WorldWideScience

Sample records for speciation meets pyrosequencing

  1. Clinical Neuropathology practice news 1-2014: Pyrosequencing meets clinical and analytical performance criteria for routine testing of MGMT promoter methylation status in glioblastoma

    Science.gov (United States)

    Preusser, Matthias; Berghoff, Anna S.; Manzl, Claudia; Filipits, Martin; Weinhäusel, Andreas; Pulverer, Walter; Dieckmann, Karin; Widhalm, Georg; Wöhrer, Adelheid; Knosp, Engelbert; Marosi, Christine; Hainfellner, Johannes A.

    2014-01-01

    Testing of the MGMT promoter methylation status in glioblastoma is relevant for clinical decision making and research applications. Two recent and independent phase III therapy trials confirmed a prognostic and predictive value of the MGMT promoter methylation status in elderly glioblastoma patients. Several methods for MGMT promoter methylation testing have been proposed, but seem to be of limited test reliability. Therefore, and also due to feasibility reasons, translation of MGMT methylation testing into routine use has been protracted so far. Pyrosequencing after prior DNA bisulfite modification has emerged as a reliable, accurate, fast and easy-to-use method for MGMT promoter methylation testing in tumor tissues (including formalin-fixed and paraffin-embedded samples). We performed an intra- and inter-laboratory ring trial which demonstrates a high analytical performance of this technique. Thus, pyrosequencing-based assessment of MGMT promoter methylation status in glioblastoma meets the criteria of high analytical test performance and can be recommended for clinical application, provided that strict quality control is performed. Our article summarizes clinical indications, practical instructions and open issues for MGMT promoter methylation testing in glioblastoma using pyrosequencing. PMID:24359605

  2. Speciation analysis of arsenic, chromium and selenium in aquatic media. Proceedings of a final research coordination meeting

    International Nuclear Information System (INIS)

    2007-03-01

    The initiation of the Coordinated Research Project (CRP) on Development and Validation of Speciation Analysis using Nuclear Techniques resulted from the recognition that knowledge of total element concentration does not provide adequate information to understand the effects of trace and heavy metals observed in the environment and in living systems. Their toxicity, bioavailability, physiological and metabolic processes, mobility and distribution are greatly dependent on the specific chemical form of the element. Speciation analysis has yet to be developed to its full potential for biochemical, clinical and environmental investigations and still more work is needed in the near future. Seven participants from seven countries participated in this CRP covering a range of analytical techniques including GC, HPLC, AAS, and ICP-MS. The first Research Coordination Meeting (RCM) of the Coordinated Research Project on the Development and Validation of Speciation Analysis using Nuclear Techniques was held at the Reactor Centre of the Jozef Stefan Institute, Podgorica (near Ljubljana), Slovenia, 20-23 June 2001. The second RCM was held at the Technical University of Vienna, 18-22 November 2002, where, in addition to the participants, two external researchers could present their views and experience in the field. The last RCM was held in Vienna, 26-29 April 2004, and this publication is a summary of the results achieved and presented at this last RCM. The participants have developed several new procedures for the reliable analysis of As, Cr, and Se species, mainly in aquatic media. A new instrument was designed and several recommendations for speciation analysis were issued. It is hoped that this publication will make a contribution to enhancing the awareness of the importance of speciation analysis and add to the reliability of speciation results in Member State laboratories

  3. Report on the consultants' meeting to: Outline a co-ordinated research project on trace element speciation to enhance technology transfer in this field by the development of suitable methodologies and/or the production of suitably characterised reference materials

    International Nuclear Information System (INIS)

    2001-01-01

    In the environment and in man, the total concentration of a given element in a sample is almost always comprised of two or more discrete chemical forms. The toxicological or nutritive impact of the element in the sample in the environment or when ingested by man will be dependent upon the properties of its individual components. Therefore, in order to make meaningful benefit or risk assessment statements, it is essential to have a knowledge of the forms and relative amounts of an element in a given matrix. When the analyte in question is only present at total concentrations at the trace level (mg.kg -1 ) or below, the problems involved in obtaining this information become much more complex. The term trace metal speciation has been coined to refer to the determination of the chemical forms and quantities of an analyte present in a sample at the trace (and ultra trace) level. Even at such relatively low levels, the presence or absence of specific forms of an analyte can have serious consequences in terms of trade, health and environmental management. In light of the PPAS External Reviewers' Report of the Consultants' Meeting on Analytical Quality Control Services (October 1997, Vienna) which recommended that characterisation of chemical species should be undertaken in AQCS reference materials, the Agency decided to convene a consultants' meeting specifically to advise it on the importance of trace metal speciation, the state of the art and the value of a CRP to address aspects of speciation in order to facilitate technology transfer and equip member states with appropriate tools to meet the challenges posed. Five scientists, recognised as experts in the field of trace metal speciation were identified and invited to the Agency's headquarters to act as consultants. The meeting was held at the Vienna International Centre from 23rd to 26th November 1998. The first day of the meeting was given over to presentations from the consultants on various aspects of trace element

  4. Removing Noise From Pyrosequenced Amplicons

    Directory of Open Access Journals (Sweden)

    Davenport Russell J

    2011-01-01

    Full Text Available Abstract Background In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms. Results AmpliconNoise outperforms alternative algorithms substantially reducing per base error rates for both the GS FLX and latest Titanium protocol. All three sources of error lead to inflation of diversity estimates. In particular, chimera formation has a hitherto unrealised importance which varies according to amplification protocol. We show that AmpliconNoise allows accurate estimates of OTU number. Just as importantly AmpliconNoise generates the right OTUs even at low sequence differences. We demonstrate that Perseus has very high sensitivity, able to find 99% of chimeras, which is critical when these are present at high

  5. Speciation analysis of radionuclides in the environment. NKS-B speciation project report 2007

    Energy Technology Data Exchange (ETDEWEB)

    Xiaolin Hou (Technical Univ. of Denmark, Risoe National Lab. for Sustainable Energy, Roskilde (Denmark)); Aldahan, A. (Uppsala Univ., Dept. of Earth Science, Uppsala (Sweden)); Possnert, G. (Uppsala Univ., Tandem Lab., Uppsala (Sweden)); Lujaniene, G. (Institute of Physics, Vilnius (Lithuania)); Lehto, J. (Univ. of Helsinki, Dept. of Chemistry, Helsinki (Finland)); Salbu, B. (Norwegian Univ. of Life Sciences (UMB), AAs (Norway))

    2008-07-15

    This report describes the work carried out under the NUK-B project SPECIATION 2007. In 2007, the project partners had two meeting in April and November, organized a NUK seminar on speciation and hot particles. SPECIATION 2007 t mainly focused on two issues on speciation (1) further development of speciation methods for radionuclides, and (2) investigation of speciation of radionuclides in environment. The report summarized the work done in partners labs, which includes: (1) Further development on the speciation of 129I and 127I in water samples; (2) Speciation method for 129I and 127I in air; (3) Dynamic system for fractionation of Pu and Am in soil and sediment; (4) Investigation on Re-absorption of Pu during the fractionation of Pu in soil and sediment; (5) Speciation of 129I in North Sea surface water; (6) Partition of 137Cs and 129I in the Nordic lake sediment, pore-water and lake water; (7) Sequential extraction of Pu in soil, sediment and concrete samples, (8) Pu sorption to Mn and Fe oxides in the geological materials, (10) Investigation of the adsorbed species of lanthanides and actinides on clays surfaces. In addition, two review articles on the speciation of plutonium and iodine in environmental are planned to be submitted to an international journal for publication. (au)

  6. Speciation analysis of radionuclides in the environment. NKS-B speciation project report 2007

    International Nuclear Information System (INIS)

    Hou, Xiaolin; Aldahan, A.; Possnert, G.; Lujaniene, G.; Lehto, J.; Salbu, B.

    2008-07-01

    This report describes the work carried out under the NUK-B project SPECIATION 2007. In 2007, the project partners had two meeting in April and November, organized a NUK seminar on speciation and hot particles. SPECIATION 2007 t mainly focused on two issues on speciation (1) further development of speciation methods for radionuclides, and (2) investigation of speciation of radionuclides in environment. The report summarized the work done in partners labs, which includes: (1) Further development on the speciation of 129I and 127I in water samples; (2) Speciation method for 129I and 127I in air; (3) Dynamic system for fractionation of Pu and Am in soil and sediment; (4) Investigation on Re-absorption of Pu during the fractionation of Pu in soil and sediment; (5) Speciation of 129I in North Sea surface water; (6) Partition of 137Cs and 129I in the Nordic lake sediment, pore-water and lake water; (7) Sequential extraction of Pu in soil, sediment and concrete samples, (8) Pu sorption to Mn and Fe oxides in the geological materials, (10) Investigation of the adsorbed species of lanthanides and actinides on clays surfaces. In addition, two review articles on the speciation of plutonium and iodine in environmental are planned to be submitted to an international journal for publication. (au)

  7. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    carefully selected waterworks (Article IV), where the bacterial metabolic diversity and its important for water purification was described. Building on this, the most important part of the thesis consists of two pyrosequencing analyses of protozoa with newly developed 18S primers. One specifically targets...... Cercozoa, a particularly abundant phylum of protozoa (Article III), on heath land that had been subjected to prolonged artificially induced drought in a Danish free-air climate-manipulation experiment (CLIMAITE). Article III showed that the testate cercozoan forms responded negatively to prolonged drought...

  8. Arsenic speciation results

    Data.gov (United States)

    U.S. Environmental Protection Agency — Linear combination fitting results of synchrotron data to determine arsenic speciation in soil samples. This dataset is associated with the following publication:...

  9. Chemical Speciation - General Information

    Science.gov (United States)

    This page includes general information about the Chemical Speciation Network that is not covered on the main page. Commonly visited documents, including calendars, site lists, and historical files for the program are listed here

  10. Searching for speciation genes

    DEFF Research Database (Denmark)

    Holt, Benjamin George; Côté, Isabelle M; Emerson, Brent C

    2011-01-01

    Closely related species that show clear phenotypic divergence, but without obvious geographic barriers, can provide opportunities to study how diversification can occur when opportunities for allopatric speciation are limited. We examined genetic divergence in the coral reef fish genus Hypoplectrus...

  11. Uranium speciation in plants

    International Nuclear Information System (INIS)

    Guenther, A.; Bernhard, G.; Geipel, G.; Reich, T.; Rossberg, A.; Nitsche, H.

    2003-01-01

    Detailed knowledge of the nature of uranium complexes formed after the uptake by plants is an essential prerequisite to describe the migration behavior of uranium in the environment. This study focuses on the determination of uranium speciation after uptake of uranium by lupine plants. For the first time, time-resolved laser-induced fluorescence spectroscopy and X-ray absorption spectroscopy were used to determine the chemical speciation of uranium in plants. Differences were detected between the uranium speciation in the initial solution (hydroponic solution and pore water of soil) and inside the lupine plants. The oxidation state of uranium did not change and remained hexavalent after it was taken up by the lupine plants. The chemical speciation of uranium was identical in the roots, shoot axis, and leaves and was independent of the uranium speciation in the uptake solution. The results indicate that the uranium is predominantly bound as uranyl(VI) phosphate to the phosphoryl groups. Dandelions and lamb's lettuce showed uranium speciation identical to lupine plants. (orig.)

  12. Strategien zur HLA-Typisierung mit PyrosequencingTM

    OpenAIRE

    Entz, Patricia

    2006-01-01

    Der Haupthistokompatibilitätskomplex ist durch seine biologische Funktion eine für die Diagnostik und Forschung äußerst wichtige Region im humanen Genom. Die Untersuchung von HLA-Genorten stellt ein wichtiges Instrument in der molekulargenetischen Praxis dar. Die Pyrosequencing-Technik ist gut geeignet, um kurze DNA-Abschnitte mit weitgehend bekannter Sequenz schnell und effizient zu untersuchen. Ziel dieser Arbeit war die Entwicklung von Pyrosequencing-basierten Methoden zur HLA-Typisierung....

  13. Meeting

    Indian Academy of Sciences (India)

    July 1989 No.19 Newsletter of the Indian Academy of Sciences. 55th Annual. Meeting ... in the world, keeping alive atthe same time his research interests, abreast .... theory made a comeback with many new ideas and with the success of the ...

  14. Speciation of long-lived radionuclides in the environment

    Energy Technology Data Exchange (ETDEWEB)

    Xiaolin Hou

    2008-11-15

    This project started in November 2005 and ended in November 2008, the work and research approaches are summarized in this report. This project studied the speciation of radionuclides in environment. A number of speciation analytical methods are developed for determination of species of 129I, 99Tc, isotopes of Pu, and 237Np in seawater, fresh water, soil, sediment, vegetations, and concrete. The developed methods are used for the investigation of the chemical speciation of these radionuclides as well as their environmental behaviours, especially in Danish environment. In addition the speciation of Pu isotopes in waste samples from the decommissioning of Danish nuclear facilities is also investigated. The report summarizes these works completed in this project. Through this research project, a number of research papers have been published in the scientific journals, the research results has also been presented in the Nordic and international conference/meeting and communicated to international colleagues. Some publications are also enclosed to this report. (au)

  15. Chemical speciation of long-lived radionuclides in the environment

    International Nuclear Information System (INIS)

    Xiaolin Hou

    2008-11-01

    This project started in November 2005 and ended in November 2008, the work and research approaches are summarized in this report. This project studied the speciation of radionuclides in environment. A number of speciation analytical methods are developed for determination of species of 129 I, 99 Tc, isotopes of Pu, and 237 Np in seawater, fresh water, soil, sediment, vegetations, and concrete. The developed methods are used for the investigation of the chemical speciation of these radionuclides as well as their environmental behaviours, especially in Danish environment. In addition the speciation of Pu isotopes in waste samples from the decommissioning of Danish nuclear facilities is also investigated. The report summarizes these works completed in this project. Through this research project, a number of research papers have been published in the scientific journals, the research results has also been presented in the Nordic and international conference/meeting and communicated to international colleagues. Some publications are also enclosed to this report. (au)

  16. Arsenic Speciation in Groundwater: Role of Thioanions

    Science.gov (United States)

    The behavior of arsenic in groundwater environments is fundamentally linked to its speciation. Understanding arsenic speciation is important because chemical speciation impacts reactivity, bioavailability, toxicity, and transport and fate processes. In aerobic environments arsen...

  17. Hitchhiking to speciation.

    Directory of Open Access Journals (Sweden)

    Daven C Presgraves

    Full Text Available The modern evolutionary synthesis codified the idea that species exist as distinct entities because intrinsic reproductive barriers prevent them from merging together. Understanding the origin of species therefore requires understanding the evolution and genetics of reproductive barriers between species. In most cases, speciation is an accident that happens as different populations adapt to different environments and, incidentally, come to differ in ways that render them reproductively incompatible. As with other reproductive barriers, the evolution and genetics of interspecific hybrid sterility and lethality were once also thought to evolve as pleiotripic side effects of adaptation. Recent work on the molecular genetics of speciation has raised an altogether different possibility-the genes that cause hybrid sterility and lethality often come to differ between species not because of adaptation to the external ecological environment but because of internal evolutionary arms races between selfish genetic elements and the genes of the host genome. Arguably one of the best examples supporting a role of ecological adaptation comes from a population of yellow monkey flowers, Mimulus guttatus, in Copperopolis, California, which recently evolved tolerance to soil contaminants from copper mines and simultaneously, as an incidental by-product, hybrid lethality in crosses with some off-mine populations. However, in new work, Wright and colleagues show that hybrid lethality is not a pleiotropic consequence of copper tolerance. Rather, the genetic factor causing hybrid lethality is tightly linked to copper tolerance and spread to fixation in Copperopolis by genetic hitchhiking.

  18. Speciation analysis of radionuclides

    International Nuclear Information System (INIS)

    Salbu, B.

    2010-01-01

    Full text: Naturally occurring and artificially produced radionuclides in the environment can be present in different physico-chemical forms (i. e. radionuclide species) varying in size (nominal molecular mass), charge properties and valence, oxidation state, structure and morphology, density, complexing ability etc. Low molecular mass (LMM) species are believed to be mobile and potentially bioavailable, while high molecular mass (HMM) species such as colloids, polymers, pseudocolloids and particles are considered inert. Due to time dependent transformation processes such as mobilization of radionuclide species from solid phases or interactions of mobile and reactive radionuclide species with components in soils and sediments, however, the original distribution of radionuclides deposited in ecosystems will change over time and influence the ecosystem behaviour. To assess the environmental impact from radionuclide contamination, information on radionuclide species deposited, interactions within affected ecosystems and the time-dependent distribution of radionuclide species influencing mobility and biological uptake is essential. The development of speciation techniques to characterize radionuclide species in waters, soils and sediments should therefore be essential for improving the prediction power of impact and risk assessment models. The present paper reviews fractionation techniques which should be utilised for radionuclide speciation purposes. (author)

  19. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    Energy Technology Data Exchange (ETDEWEB)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M. [VTT Technical Research Centre of Finland, Espoo (Finland)

    2012-06-15

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected.

  20. Allele-Specific DNA Methylation Detection by Pyrosequencing®

    DEFF Research Database (Denmark)

    Kristensen, Lasse Sommer; Johansen, Jens Vilstrup; Grønbæk, Kirsten

    2015-01-01

    DNA methylation is an epigenetic modification that plays important roles in healthy as well as diseased cells, by influencing the transcription of genes. In spite the fact that human somatic cells are diploid, most of the currently available methods for the study of DNA methylation do not provide......-effective protocol for allele-specific DNA methylation detection based on Pyrosequencing(®) of methylation-specific PCR (MSP) products including a single nucleotide polymorphism (SNP) within the amplicon....

  1. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    Energy Technology Data Exchange (ETDEWEB)

    Bomberg, M; Nyyssoenen, M; Itaevaara, M [VTT Technical Research Centre of Finland, Espoo (Finland)

    2012-06-15

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected.

  2. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    International Nuclear Information System (INIS)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M.

    2012-06-01

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected

  3. Efficient alignment of pyrosequencing reads for re-sequencing applications

    Directory of Open Access Journals (Sweden)

    Russo Luis MS

    2011-05-01

    Full Text Available Abstract Background Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects. Results We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454 system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time. Conclusions The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.

  4. Rapid Molecular Identification of Human Taeniid Cestodes by Pyrosequencing Approach

    Science.gov (United States)

    Thanchomnang, Tongjit; Tantrawatpan, Chairat; Intapan, Pewpan M.; Sanpool, Oranuch; Janwan, Penchom; Lulitanond, Viraphong; Tourtip, Somjintana; Yamasaki, Hiroshi; Maleewong, Wanchai

    2014-01-01

    Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse. PMID:24945530

  5. Rapid molecular identification of human taeniid cestodes by pyrosequencing approach.

    Directory of Open Access Journals (Sweden)

    Tongjit Thanchomnang

    Full Text Available Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1 gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse.

  6. X exceptionalism in Caenorhabditis speciation.

    Science.gov (United States)

    Cutter, Asher D

    2017-11-13

    Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to "rules" of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis. Studies to date implicate improper chromatin regulation of the X-chromosome by small RNA pathways as integral to hybrid male dysfunction. Sexual transitions in reproductive mode to self-fertilizing hermaphroditism inject distinctive molecular evolutionary features into the speciation process for some species. Caenorhabditis also provides unique opportunities for analysis in a system with XO sex determination that lacks a Y-chromosome, sex chromosome-dependent sperm competition differences and mechanisms of gametic isolation, exceptional accessibility to the development process and rapid experimental evolution. As genetic analysis of reproductive isolation matures with investigation of multiple pairs of Caenorhabditis species and new species discovery, nematodes will provide a powerful complement to more established study organisms for deciphering the genetic basis of and rules to speciation. © 2017 John Wiley & Sons Ltd.

  7. CHURCH, Category, and Speciation

    Directory of Open Access Journals (Sweden)

    Rinderknecht Jakob Karl

    2018-01-01

    Full Text Available The Roman Catholic definition of “church”, especially as applied to groups of Protestant Christians, creates a number of well-known difficulties. The similarly complex category, “species,” provides a model for applying this term so as to neither lose the centrality of certain examples nor draw a hard boundary to rule out border cases. In this way, it can help us to more adequately apply the complex ecclesiology of the Second Vatican Council. This article draws parallels between the understanding of speciation and categorization and the definition of Church since the council. In doing so, it applies the work of cognitive linguists, including George Lakoff, Zoltan Kovecses, Giles Fauconnier and Mark Turner on categorization. We tend to think of categories as containers into which we sort objects according to essential criteria. However, categories are actually built inductively by making associations between objects. This means that natural categories, including species, are more porous than we assume, but nevertheless bear real meaning about the natural world. Taxonomists dispute the border between “zebras” and “wild asses,” but this distinction arises out of genetic and evolutionary reality; it is not merely arbitrary. Genetic descriptions of species has also led recently to the conviction that there are four species of giraffe, not one. This engagement will ground a vantage point from which the Council‘s complex ecclesiology can be more easily described so as to authentically integrate its noncompetitive vision vis-a-vis other Christians with its sense of the unique place held by Catholic Church.

  8. Cancer: beyond speciation.

    Science.gov (United States)

    Vincent, Mark D

    2011-01-01

    A good account of the nature of cancer should provide not only a description of its consistent features, but also how they arise, how they are maintained, why conventional chemotherapy succeeds, and fails, and where to look for better targets. Cancer was once regarded as enigmatic and inexplicable; more recently, the "mutation theory," based on random alterations in a relatively small set of proto-oncogenes and tumor suppressor genes, has enjoyed widespread acceptance. The "mutation theory," however, is noticeable for its failure to explain the basis of differential chemosensitivity, for providing a paucity of targets, especially druggable ones, and for justifying the development of targeted therapies with, in general, disappointingly abbreviated clinical benefit. Furthermore, this theory has mistakenly predicted a widespread commonality of consistent genetic abnormalities across the range of cancers, whereas the opposite, that is, roiling macrogenomic instability, is generally the rule. In contrast, concerning what actually is consistent, that is, the suite of metabolic derangements common to virtually all, especially aggressive, cancers, the "Mutation Theory" has nothing to say. Other hypotheses merit serious consideration "aneuploidy theories" posit whole-genome instability and imbalance as causally responsible for the propagation of the tumor. Another approach, that is, "derepression atavism," suggests cancer results from the release of an ancient survival program, characterized by the emergence of remarkably primitive features such as unicellularity, fermentation, and immortality; existential goals are served by heuristic genomic instability coupled with host-to-tumor biomass interconversion, mediated by the Warburg effect, a major component of the program. Carcinogenesis is here seen as a process of de-speciation; however, genomic nonrestabilization raises issues as to where on the tree of life cancers belong, as a genuinely alternative modus vivendi

  9. CONCAWE effluent speciation project

    Energy Technology Data Exchange (ETDEWEB)

    Leonards, P.; Comber, M.; Forbes, S.; Whale, G.; Den Haan, K.

