitrogen (N), and phosphorus (P) and under greenhouse conditions. Burkholderia ambifaria Mex-5 and B. caribensis XV proved to be the most efficient strains and significantly promoted growth in both grain amaranth species tested. Increased grain yield and harvest index occurred in combination with chemical fertilization when tested in A. cruentus. Growth-promotion and improved yields correlated with increased N content in all tissues examined. Positive effects on growth also occurred in A. cruentus plants grown in a poor soil, even after N and P fertilization. No correlation between non-structural carbohydrate levels in roots of inoculated plants and growth promotion was observed. Conversely, gene expression assays performed at 3-, 5- and 7-weeks after seed inoculation in plants inoculated with B. caribensis XV identified a tissue-specific induction of several genes involved in photosynthesis, sugar- and N- metabolism and transport. It is concluded that strains of Burkholderia effectively promote growth and increase seed yields in grain amaranth. Growth promotion was particularly noticeable in plants grown in an infertile soil but also occurred in a well fertilized rich substrate. The positive effects observed may be attributed to a bio-fertilization effect that led to increased N levels in roots and shoots. The latter effect correlated with the differential induction of several genes involved in carbon and N metabolism