    2010-09-15

    In preparation for the implementation of the EU REACH regulation, a project was undertaken to transfer the high-resolution analytical method for determining hydrocarbon blocks in petroleum products by comprehensive two-dimensional gas chromatography (GCxGC) to a laboratory external to the petroleum industry (Institute for Environmental Studies (IVM) of the VU University of Amsterdam). The method was validated and used for the analysis of petroleum hydrocarbons extracted from refinery effluents. The report describes the technology transfer and the approaches used to demonstrate the successful transfer and application of the GCxGC methodology from analysing petroleum products to the quantitative determination of hydrocarbon blocks in refinery effluents. The report describes all the methods used for all the determinations on the effluent samples along with an overview of the results obtained which are presented in summary tables and graphs. These data have significantly improved CONCAWE's knowledge of what refineries emit in their effluents. A total of 111 Effluent Discharge Samples from 105 CONCAWE refineries in Europe were obtained in the period June 2008 to March 2009. These effluents were analysed for metals, standard effluent parameters (including COD, BOD), oil in water, BTEX and volatile organic compounds. The hydrocarbon speciation determinations and other hydrocarbon analyses are also reported. The individual refinery analytical results are included into this report, coded as per the CONCAWE system. These data will be, individually, communicated to companies and refineries. The report demonstrates that it is feasible to conduct a research programme to investigate the fate and effects of hydrocarbon blocks present in discharged refinery effluents.

  10. Sympatric Speciation in Threespine Stickleback: Why Not?

    Directory of Open Access Journals (Sweden)

    Daniel I. Bolnick

    2011-01-01

    Full Text Available Numerous theoretical models suggest that sympatric speciation is possible when frequency-dependent interactions such as intraspecific competition drive disruptive selection on a trait that is also subject to assortative mating. Here, I review recent evidence that both conditions are met in lake populations of threespine stickleback (Gasterosteus aculeatus. Nonetheless, sympatric speciation appears to be rare or absent in stickleback. If stickleback qualitatively fit the theoretical requirements for sympatric speciation, why do they not undergo sympatric speciation? I present simulations showing that disruptive selection and assortative mating in stickleback, though present, are too weak to drive speciation. Furthermore, I summarize empirical evidence that disruptive selection in stickleback drives other forms of evolutionary diversification (plasticity, increased trait variance, and sexual dimorphism instead of speciation. In conclusion, core assumptions of sympatric speciation theory seem to be qualitatively reasonable for stickleback, but speciation may nevertheless fail because of (i quantitative mismatches with theory and (ii alternative evolutionary outcomes.

  11. [Sensitivity and specificity of nested PCR pyrosequencing in hepatitis B virus drug resistance gene testing].

    Science.gov (United States)

    Sun, Shumei; Zhou, Hao; Zhou, Bin; Hu, Ziyou; Hou, Jinlin; Sun, Jian

    2012-05-01

    To evaluate the sensitivity and specificity of nested PCR combined with pyrosequencing in the detection of HBV drug-resistance gene. RtM204I (ATT) mutant and rtM204 (ATG) nonmutant plasmids mixed at different ratios were detected for mutations using nested-PCR combined with pyrosequencing, and the results were compared with those by conventional PCR pyrosequencing to analyze the linearity and consistency of the two methods. Clinical specimens with different viral loads were examined for drug-resistant mutations using nested PCR pyrosequencing and nested PCR combined with dideoxy sequencing (Sanger) for comparison of the detection sensitivity and specificity. The fitting curves demonstrated good linearity of both conventional PCR pyrosequencing and nested PCR pyrosequencing (R(2)>0.99, PNested PCR showed a better consistency with the predicted value than conventional PCR, and was superior to conventional PCR for detection of samples containing 90% mutant plasmid. In the detection of clinical specimens, Sanger sequencing had a significantly lower sensitivity than nested PCR pyrosequencing (92% vs 100%, Pnested PCR and Sanger sequencing method, nested PCR pyrosequencing has a higher sensitivity especially in clinical specimens with low viral copies, which can be important for early detection of HBV mutant strains and hence more effective clinical management.

  12. Pyrosequencing assessment of rhizosphere fungal communities from a soybean field.

    Science.gov (United States)

    Sugiyama, Akifumi; Ueda, Yoshikatsu; Takase, Hisabumi; Yazaki, Kazufumi

    2014-10-01

    Soil fungal communities play essential roles in soil ecosystems, affecting plant growth and health. Rhizosphere bacterial communities have been shown to undergo dynamic changes during plant growth. This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth. Members of the Ascomycota and Basiodiomycota dominated in all soils. There were no statistically significant changes at the phylum level among growth stages or between bulk and rhizosphere soils. In contrast, the relative abundance of small numbers of operational taxonomic units, 4 during growth and 28 between bulk and rhizosphere soils, differed significantly. Clustering analysis revealed that rhizosphere fungal communities were different from bulk fungal communities during growth stages of soybeans. Taken together, these results suggest that in contrast to rhizosphere bacterial communities, most constituents of rhizosphere fungal communities remained stable during soybean growth.

  13. Bacterial flora-typing with targeted, chip-based Pyrosequencing

    Directory of Open Access Journals (Sweden)

    El-Sayed Yasser Y

    2007-11-01

    Full Text Available Abstract Background The metagenomic analysis of microbial communities holds the potential to improve our understanding of the role of microbes in clinical conditions. Recent, dramatic improvements in DNA sequencing throughput and cost will enable such analyses on individuals. However, such advances in throughput generally come at the cost of shorter read-lengths, limiting the discriminatory power of each read. In particular, classifying the microbial content of samples by sequencing the Results We describe a method for identifying the phylogenetic content of bacterial samples using high-throughput Pyrosequencing targeted at the 16S rRNA gene. Our analysis is adapted to the shorter read-lengths of such technology and uses a database of 16S rDNA to determine the most specific phylogenetic classification for reads, resulting in a weighted phylogenetic tree characterizing the content of the sample. We present results for six samples obtained from the human vagina during pregnancy that corroborates previous studies using conventional techniques. Next, we analyze the power of our method to classify reads at each level of the phylogeny using simulation experiments. We assess the impacts of read-length and database completeness on our method, and predict how we do as technology improves and more bacteria are sequenced. Finally, we study the utility of targeting specific 16S variable regions and show that such an approach considerably improves results for certain types of microbial samples. Using simulation, our method can be used to determine the most informative variable region. Conclusion This study provides positive validation of the effectiveness of targeting 16S metagenomes using short-read sequencing technology. Our methodology allows us to infer the most specific assignment of the sequence reads within the phylogeny, and to identify the most discriminative variable region to target. The analysis of high-throughput Pyrosequencing on human flora

  14. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  15. Neutral Models with Generalised Speciation

    NARCIS (Netherlands)

    Haegeman, Bart; Etienne, Rampal S.

    Hubbell's neutral theory claims that ecological patterns such as species abundance distributions can be explained by a stochastic model based on simple assumptions. One of these assumptions, the point mutation assumption, states that every individual has the same probability to speciate. Etienne et

  16. Aspects of speciation in foodstuffs

    International Nuclear Information System (INIS)

    Crews, Helen M.

    2001-01-01

    Food is the primary source of trace elements for humans and it is now generally accepted that the bioavailability of a given element and its behaviour in the body depends upon its chemical form. This point was illustrated with the example of arsenic speciation in fish in which bioaccumulation takes place in the marine food chain, however, the species of arsenic ingested by man when the fish is consumed are not toxic. It was pointed out that species information will be vital in deciding upon realistic average dietary requirements for trace elements, particularly because both deficiency or excess of an element can have detrimental consequences on an individual's health. Two examples of speciation studies with food (Cd and Se) were presented and the importance of the use of label technology which will allow studies of target analytes at physiological levels, was stressed

  17. Pyrosequencing the Canine Faecal Microbiota: Breadth and Depth of Biodiversity

    Science.gov (United States)

    Hand, Daniel; Wallis, Corrin; Colyer, Alison; Penn, Charles W.

    2013-01-01

    Mammalian intestinal microbiota remain poorly understood despite decades of interest and investigation by culture-based and other long-established methodologies. Using high-throughput sequencing technology we now report a detailed analysis of canine faecal microbiota. The study group of animals comprised eleven healthy adult miniature Schnauzer dogs of mixed sex and age, some closely related and all housed in kennel and pen accommodation on the same premises with similar feeding and exercise regimes. DNA was extracted from faecal specimens and subjected to PCR amplification of 16S rDNA, followed by sequencing of the 5′ region that included variable regions V1 and V2. Barcoded amplicons were sequenced by Roche-454 FLX high-throughput pyrosequencing. Sequences were assigned to taxa using the Ribosomal Database Project Bayesian classifier and revealed dominance of Fusobacterium and Bacteroidetes phyla. Differences between animals in the proportions of different taxa, among 10,000 reads per animal, were clear and not supportive of the concept of a “core microbiota”. Despite this variability in prominent genera, littermates were shown to have a more similar faecal microbial composition than unrelated dogs. Diversity of the microbiota was also assessed by assignment of sequence reads into operational taxonomic units (OTUs) at the level of 97% sequence identity. The OTU data were then subjected to rarefaction analysis and determination of Chao1 richness estimates. The data indicated that faecal microbiota comprised possibly as many as 500 to 1500 OTUs. PMID:23382835

  18. Pyrosequencing the canine faecal microbiota: breadth and depth of biodiversity.

    Directory of Open Access Journals (Sweden)

    Daniel Hand

    Full Text Available Mammalian intestinal microbiota remain poorly understood despite decades of interest and investigation by culture-based and other long-established methodologies. Using high-throughput sequencing technology we now report a detailed analysis of canine faecal microbiota. The study group of animals comprised eleven healthy adult miniature Schnauzer dogs of mixed sex and age, some closely related and all housed in kennel and pen accommodation on the same premises with similar feeding and exercise regimes. DNA was extracted from faecal specimens and subjected to PCR amplification of 16S rDNA, followed by sequencing of the 5' region that included variable regions V1 and V2. Barcoded amplicons were sequenced by Roche-454 FLX high-throughput pyrosequencing. Sequences were assigned to taxa using the Ribosomal Database Project Bayesian classifier and revealed dominance of Fusobacterium and Bacteroidetes phyla. Differences between animals in the proportions of different taxa, among 10,000 reads per animal, were clear and not supportive of the concept of a "core microbiota". Despite this variability in prominent genera, littermates were shown to have a more similar faecal microbial composition than unrelated dogs. Diversity of the microbiota was also assessed by assignment of sequence reads into operational taxonomic units (OTUs at the level of 97% sequence identity. The OTU data were then subjected to rarefaction analysis and determination of Chao1 richness estimates. The data indicated that faecal microbiota comprised possibly as many as 500 to 1500 OTUs.

  19. Pyrosequencing Analysis of Subgingival Microbiota in Distinct Periodontal Conditions.

    Science.gov (United States)

    Park, O-J; Yi, H; Jeon, J H; Kang, S-S; Koo, K-T; Kum, K-Y; Chun, J; Yun, C-H; Han, S H

    2015-07-01

    Subgingival microorganisms are potentially associated with periodontal diseases. However, changes in the subgingival microbiota during the progress of periodontal diseases are poorly understood. In this study, we analyzed bacterial communities in the subgingival paper point samples from 32 Korean individuals with no sign of disease, gingivitis, or periodontitis using 454 FLX Titanium pyrosequencing. A total of 256,113 reads representing 26 phyla, 433 genera, and 1,016 species were detected. Bacteroidetes, Fusobacteria, Synergistetes, and Spirochaetes were the abundant phyla in periodontitis subjects, whereas Firmicutes and Proteobacteria were identified as the dominant phyla in the gingivitis and healthy subjects, respectively. Although high levels of Porphyromonas, Fusobacterium, Fretibacterium, Rothia, Filifactor, and Treponema genera were observed in the periodontitis subjects, Streptococcus, Capnocytophaga, Leptotrichia, and Haemophilus genera were found at high frequency in the gingivitis subjects. Species including Porphyromonas gingivalis, Fusobacterium nucleatum, and Fretibacterium fastidiosum were significantly increased in periodontitis subjects. On the other hand, Streptococcus pseudopneumoniae, Haemophilus parainfluenzae, and Leptotrichia hongkongensis were preferentially observed in the gingivitis subjects. Intriguingly, the halophile Halomonas hamiltonii was revealed as a predominant species in the healthy subjects. Based on Fast UniFrac analysis, distinctive bacterial clusters were classified for the healthy, gingivitis, and periodontitis state. The current findings might be useful for understanding the pathogenesis, diagnosis, and treatment of periodontal diseases. © International & American Associations for Dental Research 2015.

  20. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    Science.gov (United States)

    Park, J. E.; Lee, B. T.; Son, A.

    2015-12-01

    Heavy metals leached from exhausted mines have been causing severe environmental problems in nearby soils and groundwater. Environmental mitigation was performed based on the heavy metal stabilization using Calcite and steel slag in Korea. Since the soil stabilization only temporarily immobilizes the contaminants to soil matrix, the potential risk of re-leaching heavy metal still exists. Therefore the follow-up management of stabilized soils and the corresponding evaluation methods are required to avoid the consequent contamination from the stabilized soils. In this study, microbial community analysis using pyrosequencing was performed for assessing the potential leaching of the stabilized soils. As a result of rarefaction curve and Chao1 and Shannon indices, the stabilized soil has shown lower richness and diversity as compared to non-contaminated negative control. At the phyla level, as the degree of contamination increases, most of phyla decreased with only exception of increased proteobacteria. Among proteobacteria, gamma-proteobacteria increased against the heavy metal contamination. At the species level, Methylobacter tundripaludum of gamma-proteobacteria showed the highest relative portion of microbial community, indicating that methanotrophs may play an important role in either solubilization or immobilization of heavy metals in stabilized soils.

  1. Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.

  2. 454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology

    Directory of Open Access Journals (Sweden)

    David J. Rooks

    2010-07-01

    Full Text Available Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785 were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%. The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases.

  3. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon; Wang, Yong; Yang, Jiangke; Lafi, Feras Fawzi; Al-Suwailem, Abdulaziz M.; Qian, Peiyuan

    2010-01-01

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus

  4. The ambrosia symbiosis is specific in some species and promiscuous in others: evidence from community pyrosequencing

    Czech Academy of Sciences Publication Activity Database

    Kostovčík, Martin; Bateman, C.C.; Kolařík, Miroslav; Stelinski, L.L.; Jordal, B.H.; Hulcr, J.

    2015-01-01

    Roč. 9, č. 1 (2015), s. 126-138 ISSN 1751-7362 Institutional support: RVO:61388971 Keywords : ambrosia symbiosis * pyrosequencing Subject RIV: EE - Microbiology, Virology Impact factor: 9.328, year: 2015

  5. MODELING MONOMETHYLMERCURY AND TRIBUTYLTIN SPECIATION WITH EPA'S GEOCHEMICAL SPECIATION MODEL MINTEQA2

    Science.gov (United States)

    Given the complexity of the various, simultaneous (and competing) equilibrium reactions governing the speciation of ionic species in aquatic systems, EPA has developed and distributed the geochemical speciation model MINTEQA2 (Brown and Allison, 1987, Allison et al., 1991; Hydrog...

  6. Uranium speciation in Fernald soils

    International Nuclear Information System (INIS)

    Morris, D.E.; Conradson, S.D.; Tait, C.D.; Chisholm-Brause, C.J.; Berg, J.; Musgrave, J.

    1992-01-01

    This report details progress made from January 1 to May 31, 1992 in this analytical support task to determine the speciation of uranium in contaminated soil samples from the Fernald Environmental Management Project site under the auspices of the Uranium in Soils Integrated Demonstration funded through the US DOE's Office of Technology Development. The authors' efforts have focused on characterization of soil samples collected by S.Y. Lee (Oak Ridge National Laboratory) from five locales at the Fernald site. These were chosen to sample a broad range of uranium source terms. On the basis of x-ray absorption spectroscopy data, they have determined that the majority of uranium (> 80--90%) exists in the hexavalent oxidation state for all samples examined. This is a beneficial finding from the perspective of remediation, because U(VI) species are more soluble in general than uranium species in other oxidation states. Optical luminescence data from many of the samples show the characteristic structured yellow-green emission from the uranyl (UO 2 2+ ) moiety. The luminescence data also suggest that much of the uranium in these soils is present as well-crystallized UO 2 2+ species. Some clear spectroscopic distinctions have been noted for several samples that illustrate significant differences in the speciation (1) from site to site, (2) within different horizons at the same site, and (3) within different size fractions of the soils in the same horizon at the same site. This marked heterogeneity in uranyl speciation suggests that several soil washing strategies may be necessary to reduce the total uranium concentrations within these soils to regulatory limits

  7. Speciation of Pb in industrially polluted soils

    DEFF Research Database (Denmark)

    Jensen, Pernille Erland; Ottosen, Lisbeth M.; Pedersen, Anne Juul

    2006-01-01

    This study was aimed at elucidating the importance of original Pb-speciation versus soil-characteristics to mobility and distribution of Pb in industrially polluted soils. Ten industrially polluted Danish surface soils were characterized and Pb speciation was evaluated through SEM-EDX studies...

  8. Advances in Ecological Speciation: an integrative approach.

    Science.gov (United States)

    Faria, Rui; Renaut, Sebastien; Galindo, Juan; Pinho, Catarina; Melo-Ferreira, José; Melo, Martim; Jones, Felicity; Salzburger, Walter; Schluter, Dolph; Butlin, Roger

    2014-02-01

    The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference 'Advances in Ecological Speciation' organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation. © 2013 John Wiley & Sons Ltd.

  9. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    Science.gov (United States)

    Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E

    2006-01-01

    Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid

  10. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    Directory of Open Access Journals (Sweden)

    Farmerie William G

    2006-08-01

    Full Text Available Abstract Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20 System (454 Life Sciences Corporation, to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae and Platanus occidentalis (Platanaceae. Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy

  11. 15. ESRF users meeting

    Energy Technology Data Exchange (ETDEWEB)

    Fotis C, Kafatos; Ulrich, K.U.; Weib, S.; Rossberg, A.; Scheinost, A.C.; Foerstendorf, H.; Zanker, H.; Meyerheim, H.L.; Sander, D.; Popescu, R.; Kirschner, J.; Robach, O.; Ferrer, S.; Lyman, P.F.; Shneerson, V.L.; Fung, R.; Harder, R.J.; Parihar, S.S.; Johnson-Steigelman, H.T.; Lu, E.D.; Saldin, D.K.; Eastwood, D.S.; Atkinson, D.; Tanner, B.K.; Hase, T.P.A.; Van Kampen, M.; Hjorvarsson, B.; Brown, S.; Thompson, P.; Konovalov, O.; Saint-Martin, E.; Daillant, J.; Luzet, D.; Szlachetko, J.; Barrett, R.; Berset, M.; Dousse, J.C.; Fennane, K.; Hoszowska, J.; Kubala-Kukus, A.; Pajek, M.; Szlachetko, M.; Monaco, A.; Chumakov, A.; Crichton, W.; Van Buerck, I.; Wortmann, G.; Meyer, A.; Ponkratz, U.; Ruffer, R.; Sakurai, Y.; Hiraoka, N.; Itou, M.; Buslaps, T.; Honkimki, V.; Maeno, Y.; Collart, E.; Shukla, A.; Rueff, J.P.; Leininger, Ph.; Ishii, H.; Cai, Y.; Cheong, S.W.; Martins, R.M.S.; Schell, N.; Beckers, M.; Silva, R.; Braz Fernandes, F.M.; Acapito, F.; Seta, M. de; Capelini, G.; Giorgi, M.; Schorr, G.; Geandier, G.; Alves Marques, M.; Barros Marquesa, M.I. de; Cabaco, M.I.; Gaspara, A.M.; Marques, M.P.M.; Amado, A.M.; Amorim da Costa, A.M.; Bruneseaux, F.; Weisbecker, P.; Brandao, M.J.; Aeby-Gautier, E.; Simmonds, H.; Lei, C.; Das, A.; Trolley, D.; Thomas, H.E.; Macdonald, J.E.; Wiegart, L.; Tolan, M.; Struth, B.; Petukhov, A.V.; Thijssen, J.H.J.; Hart, D.C.; Imhof, A.; Van Blaaderen, A.; Dolbnya, I.P.; Snigirev, A.; Mossaid, A.; Snigireva, I.; Reconditi, M.; Brunello, E

    2005-07-01

    This document gathers the posters presented on the one day and a half long plenary meeting workshop. This meeting workshop is a privileged forum where ESRF users can exchange their views on the latest scientific and technical development involving synchrotron radiation. One poster deals with the investigation of colloid composition and uranium bond structure to see whether the migration of contaminants from abandoned mines could be stimulated or attenuated by colloids. Another poster is dedicated to the investigation of the uranium speciation in covered mine tailings by a combination of micro-spectroscopic and wet chemical approaches. 2 posters deal with the contribution of synchrotron radiation to radiotherapy.

  12. 15. ESRF users meeting

    International Nuclear Information System (INIS)

    Fotis C, Kafatos; Ulrich, K.U.; Weib, S.; Rossberg, A.; Scheinost, A.C.; Foerstendorf, H.; Zanker, H.; Meyerheim, H.L.; Sander, D.; Popescu, R.; Kirschner, J.; Robach, O.; Ferrer, S.; Lyman, P.F.; Shneerson, V.L.; Fung, R.; Harder, R.J.; Parihar, S.S.; Johnson-Steigelman, H.T.; Lu, E.D.; Saldin, D.K.; Eastwood, D.S.; Atkinson, D.; Tanner, B.K.; Hase, T.P.A.; Van Kampen, M.; Hjorvarsson, B.; Brown, S.; Thompson, P.; Konovalov, O.; Saint-Martin, E.; Daillant, J.; Luzet, D.; Szlachetko, J.; Barrett, R.; Berset, M.; Dousse, J.C.; Fennane, K.; Hoszowska, J.; Kubala-Kukus, A.; Pajek, M.; Szlachetko, M.; Monaco, A.; Chumakov, A.; Crichton, W.; Van Buerck, I.; Wortmann, G.; Meyer, A.; Ponkratz, U.; Ruffer, R.; Sakurai, Y.; Hiraoka, N.; Itou, M.; Buslaps, T.; Honkimki, V.; Maeno, Y.; Collart, E.; Shukla, A.; Rueff, J.P.; Leininger, Ph.; Ishii, H.; Cai, Y.; Cheong, S.W.; Martins, R.M.S.; Schell, N.; Beckers, M.; Silva, R.; Braz Fernandes, F.M.; Acapito, F.; Seta, M. de; Capelini, G.; Giorgi, M.; Schorr, G.; Geandier, G.; Alves Marques, M.; Barros Marquesa, M.I. de; Cabaco, M.I.; Gaspara, A.M.; Marques, M.P.M.; Amado, A.M.; Amorim da Costa, A.M.; Bruneseaux, F.; Weisbecker, P.; Brandao, M.J.; Aeby-Gautier, E.; Simmonds, H.; Lei, C.; Das, A.; Trolley, D.; Thomas, H.E.; Macdonald, J.E.; Wiegart, L.; Tolan, M.; Struth, B.; Petukhov, A.V.; Thijssen, J.H.J.; Hart, D.C.; Imhof, A.; Van Blaaderen, A.; Dolbnya, I.P.; Snigirev, A.; Mossaid, A.; Snigireva, I.; Reconditi, M.; Brunello, E.

    2005-01-01

    This document gathers the posters presented on the one day and a half long plenary meeting workshop. This meeting workshop is a privileged forum where ESRF users can exchange their views on the latest scientific and technical development involving synchrotron radiation. One poster deals with the investigation of colloid composition and uranium bond structure to see whether the migration of contaminants from abandoned mines could be stimulated or attenuated by colloids. Another poster is dedicated to the investigation of the uranium speciation in covered mine tailings by a combination of micro-spectroscopic and wet chemical approaches. 2 posters deal with the contribution of synchrotron radiation to radiotherapy

  13. Metabarcoding Analysis of Phytophthora Diversity Using Genus-Specific Primers and 454 Pyrosequencing.

    Science.gov (United States)

    Prigigallo, Maria I; Abdelfattah, Ahmed; Cacciola, Santa O; Faedda, Roberto; Sanzani, Simona M; Cooke, David E L; Schena, L

    2016-03-01

    A metabarcoding method based on genus-specific primers and 454 pyrosequencing was utilized to investigate the genetic diversity of Phytophthora spp. in soil and root samples of potted plants, from eight nurseries. Pyrosequencing enabled the detection of 25 Phytophthora phylotypes distributed in seven different clades and provided a much higher resolution than a corresponding cloning/Sanger sequencing approach. Eleven of these phylotypes, including P. cactorum, P. citricola s.str., P. palmivora, P. palmivora-like, P. megasperma or P. gonapodyides, P. ramorum, and five putative new Phytophthora species phylogenetically related to clades 1, 2, 4, 6, and 7 were detected only with the 454 pyrosequencing approach. We also found an additional 18 novel records of a phylotype in a particular nursery that were not detected with cloning/Sanger sequencing. Several aspects confirmed the reliability of the method: (i) many identical sequence types were identified independently in different nurseries, (ii) most sequence types identified with 454 pyrosequencing were identical to those from the cloning/Sanger sequencing approach and/or perfectly matched GenBank deposited sequences, and (iii) the divergence noted between sequence types of putative new Phytophthora species and all other detected sequences was sufficient to rule out sequencing errors. The proposed method represents a powerful tool to study Phytophthora diversity providing that particular attention is paid to the analysis of 454 pyrosequencing raw read sequences and to the identification of sequence types.

  14. Pyrosequencing for Rapid Detection of Mycobacterium tuberculosis Resistance to Rifampin, Isoniazid, and Fluoroquinolones ▿

    Science.gov (United States)

    Bravo, Lulette Tricia C.; Tuohy, Marion J.; Ang, Concepcion; Destura, Raul V.; Mendoza, Myrna; Procop, Gary W.; Gordon, Steven M.; Hall, Geraldine S.; Shrestha, Nabin K.

    2009-01-01

    After isoniazid and rifampin (rifampicin), the next pivotal drug class in Mycobacterium tuberculosis treatment is the fluoroquinolone class. Mutations in resistance-determining regions (RDR) of the rpoB, katG, and gyrA genes occur with frequencies of 97%, 50%, and 85% among M. tuberculosis isolates resistant to rifampin, isoniazid, and fluoroquinolones, respectively. Sequences are highly conserved, and certain mutations correlate well with phenotypic resistance. We developed a pyrosequencing assay to determine M. tuberculosis genotypic resistance to rifampin, isoniazid, and fluoroquinolones. We characterized 102 M. tuberculosis clinical isolates from the Philippines for susceptibility to rifampin, isoniazid, and ofloxacin by using the conventional submerged-disk proportion method and validated our pyrosequencing assay using these isolates. DNA was extracted and amplified by using PCR primers directed toward the RDR of the rpoB, katG, and gyrA genes, and pyrosequencing was performed on the extracts. The M. tuberculosis H37Rv strain (ATCC 25618) was used as the reference strain. The sensitivities and specificities of pyrosequencing were 96.7% and 97.3%, 63.8% and 100%, and 70.0% and 100% for the detection of resistance to rifampin, isoniazid, and ofloxacin, respectively. Pyrosequencing is thus a rapid and accurate method for detecting M. tuberculosis resistance to these three drugs. PMID:19846642

  15. US EPA's SPECIATE 4.4 Database: Development and Uses

    Science.gov (United States)

    SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, volatile o...

  16. Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim.

    Science.gov (United States)

    Balzer, Susanne; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge

    2010-09-15

    The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to approximately 500 base pairs and are thus approaching read lengths obtained from traditional Sanger sequencing. Study design of sequencing projects would benefit from being able to simulate experiments. We explore 454 raw data to investigate its characteristics and derive empirical distributions for the flow values generated by pyrosequencing. Based on our findings, we implement Flowsim, a simulator that generates realistic pyrosequencing data files of arbitrary size from a given set of input DNA sequences. We finally use our simulator to examine the impact of sequence lengths on the results of concrete whole-genome assemblies, and we suggest its use in planning of sequencing projects, benchmarking of assembly methods and other fields. Flowsim is freely available under the General Public License from http://blog.malde.org/index.php/flowsim/.

  17. Speciation Analysis of Radionuclides in the Environment - NSK-B SPECIATION project report 2009

    DEFF Research Database (Denmark)

    Hou, Xiaolin; Aldahan, Ala; Possnert, Göran

    . Speciation of radionuclides in soils and sediments includes: Sequential extraction of radionuclides in sediments and of trace elements in soil samples. Sequential extraction of radionuclides in aerosols and particles has also been performed. Further-more, sorption experiments have been performed......, sediments, particles); and (3) Intercomparison excise for speciation analysis of radionu-clides in soil and sediment. This report summarizes the work completed in the project partners’ laboratories, Method developments include: Development of an rapid and in-suit separation method for the speciation...... analysis of 129I in seawater samples; Development of a simple method for the speciation analysis of 129I in fresh water and seawater samples; Development of an on-line HPLC-ICP-MS method for the direct speciation analysis of 127I in water and leachate samples; Speciation of radionuclides in water includes...

  18. Speciation analysis of radionuclides in the environment - NSK-B SPECIATION project report 2009

    International Nuclear Information System (INIS)

    Hou, X.; Aldahan, A.; Possnert, G.; Lujaniene, G.; Lehto, J.; Skipperud, L.; Lind, O.C.; Salbu, B.

    2009-10-01

    The second stage of the NKS-B project SPECIATION was complemented in 2008-2009, which mainly focus on three aspects: (1) Further improvement and development of methods for speciation analysis of radionuclides; (2) Investigation of speciation of some radionuclides in the environment (water, sediments, particles); and (3) Intercomparison excise for speciation analysis of radionuclides in soil and sediment. This report summarizes the work completed in the project partners' laboratories. Method developments include: Development of an rapid and in-suit separation method for the speciation analysis of 129I in seawater samples; Development of a simple method for the speciation analysis of 129I in fresh water and seawater samples; Development of an on-line HPLC-ICP-MS method for the direct speciation analysis of 127I in water and leachate samples; Speciation of radionuclides in water includes: Speciation of 129I and 127I in time-series precipitation samples collected in Denmark 2001-2006 and its application for the investigation of geochemistry and atmospheric chemistry of iodine, Speciation of radionuclides in Ob and Yenisey Rivers, and Speciation of 129I and 127I in Lake Heimdalen water. Speciation of radionuclides in soils and sediments includes: Sequential extraction of radionuclides in sediments and of trace elements in soil samples. Sequential extraction of radionuclides in aerosols and particles has also been performed. Furthermore, sorption experiments have been performed to investigate the association of Pu, Am and Cs with different geological materials. The intercomparison exercises included sequential extraction of Pu, 137Cs, U, Th, and 129I in one soil and one sediment standard reference materials (NIST-4354, IAEA-375) and Pu in sediment collected from the Lake Heimdalen, Norway. (author)

  19. Speciation analysis of radionuclides in the environment - NSK-B SPECIATION project report 2009

    Energy Technology Data Exchange (ETDEWEB)

    Hou, X. (Technical Univ. of Denmark, Risoe National Lab. for Sustainable Energy, Roskilde (Denmark)); Aldahan, A. (Uppsala Univ., Dept. of Earth Science (Sweden)); Possnert, G. (Uppsala Univ., Tandem Lab. (Sweden)); Lujaniene, G. (Univ. of Helsinki, Lab. of Radiochemistry (Finland)); Lehto, J. (Institute of Physics (Lithuania)); Skipperud, L.; Lind, O.C.; Salbu, B. (Norwegian Univ. of Life Sciences, Isotope Lab., AAs (Norway))

    2009-10-15

    The second stage of the NKS-B project SPECIATION was complemented in 2008-2009, which mainly focus on three aspects: (1) Further improvement and development of methods for speciation analysis of radionuclides; (2) Investigation of speciation of some radionuclides in the environment (water, sediments, particles); and (3) Intercomparison excise for speciation analysis of radionuclides in soil and sediment. This report summarizes the work completed in the project partners' laboratories. Method developments include: Development of an rapid and in-suit separation method for the speciation analysis of 129I in seawater samples; Development of a simple method for the speciation analysis of 129I in fresh water and seawater samples; Development of an on-line HPLC-ICP-MS method for the direct speciation analysis of 127I in water and leachate samples; Speciation of radionuclides in water includes: Speciation of 129I and 127I in time-series precipitation samples collected in Denmark 2001-2006 and its application for the investigation of geochemistry and atmospheric chemistry of iodine, Speciation of radionuclides in Ob and Yenisey Rivers, and Speciation of 129I and 127I in Lake Heimdalen water. Speciation of radionuclides in soils and sediments includes: Sequential extraction of radionuclides in sediments and of trace elements in soil samples. Sequential extraction of radionuclides in aerosols and particles has also been performed. Furthermore, sorption experiments have been performed to investigate the association of Pu, Am and Cs with different geological materials. The intercomparison exercises included sequential extraction of Pu, 137Cs, U, Th, and 129I in one soil and one sediment standard reference materials (NIST-4354, IAEA-375) and Pu in sediment collected from the Lake Heimdalen, Norway. (author)

  20. Radionuclide speciation in the environment: a review

    International Nuclear Information System (INIS)

    Moulin, V.; Moulin, C.

    2001-01-01

    Speciation determination is of prime importance to explain and evaluate the mobility, the toxicity and the risk resulting from the presence of trace elements in natural systems, in particular in the case of radionuclides, in the framework of environment and waste management purposes. The present paper will then focus more specifically on the physico-chemical speciation of radionuclides, and more particularly of actinides, in the environment, with emphasis on the behavior in solution: from a chemical point of view (with important ligands including colloidal phases) using experimental data and speciation calculations, as well as from a more technical point of view (with analytical methods for in situ speciation determination and thermodynamic data determination). A review of recent papers (mainly from CEA) is presented. (orig.)

  1. Pb speciation results in amended soils

    Data.gov (United States)

    U.S. Environmental Protection Agency — The dataset shows the distribution of Pb phases resulting from various amendments to change Pb speciation. This dataset is associated with the following publication:...

  2. Speciation of radionuclides in the environment

    International Nuclear Information System (INIS)

    Gunten, H.R. von; Benes, P.

    1994-02-01

    Methods for the determination of the speciation of radionuclides in aerosols, in aquatic solutions, in sediments, soils and rocks are reviewed. At present, most of the results about speciation are deduced from model calculations, model experiments, and separation of species (forms) of radionuclides, e.g., by sequential extraction procedures. Methods of direct determination of speciation of radionuclides (e.g. by laser induced spectroscopy) are in general not yet sensitive enough for a measurement of the very low concentrations of radionuclides in the environment. The methodological part of this paper is followed by a review of the very abundant literature about speciation of important radionuclides in the environment, i.e. in the atmosphere, hydrosphere and lithosphere. The review does not include the biosphere. Literature up to spring 1993 is included (with a few more recent additions). (author)

  3. Evolution: sympatric speciation the eusocial way

    DEFF Research Database (Denmark)

    Boomsma, Jacobus Jan; Nash, David Richard

    2014-01-01

    Sympatric speciation normally requires particular conditions of ecological niche differentiation. However, ant social parasites have been suspected to arise sympatrically, because (dis)loyalty to eusocial kin-structures induces disruptive selection for dispersal and inbreeding. A new study docume...

  4. Dearborn GC-MS organic speciation data

    Data.gov (United States)

    U.S. Environmental Protection Agency — Ambient particulate matter organic speciation data from July - August, 2011. This dataset is associated with the following publication: Lynam, M., T. Dvonch, J....

  5. Aerosol Chemical Speciation Monitor (ACSM) Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Thomas B. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2017-08-15

    The Aerodyne Aerosol Chemical Speciation Monitor (ACSM) measures particle mass loading and chemical composition in real time for non-refractory sub-micron aerosol particles. The ACSM is designed for long-term unattended deployment and routine monitoring applications.

  6. Research on the chemical speciation of actinides

    International Nuclear Information System (INIS)

    Jung, Euo Chang; Park, K. K.; Cho, H. R.

    2012-04-01

    A demand for the safe and effective management of spent nuclear fuel and radioactive waste generated from nuclear power plant draws increasing attention with the growth of nuclear power industry. The objective of this project is to establish the basis of research on the actinide chemistry by using highly sensitive and advanced laser-based spectroscopic systems. Researches on the chemical speciation of actinides are prerequisite for the development of technologies related to nuclear fuel cycles, especially, such as the safe management of high level radioactive wastes and the chemical examination of irradiated nuclear fuels. For supporting these technologies, laser-based spectroscopies have been applied for the chemical speciation of actinide in aqueous solutions and the quantitative analysis of actinide isotopes in spent nuclear fuels. In this report, results on the following subjects have been summarized. Development of TRLFS technology for the chemical speciation of actinides, Development of laser-induced photo-acoustic spectroscopy (LPAS) system, Application of LIBD technology to investigate dynamic behaviors of actinides dissolution reactions, Development of nanoparticle analysis technology in groundwater using LIBD, Chemical speciation of plutonium complexes by using a LWCC system, Development of LIBS technology for the quantitative analysis of actinides, Evaluation on the chemical reactions between actinides and humic substances, Spectroscopic speciation of uranium-ligand complexes in aqueous solution, Chemical speciation of actinides adsorbed on metal oxides surfaces

  7. Research on the chemical speciation of actinides

    International Nuclear Information System (INIS)

    Jung, Euo Chang; Park, K. K.; Cho, H. R.

    2010-04-01

    A demand for the safe and effective management of spent nuclear fuel and radioactive waste generated from nuclear power plant draws increasing attention with the growth of nuclear power industry. The objective of this project is to establish the basis of research on the actinide chemistry by using advanced laser-based highly sensitive spectroscopic systems. Researches on the chemical speciation of actinides are prerequisite for the development of technologies related to nuclear fuel cycles, especially, such as the safe management of high level radioactive wastes and the chemical examination of irradiated nuclear fuels. For supporting these technologies, laser-based spectroscopies have been performed for the chemical speciation of actinide in an aqueous solutions and the quantitative analysis of actinide isotopes in spent nuclear fuels. In this report, results on the following subjects have been summarized. (1) Development of TRLFS technology for chemical speciation of actinides, (2) Development of LIBD technology for measuring solubility of actinides, (3) Chemical speciation of plutonium complexes by using a LWCC system, (4) Development of LIBS technology for the quantitative analysis of actinides, (5) Development of technology for the chemical speciation of actinides by CE, (6) Evaluation on the chemical reactions between actinides and humic substances, (7) Chemical speciation of actinides adsorbed on metal oxides surfaces, (8) Determination of actinide source terms of spent nuclear fuel

  8. Pyrosequencing of environmental soil samples reveals biodiversity of the Phytophthora resident community in chestnut forests.

    Science.gov (United States)

    Vannini, Andrea; Bruni, Natalia; Tomassini, Alessia; Franceschini, Selma; Vettraino, Anna Maria

    2013-09-01

    Pyrosequencing analysis was performed on soils from Italian chestnut groves to evaluate the diversity of the resident Phytophthora community. Sequences analysed with a custom database discriminated 15 pathogenic Phytophthoras including species common to chestnut soils, while a total of nine species were detected with baiting. The two sites studied differed in Phytophthora diversity and the presence of specific taxa responded to specific ecological traits of the sites. Furthermore, some species not previously recorded were represented by a discrete number of reads; among these species, Phytophthora ramorum was detected at both sites. Pyrosequencing was demonstrated to be a very sensitive technique to describe the Phytophthora community in soil and was able to detect species not easy to be isolated from soil with standard baiting techniques. In particular, pyrosequencing is an highly efficient tool for investigating the colonization of new environments by alien species, and for ecological and adaptive studies coupled with biological detection methods. This study represents the first application of pyrosequencing for describing Phytophthoras in environmental soil samples. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  9. A sensitive issue: Pyrosequencing as a valuable forensic SNP typing platform

    DEFF Research Database (Denmark)

    Harrison, C.; Musgrave-Brown, E.; Bender, K.

    2006-01-01

    Analysing minute amounts of DNA is a routine challenge in forensics in part due to the poor sensitivity of an instrument and its inability to detect results from forensic samples. In this study, the sensitivity of the Pyrosequencing method is investigated using varying concentrations of DNA and f...

  10. Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

    Science.gov (United States)

    Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

    2015-01-01

    Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

  11. Selfish X chromosomes and speciation.

    Science.gov (United States)

    Patten, Manus M

    2017-12-27

    In two papers published at about the same time almost thirty years ago, Frank (Evolution, 45, 1991a, 262) and Hurst and Pomiankowski (Genetics, 128, 1991, 841) independently suggested that divergence of meiotic drive systems-comprising genes that cheat meiosis and genes that suppress this cheating-might provide a general explanation for Haldane's rule and the large X-effect in interspecific hybrids. Although at the time, the idea was met with skepticism and a conspicuous absence of empirical support, the tide has since turned. Some of the clearest mechanistic explanations we have for hybrid male sterility involve meiotic drive systems, and several other cases of hybrid sterility are suggestive of a role for meiotic drive. In this article, I review these ideas and their descendants and catalog the current evidence for the meiotic drive model of speciation. In addition, I suggest that meiotic drive is not the only intragenomic conflict to involve the X chromosome and contribute to hybrid incompatibility. Sexually and parentally antagonistic selection pressures can also pit the X chromosome and autosomes against each other. The resulting intragenomic conflicts should lead to co-evolution within populations and divergence between them, thus increasing the likelihood of incompatibilities in hybrids. I provide a sketch of these ideas and interpret some empirical patterns in the light of these additional X-autosome conflicts. © 2017 John Wiley & Sons Ltd.

  12. Liquid phase microextraction for the analysis of trace elements and their speciation

    International Nuclear Information System (INIS)

    Hu, Bin; He, Man; Chen, Beibei; Xia, Linbo

    2013-01-01

    Trace/ultra-trace elements and their speciation analysis in complex matrices usually require sample preparation procedures to achieve sample clean-up and analyte preconcentration. Sample preparation is often the bottleneck in trace elements and their speciation analysis which has a direct impact on accuracy, precision and limits of detection and is often the rate-determining step of the analytical process. Recent trends in sample preparation include miniaturization, automation, high-throughput performance and reduction in solvent/sample consumption and operation time. Liquid-phase microextraction (LPME) technique as a novel and promising alternative in sample preparation can meet these requirements and has become a very efficient sample preparation technique. This review updates the state of art of LPME for trace elements and their speciation analysis and discusses its promising prospects. The major thrust of the article highlights the applications of LPME including single-drop microextraction (SDME), hollow fiber-liquid phase microextraction (HF-LPME), dispersive liquid liquid microextraction (DLLME) and solidified floating organic drop microextraction (SFODME) to the fields of elemental and their speciation analysis by atomic spectrometry-based methods, especially inductively coupled plasma mass spectrometry. General and specific concepts, different extraction formats and characteristics of LPME are described and compared, along with examples of recent innovations and applications presented to demonstrate its potential for trace elements and their speciation analysis in biological and environmental fields. Moreover, the application potential and an outlook on the combination of LPME and atomic spectrometry-based techniques for inorganic analysis are commentated. - Highlights: • The state of art of LPME for trace elements and their speciation analysis is updated. • Different extraction formats of LPME are described. • The application potential and future

  13. Speciation distribution and mass balance of copper and zinc in urban rain, sediments, and road runoff.

    Science.gov (United States)

    Zuo, Xiaojun; Fu, Dafang; Li, He

    2012-11-01

    Heavy metal pollution in road runoff had caused widespread concern since the last century. However, there are little references on metal speciation in multiple environmental media (e.g., rain, road sediments, and road runoff). Our research targeted the investigation of metal speciation in rain, road sediments, and runoff; the analysis of speciation variation and mass balance of metals among rain, road sediments, and runoff; the selection of main factors by principal component analysis (PCA); and the establishment of equation to evaluate the impact of rain and road sediments to metals in road runoff. Sequential extraction procedure contains five steps for the chemical fractionation of metals. Flame atomic absorption spectrometry (Shimadzu, AA-6800) was used to determine metal speciation concentration, as well as the total and dissolved fractions. The dissolved fractions for both Cu and Zn were dominant in rain. The speciation distribution of Zn was different from that of Cu in road sediments, while speciation distribution of Zn is similar to that of Cu in runoff. The bound to carbonates for both Cu and Zn in road sediments were prone to be dissolved by rain. The levels of Cu and Zn in runoff were not obviously influenced by rain, but significantly influenced by road sediments. The masses for both Cu and Zn among rain, road sediments, and road runoff approximately meet the mass balance equation for all rainfall patterns. Five principal factors were selected for metal regression equation based on PCA, including rainfall, average rainfall intensity, antecedent dry periods, total suspended particles, and temperature. The established regression equations could be used to predict the effect of road runoff on receiving environments.

  14. Bacterial communities in the gut and reproductive organs of Bactrocera minax (Diptera: Tephritidae) based on 454 pyrosequencing.

    Science.gov (United States)

    Wang, Ailin; Yao, Zhichao; Zheng, Weiwei; Zhang, Hongyu

    2014-01-01

    The citrus fruit fly Bactrocera minax is associated with diverse bacterial communities. We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax. Our dataset consisted of 100,749 reads with an average length of 400 bp. The saturated rarefaction curves and species richness indices indicate that the sampling was comprehensive. We found highly diverse bacterial communities, with individual sample containing approximately 361 microbial operational taxonomic units (OTUs). A total of 17 bacterial phyla were obtained from the flies. A phylogenetic analysis of 16S rDNA revealed that Proteobacteria was dominant in all samples (75%-95%). Actinobacteria and Firmicutes were also commonly found in the total clones. Klebsiella, Citrobacter, Enterobacter, and Serratia were the major genera. However, bacterial diversity (Chao1, Shannon and Simpson indices) and community structure (PCA analysis) varied across samples. Female ovary has the most diverse bacteria, followed by male testis, and the bacteria diversity of reproductive organs is richer than that of the gut. The observed variation can be caused by sex and tissue, possibly to meet the host's physiological demands.

  15. Bacterial communities in the gut and reproductive organs of Bactrocera minax (Diptera: Tephritidae based on 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Ailin Wang

    Full Text Available The citrus fruit fly Bactrocera minax is associated with diverse bacterial communities. We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax. Our dataset consisted of 100,749 reads with an average length of 400 bp. The saturated rarefaction curves and species richness indices indicate that the sampling was comprehensive. We found highly diverse bacterial communities, with individual sample containing approximately 361 microbial operational taxonomic units (OTUs. A total of 17 bacterial phyla were obtained from the flies. A phylogenetic analysis of 16S rDNA revealed that Proteobacteria was dominant in all samples (75%-95%. Actinobacteria and Firmicutes were also commonly found in the total clones. Klebsiella, Citrobacter, Enterobacter, and Serratia were the major genera. However, bacterial diversity (Chao1, Shannon and Simpson indices and community structure (PCA analysis varied across samples. Female ovary has the most diverse bacteria, followed by male testis, and the bacteria diversity of reproductive organs is richer than that of the gut. The observed variation can be caused by sex and tissue, possibly to meet the host's physiological demands.

  16. How Facilitation May Interfere with Ecological Speciation

    Directory of Open Access Journals (Sweden)

    P. Liancourt

    2012-01-01

    Full Text Available Compared to the vast literature linking competitive interactions and speciation, attempts to understand the role of facilitation for evolutionary diversification remain scarce. Yet, community ecologists now recognize the importance of positive interactions within plant communities. Here, we examine how facilitation may interfere with the mechanisms of ecological speciation. We argue that facilitation is likely to (1 maintain gene flow among incipient species by enabling cooccurrence of adapted and maladapted forms in marginal habitats and (2 increase fitness of introgressed forms and limit reinforcement in secondary contact zones. Alternatively, we present how facilitation may favour colonization of marginal habitats and thus enhance local adaptation and ecological speciation. Therefore, facilitation may impede or pave the way for ecological speciation. Using a simple spatially and genetically explicit modelling framework, we illustrate and propose some first testable ideas about how, when, and where facilitation may act as a cohesive force for ecological speciation. These hypotheses and the modelling framework proposed should stimulate further empirical and theoretical research examining the role of both competitive and positive interactions in the formation of incipient species.

  17. Speciation of zinc in contaminated soils

    International Nuclear Information System (INIS)

    Stephan, Chadi H.; Courchesne, Francois; Hendershot, William H.; McGrath, Steve P.; Chaudri, Amar M.; Sappin-Didier, Valerie; Sauve, Sebastien

    2008-01-01

    The chemical speciation of zinc in soil solutions is critical to the understanding of its bioavailability and potential toxic effects. We studied the speciation of Zn in soil solution extracts from 66 contaminated soils representative of a wide range of field conditions in both North America and Europe. Within this dataset, we evaluated the links among the dissolved concentrations of zinc and the speciation of Zn 2+ , soil solution pH, total soil Zn, dissolved organic matter (DOM), soil organic matter (SOM) and the concentrations of different inorganic anions. The solid-liquid partitioning coefficient (K d ) for Zn ranged from 17 to 13,100 L kg -1 soil. The fraction of dissolved Zn bound to DOM varied from 60% to 98% and the soil solution free Zn 2+ varied from 40% to 60% of the labile Zn. Multiple regression equations to predict free Zn 2+ , dissolved Zn and the solid-liquid partitioning of Zn are given for potential use in environmental fate modeling and risk assessment. The multiple regressions also highlight some of the most important soil properties controlling the solubility and chemical speciation of zinc in contaminated soils. - We studied the relationships among the chemical speciation of Zn in soil solution extracts from 66 contaminated soils and various physicochemical properties of the soils

  18. Speciation by Symbiosis: the Microbiome and Behavior.

    Science.gov (United States)

    Shropshire, J Dylan; Bordenstein, Seth R

    2016-03-31

    Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species. Copyright © 2016 Shropshire and Bordenstein.

  19. Speciation from photon to ion detection

    International Nuclear Information System (INIS)

    Moulin, C.

    2001-01-01

    New analytical techniques allowing to perform speciation in the framework of the nuclear fuel cycle are more and more needed. Among them, several laser-based analytical techniques present several advantages (non intrusive). Hence, Thermal Lensing (TL)/Photoacoustic (LIPAS), Time Resolved selective, sensitive Laser-Induced Fluorescence (TRLIF) have been used for actinides/lanthanides interaction and speciation studies in inorganic and organic matrices, Laser Ablation-Optical Emission Spectroscopy (LA-OES or LIBS) for direct studies on solids, liquids,... where in situ measurements (elemental or isotopic) are mandatory. In complementary to these photon-based methods, new ion detection methods such as ElectroSpray-Mass Spectrometry (ES-MS) seems promising for speciation studies. Principle, advantages and limitations as well as results obtained and trends for these different methods will be presented. (author)

  20. Anaerobic Digestion Alters Copper and Zinc Speciation.

    Science.gov (United States)

    Legros, Samuel; Levard, Clément; Marcato-Romain, Claire-Emmanuelle; Guiresse, Maritxu; Doelsch, Emmanuel

    2017-09-19

    Anaerobic digestion is a widely used organic waste treatment process. However, little is known on how it could alter the speciation of contaminants in organic waste. This study was focused on determining the influence of anaerobic digestion on the speciation of copper and zinc, two metals that generally occur at high concentration in organic waste. Copper and zinc speciation was investigated by X-ray absorption spectroscopy in four different raw organic wastes (predigestion) and their digested counterparts (postdigestion, i.e., digestates). The results highlighted an increase in the digestates of the proportion of amorphous or nanostructured copper sulfides as well as amorphous or nanostructured zinc sulfides and zinc phosphate as compared to raw waste. We therefore suggest that the environmental fate of these elements would be different when spreading either digestates or raw waste on cropland.

  1. Loss of speciation rate will impoverish future diversity

    OpenAIRE

    Rosenzweig, Michael L.

    2001-01-01

    Human activities have greatly reduced the amount of the earth's area available to wild species. As the area they have left declines, so will their rates of speciation. This loss of speciation will occur for two reasons: species with larger geographical ranges speciate faster; and loss of area drives up extinction rates, thus reducing the number of species available for speciation. Theory predicts steady states in species diversity, and fossils suggest that these have t...

  2. Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

    DEFF Research Database (Denmark)

    Rask, Thomas Salhøj; Petersen, Bent; Chen, Donald S.

    2016-01-01

    . The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data....... This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene...... family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon...

  3. Analysis of genetically modified organisms by pyrosequencing on a portable photodiode-based bioluminescence sequencer.

    Science.gov (United States)

    Song, Qinxin; Wei, Guijiang; Zhou, Guohua

    2014-07-01

    A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array. Pyrosequencing on eight genes (zSSIIb, Bt11 and Bt176 gene of genetically modified maize; Lectin, 35S-CTP4, CP4EPSPS, CaMV35S promoter and NOS terminator of the genetically modified Roundup ready soya) was successfully detected with this instrument. The corresponding limit of detection (LOD) was 0.01% with 35 PCR cycles. The maize and soya available from three different provenances in China were detected. The results indicate that pyrosequencing using the small size of the detector is a simple, inexpensive, and reliable way in a farm/field test of GMO analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. The development of chemical speciation analysis

    International Nuclear Information System (INIS)

    Martin, R.; Santana, J.L.; Lima, L.; De La Rosa, D.; Melchor, K.

    2003-01-01

    The knowledge of many metals species on the environmental, its bioaccumulation, quantification and its effect in human body has been studied by a wide researchers groups in the last two decades. The development of speciation analysis has an vertiginous advance close to the developing of novel analytical techniques. Separation and quantification at low level is a problem that's has been afford by a coupling of high resolution chromatographic techniques like HPLC and HRGC with a specific method of detection (ICP-MS or CV-AAS). This methodological approach make possible the success in chemical speciation nowadays

  5. Incidence and Speciation of Candida Species among Non-gravid ...

    African Journals Online (AJOL)

    This study investigated the incidence and speciation of Candida species among non-gravid young females, using commercially available chromogenic Candida speciation media (CHROM agar) for the identification/speciation of medically important yeast and yeastlike organisms in a routine clinical mycology laboratory.

  6. EPAs SPECIATE 4.4 Database: Development and Uses

    Science.gov (United States)

    SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of source category-specific particulate matter (PM), volatile organic gas, and other gas speciation profiles of air pollutant emissions. Abt Associates, Inc. developed SPECIATE 4.4 through a collaborat...

  7. Rapid strategy for screening by pyrosequencing of influenza virus reassortants--candidates for live attenuated vaccines.

    Science.gov (United States)

    Shcherbik, Svetlana V; Pearce, Nicholas C; Levine, Marnie L; Klimov, Alexander I; Villanueva, Julie M; Bousse, Tatiana L

    2014-01-01

    Live attenuated influenza vaccine viruses (LAIVs) can be generated by classical reassortment of gene segments between a cold adapted, temperature sensitive and attenuated Master Donor Virus (MDV) and a seasonal wild-type (wt) virus. The vaccine candidates contain hemagglutinin (HA) and neuraminidase (NA) genes derived from the circulating wt viruses and the remaining six genes derived from the MDV strains. Rapid, efficient selection of the viruses with 6∶2 genome compositions from the large number of genetically different viruses generated during reassortment is essential for the biannual production schedule of vaccine viruses. This manuscript describes a new approach for the genotypic analysis of LAIV reassortant virus clones based on pyrosequencing. LAIV candidate viruses were created by classical reassortment of seasonal influenza A (H3N2) (A/Victoria/361/2011, A/Ohio/02/2012, A/Texas/50/2012) or influenza A (H7N9) (A/Anhui/1/2013) wt viruses with the MDV A/Leningrad/134/17/57(H2N2). Using strain-specific pyrosequencing assays, mixed gene variations were detected in the allantoic progenies during the cloning procedure. The pyrosequencing analysis also allowed for estimation of the relative abundance of segment variants in mixed populations. This semi-quantitative approach was used for selecting specific clones for the subsequent cloning procedures. The present study demonstrates that pyrosequencing analysis is a useful technique for rapid and reliable genotyping of reassortants and intermediate clones during the preparation of LAIV candidates, and can expedite the selection of vaccine virus candidates.

  8. Rapid strategy for screening by pyrosequencing of influenza virus reassortants--candidates for live attenuated vaccines.

    Directory of Open Access Journals (Sweden)

    Svetlana V Shcherbik

    Full Text Available BACKGROUND: Live attenuated influenza vaccine viruses (LAIVs can be generated by classical reassortment of gene segments between a cold adapted, temperature sensitive and attenuated Master Donor Virus (MDV and a seasonal wild-type (wt virus. The vaccine candidates contain hemagglutinin (HA and neuraminidase (NA genes derived from the circulating wt viruses and the remaining six genes derived from the MDV strains. Rapid, efficient selection of the viruses with 6∶2 genome compositions from the large number of genetically different viruses generated during reassortment is essential for the biannual production schedule of vaccine viruses. METHODOLOGY/PRINCIPAL FINDINGS: This manuscript describes a new approach for the genotypic analysis of LAIV reassortant virus clones based on pyrosequencing. LAIV candidate viruses were created by classical reassortment of seasonal influenza A (H3N2 (A/Victoria/361/2011, A/Ohio/02/2012, A/Texas/50/2012 or influenza A (H7N9 (A/Anhui/1/2013 wt viruses with the MDV A/Leningrad/134/17/57(H2N2. Using strain-specific pyrosequencing assays, mixed gene variations were detected in the allantoic progenies during the cloning procedure. The pyrosequencing analysis also allowed for estimation of the relative abundance of segment variants in mixed populations. This semi-quantitative approach was used for selecting specific clones for the subsequent cloning procedures. CONCLUSIONS/SIGNIFICANCE: The present study demonstrates that pyrosequencing analysis is a useful technique for rapid and reliable genotyping of reassortants and intermediate clones during the preparation of LAIV candidates, and can expedite the selection of vaccine virus candidates.

  9. Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets.

    OpenAIRE

    Carda Diéguez, Miguel; Mira, Alex; Fouz Rodríguez, Belén

    2014-01-01

    The routine use of chemotherapy to control bacterial diseases in aquatic populations has resulted in the development and spread of antibiotic resistance. The inclusion of immunostimulants in fish diets (functional diets) is one of the main strategies to solve this threat. This study aimed to analyse the intestinal microbiota of cultured European sea bass (Dicentrarchus labrax) fed two functional diets applying pyrosequencing of PCR-amplified 16S rRNA gene. Quality-filtered reads were assigned...

  10. Development and characterization of microsatellite markers from the humivorous termite Cavitermes tuberosus (Isoptera: Termitinae) using pyrosequencing technology

    Czech Academy of Sciences Publication Activity Database

    Fournier, D.; Hanus, Robert; Roisin, Y.

    2015-01-01

    Roč. 7, č. 2 (2015), s. 521-524 ISSN 1877-7252 Institutional support: RVO:61388963 Keywords : Cavitermes tuberosus * termite * microsatellite * pyrosequencing * population genetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.446, year: 2015

  11. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.; Yang, J.; Bougouffa, S.; Wang, Y.; Batang, Zenon B.; Tian, R.; Al-Suwailem, A.; Qian, P.-Y.

    2012-01-01

    -pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than

  12. Actinide speciation in the environment

    International Nuclear Information System (INIS)

    Choppin, G.R.

    2007-01-01

    Nuclear test explosions and nuclear reactor wastes and accidents have released large amounts of radioactivity into the environment. Actinide ions in waters often are not in a state of thermodynamic equilibrium and their solubility and migration behavior is related to the form in which the nuclides are introduced into the aquatic system. Chemical speciation, oxidation state, redox reactions, and sorption characteristics are necessary in predicting solubility of the different actinides, their migration behaviors and their potential effects on marine biota. The most significant of these variables is the oxidation state of the metal ion as the simultaneous presence of more than one oxidation state for some actinides in a solution complicates actinide environmental behavior. Both Np(V)O 2 + and Pu(V)O 2 + , the most significant soluble states in natural oxic waters, are relatively noncomplexing and resistant to hydrolysis and subsequent precipitation. The solubility of NpO 2 + can be as high as 10 -4 M while that of PuO 2 + is much more limited by reduction to the insoluble tetravalent species, Pu(OH) 4 , (pK sp ≥56) but which can be present in the pentavalent form in aqautic phases as colloidal material. The solubility of hexavalent UO 2 2+ in sea water is relatively high due to formation of carbonate complexes. The insoluble trivalent americium hydroxocarbonate, Am(OH)(CO 3 ) is the limiting species for the solubility of Am(III) in sea water. Thorium(IV) is present as Th(OH) 4 , in colloidal form. The chemistry of actinide ions in the environment is reviewed to show the spectrum of reactions that can occur in natural waters which must be considered in assessing the environmental behavior of actinides. Much is understood about sorption of actinides on surfaces, the mode of migration of actinides in such waters and the potential effects of these radioactive species on marine biota, but much more understanding of the behavior of the actinides in the environment is

  13. Potential human pathogenic bacteria in a mixed urban watershed as revealed by pyrosequencing.

    Directory of Open Access Journals (Sweden)

    A Mark Ibekwe

    Full Text Available Current microbial source tracking (MST methods for water depend on testing for fecal indicator bacterial counts or specific marker gene sequences to identify fecal contamination where potential human pathogenic bacteria could be present. In this study, we applied 454 high-throughput pyrosequencing to identify bacterial pathogen DNA sequences, including those not traditionally monitored by MST and correlated their abundances to specific sources of contamination such as urban runoff and agricultural runoff from concentrated animal feeding operations (CAFOs, recreation park area, waste-water treatment plants, and natural sites with little or no human activities. Samples for pyrosequencing were surface water, and sediment collected from 19 sites. A total of 12,959 16S rRNA gene sequences with average length of ≤400 bp were obtained, and were assigned to corresponding taxonomic ranks using ribosomal database project (RDP, Classifier and Greengenes databases. The percent of total potential pathogens were highest in urban runoff water (7.94%, agricultural runoff sediment (6.52%, and Prado Park sediment (6.00%, respectively. Although the numbers of DNA sequence tags from pyrosequencing were very high for the natural site, corresponding percent potential pathogens were very low (3.78-4.08%. Most of the potential pathogenic bacterial sequences identified were from three major phyla, namely, Proteobacteria, Bacteroidetes, and Firmicutes. The use of deep sequencing may provide improved and faster methods for the identification of pathogen sources in most watersheds so that better risk assessment methods may be developed to enhance public health.

  14. Pyrosequencing analysis of the gyrB gene to differentiate bacteria responsible for diarrheal diseases.

    Science.gov (United States)

    Hou, X-L; Cao, Q-Y; Jia, H-Y; Chen, Z

    2008-07-01

    Pathogens causing acute diarrhea include a large variety of species from Enterobacteriaceae and Vibrionaceae. A method based on pyrosequencing was used here to differentiate bacteria commonly associated with diarrhea in China; the method is targeted to a partial amplicon of the gyrB gene, which encodes the B subunit of DNA gyrase. Twenty-eight specific polymorphic positions were identified from sequence alignment of a large sequence dataset and targeted using 17 sequencing primers. Of 95 isolates tested, belonging to 13 species within 7 genera, most could be identified to the species level; O157 type could be differentiated from other E. coli types; Salmonella enterica subsp. enterica could be identified at the serotype level; the genus Shigella, except for S. boydii and S. dysenteriae, could also be identified. All these isolates were also subjected to conventional sequencing of a relatively long ( approximately1.2 kb) region of gyrB DNA; these results confirmed those with pyrosequencing. Twenty-two fecal samples were surveyed, the results of which were concordant with culture-based bacterial identification, and the pathogen detection limit with simulated stool specimens was 10(4) CFU/ml. DNA from different pathogens was also mixed to simulate a case of multibacterial infection, and the generated signals correlated well with the mix ratio. In summary, the gyrB-based pyrosequencing approach proved to have significant reliability and discriminatory power for enteropathogenic bacterial identification and provided a fast and effective method for clinical diagnosis.

  15. Pyrosequencing Analysis of Cryogenically Ground Samples from Primary and Secondary/Persistent Endodontic Infections.

    Science.gov (United States)

    Keskin, Cangül; Demiryürek, Ebru Özsezer; Onuk, Ertan Emek

    2017-08-01

    This study aimed to characterize the microbial communities of primary and secondary/persistent endodontic infections using high-throughput pyrosequencing from the pulverized samples. The roots of 20 extracted human teeth with primary endodontic infection and 20 teeth with secondary/persistent endodontic infection were collected. The outer surfaces of the roots were disinfected, and whole roots were cryopulverized. 16S amplicon pyrosequencing data from the DNA extracted from the pulverized root powders were obtained, and microorganism abundance and diversity were calculated. Data were analyzed using statistical and bioinformatic methods. Pyrosequencing analysis resulted a total of 2,606,128 sequences from 40 samples. A total of 15 phyla, 160 genera, and 368 species were detected. No significant difference between primary and secondary/persistent endodontic infections was found regarding the diversity and richness of operational taxonomic units at the phyla, genera, and species levels (P > .005). The present study revealed that the microbial diversity of secondary/persistent endodontic infections did not differ than those of primary endodontic infections. A new archaeal species, Candidatus Nitrosoarchaeum limnia, was detected in root canals of 1 patient with primary endodontic infection for the first time. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  16. Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Engelbrektson, Anna; Ochman, Howard; Hugenholtz, Philip

    2009-08-01

    Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the 'rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on diversity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial diversity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere.

  17. Microbial analysis in primary and persistent endodontic infections by using pyrosequencing.

    Science.gov (United States)

    Hong, Bo-Young; Lee, Tae-Kwon; Lim, Sang-Min; Chang, Seok Woo; Park, Joonhong; Han, Seung Hyun; Zhu, Qiang; Safavi, Kamran E; Fouad, Ashraf F; Kum, Kee Yeon

    2013-09-01

    The aim of this study was to investigate the bacterial community profile of intracanal microbiota in primary and persistent endodontic infections associated with asymptomatic chronic apical periodontitis by using GS-FLX Titanium pyrosequencing. The null hypothesis was that there is no difference in diversity of overall bacterial community profiles between primary and persistent infections. Pyrosequencing analysis from 10 untreated and 8 root-filled samples was conducted. Analysis from 18 samples yielded total of 124,767 16S rRNA gene sequences (with a mean of 6932 reads per sample) that were taxonomically assigned into 803 operational taxonomic units (3% distinction), 148 genera, and 10 phyla including unclassified. Bacteroidetes was the most abundant phylum in both primary and persistent infections. There were no significant differences in bacterial diversity between the 2 infection groups (P > .05). The bacterial community profile that was based on dendrogram showed that bacterial population in both infections was not significantly different in their structure and composition (P > .05). The present pyrosequencing study demonstrates that persistent infections have as diverse bacterial community as primary infections. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  18. Electrochemical metal speciation in colloidal dispersions

    NARCIS (Netherlands)

    Wonders, J.H.A.M.

    1995-01-01

    The term "heavy metals" is connected with toxicity. They form strong complexes with enzymes, other proteins and DNA in living organisms, which causes dysfunctioning and hence poisoning. In combination with the uptake mechanism of the organism, speciation of heavy metal determines the

  19. ARSENIC SPECIATION ANALYSIS IN HUMAN SALIVA

    Science.gov (United States)

    Background: Determination of arsenic species in human saliva is potentially useful for biomonitoring of human exposure to arsenic and for studying arsenic metabolism. However, there is no report on the speciation analysis of arsenic in saliva. Methods: Arsenic species in saliva ...

  20. Magic cues versus magic preferences in speciation

    NARCIS (Netherlands)

    Maan, Martine E.; Seehausen, Ole

    Question: How does divergent natural selection lead to divergence in mating traits and the evolution of reproductive isolation? Background: Ecological speciation of non-allopatric taxa usually requires the evolution of an association between selective mating and the traits underlying ecological

  1. Biogeochemical speciation of Fe in ocean water

    NARCIS (Netherlands)

    Hiemstra, T.; Riemsdijk, van W.H.

    2006-01-01

    The biogeochemical speciation of Fe in seawater has been evaluated using the consistent Non-Ideal Competitive Adsorption model (NICA¿Donnan model). Two types of data sets were used, i.e. Fe-hydroxide solubility data and competitive ligand equilibration/cathodic stripping voltammetry (CLE/CSV) Fe

  2. Biosensor for metal analysis and speciation

    Science.gov (United States)

    Aiken, Abigail M.; Peyton, Brent M.; Apel, William A.; Petersen, James N.

    2007-01-30

    A biosensor for metal analysis and speciation is disclosed. The biosensor comprises an electron carrier immobilized to a surface of an electrode and a layer of an immobilized enzyme adjacent to the electrode. The immobilized enzyme comprises an enzyme having biological activity inhibited by a metal to be detected by the biosensor.

  3. The speciation of iodine in the environment

    International Nuclear Information System (INIS)

    Bulman, R.A.

    1986-01-01

    The speciation of iodine in the environment is discussed under the following topics: (i) sea surface to atmosphere, (ii) chemistry in bulk seawater, (iii) iodine in rocks, (iv) iodine in soils, (v) iodine in plants and (vi) iodine in solidified wastes. (author)

  4. Polarographic validation of chemical speciation models

    International Nuclear Information System (INIS)

    Duffield, J.R.; Jarratt, J.A.

    2001-01-01

    It is well established that the chemical speciation of an element in a given matrix, or system of matrices, is of fundamental importance in controlling the transport behaviour of the element. Therefore, to accurately understand and predict the transport of elements and compounds in the environment it is a requirement that both the identities and concentrations of trace element physico-chemical forms can be ascertained. These twin requirements present the analytical scientist with considerable challenges given the labile equilibria, the range of time scales (from nanoseconds to years) and the range of concentrations (ultra-trace to macro) that may be involved. As a result of this analytical variability, chemical equilibrium modelling has become recognised as an important predictive tool in chemical speciation analysis. However, this technique requires firm underpinning by the use of complementary experimental techniques for the validation of the predictions made. The work reported here has been undertaken with the primary aim of investigating possible methodologies that can be used for the validation of chemical speciation models. However, in approaching this aim, direct chemical speciation analyses have been made in their own right. Results will be reported and analysed for the iron(II)/iron(III)-citrate proton system (pH 2 to 10; total [Fe] = 3 mmol dm -3 ; total [citrate 3- ] 10 mmol dm -3 ) in which equilibrium constants have been determined using glass electrode potentiometry, speciation is predicted using the PHREEQE computer code, and validation of predictions is achieved by determination of iron complexation and redox state with associated concentrations. (authors)

  5. Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains.

    Science.gov (United States)

    Trémeaux, P; Caporossi, A; Ramière, C; Santoni, E; Tarbouriech, N; Thélu, M-A; Fusillier, K; Geneletti, L; François, O; Leroy, V; Burmeister, W P; André, P; Morand, P; Larrat, S

    2016-05-01

    Directly acting antiviral drugs have contributed considerable progress to hepatitis C virus (HCV) treatment, but they show variable activity depending on virus genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the HCV near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV 1a, 1b, 3a and 4a, 16/22) and 45% for recombinant forms RF_2k/1b (5/11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in seven of 13 samples at baseline, in the NS3 (n = 3) or NS5A (n = 4) region. Of these samples, the treatment of one patient included daclatasvir, and that patient experienced a relapse. Virus sequences from pre- and posttreatment samples of four patients who experienced relapse after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proven to be successful for both genotyping and resistance-associated variant detection on several HCV types. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  6. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing.

    Science.gov (United States)

    Ling, Zongxin; Kong, Jianming; Jia, Peng; Wei, Chaochun; Wang, Yuezhu; Pan, Zhiwen; Huang, Wujing; Li, Lanjuan; Chen, Hui; Xiang, Charlie

    2010-10-01

    Oral microbiota plays a vital role in maintaining the homeostasis of oral cavity. Dental caries are among the most common oral diseases in children and pathogenic bacteria contribute to the development of the disease. However, the overall structure of bacterial communities in the oral cavity from children with dental caries has not been explored deeply heretofore. We used high-throughput barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) to examine bacterial diversity of oral microbiota in saliva and supragingival plaques from 60 children aged 3 to 6 years old with and without dental caries from China. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers. As PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results of both approaches were compared. A total of 186,787 high-quality sequences were obtained for evaluating bacterial diversity and 41,905 unique sequences represented all phylotypes. We found that the oral microbiota in children was far more diverse than previous studies reported, and more than 200 genera belonging to ten phyla were found in the oral cavity. The phylotypes in saliva and supragingival plaques were significantly different and could be divided into two distinct clusters (p oral microbiome analyzed by PCR-DGGE and barcoded pyrosequencing was employed to cross validate the data sets. The genera of Streptococcus, Veillonella, Actinomyces, Granulicatella, Leptotrichia, and Thiomonas in plaques were significantly associated with dental caries (p oral microbiota allowed for a better understanding of oral microecosystem, and these pathogenic populations in plaque provide new insights into the etiology of dental caries and suggest new targets for interventions of the disease.

  7. Shotgun pyrosequencing metagenomic analyses of dusts from swine confinement and grain facilities.

    Science.gov (United States)

    Boissy, Robert J; Romberger, Debra J; Roughead, William A; Weissenburger-Moser, Lisa; Poole, Jill A; LeVan, Tricia D

    2014-01-01

    Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e.g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance). The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70%) at the phylum level, Clostridia (44%) at the Class level, and Clostridiales at the Order level (41%). In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the bioinformatic analyses

  8. Shotgun pyrosequencing metagenomic analyses of dusts from swine confinement and grain facilities.

    Directory of Open Access Journals (Sweden)

    Robert J Boissy

    Full Text Available Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e.g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance. The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70% at the phylum level, Clostridia (44% at the Class level, and Clostridiales at the Order level (41%. In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the

  9. Rapid detection and identification of Bacillus anthracis in food using pyrosequencing technology.

    Science.gov (United States)

    Amoako, Kingsley K; Janzen, Timothy W; Shields, Michael J; Hahn, Kristen R; Thomas, Matthew C; Goji, Noriko

    2013-08-01

    The development of advanced methodologies for the detection of Bacillus anthracis has been evolving rapidly since the release of the anthrax spores in the mail in 2001. Recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence based such as pyrosequencing, which has the capability to determine short DNA stretches in real-time using biotinylated PCR amplicons, has potential biodefense applications. Using markers from the virulence plasmids (pXO1 and pXO2) and chromosomal regions, we have demonstrated the power of this technology in the rapid, specific and sensitive detection of B. anthracis spores in food matrices including milk, juice, bottled water, and processed meat. The combined use of immunomagnetic separation and pyrosequencing showed positive detection when liquid foods (bottled water, milk, juice), and processed meat were experimentally inoculated with 6CFU/mL and 6CFU/g, respectively, without an enrichment step. Pyrosequencing is completed in about 60min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence. The entire assay (from sample preparation to sequencing information) can be completed in about 7.5h. A typical run on food samples yielded 67-80bp reads with 94-100% identity to the expected sequence. This sequence based approach is a novel application for the detection of anthrax spores in food with potential application in foodborne bioterrorism response and biodefense involving the use of anthrax spores. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  10. Characterization of microsatellite loci from two-spotted octopus Octopus bimaculatus Verrill 1883 from pyrosequencing reads

    Science.gov (United States)

    Domínguez-Contreras, J. F.; Munguía-Vega, A.; Ceballos-Vázquez, B. P.; Arellano-Martínez, M.; Culver, Melanie

    2014-01-01

    We characterized 22 novel microsatellite loci in the two-spotted octopus Octopus bimaculatus using 454 pyrosequencing reads. All loci were polymorphic and will be used in studies of marine connectivity aimed at increasing sustainability of the resource. The mean number alleles per locus was 13.09 (range 7–19) and observed heterozygosities ranged from 0.50 to 1.00. Four loci pairs were linked and three deviated from Hardy–Weinberg equilibrium. Eighteen and 12 loci were polymorphic in Octopus bimaculoides and Octopus hubbsorum, respectively.

  11. Trace element speciation in the environment

    International Nuclear Information System (INIS)

    Heumann, Klaus G.

    2001-01-01

    The production of methylated heavy metal species in the ocean was reviewed and shown to be correlated with biological parameters demonstrating them to be of biogenic origin. Methods for the determination of the species were discussed. The potential for the use of isotopic spiking either in 'species specific' or 'non-species specific' formats was identified as a valuable tool in the struggle for accuracy, specificity and precision in speciation analysis. The value of using a size exclusion chromatographic method in conjunction with non-species specific spiking IDMS was highlighted with an example illustrating the molecular mass fractions associated with halogenated species from a humic sample. Additional recommendations that the Agency might wish to consider when evaluating its potential role as a service to Member States engaged in speciation activities are also given

  12. Speciation and zoogeography of amphibian in Sundaland

    Directory of Open Access Journals (Sweden)

    Nia Kurniawan

    2015-12-01

    Full Text Available Sundaland is an interesting area to be explored based on its geological history, topography, and climate. Sundaland consists of Penisular Malaysia, Sumatra, Borneo, and Java which experienced some emergence and submergence process in the past. During 1981-2015, most of research in Sundaland found that amphibian family in Sundaland was dominated by Bufonidae, Ranidae, Microhylidae, Megophrydae, Rachophoridae, and Dicroglossidae which experienced lot of speciation in its history. Among of 4 major islands in Sundaland, Borneo has the highest number of species diversity, then Peninsular Malaysia, Sumatra, and Java. During those years, Sumatra and Java got least concern by researcher. Therefore, it is suggested for further study to explore more in Sumatra and Java. Keywords: Sundaland, amphibian, speciation, zoogeography.

  13. Speciation studies of cobalt in sea water

    International Nuclear Information System (INIS)

    Toteja, R.S.D.; Sudersanan, M.; Iyer, R.K.

    1995-01-01

    Recent results on the speciation of cobalt in simulated and actual sea water is reported using ion exchangers. The influence of magnesium ions in affecting the composition of ion exchangers and subsequent interpretation of the results is discussed. The results indicated that Co +2 may predominate in both the simulated and actual sea water and the presence of other constituents in sea water does not affect the nature of complex species present. (author). 2 refs., 3 tabs., 1 fig

  14. Tungsten Speciation in Firing Range Soils

    Science.gov (United States)

    2011-01-01

    satisfactorily, such as: which tungsten mineral phase is present in soil and to what extent is adsorption important in regu- lating soil solution concentrations... soil solution rather than discrete mineral phases. Information provided in this report will assist the following organizations in future decision...the soil solution ERDC TR-11-1 43 must affect tungsten speciation in other ways. The precipitation of soil minerals also would limit tungsten

  15. Detection of polyoma virus in brain tissue of patients with progressive multifocal leukoencephalopathy by real-time PCR and pyrosequencing.

    Science.gov (United States)

    Beck, Rose C; Kohn, Debra J; Tuohy, Marion J; Prayson, Richard A; Yen-Lieberman, Belinda; Procop, Gary W

    2004-03-01

    We evaluated 2 methods, a LightCycler PCR assay and pyrosequencing for the detection of the JC polyoma virus (JCV) in fixed brain tissue of 10 patients with and 3 control patients without progressive multifocal leukoencephalopathy (PML). Nucleic acid extraction was performed after deparaffinization and proteinase K digestion. The LightCycler assay differentiates the BK virus (BKV), JCV, and SV40 using melt curve analysis. Conventional PCR was used with the same primers to generate products for pyrosequencing. Two sequencing primers were used that differentiate the polyoma viruses. Seven of 11 biopsies (1 patient had 2 biopsies) with PML were positive for JCV by real-time PCR and/or PCR/pyrosequencing. Three of 4 remaining biopsies were positive by real-time PCR but had melting points between JCV and SV40. The 4 specimens that were negative or atypical by LightCycler PCR were positive by traditional PCR, but 1 had an amplicon of lower molecular weight by gel electrophoresis. These were shown to represent JCV by at least 1 of the 2 pyrosequencing primers. The biopsies from patients without PML were PCR negative. Both the LightCycler and pyrosequencing assays are useful for confirming JCV in brain biopsies from patients with PML, but variant JCVs may require supplementary methods to confirm JCV infection.

  16. The genetics of speciation by reinforcement.

    Directory of Open Access Journals (Sweden)

    Daniel Ortiz-Barrientos

    2004-12-01

    Full Text Available Reinforcement occurs when natural selection strengthens behavioral discrimination to prevent costly interspecies matings, such as when matings produce sterile hybrids. This evolutionary process can complete speciation, thereby providing a direct link between Darwin's theory of natural selection and the origin of new species. Here, by examining a case of speciation by reinforcement in Drosophila,we present the first high-resolution genetic study of variation within species for female mating discrimination that is enhanced by natural selection. We show that reinforced mating discrimination is inherited as a dominant trait, exhibits variability within species, and may be influenced by a known set of candidate genes involved in olfaction. Our results show that the genetics of reinforced mating discrimination is different from the genetics of mating discrimination between species, suggesting that overall mating discrimination might be a composite phenomenon, which in Drosophila could involve both auditory and olfactory cues. Examining the genetics of reinforcement provides a unique opportunity for both understanding the origin of new species in the face of gene flow and identifying the genetic basis of adaptive female species preferences, two major gaps in our understanding of speciation.

  17. First passage time to allopatric speciation.

    Science.gov (United States)

    Yamaguchi, Ryo; Iwasa, Yoh

    2013-12-06

    Allopatric speciation is a mechanism to evolve reproductive isolation; it is caused by the accumulation of genetic differences between populations while they are geographically isolated. Here, we studied a simple stochastic model for the time until speciation caused by geographical isolation in fragmented populations that experience recurrent but infrequent migration between subpopulations. We assumed that mating incompatibility is controlled by a number of loci that behave as neutral characters in the accumulation of novel mutations within each population. Genetic distance between populations was defined as the number of incompatibility-controlling loci that differ between them. Genetic distance increases through the separate accumulation of mutations in different populations, but decreases after a successful migration event followed by genetic mixing between migrants and residents. We calculated the time to allopatric speciation, which occurs when the genetic distance exceeds a specified threshold. If the number of invasive individuals relative to the resident population is not very large, diffusion approximation provides an accurate prediction. There is an intermediate optimal rate of migration that maximizes the rate of species creation by recurrent invasion and diversification. We also examined cases that involved more than two populations.

  18. Arsenic speciation and sorption in natural environments

    Science.gov (United States)

    Campbell, Kate M.; Nordstrom, D. Kirk

    2014-01-01

    Aqueous arsenic speciation, or the chemical forms in which arsenic exists in water, is a challenging, interesting, and complicated aspect of environmental arsenic geochemistry. Arsenic has the ability to form a wide range of chemical bonds with carbon, oxygen, hydrogen, and sulfur, resulting in a large variety of compounds that exhibit a host of chemical and biochemical properties. Besides the intriguing chemical diversity, arsenic also has the rare capacity to capture our imaginations in a way that few elements can duplicate: it invokes images of foul play that range from sinister to comedic (e.g., “inheritance powder” and arsenic-spiked elderberry wine). However, the emergence of serious large-scale human health problems from chronic arsenic exposure in drinking water has placed a high priority on understanding environmental arsenic mobility, toxicity, and bioavailability, and chemical speciation is key to these important questions. Ultimately, the purpose of arsenic speciation research is to predict future occurrences, mitigate contamination, and provide successful management of water resources.

  19. Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms.

    Science.gov (United States)

    Brown, David S; Jarman, Simon N; Symondson, William O C

    2012-03-01

    Little quantitative ecological information exists on the diets of most invertebrate feeding reptiles, particularly nocturnal or elusive species that are difficult to observe. In the UK and elsewhere, reptiles are legally required to be relocated before land development can proceed, but without knowledge of their dietary requirements, the suitability of receptor sites cannot be known. Here, we tested the ability of non-invasive DNA-based molecular diagnostics (454 pyrosequencing) to analyse reptile diets, with the specific aims of determining which earthworm species are exploited by slow worms (the legless lizard Anguis fragilis) and whether they feed on the deeper-living earthworm species that only come to the surface at night. Slow worm faecal samples from four different habitats were analysed using earthworm-specific PCR primers. We found that 86% of slow worms (N=80) had eaten earthworms. In lowland heath and marshy/acid grassland, Lumbricus rubellus, a surface-dwelling epigeic species, dominated slow worm diet. In two other habitats, riverside pasture and calciferous coarse grassland, diet was dominated by deeper-living anecic and endogeic species. We conclude that all species of earthworm are exploited by these reptiles and lack of specialization allows slow worms to thrive in a wide variety of habitats. Pyrosequencing of prey DNA in faeces showed promise as a practical, rapid and relatively inexpensive means of obtaining detailed and valuable ecological information on the diets of reptiles. © 2011 Blackwell Publishing Ltd.

  20. Comparisons of the fungal and protistan communities among different marine sponge holobionts by pyrosequencing.

    Science.gov (United States)

    He, Liming; Liu, Fang; Karuppiah, Valliappan; Ren, Yi; Li, Zhiyong

    2014-05-01

    To date, the knowledge of eukaryotic communities associated with sponges remains limited compared with prokaryotic communities. In a manner similar to prokaryotes, it could be hypothesized that sponge holobionts have phylogenetically diverse eukaryotic symbionts, and the eukaryotic community structures in different sponge holobionts were probably different. In order to test this hypothesis, the communities of eukaryota associated with 11 species of South China Sea sponges were compared with the V4 region of 18S ribosomal ribonucleic acid gene using 454 pyrosequencing. Consequently, 135 and 721 unique operational taxonomic units (OTUs) of fungi and protists were obtained at 97 % sequence similarity, respectively. These sequences were assigned to 2 phyla of fungi (Ascomycota and Basidiomycota) and 9 phyla of protists including 5 algal phyla (Chlorophyta, Haptophyta, Streptophyta, Rhodophyta, and Stramenopiles) and 4 protozoal phyla (Alveolata, Cercozoa, Haplosporidia, and Radiolaria) including 47 orders (12 fungi, 35 protists). Entorrhizales of fungi and 18 orders of protists were detected in marine sponges for the first time. Particularly, Tilletiales of fungi and Chlorocystidales of protists were detected for the first time in marine habitats. Though Ascomycota, Alveolata, and Radiolaria were detected in all the 11 sponge species, sponge holobionts have different fungi and protistan communities according to OTU comparison and principal component analysis at the order level. This study provided the first insights into the fungal and protistan communities associated with different marine sponge holobionts using pyrosequencing, thus further extending the knowledge on sponge-associated eukaryotic diversity.

  1. Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing.

    Science.gov (United States)

    Ye, Lin; Zhang, Tong

    2011-09-01

    This study applied 454 high-throughput pyrosequencing to analyze potentially pathogenic bacteria in activated sludge from 14 municipal wastewater treatment plants (WWTPs) across four countries (China, U.S., Canada, and Singapore), plus the influent and effluent of one of the 14 WWTPs. A total of 370,870 16S rRNA gene sequences with average length of 207 bps were obtained and all of them were assigned to corresponding taxonomic ranks by using RDP classifier and MEGAN. It was found that the most abundant potentially pathogenic bacteria in the WWTPs were affiliated with the genera of Aeromonas and Clostridium. Aeromonas veronii, Aeromonas hydrophila, and Clostridium perfringens were species most similar to the potentially pathogenic bacteria found in this study. Some sequences highly similar (>99%) to Corynebacterium diphtheriae were found in the influent and activated sludge samples from a saline WWTP. Overall, the percentage of the sequences closely related (>99%) to known pathogenic bacteria sequences was about 0.16% of the total sequences. Additionally, a platform-independent Java application (BAND) was developed for graphical visualization of the data of microbial abundance generated by high-throughput pyrosequencing. The approach demonstrated in this study could examine most of the potentially pathogenic bacteria simultaneously instead of one-by-one detection by other methods.

  2. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Yi-Mo Deng

    Full Text Available BACKGROUND: Given the continuing co-circulation of the 2009 H1N1 pandemic influenza A viruses with seasonal H3N2 viruses, rapid and reliable detection of newly emerging influenza reassortant viruses is important to enhance our influenza surveillance. METHODOLOGY/PRINCIPAL FINDINGS: A novel pyrosequencing assay was developed for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus. Except for HA and NA genes, one universal set of primers was used to amplify and subtype each of the six internal genes. With this method, all eight gene segments of 57 laboratory isolates and 17 original specimens of seasonal H1N1, H3N2 and 2009 H1N1 pandemic viruses were correctly matched with their corresponding subtypes. In addition, this method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all 8 gene segments from three vaccine production reassortant viruses and three H1N2 viruses. CONCLUSIONS/SIGNIFICANCE: In summary, this pyrosequencing assay is a sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses, which is more rapid and cheaper than using conventional sequencing approaches.

  3. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing.

    Science.gov (United States)

    Deng, Yi-Mo; Caldwell, Natalie; Barr, Ian G

    2011-01-01

    Given the continuing co-circulation of the 2009 H1N1 pandemic influenza A viruses with seasonal H3N2 viruses, rapid and reliable detection of newly emerging influenza reassortant viruses is important to enhance our influenza surveillance. A novel pyrosequencing assay was developed for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus. Except for HA and NA genes, one universal set of primers was used to amplify and subtype each of the six internal genes. With this method, all eight gene segments of 57 laboratory isolates and 17 original specimens of seasonal H1N1, H3N2 and 2009 H1N1 pandemic viruses were correctly matched with their corresponding subtypes. In addition, this method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all 8 gene segments from three vaccine production reassortant viruses and three H1N2 viruses. In summary, this pyrosequencing assay is a sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses, which is more rapid and cheaper than using conventional sequencing approaches.

  4. 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters.

    Science.gov (United States)

    Sundberg, Carina; Al-Soud, Waleed A; Larsson, Madeleine; Alm, Erik; Yekta, Sepehr S; Svensson, Bo H; Sørensen, Søren J; Karlsson, Anna

    2013-09-01

    The microbial community of 21 full-scale biogas reactors was examined using 454 pyrosequencing of 16S rRNA gene sequences. These reactors included seven (six mesophilic and one thermophilic) digesting sewage sludge (SS) and 14 (ten mesophilic and four thermophilic) codigesting (CD) various combinations of wastes from slaughterhouses, restaurants, households, etc. The pyrosequencing generated more than 160,000 sequences representing 11 phyla, 23 classes, and 95 genera of Bacteria and Archaea. The bacterial community was always both more abundant and more diverse than the archaeal community. At the phylum level, the foremost populations in the SS reactors included Actinobacteria, Proteobacteria, Chloroflexi, Spirochetes, and Euryarchaeota, while Firmicutes was the most prevalent in the CD reactors. The main bacterial class in all reactors was Clostridia. Acetoclastic methanogens were detected in the SS, but not in the CD reactors. Their absence suggests that methane formation from acetate takes place mainly via syntrophic acetate oxidation in the CD reactors. A principal component analysis of the communities at genus level revealed three clusters: SS reactors, mesophilic CD reactors (including one thermophilic CD and one SS), and thermophilic CD reactors. Thus, the microbial composition was mainly governed by the substrate differences and the process temperature. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  5. Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.

    Science.gov (United States)

    Mark, Kristiina; Cornejo, Carolina; Keller, Christine; Flück, Daniela; Scheidegger, Christoph

    2016-09-01

    Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichen-forming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).

  6. Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence.

    Science.gov (United States)

    Pauchet, Y; Wilkinson, P; Vogel, H; Nelson, D R; Reynolds, S E; Heckel, D G; ffrench-Constant, R H

    2010-02-01

    The tobacco hornworm Manduca sexta is an important model for insect physiology but genomic and transcriptomic data are currently lacking. Following a recent pyrosequencing study generating immune related expressed sequence tags (ESTs), here we use this new technology to define the M. sexta larval midgut transcriptome. We generated over 387,000 midgut ESTs, using a combination of Sanger and 454 sequencing, and classified predicted proteins into those involved in digestion, detoxification and immunity. In many cases the depth of 454 pyrosequencing coverage allowed us to define the entire cDNA sequence of a particular gene. Many new M. sexta genes are described including up to 36 new cytochrome P450s, some of which have been implicated in the metabolism of host plant-derived nicotine. New lepidopteran gene families such as the beta-fructofuranosidases, previously thought to be restricted to Bombyx mori, are also described. An unexpectedly high number of ESTs were involved in immunity, for example 39 contigs encoding serpins, and the increasingly appreciated role of the midgut in insect immunity is discussed. Similar studies of other tissues will allow for a tissue by tissue description of the M. sexta transcriptome and will form an essential complimentary step on the road to genome sequencing and annotation.

  7. Investigation of the koala (Phascolarctos cinereus) hindgut microbiome via 16S pyrosequencing.

    Science.gov (United States)

    Barker, Christopher J; Gillett, Amber; Polkinghorne, Adam; Timms, Peter

    2013-12-27

    As a dietary source, the foliage of Eucalyptus spp. is low in available protein and carbohydrate while containing polyphenolic compounds that interfere with enzymatic digestion. To overcome this, the koala (Phascolarctos cinereus) has evolved a range of anatomical and physiological adaptations to assist with digestion and absorption of nutrients from this food source. Microbial fermentation of partially digested eucalyptus leaves is thought to be critical in this process, however, little is known about the composition and diversity of microorganisms that are associated with digestive health in this native species. In this study, we performed 16S rRNA gene pyrosequencing of caecum, colon and faecal pellet samples from two wild, free ranging, Queensland koalas. Our results reveal a highly complex and diverse ecosystem with considerable intra-individual variation. Although samples were dominated by sequences from the Bacteroidetes and Firmicutes phyla there was considerable variation at the genus level. This study is the first non-culture based microbiota analysis, using 454-amplicon pyrosequencing, and provides preliminary data to expand our understanding of the koala hindgut. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea.

    Science.gov (United States)

    Sun, Wei; Zhang, Fengli; He, Liming; Li, Zhiyong

    2014-05-01

    Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.

  9. Thermodynamics proposes, kinetics decides, speciation dares: speciation of actinides in biological media

    International Nuclear Information System (INIS)

    Ansoborlo, E.

    2005-06-01

    After having recalled the content and purpose of his research thesis, the author proposes a detailed overview of the research works he performed thereafter in the field of the speciation of actinides at the level of the organism entry gates and in target tissues. These works therefore concern four important areas of research in radioprotection: bio-kinetic, toxicology, decorporation, and dosimetry studies. The author outlines how speciation studies can be useful for these different areas, and to better understand and describe, and therefore foresee, the biokinetics and toxicity of radionuclides

  10. Electrospray mass spectrometry for actinides and lanthanide speciation

    International Nuclear Information System (INIS)

    Moulin, C.; Amekraz, B.; Colette, S.; Doizi, D.; Jacopin, C.; Lamouroux, C.; Plancque, G.

    2006-01-01

    Electrospray mass spectrometry (ES-MS) is a new speciation technique that has the great interest to be able to probe the element, the ligand and the complex in order to reach the speciation. This paper will focus on the use of ES-MS for the speciation of actinides/lanthanides on several systems of interest in various fields such as the interaction between DTPA (decorporant) and europium, HEBP and uranium, BTP (new extracting agent) and lanthanides with comparison with known chemistry as well as whenever possible with other speciation techniques

  11. Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing® technology

    Directory of Open Access Journals (Sweden)

    Gallagher Margaret L

    2009-08-01

    Full Text Available Abstract Background Identification of CYP2A6 alleles associated with reduced enzyme activity is important in the study of inter-individual differences in drug metabolism. CYP2A6*12 is a hybrid allele that results from unequal crossover between CYP2A6 and CYP2A7 genes. The 5' regulatory region and exons 1–2 are derived from CYP2A7, and exons 3–9 are derived from CYP2A6. Conventional methods for detection of CYP2A6*12 consist of two-step PCR protocols that are laborious and unsuitable for high-throughput genotyping. We developed a rapid and accurate method to detect the CYP2A6*12 allele by Pyrosequencing technology. Methods A single set of PCR primers was designed to specifically amplify both the CYP2A6*1 wild-type allele and the CYP2A6*12 hybrid allele. An internal Pyrosequencing primer was used to generate allele-specific sequence information, which detected homozygous wild-type, heterozygous hybrid, and homozygous hybrid alleles. We first validated the assay on 104 DNA samples that were also genotyped by conventional two-step PCR and by cycle sequencing. CYP2A6*12 allele frequencies were then determined using the Pyrosequencing assay on 181 multi-ethnic DNA samples from subjects of African American, European Caucasian, Pacific Rim, and Hispanic descent. Finally, we streamlined the Pyrosequencing assay by integrating liquid handling robotics into the workflow. Results Pyrosequencing results demonstrated 100% concordance with conventional two-step PCR and cycle sequencing methods. Allele frequency data showed slightly higher prevalence of the CYP2A6*12 allele in European Caucasians and Hispanics. Conclusion This Pyrosequencing assay proved to be a simple, rapid, and accurate alternative to conventional methods, which can be easily adapted to the needs of higher-throughput studies.

  12. Combining flow cytometry and 16S rRNA gene pyrosequencing: A promising approach for drinking water monitoring and characterization

    KAUST Repository

    Prest, Emmanuelle I E C

    2014-10-01

    The combination of flow cytometry (FCM) and 16S rRNA gene pyrosequencing data was investigated for the purpose of monitoring and characterizing microbial changes in drinking water distribution systems. High frequency sampling (5min intervals for 1h) was performed at the outlet of a treatment plant and at one location in the full-scale distribution network. In total, 52 bulk water samples were analysed with FCM, pyrosequencing and conventional methods (adenosine-triphosphate, ATP; heterotrophic plate count, HPC). FCM and pyrosequencing results individually showed that changes in the microbial community occurred in the water distribution system, which was not detected with conventional monitoring. FCM data showed an increase in the total bacterial cell concentrations (from 345±15×103 to 425±35×103cellsmL-1) and in the percentage of intact bacterial cells (from 39±3.5% to 53±4.4%) during water distribution. This shift was also observed in the FCM fluorescence fingerprints, which are characteristic of each water sample. A similar shift was detected in the microbial community composition as characterized with pyrosequencing, showing that FCM and genetic fingerprints are congruent. FCM and pyrosequencing data were subsequently combined for the calculation of cell concentration changes for each bacterial phylum. The results revealed an increase in cell concentrations of specific bacterial phyla (e.g., Proteobacteria), along with a decrease in other phyla (e.g., Actinobacteria), which could not be concluded from the two methods individually. The combination of FCM and pyrosequencing methods is a promising approach for future drinking water quality monitoring and for advanced studies on drinking water distribution pipeline ecology. © 2014 Elsevier Ltd.

  13. Combining flow cytometry and 16S rRNA gene pyrosequencing: a promising approach for drinking water monitoring and characterization.

    Science.gov (United States)

    Prest, E I; El-Chakhtoura, J; Hammes, F; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

    2014-10-15

    The combination of flow cytometry (FCM) and 16S rRNA gene pyrosequencing data was investigated for the purpose of monitoring and characterizing microbial changes in drinking water distribution systems. High frequency sampling (5 min intervals for 1 h) was performed at the outlet of a treatment plant and at one location in the full-scale distribution network. In total, 52 bulk water samples were analysed with FCM, pyrosequencing and conventional methods (adenosine-triphosphate, ATP; heterotrophic plate count, HPC). FCM and pyrosequencing results individually showed that changes in the microbial community occurred in the water distribution system, which was not detected with conventional monitoring. FCM data showed an increase in the total bacterial cell concentrations (from 345 ± 15 × 10(3) to 425 ± 35 × 10(3) cells mL(-1)) and in the percentage of intact bacterial cells (from 39 ± 3.5% to 53 ± 4.4%) during water distribution. This shift was also observed in the FCM fluorescence fingerprints, which are characteristic of each water sample. A similar shift was detected in the microbial community composition as characterized with pyrosequencing, showing that FCM and genetic fingerprints are congruent. FCM and pyrosequencing data were subsequently combined for the calculation of cell concentration changes for each bacterial phylum. The results revealed an increase in cell concentrations of specific bacterial phyla (e.g., Proteobacteria), along with a decrease in other phyla (e.g., Actinobacteria), which could not be concluded from the two methods individually. The combination of FCM and pyrosequencing methods is a promising approach for future drinking water quality monitoring and for advanced studies on drinking water distribution pipeline ecology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Rapid allopatric speciation in logperch darters (Percidae: Percina).

    Science.gov (United States)

    Near, Thomas J; Benard, Michael F

    2004-12-01

    Theory predicts that clades diversifying via sympatric speciation will exhibit high diversification rates. However, the expected rate of diversification in clades characterized by allopatric speciation is less clear. Previous studies have documented significantly higher speciation rates in freshwater fish clades diversifying via sympatric versus allopatric modes, leading to suggestions that the geographic pattern of speciation can be inferred solely from knowledge of the diversification rate. We tested this prediction using an example from darters, a clade of approximately 200 species of freshwater fishes endemic to eastern North America. A resolved phylogeny was generated using mitochondrial DNA gene sequences for logperches, a monophyletic group of darters composed of 10 recognized species. Divergence times among logperch species were estimated using a fossil calibrated molecular clock in centrarchid fishes, and diversification rates in logperches were estimated using several methods. Speciation events in logperches are recent, extending from 4.20 +/- 1.06 million years ago (mya) to 0.42 +/- 0.22 mya, with most speciation events occurring in the Pleistocene. Diversification rates are high in logperches, at some nodes exceeding rates reported for well-studied adaptive radiations such as Hawaiian silverswords. The geographic pattern of speciation in logperches was investigated by examining the relationship between degree of sympatry and the absolute age of the contrast, with the result that diversification in logperches appears allopatric. The very high diversification rate observed in the logperch phylogeny is more similar to freshwater fish clades thought to represent examples of sympatric speciation than to clades representing allopatric speciation. These results demonstrate that the geographic mode of speciation for a clade cannot be inferred from the diversification rate. The empirical observation of high diversification rates in logperches demonstrates that

  15. Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

    DEFF Research Database (Denmark)

    Masoud, Wafa Mahmoud Hasan; Takamiya, Monica K Wik; Vogensen, Finn Kvist

    2011-01-01

    ripening. Other bacteria like Corynebacterium, Halomonas, Pediococcus, Micrococcus and Staphylococcus, which were encountered in some cheese samples at low percentages compared with the total bacterial populations, were only detected by pyrosequencing. 16S rRNA gene pyrosequencing is an efficient method...

  16. Complementary arsenic speciation methods: A review

    Energy Technology Data Exchange (ETDEWEB)

    Nearing, Michelle M., E-mail: michelle.nearing@rmc.ca; Koch, Iris, E-mail: koch-i@rmc.ca; Reimer, Kenneth J., E-mail: reimer-k@rmc.ca

    2014-09-01

    The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk. High performance liquid chromatography with inductively coupled mass spectrometry (HPLC–ICP-MS) is the most common analysis used for arsenic speciation but it has two major limitations: it relies on an extraction step (usually from a solid sample) that can be incomplete or alter the arsenic compounds; and it provides no structural information, relying on matching sample peaks to standard peaks. The use of additional analytical methods in a complementary manner introduces the ability to address these disadvantages. The use of X-ray absorption spectroscopy (XAS) with HPLC–ICP-MS can be used to identify compounds not extracted for HPLC–ICP-MS and provide minimal processing steps for solid state analysis that may help preserve labile compounds such as those containing arsenic-sulfur bonds, which can degrade under chromatographic conditions. On the other hand, HPLC–ICP-MS is essential in confirming organoarsenic compounds with similar white line energies seen by using XAS, and identifying trace arsenic compounds that are too low to be detected by XAS. The complementary use of electrospray mass spectrometry (ESI–MS) with HPLC–ICP-MS provides confirmation of arsenic compounds identified during the HPLC–ICP-MS analysis, identification of unknown compounds observed during the HPLC–ICP-MS analysis and further resolves HPLC–ICP-MS by identifying co-eluting compounds. In the complementary use of HPLC–ICP-MS and ESI–MS, HPLC–ICP-MS helps to focus the ESI–MS selection of ions. Numerous studies have shown that the information obtained from HPLC–ICP-MS analysis can be greatly enhanced by complementary approaches. - Highlights: • HPLC–ICP-MS is the most common method used for arsenic speciation. • HPLC limitations include

  17. Plutonium Speciation, Solubilization and Migration in Soils

    International Nuclear Information System (INIS)

    Neu, M.; Runde, W.

    1999-01-01

    This report summarizes research completed in the first half of a three-year project. As outlined in the authors' proposal they are focusing on (1) characterizing the plutonium at an actinide contaminated site, RFETS, including determining the origin, dispersion, and speciation of the plutonium, (2) studying environmentally important plutonium complexes, primarily hydroxides and carbonates, and (3) examining the interactions of plutonium species with manganese minerals. In the first year the authors focused on site based studies. This year they continue to characterize samples from the RFETS, study the formation and structural and spectroscopic features of environmentally relevant Pu species, and begin modeling the environmental behavior of plutonium

  18. Speciation of arsenic in biological samples.

    Science.gov (United States)

    Mandal, Badal Kumar; Ogra, Yasumitsu; Anzai, Kazunori; Suzuki, Kazuo T

    2004-08-01

    Speciation of arsenicals in biological samples is an essential tool to gain insight into its distribution in tissues and its species-specific toxicity to target organs. Biological samples (urine, hair, fingernail) examined in the present study were collected from 41 people of West Bengal, India, who were drinking arsenic (As)-contaminated water, whereas 25 blood and urine samples were collected from a population who stopped drinking As contaminated water 2 years before the blood collection. Speciation of arsenicals in urine, water-methanol extract of freeze-dried red blood cells (RBCs), trichloroacetic acid treated plasma, and water extract of hair and fingernail was carried out by high-performance liquid chromatography (HPLC)-inductively coupled argon plasma mass spectrometry (ICP MS). Urine contained arsenobetaine (AsB, 1.0%), arsenite (iAs(III), 11.3), arsenate (iAs(V), 10.1), monomethylarsonous acid (MMA(III), 6.6), monomethylarsonic acid (MMA(V), 10.5), dimethylarsinous acid (DMA(III), 13.0), and dimethylarsinic acid (DMA(V), 47.5); fingernail contained iAs(III) (62.4%), iAs(V) (20.2), MMA(V) (5.7), DMA(III) (8.9), and DMA(V) (2.8); hair contained iAs(III) (58.9%), iAs(V) (34.8), MMA(V) (2.9), and DMA(V) (3.4); RBCs contained AsB (22.5%) and DMA(V) (77.5); and blood plasma contained AsB (16.7%), iAs(III) (21.1), MMA(V) (27.1), and DMA(V) (35.1). MMA(III), DMA(III), and iAs(V) were not found in any plasma and RBCs samples, but urine contained all of them. Arsenic in urine, fingernails, and hair are positively correlated with water As, suggesting that any of these measurements could be considered as a biomarker to As exposure. Status of urine and exogenous contamination of hair urgently need speciation of As in these samples, but speciation of As in nail is related to its total As (tAs) concentration. Therefore, total As concentrations of nails could be considered as biomarker to As exposure in the endemic areas.

  19. Speciation of arsenic in biological samples

    International Nuclear Information System (INIS)

    Mandal, Badal Kumar; Ogra, Yasumitsu; Anzai, Kazunori; Suzuki, Kazuo T.

    2004-01-01

    Speciation of arsenicals in biological samples is an essential tool to gain insight into its distribution in tissues and its species-specific toxicity to target organs. Biological samples (urine, hair, fingernail) examined in the present study were collected from 41 people of West Bengal, India, who were drinking arsenic (As)-contaminated water, whereas 25 blood and urine samples were collected from a population who stopped drinking As contaminated water 2 years before the blood collection. Speciation of arsenicals in urine, water-methanol extract of freeze-dried red blood cells (RBCs), trichloroacetic acid treated plasma, and water extract of hair and fingernail was carried out by high-performance liquid chromatography (HPLC)-inductively coupled argon plasma mass spectrometry (ICP MS). Urine contained arsenobetaine (AsB, 1.0%), arsenite (iAs III , 11.3), arsenate (iAs V , 10.1), monomethylarsonous acid (MMA III , 6.6), monomethylarsonic acid (MMA V , 10.5), dimethylarsinous acid (DMA III , 13.0), and dimethylarsinic acid (DMA V , 47.5); fingernail contained iAs III (62.4%), iAs V (20.2), MMA V (5.7), DMA III (8.9), and DMA V (2.8); hair contained iAs III (58.9%), iAs V (34.8), MMA V (2.9), and DMA V (3.4); RBCs contained AsB (22.5%) and DMA V (77.5); and blood plasma contained AsB (16.7%), iAs III (21.1), MMA V (27.1), and DMA V (35.1). MMA III , DMA III , and iAs V were not found in any plasma and RBCs samples, but urine contained all of them. Arsenic in urine, fingernails, and hair are positively correlated with water As, suggesting that any of these measurements could be considered as a biomarker to As exposure. Status of urine and exogenous contamination of hair urgently need speciation of As in these samples, but speciation of As in nail is related to its total As (tAs) concentration. Therefore, total As concentrations of nails could be considered as biomarker to As exposure in the endemic areas

  20. Complementary arsenic speciation methods: A review

    International Nuclear Information System (INIS)

    Nearing, Michelle M.; Koch, Iris; Reimer, Kenneth J.

    2014-01-01

    The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk. High performance liquid chromatography with inductively coupled mass spectrometry (HPLC–ICP-MS) is the most common analysis used for arsenic speciation but it has two major limitations: it relies on an extraction step (usually from a solid sample) that can be incomplete or alter the arsenic compounds; and it provides no structural information, relying on matching sample peaks to standard peaks. The use of additional analytical methods in a complementary manner introduces the ability to address these disadvantages. The use of X-ray absorption spectroscopy (XAS) with HPLC–ICP-MS can be used to identify compounds not extracted for HPLC–ICP-MS and provide minimal processing steps for solid state analysis that may help preserve labile compounds such as those containing arsenic-sulfur bonds, which can degrade under chromatographic conditions. On the other hand, HPLC–ICP-MS is essential in confirming organoarsenic compounds with similar white line energies seen by using XAS, and identifying trace arsenic compounds that are too low to be detected by XAS. The complementary use of electrospray mass spectrometry (ESI–MS) with HPLC–ICP-MS provides confirmation of arsenic compounds identified during the HPLC–ICP-MS analysis, identification of unknown compounds observed during the HPLC–ICP-MS analysis and further resolves HPLC–ICP-MS by identifying co-eluting compounds. In the complementary use of HPLC–ICP-MS and ESI–MS, HPLC–ICP-MS helps to focus the ESI–MS selection of ions. Numerous studies have shown that the information obtained from HPLC–ICP-MS analysis can be greatly enhanced by complementary approaches. - Highlights: • HPLC–ICP-MS is the most common method used for arsenic speciation. • HPLC limitations include

  1. Dynamic speciation analysis and bioavailability of metals in aquatic systems

    NARCIS (Netherlands)

    Leeuwen, van H.P.; Town, R.M.; Buffle, J.; Cleven, R.F.M.J.; Davison, W.; Puy, J.; Riemsdijk, van W.H.; Sigg, L.

    2005-01-01

    Dynamic metal speciation analysis in aquatic ecosystems is emerging as a powerful basis for development of predictions of bioavailability and reliable risk assessment strategies. A given speciation sensor is characterized by an effective time scale or kinetic window that defines the measurable metal

  2. Parasites Promote and When Might They Constrain Ecological Speciation?

    Directory of Open Access Journals (Sweden)

    Anssi Karvonen

    2012-01-01

    Full Text Available Research on speciation and adaptive radiation has flourished during the past decades, yet factors underlying initiation of reproductive isolation often remain unknown. Parasites represent important selective agents and have received renewed attention in speciation research. We review the literature on parasite-mediated divergent selection in context of ecological speciation and present empirical evidence for three nonexclusive mechanisms by which parasites might facilitate speciation: reduced viability or fecundity of immigrants and hybrids, assortative mating as a pleiotropic by-product of host adaptation, and ecologically-based sexual selection. We emphasise the lack of research on speciation continuums, which is why no study has yet made a convincing case for parasite driven divergent evolution to initiate the emergence of reproductive isolation. We also point interest towards selection imposed by single versus multiple parasite species, conceptually linking this to strength and multifariousness of selection. Moreover, we discuss how parasites, by manipulating behaviour or impairing sensory abilities of hosts, may change the form of selection that underlies speciation. We conclude that future studies should consider host populations at variable stages of the speciation process, and explore recurrent patterns of parasitism and resistance that could pinpoint the role of parasites in imposing the divergent selection that initiates ecological speciation.

  3. Self-consistent approach for neutral community models with speciation

    NARCIS (Netherlands)

    Haegeman, Bart; Etienne, Rampal S.

    Hubbell's neutral model provides a rich theoretical framework to study ecological communities. By incorporating both ecological and evolutionary time scales, it allows us to investigate how communities are shaped by speciation processes. The speciation model in the basic neutral model is

  4. The neutral theory of biodiversity with random fission speciation

    NARCIS (Netherlands)

    Etienne, Rampal S.; Haegeman, Bart

    The neutral theory of biodiversity and biogeography emphasizes the importance of dispersal and speciation to macro-ecological diversity patterns. While the influence of dispersal has been studied quite extensively, the effect of speciation has not received much attention, even though it was already

  5. What do we need to know about speciation?

    NARCIS (Netherlands)

    Butlin, Roger; Debelle, Allan; Kerth, Claudius; Snook, Rhonda R.; Beukeboom, Leo W.; Castillo Cajas, Ruth; Diao, Wenwen; Maan, Martine E.; Paolucci, Silvia; Weissing, Franz J.; van de Zande, Louis; Hoikkala, Anneli; Geuverink, Elzemiek; Jennings, Jackson; Kankare, Maaria; Knott, K. Emily; Tyukmaeva, Venera I.; Zoumadakis, Christos; Ritchie, Michael G.; Barker, Daniel; Immonen, Elina; Kirkpatrick, Mark; Noor, Mohamed; Macias Garcia, Constantino; Schmitt, Thomas; Schilthuizen, Menno

    Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical

  6. Speciation imperatives for waste management and environmental pollution

    International Nuclear Information System (INIS)

    Wymer, R.G.

    2001-01-01

    This paper addresses speciation requirements in the context of problems produced by nuclear energy and nuclear weapons production. These problems are primarily in the areas of waste management, material contamination, and environmental pollution. They pose difficult and important measurement and speciation challenges. Examples of speciation requirements in the context of national and international regulations are presented to exemplify and make quantitative the types of problems posed by waste management, material contamination, and environmental pollution. The importance of identifying species present in the natural environment as well as in wastes from chemical and physical processing and from waste management activities and accidental releases is addressed. Differing speciation requirements for macro and micro concentrations of species are discussed. The role of speciation in modelling studies is discussed. (author)

  7. Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing

    Directory of Open Access Journals (Sweden)

    Alex Mira

    2014-06-01

    Pyrosequencing of the samples resulted in a total of 18520 sequences (3000 per sample, approximately with an average length of 325 bp (base pairs. The taxonomic assignment of sequences allowed the identification to the genus level, being observed a large bacterial diversity with over 110 genera. The most prevalent genera in the samples were Hydrotalea, Acinetobacter, Delftia, Sediminibacter and Pseudomonas, among others. Differences in the microbial communities were observed among the samples, and the PCoA analysis allowed their separation by means on their gender and if they proceed from sampling before or after the spawning. Nevertheless, the rarefaction curves obtained for each sample failed to reach a saturation phase, indicating that more sequencing effort would be necessary.

  8. Development of an ELA-DRA gene typing method based on pyrosequencing technology.

    Science.gov (United States)

    Díaz, S; Echeverría, M G; It, V; Posik, D M; Rogberg-Muñoz, A; Pena, N L; Peral-García, P; Vega-Pla, J L; Giovambattista, G

    2008-11-01

    The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throughput genotyping of major histocompatibility complex genes in horses and other animal species, making this system interesting as a rapid screening method for animal genotyping of immune-related genes.

  9. Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED

    Czech Academy of Sciences Publication Activity Database

    Větrovský, Tomáš; Baldrian, Petr

    2013-01-01

    Roč. 49, č. 8 (2013), s. 1027-1037 ISSN 0178-2762 R&D Projects: GA MŠk LD12050; GA MŠk LD12048; GA ČR GAP504/12/0709 Institutional support: RVO:61388971 Keywords : Fungal community * Internal transcribed spacer * Pyrosequencing pipeline Subject RIV: EE - Microbiology, Virology Impact factor: 3.396, year: 2013

  10. Pyrosequencing Analysis of Norovirus Genogroup II Distribution in Sewage and Oysters: First Detection of GII.17 Kawasaki 2014 in Oysters.

    Science.gov (United States)

    Pu, Jian; Kazama, Shinobu; Miura, Takayuki; Azraini, Nabila Dhyan; Konta, Yoshimitsu; Ito, Hiroaki; Ueki, You; Cahyaningrum, Ermaya Eka; Omura, Tatsuo; Watanabe, Toru

    2016-12-01

    Norovirus GII.3, GII.4, and GII.17 were detected using pyrosequencing in sewage and oysters in January and February 2015, in Japan. The strains in sewage and oyster samples were genetically identical or similar, predominant strains belonging to GII.17 Kawasaki 2014 lineage. This is the first report of GII.17 Kawasaki 2014 in oysters.

  11. Comparison Study of MS-HRM and Pyrosequencing Techniques for Quantification of APC and CDKN2A Gene Methylation

    Science.gov (United States)

    Migheli, Francesca; Stoccoro, Andrea; Coppedè, Fabio; Wan Omar, Wan Adnan; Failli, Alessandra; Consolini, Rita; Seccia, Massimo; Spisni, Roberto; Miccoli, Paolo; Mathers, John C.; Migliore, Lucia

    2013-01-01

    There is increasing interest in the development of cost-effective techniques for the quantification of DNA methylation biomarkers. We analyzed 90 samples of surgically resected colorectal cancer tissues for APC and CDKN2A promoter methylation using methylation sensitive-high resolution melting (MS-HRM) and pyrosequencing. MS-HRM is a less expensive technique compared with pyrosequencing but is usually more limited because it gives a range of methylation estimates rather than a single value. Here, we developed a method for deriving single estimates, rather than a range, of methylation using MS-HRM and compared the values obtained in this way with those obtained using the gold standard quantitative method of pyrosequencing. We derived an interpolation curve using standards of known methylated/unmethylated ratio (0%, 12.5%, 25%, 50%, 75%, and 100% of methylation) to obtain the best estimate of the extent of methylation for each of our samples. We observed similar profiles of methylation and a high correlation coefficient between the two techniques. Overall, our new approach allows MS-HRM to be used as a quantitative assay which provides results which are comparable with those obtained by pyrosequencing. PMID:23326336

  12. Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units.

    Science.gov (United States)

    Vettraino, A M; Bonants, P; Tomassini, A; Bruni, N; Vannini, A

    2012-11-01

    To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight Phytophthora spp. and Pythium vexans. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0·63% and comprised mainly mismatches (0·25%) Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of Phytophthora spp. in environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods. Phytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of Phytophthora complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments. © 2012 The Authors Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

  13. Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing

    DEFF Research Database (Denmark)

    Reyes, Carlen; Dellwig, Olaf; Dähnke, K.

    2016-01-01

    To gain insight into the bacterial communities involved in iron-(Fe) cycling under marine conditions, we analysed sediments with Fe-contents (0.5-1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing....

  14. Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.

    Science.gov (United States)

    Jeanne, Nicolas; Saliou, Adrien; Carcenac, Romain; Lefebvre, Caroline; Dubois, Martine; Cazabat, Michelle; Nicot, Florence; Loiseau, Claire; Raymond, Stéphanie; Izopet, Jacques; Delobel, Pierre

    2015-11-20

    HIV-1 coreceptor usage must be accurately determined before starting CCR5 antagonist-based treatment as the presence of undetected minor CXCR4-using variants can cause subsequent virological failure. Ultra-deep pyrosequencing of HIV-1 V3 env allows to detect low levels of CXCR4-using variants that current genotypic approaches miss. However, the computation of the mass of sequence data and the need to identify true minor variants while excluding artifactual sequences generated during amplification and ultra-deep pyrosequencing is rate-limiting. Arbitrary fixed cut-offs below which minor variants are discarded are currently used but the errors generated during ultra-deep pyrosequencing are sequence-dependant rather than random. We have developed an automated processing of HIV-1 V3 env ultra-deep pyrosequencing data that uses biological filters to discard artifactual or non-functional V3 sequences followed by statistical filters to determine position-specific sensitivity thresholds, rather than arbitrary fixed cut-offs. It allows to retain authentic sequences with point mutations at V3 positions of interest and discard artifactual ones with accurate sensitivity thresholds.

  15. Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Man Kit Cheung

    Full Text Available BACKGROUND: Tuberculosis (TB remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease. METHODOLOGY/PRINCIPAL FINDINGS: Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples. CONCLUSIONS/SIGNIFICANCE: The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.

  16. Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses.

    Directory of Open Access Journals (Sweden)

    Patricia Moya

    Full Text Available The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method seems to underestimate the diversity. Here, we aim to analyze both the microalgal diversity and its community structure in a single thallus of the lichen R. farinacea by applying a 454 pyrosequencing approach coupled with a careful ad hoc-performed protocol for lichen sample processing prior to DNA extraction. To ascertain the reliability of the pyrosequencing results and the applied bioinformatics pipeline results, the thalli were divided into three sections (apical, middle and basal zones, and a mock community sample was used. The developed methodology allowed 40448 filtered algal reads to be obtained from a single lichen thallus, which encompassed 31 OTUs representative of different microalgae genera. In addition to corroborating the coexistence of the two Trebouxia sp. TR9 and T. jamesii taxa in the same thallus, this study showed a much higher microalgal diversity associated with the lichen. Along the thallus ramifications, we also detected variations in phycobiont distribution that might correlate with different microenvironmental conditions. These results highlight R. farinacea as a suitable material for studying microalgal diversity and further strengthen the concept of lichens as multispecies microecosystems. Future analyses will be relevant to

  17. Pyrosequencing based assessment of bacterial diversity in Turkish Rhipicephalus annulatus and Dermacentor marginatus ticks (Acari: Ixodidae).

    Science.gov (United States)

    Tekin, Saban; Dowd, Scot E; Davinic, Marko; Bursali, Ahmet; Keskin, Adem

    2017-03-01

    Ticks continue to be a threat to human and animal health in Turkey, as they are considered important vectors of human and animal diseases. The objectives of this investigation are to characterize the microbial communities of two tick species, Rhipicephalus annulatus and Dermacenter marginatus, analyze patterns of co-occurrence among microbial taxa, identify and compare pathogens contributing human diseases, and determine whether avirulent symbionts could exclude human pathogens from tick communities. Furthermore, this study explores a microbiome of the R. annulatus and D. marginatus via the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to describe their bacterial diversity. Pyrosequencing was performed on adult males and females isolated from humans from two high-risk Turkish provinces, Sivas and Amasya, during tick outbreaks in 2009. A total of 36,253 sequences were utilized for analyses of the 8 tick samples. Several pathogenic genera such as Francisella, Coxiella, Rickettsia, and Shigella were detected in the ticks tested. The most distinguishable difference between the two species of ticks was the lack of known human pathogen Rickettsia in R. annulatus and in samples 9 and 10 of D. marginatus. These samples had higher relative abundance of Flavobacterium sp., Curvibacter sp., Acidovorax sp., and Bacteroidaceae genera mostly representing symbionts which form a large component of normal tick microbiota. The outcome of this study is consistent with the predictions of the community ecological theory that diversity-rich bacteriomes are more resistant to bacterial invasion (and consequent pathogen dissemination) than diversity-deprived ones.

  18. Pyrosequencing as a tool for the identification of common isolates of Mycobacterium sp.

    Science.gov (United States)

    Tuohy, Marion J; Hall, Gerri S; Sholtis, Mary; Procop, Gary W

    2005-04-01

    Pyrosequencing technology, sequencing by addition, was evaluated for categorization of mycobacterial isolates. One hundred and eighty-nine isolates, including 18 ATCC and Trudeau Mycobacterial Culture Collection (TMC) strains, were studied. There were 38 Mycobacterium tuberculosis complex, 27 M. kansasii, 27 MAI complex, 21 M. marinum, 14 M. gordonae, 20 M. chelonae-abscessus group, 10 M. fortuitum, 5 M. xenopi, 3 M. celatum, 2 M. terrae complex, 20 M. mucogenicum, and 2 M. scrofulaceum. Nucleic acid extracts were prepared from solid media or MGIT broth. Traditional PCR was performed with one of the primers biotinylated; the assay targeted a portion of the 16S rRNA gene that contains a hypervariable region, which has been previously shown to be useful for the identification of mycobacteria. The PSQ Sample Preparation Kit was used, and the biotinylated PCR product was processed to a single-stranded DNA template. The sequencing primer was hybridized to the DNA template in a PSQ96 plate. Incorporation of the complementary nucleotides resulted in light generation peaks, forming a pyrogram, which was evaluated by the instrument software. Thirty basepairs were used for isolate categorization. Manual interpretation of the sequences was performed if the quality of the 30-bp sequence was in doubt or if more than 4 bp homopolymers were recognized. Sequences with more than 5 bp of bad quality were deemed unacceptable. When blasted against GenBank, 179 of 189 sequences (94.7%) assigned isolates to the correct molecular genus or group. Ten M. gordonae isolates had more than 5 bp of bad quality sequence and were not accepted. Pyrosequencing of this hypervariable region afforded rapid and acceptable characterization of common, routinely isolated clinical Mycobacterium sp. Algorithms are recommended for further differentiation with an additional sequencing primer or additional biochemicals.

  19. The comparison of pyrosequencing molecular Gram stain, culture, and conventional Gram stain for diagnosing orthopaedic infections.

    Science.gov (United States)

    Kobayashi, Naomi; Bauer, Thomas W; Tuohy, Marion J; Lieberman, Isador H; Krebs, Viktor; Togawa, Daisuke; Fujishiro, Takaaki; Procop, Gary W

    2006-08-01

    We have developed a combined real-time PCR and pyrosequencing assay that successfully differentiated the vast majority of gram-positive and gram-negative bacteria when bacterial isolates were tested. The purpose of this study was to evaluate this assay on clinical specimens obtained from orthopedic surgeries, and to prospectively compare the results of "molecular Gram stain" with culture and conventional direct Gram stain. Forty-five surgical specimens were obtained from patients who underwent orthopedic surgery procedures. The DNA was extracted and a set of broad-range PCR primers that targeted a part of the 16S rDNA gene was used for pan-bacterial PCR. The amplicons were submitted for pyrosequencing and the resulting molecular Gram stain characteristics were recorded. Culture and direct Gram staining were performed using standard methods for all cases. Surgical specimens were reviewed histologically for all cases that had a discrepancy between culture and molecular results. There was an 86.7% (39/45) agreement between the traditional and molecular methods. In 12/14 (85.7%) culture-proven cases of bacterial infection, molecular Gram stain characteristics were in agreement with the culture results, while the conventional Gram stain result was in agreement only for five cases (35.7%). In the 31 culture negative cases, 27 cases were also PCR negative, whereas 4 were PCR positive. Three of these were characterized as gram negative and one as gram positive by this molecular method. Molecular determination of the Gram stain characteristics of bacteria that cause orthopedic infections may be achieved, in most instances, by this method. Further studies are necessary to understand the clinical importance of PCR-positive/culture-negative results.

  20. Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2017-01-01

    Full Text Available Objective The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep’s health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum of sheep. Methods This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. Results The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum, small intestine (duodenum, jejunum, and ileum, and large intestine (cecum, colon, and rectum. Conclusion This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.

  1. The rate test of speciation: estimating the likelihood of non-allopatric speciation from reproductive isolation rates in Drosophila.

    Science.gov (United States)

    Yukilevich, Roman

    2014-04-01

    Among the most debated subjects in speciation is the question of its mode. Although allopatric (geographical) speciation is assumed the null model, the importance of parapatric and sympatric speciation is extremely difficult to assess and remains controversial. Here I develop a novel approach to distinguish these modes of speciation by studying the evolution of reproductive isolation (RI) among taxa. I focus on the Drosophila genus, for which measures of RI are known. First, I incorporate RI into age-range correlations. Plots show that almost all cases of weak RI are between allopatric taxa whereas sympatric taxa have strong RI. This either implies that most reproductive isolation (RI) was initiated in allopatry or that RI evolves too rapidly in sympatry to be captured at incipient stages. To distinguish between these explanations, I develop a new "rate test of speciation" that estimates the likelihood of non-allopatric speciation given the distribution of RI rates in allopatry versus sympatry. Most sympatric taxa were found to have likely initiated RI in allopatry. However, two putative candidate species pairs for non-allopatric speciation were identified (5% of known Drosophila). In total, this study shows how using RI measures can greatly inform us about the geographical mode of speciation in nature. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  2. Relative Bioavailability and Bioaccessability and Speciation of ...

    Science.gov (United States)

    Background: Assessment of soil arsenic (As) bioavailability may profoundly affect the extent of remediation required at contaminated sites by improving human exposure estimates. Because small adjustments in soil As bioavailability estimates can significantly alter risk assessments and remediation goals, convenient, rapid, reliable, and inexpensive tools are needed to determine soil As bioavailability. Objectives: We evaluated inexpensive methods for assessing As bioavailability in soil as a means to improve human exposure estimates and potentially reduce remediation costs. Methods: Nine soils from residential sites affected by mining or smelting activity and two National Institute of Standards and Technology standard reference materials were evaluated for As bioavailability, bioaccessibility, and speciation. Arsenic bioavailability was determined using an in vivo mouse model, and As bioaccessibility was determined using the Solubility/Bioavailability Research Consortium in vitro assay. Arsenic speciation in soil and selected soil physicochemical properties were also evaluated to determine whether these parameters could be used as predictors of As bio¬availability and bioaccessibility. Results: In the mouse assay, we compared bioavailabilities of As in soils with that for sodium arsenate. Relative bioavailabilities (RBAs) of soil As ranged from 11% to 53% (mean, 33%). In vitro soil As bioaccessibility values were strongly correlated with soil As RBAs (R

  3. Uranium(VI) speciation by spectroscopy

    International Nuclear Information System (INIS)

    Meinrath, G.

    1997-01-01

    The application of UV-Vis and time-resolved laser-induced fluorescence (TRLF) spectroscopies to direct of uranium(VI) in environmental samples offers various prospects that have, however, serious limitations. While UV-Vis spectroscopy is probably not sensitive enough to detect uranium(VI) species in the majority of environmental samples, TRLFS is principially able to speciate uranium(VI) at very low concentration levels in the nanomol range. Speciation by TRLFS can be based on three parameters: excitation spectrum, emission spectrum and lifetime of the fluorescence emission process. Due to quenching effects, the lifetime may not be expected to be as characteristics as, e.g., the emission spectrum. Quenching of U(VI) fluorescence by reaction with organic substances, inorganic ions and formation of carbonate radicals is one important limiting factor in the application of U(VI) fluorescence spectroscopy. Fundamental photophysical criteria are illustrated using UV-Vis and fluorescence spectra of U(VI) hydrolysis and carbonato species as examples. (author)

  4. Resolving uncertainty in chemical speciation determinations

    Science.gov (United States)

    Smith, D. Scott; Adams, Nicholas W. H.; Kramer, James R.

    1999-10-01

    Speciation determinations involve uncertainty in system definition and experimentation. Identification of appropriate metals and ligands from basic chemical principles, analytical window considerations, types of species and checking for consistency in equilibrium calculations are considered in system definition uncertainty. A systematic approach to system definition limits uncertainty in speciation investigations. Experimental uncertainty is discussed with an example of proton interactions with Suwannee River fulvic acid (SRFA). A Monte Carlo approach was used to estimate uncertainty in experimental data, resulting from the propagation of uncertainties in electrode calibration parameters and experimental data points. Monte Carlo simulations revealed large uncertainties present at high (>9-10) and low (monoprotic ligands. Least-squares fit the data with 21 sites, whereas linear programming fit the data equally well with 9 sites. Multiresponse fitting, involving simultaneous fluorescence and pH measurements, improved model discrimination. Deconvolution of the excitation versus emission fluorescence surface for SRFA establishes a minimum of five sites. Diprotic sites are also required for the five fluorescent sites, and one non-fluorescent monoprotic site was added to accommodate the pH data. Consistent with greater complexity, the multiresponse method had broader confidence limits than the uniresponse methods, but corresponded better with the accepted total carboxylic content for SRFA. Overall there was a 40% standard deviation in total carboxylic content for the multiresponse fitting, versus 10% and 1% for least-squares and linear programming, respectively.

  5. Chromium fractionation and speciation in natural waters.

    Science.gov (United States)

    Pereira, Catarinie Diniz; Techy, João Gabriel; Ganzarolli, Edgard Moreira; Quináia, Sueli Pércio

    2012-05-01

    It is common for leather industries to dump chromium-contaminated effluent into rivers and other bodies of water. Thus, it is crucial to know the impacts caused by this practice to the environment. A study on chromium partitioning and speciation, with determination at trace levels, was carried out in a potentially contaminated creek. Chromium fractionation and speciation was performed using a flow-injection preconcentration system and detection by flame atomic absorption spectrometry. High levels of this element were found in the particulate material (449-9320 mg kg(-1)), which indicates its compatibility with this fraction. The concentration of Cr(iii) in the water samples collected ranged from 5.2-105.2 μg L(-1). Cr(vi) was always below of the DL (0.3 μg L(-1)). Chromium accumulation observed in the sediment (873-1691 mg kg(-1)) may confirm contamination due to the long term release of contaminated effluents in the creek.

  6. Speciation of animal fat: Needs and challenges.

    Science.gov (United States)

    Hsieh, Yun-Hwa Peggy; Ofori, Jack Appiah

    2017-05-24

    The use of pork fat is a concern for Muslims and Jews, who for religious reasons avoid consuming anything that is pig-derived. The use of bovine materials, including beef fat, is prohibited in Hinduism and may also pose a risk of carrying the infectious agent for bovine spongiform encephalopathy. Vegetable oils are sometimes adulterated with animal fat or pork fat with beef fat for economic gain. The development of methods to determine the species origin of fat has therefore become a priority due to the complex and global nature of the food trade, which creates opportunities for the fraudulent use of these animal fats as food ingredients. However, determining the species origin of fats in processed foods or composite blends is an arduous task as the adulterant has a composition that is very similar to that of the original fat or oil. This review examines some of the methods that have been developed for fat speciation, including both fat-based and DNA-based methods, their shortcomings, and the need for additional alternatives. Protein-based methods, specifically immunoassays targeting residual proteins in adipose tissue, that are being explored by researchers as a new tool for fat speciation will also be discussed.

  7. The diversity and structure of marine protists in the coastal waters of China revealed by morphological observation and 454 pyrosequencing

    Science.gov (United States)

    Liu, Yun; Song, Shuqun; Chen, Tiantian; Li, Caiwen

    2017-04-01

    Pyrosequencing of the 18S rRNA gene has been widely adopted to study the eukaryotic diversity in various types of environments, and has an advantage over traditional morphology methods in exploring unknown microbial communities. To comprehensively assess the diversity and community composition of marine protists in the coastal waters of China, we applied both morphological observations and high-throughput sequencing of the V2 and V3 regions of 18S rDNA simultaneously to analyze samples collected from the surface layer of the Yellow and East China Seas. Dinoflagellates, diatoms and ciliates were the three dominant protistan groups as revealed by the two methods. Diatoms were the first dominant protistan group in the microscopic observations, with Skeletonema mainly distributed in the nearshore eutrophic waters and Chaetoceros in higher temperature and higher pH waters. The mixotrophic dinoflagellates, Gymnodinium and Gyrodinium, were more competitive in the oligotrophic waters. The pyrosequencing method revealed an extensive diversity of dinoflagellates. Chaetoceros was the only dominant diatom group in the pyrosequencing dataset. Gyrodinium represented the most abundant reads and dominated the offshore oligotrophic protistan community as they were in the microscopic observations. The dominance of parasitic dinoflagellates in the pyrosequencing dataset, which were overlooked in the morphological observations, indicates more attention should be paid to explore the potential role of this group. Both methods provide coherent clustering of samples. Nutrient levels, salinity and pH were the main factors influencing the distribution of protists. This study demonstrates that different primer pairs used in the pyrosequencing will indicate different protistan community structures. A suitable marker may reveal more comprehensive composition of protists and provide valuable information on environmental drivers.

  8. EPA’s SPECIATE 4.4 Database:Development and Uses

    Science.gov (United States)

    SPECIATE is the U.S. Environmental Protection Agency's (EPA)repository of volatile organic gas and particulate matter (PM) speciation profiles for air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, VOC, total...

  9. Sexual selection and magic traits in speciation with gene flow

    Directory of Open Access Journals (Sweden)

    Maria R. SERVEDIO, Michael KOPP

    2012-06-01

    Full Text Available The extent to which sexual selection is involved in speciation with gene flow remains an open question and the subject of much research. Here, we propose that some insight can be gained from considering the concept of magic traits (i.e., traits involved in both reproductive isolation and ecological divergence. Both magic traits and other, “non-magic”, traits can contribute to speciation via a number of specific mechanisms. We argue that many of these mechanisms are likely to differ widely in the extent to which they involve sexual selection. Furthermore, in some cases where sexual selection is present, it may be prone to inhibit rather than drive speciation. Finally, there are a priori reasons to believe that certain categories of traits are much more effective than others in driving speciation. The combination of these points suggests a classification of traits that may shed light on the broader role of sexual selection in speciation with gene flow. In particular, we suggest that sexual selection can act as a driver of speciation in some scenarios, but may play a negligible role in potentially common categories of magic traits, and may be likely to inhibit speciation in common categories of non-magic traits [Current Zoology 58 (3: 507–513, 2012].

  10. Speciation issues in food control - are we ready?

    International Nuclear Information System (INIS)

    Sloth, J.J.; Hedegaard, R.V.; Julshamn, K.; Trier, X.T.; Larsen, E.H.

    2009-01-01

    Full text: Our understanding of the mechanisms of biological activities and biotransformation of trace elements has improved during recent years with the help of chemical speciation studies. However, the most important practical application of elemental speciation is in the area of toxicology. Toxicological knowledge on the individual chemical elemental species should lead to more specific legislation of hazardous substances. Presently, European legislation concerning food safety is based on total element concentrations expressed as maximum limits. The lecture focuses on the present situation for speciation in food control and discusses the latest and expected future developments within this area. (author)

  11. NICKEL SPECIATION OF URBAN PARTICULATE MATTER

    Energy Technology Data Exchange (ETDEWEB)

    Kevin C. Galbreath; Charlene R. Crocker; Carolyn M. Nyberg; Frank E. Huggins; Gerald P. Huffman

    2003-10-01

    A four-step sequential Ni extraction method, summarized in Table AB-1, was evaluated for identifying and quantifying the Ni species occurring in urban total suspended particulate (TSP) matter and fine particulate matter (<10 {micro}m [PM{sub 10}] and <2.5 {micro}m [PM{sub 2.5}] in aerodynamic diameter). The extraction method was originally developed for quantifying soluble, sulfidic, elemental, and oxidic forms of Ni that may occur in industrial atmospheres. X-ray diffraction (XRD) and x-ray absorption fine structure (XAFS) spectroscopy were used to evaluate the Ni species selectivity of the extraction method. Uncertainties in the chemical speciation of Ni in urban PM{sub 10} and PM{sub 2.5} greatly affect inhalation health risk estimates, primarily because of the large variability in acute, chronic, and cancer-causing effects for different Ni compounds.

  12. Selenium speciation from farm to faeces

    International Nuclear Information System (INIS)

    Larsen, E.H.; Kapolna, E.; Hillestroem, P.R.; Laursen, K.; Budek, A.; Husted, S.; Buegel, S.

    2009-01-01

    Full text:The content and speciation of Se were studied in food crops originating from organic and conventional cultivation schemes. Additionally, carrots and onions were biofortified and intrinsically labelled using foliar spraying with isotopically enriched 77 SeO 3 -2 . HPLC-ICPMS and HPLC-ESIMS/MS analysis revealed that Se was mainly metabolized to 77 SeMet and to Me 77 SeCys, also in carrot. The 77 Se plants were processed to food (50 μg 77 Se/d) for a human intervention study. The isotopic enrichment by 77 Se as well as 67 Zn and 65 Cu in urine and faeces was determined by ICP(DRC)MS and the mineral absorption rates estimated. (author)

  13. Chemical speciation of radionuclides migrating in groundwaters

    International Nuclear Information System (INIS)

    Robertson, D.; Schilk, A.; Abel, K.; Lepel, E.; Thomas, C.; Pratt, S.; Cooper, E.; Hartwig, P.; Killey, R.

    1994-04-01

    In order to more accurately predict the rates and mechanisms of radionuclide migration from low-level waste disposal facilities via groundwater transport, ongoing studies are being conducted at field sites at Chalk River Laboratories to identify and characterize the chemical speciation of mobile, long-lived radionuclides migrating in groundwaters. Large-volume water sampling techniques are being utilized to separate and concentrate radionuclides into particular, cationic, anionic, and nonionic chemical forms. Most radionuclides are migrating as soluble, anionic species that appear to be predominantly organoradionuclide complexes. Laboratory studies utilizing anion exchange chromatography have separated several anionically complexed radionuclides, e.g., 60 Co and 106 Ru, into a number of specific compounds or groups of compounds. Further identification of the anionic organoradionuclide complexes is planned utilizing high resolution mass spectrometry. Large-volume ultra-filtration experiments are characterizing the particulate forms of radionuclides being transported in these groundwaters

  14. Sex chromosomes and speciation in Drosophila

    Science.gov (United States)

    Presgraves, Daven C.

    2010-01-01

    Two empirical rules suggest that sex chromosomes play a special role in speciation. The first is Haldane's rule— the preferential sterility and inviability of species hybrids of the heterogametic (XY) sex. The second is the disproportionately large effect of the X chromosome in genetic analyses of hybrid sterility. Whereas the causes of Haldane's rule are well established, the causes of the ‘large X-effect’ have remained controversial. New genetic analyses in Drosophila confirm that the X is a hotspot for hybrid male sterility factors, providing a proximate explanation for the large X-effect. Several other new findings— on faster X evolution, X chromosome meiotic drive, and the regulation of the X chromosome in the male-germline— provide plausible evolutionary explanations for the large X-effect. PMID:18514967

  15. Speciation of actinides in marine waters

    International Nuclear Information System (INIS)

    Roberts, R.A.

    1984-01-01

    The oxidation state distribution of plutonium in seawater, pore water from marine sediments, and a series of model solutions similar to seawater was measured using a TTA solvent extraction technique and α liquid scintillation counting methods. Electromigration was used to compare migration behavior of americium in 0.7M NaCl solutions (pH 6.5 to 8.0) with the behavior calculated from predicted speciation. In all pH 8 solutions studied, Pu(VI) was rapidly reduced to Pu(V). In 0.7M NaCl, pH 8.0, and artifical seawater (no organics), the Pu(V) formed was stable. In real seawater (with organic components), a rapid reduction of Pu(VI) to Pu(IV) was also observed. The Pu(V) formed in seawater was metastable; a very slow reduction to Pu(IV) occurred. This reduction was catalyzed by light. Humic acid (obtained from marine sediments from the Bahama Islands), was added to 0.7M NaCl, pH 8.0 solutions to determine its effect on Pu redox reactions. The effect was similar to the reductions in seawater. Increasing the humic acid concentration decreased the amount of Pu(V) which was formed and favored the IV state. The americium electromigration experiments showed a +0.12 net charge for the Am complexes formed in 0.7M NaCl solutions from pH 7.0 to 8.0. This value was smaller than the charge of +0.94 calculated from predicted speciation

  16. Identification and analysis of common bean (Phaseolus vulgaris L. transcriptomes by massively parallel pyrosequencing

    Directory of Open Access Journals (Sweden)

    Thimmapuram Jyothi

    2011-10-01

    Full Text Available Abstract Background Common bean (Phaseolus vulgaris is the most important food legume in the world. Although this crop is very important to both the developed and developing world as a means of dietary protein supply, resources available in common bean are limited. Global transcriptome analysis is important to better understand gene expression, genetic variation, and gene structure annotation in addition to other important features. However, the number and description of common bean sequences are very limited, which greatly inhibits genome and transcriptome research. Here we used 454 pyrosequencing to obtain a substantial transcriptome dataset for common bean. Results We obtained 1,692,972 reads with an average read length of 207 nucleotides (nt. These reads were assembled into 59,295 unigenes including 39,572 contigs and 19,723 singletons, in addition to 35,328 singletons less than 100 bp. Comparing the unigenes to common bean ESTs deposited in GenBank, we found that 53.40% or 31,664 of these unigenes had no matches to this dataset and can be considered as new common bean transcripts. Functional annotation of the unigenes carried out by Gene Ontology assignments from hits to Arabidopsis and soybean indicated coverage of a broad range of GO categories. The common bean unigenes were also compared to the bean bacterial artificial chromosome (BAC end sequences, and a total of 21% of the unigenes (12,724 including 9,199 contigs and 3,256 singletons match to the 8,823 BAC-end sequences. In addition, a large number of simple sequence repeats (SSRs and transcription factors were also identified in this study. Conclusions This work provides the first large scale identification of the common bean transcriptome derived by 454 pyrosequencing. This research has resulted in a 150% increase in the number of Phaseolus vulgaris ESTs. The dataset obtained through this analysis will provide a platform for functional genomics in common bean and related legumes and

  17. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus microplus through tag-encoded pyrosequencing

    Directory of Open Access Journals (Sweden)

    Bendele Kylie G

    2011-01-01

    Full Text Available Abstract Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be

  18. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing

    Science.gov (United States)

    2011-01-01

    Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus) microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be pathogenic to its vertebrate hosts

  19. saosakwe@yahoo.com Chemical Speciation and Mobility of Some

    African Journals Online (AJOL)

    Michael Horsfall

    ABSTRACT: The mobility of some heavy metals (Fe, Co, Ni and Mn) in soils around ... Sampling and Analysis: Soil samples were collected ..... Speciation Studies of trace elements levels in .... Characterization of Radioactive Particles in the.

  20. Pb Speciation Data to Estimate Lead Bioavailability to Quail

    Data.gov (United States)

    U.S. Environmental Protection Agency — Linear combination fitting data for lead speciation of soil samples evaluated through an in-vivo/in-vitro correlation for quail exposure. This dataset is associated...

  1. Speciation of arsenic and mercury in feed: why and how?

    DEFF Research Database (Denmark)

    Hedegaard, Rikke Susanne Vingborg; Sloth, Jens Jørgen

    2011-01-01

    The understanding of the mechanisms of biological activities and biotransformation of trace elements such as arsenic and mercury has improved during recent years with the help of chemical speciation studies. However, the most important practical application of elemental speciation is in the area ...... in feed as well as initiatives for the establishment of standardized methods for determination of inorganic arsenic and methylmercury are presented.......The understanding of the mechanisms of biological activities and biotransformation of trace elements such as arsenic and mercury has improved during recent years with the help of chemical speciation studies. However, the most important practical application of elemental speciation is in the area...... of toxicology. Toxicological knowledge on the individual trace element species can lead to more specific legislation of hazardous substances found in feed. Examples here are arsenic, where the inorganic forms are the most toxic, and mercury, where the organic form methylmercury is more toxic than inorganic...

  2. Speciation and Persistence of Dimethoate in the Aquatic Environment

    African Journals Online (AJOL)

    Speciation and Persistence of Dimethoate in the Aquatic Environment: Characterization in Terms of a Rate Model that Takes Into Account Hydrolysis, Photolysis, Microbial Degradation and Adsorption of the Pesticide by Colloidal and Sediment Particles.

  3. Speciation and internal dosimetry: from chemical species to dosimetric models

    International Nuclear Information System (INIS)

    Paquet, F.; Frelon, S.; Cote, G.; Madic, C.

    2004-01-01

    Speciation studies refer to the distribution of species in a particular sample or matrix. These studies are necessary to improve the description, understanding and prediction of trace element kinetics and toxicity. In case of internal contamination with radionuclides, speciation studies could help to improve both the biokinetic and dosimetric models for radionuclides. There are different methods to approach the speciation of radionuclide in a biological system, depending on the degree of accuracy needed and the level of uncertainties accepted. Among them, computer modelling and experimental determination are complementary approaches. This paper describes what is known about speciation of actinides in blood, GI-tract, liver and skeleton and of their consequences in terms of internal dosimetry. The conclusion is that such studies provide very valuable data and should be targeted in the future on some specific tissues and biomolecules. (authors)

  4. The contribution of chemical speciation to internal dosimetry

    International Nuclear Information System (INIS)

    Paquet, F.; Frelon, S.; Cote, G.; Madic, C.

    2003-01-01

    Speciation studies refer to the distribution of species in a particular sample or matrix. These studies are necessary to improve the description, understanding and prediction of trace element kinetics and toxicity. In the case of internal contamination with radionuclides, speciation studies could help to improve both the biokinetic and dosimetric models for radionuclides. There are different methods to approach the speciation of radionuclides in a biological system, depending on the degree of accuracy needed and the level of uncertainties accepted. Among them, computer modelling and experimental determination are complementary approaches. This paper describes what is known about speciation of actinides in blood, GI tract, liver and skeleton and of their consequences in terms of internal dosimetry. The conclusion is that such studies provide very valuable data and should be targeted in the future on some specific tissues and biomolecules. (author)

  5. Genomic support for speciation and specificity of baculoviruses

    NARCIS (Netherlands)

    Jakubowska, A.K.

    2010-01-01

    Keywords: baculovirus, insects, speciation, genomics, phylogeny, host specificity

    The Baculoviridae comprise a large family of double-stranded DNA viruses infecting
    arthropods. In this thesis two baculoviruses, Leucoma salicis nucleopolyhedrovirus
    (LesaNPV) and Agrotis

  6. The reality and importance of founder speciation in evolution.

    Science.gov (United States)

    Templeton, Alan R

    2008-05-01

    A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone. (c) 2008 Wiley Periodicals, Inc.

  7. Electrochemical metal speciation in natural and model polyelectrolyte systems

    OpenAIRE

    Hoop, van den, M.A.G.T.

    1994-01-01

    The purpose of the research described in this thesis was to examine the applicability of electro-analytical techniques in obtaining information on the speciation of metals, i.e. their distribution over different physico-chemical forms, in aquatic systems containing charged macromolecules. In chapter 1 a general introduction is given to (i) metal speciation in aquatic systems, (ii) (bio)polyelectrolytes and their counterion distributions and (iii) electrochemical ...

  8. How humans drive speciation as well as extinction

    DEFF Research Database (Denmark)

    Bull, Joseph William; Maron, M.

    2016-01-01

    influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature— considering phylogenetic diversity...... and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity....

  9. Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing.

    Science.gov (United States)

    Peng, Qian; Yang, Yanping; Guo, Yanyun; Han, Ye

    2015-08-01

    The vinegar pei harbors complex bacterial communities. Prior studies revealing the bacterial diversity involved were mainly conducted by culture-dependent methods and PCR-DGGE. In this study, 454 pyrosequencing was used to investigate the bacterial communities in vinegar pei during the acetic acid fermentation (AAF) of Tianjin Duliu aged vinegar (TDAV). The results showed that there were 7 phyla and 24 families existing in the vinegar pei, with 2 phyla (Firmicutes, Protebacteria) and 4 families (Lactobacillaceae, Acetobacteracae, Enterobacteriaceae, Chloroplast) predominating. The genus-level identification revealed that 9 genera were the relatively stable, consistent components in different stages of AAF, including the most abundant genus Lactobacillus followed by Acetobacter and Serratia. Additionally, the bacterial community in the early fermentation stage was more complex than those in the later stages, indicating that the accumulation of organic acids provided an appropriate environment to filter unwanted bacteria and to accelerate the growth of required ones. This study provided basic information of bacterial patterns in vinegar pei and relevant changes during AAF of TDAV, and could be used as references in the following study on the implementation of starter culture as well as the improvement of AAF process.

  10. Complete genome sequence of a novel Plum pox virus strain W isolate determined by 454 pyrosequencing.

    Science.gov (United States)

    Sheveleva, Anna; Kudryavtseva, Anna; Speranskaya, Anna; Belenikin, Maxim; Melnikova, Natalia; Chirkov, Sergei

    2013-10-01

    The near-complete (99.7 %) genome sequence of a novel Russian Plum pox virus (PPV) isolate Pk, belonging to the strain Winona (W), has been determined by 454 pyrosequencing with the exception of the thirty-one 5'-terminal nucleotides. This region was amplified using 5'RACE kit and sequenced by the Sanger method. Genomic RNA released from immunocaptured PPV particles was employed for generation of cDNA library using TransPlex Whole transcriptome amplification kit (WTA2, Sigma-Aldrich). The entire Pk genome has identity level of 92.8-94.5 % when compared to the complete nucleotide sequences of other PPV-W isolates (W3174, LV-141pl, LV-145bt, and UKR 44189), confirming a high degree of variability within the PPV-W strain. The isolates Pk and LV-141pl are most closely related. The Pk has been found in a wild plum (Prunus domestica) in a new region of Russia indicating widespread dissemination of the PPV-W strain in the European part of the former USSR.

  11. Isolation of 18 Microsatellite Loci in the Desert Mistletoe Phoradendron californicum (Santalaceae Via 454 Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Juan M. Arroyo

    2013-12-01

    Full Text Available Premise of the study: Microsatellite primers were developed for the parasitic mistletoe Phoradendron californicum to investigate to what extent population genetic structure depends on host tree distribution within a highly fragmented landscape. Methods and Results: Fourteen unlinked polymorphic and four monomorphic nuclear microsatellite markers were developed using a genomic shotgun pyrosequencing method. A total of 187 alleles plus four monomorphic loci alleles were found in 98 individuals sampled in three populations from the Sonoran Desert in the Baja California peninsula (Mexico. Loci averaged 13.3 alleles per locus (range 4–28, and observed and expected heterozygosities within populations varied from 0.167–0.879 and 0.364–0.932, respectively. Conclusions: Levels of polymorphism of the reported markers are adequate for studies of diversity and fragmentation in natural populations of this parasitic plant. Cross-species amplifications in P. juniperinum and P. diguetianum only showed four markers that could be useful in P. diguetianum.

  12. Arbuscular mycorrhizal fungi assemblages in Chernozem great groups revealed by massively parallel pyrosequencing.

    Science.gov (United States)

    Dai, Mulan; Hamel, Chantal; St Arnaud, Marc; He, Yong; Grant, Cynthia; Lupwayi, Newton; Janzen, Henry; Malhi, Sukhdev S; Yang, Xiaohong; Zhou, Zhiqin

    2012-01-01

    The arbuscular mycorrhizal (AM) fungal resources present in wheat fields of the Canadian Prairie were explored using 454 pyrosequencing. Of the 33 dominant AM fungal operational taxonomic units (OTUs) found in the 76 wheat fields surveyed at anthesis in 2009, 14 clustered as Funneliformis - Rhizophagus, 16 as Claroideoglomus, and 3 as Diversisporales. An OTU of Funneliformis mosseae and one OTU of Diversisporales each accounted for approximately 16% of all AM fungal OTUs. The former was ubiquitous, and the latter was mainly restricted to the Black and Dark Brown Chernozems. AM fungal OTU community composition was better explained by the Chernozem great groups (P = 0.044) than by measured soil properties. Fifty-two percent of the AM fungal OTUs were unrelated to measured soil properties. Black Chernozems hosted the largest AM fungal OTU diversity and almost twice the number of AM fungal sequences seen in Dark Brown Chernozems, the great group ranking second for AM fungal sequence abundance. Brown Chernozems hosted the lowest AM fungal abundance and an AM fungal diversity as low as that seen in Gray soils. We concluded that Black Chernozems are most conducive to AM fungal proliferation. AM fungi are generally distributed according to Chernozem great groups in the Canadian Prairie, although some taxa are evenly distributed in all soil groups.

  13. Pyrosequencing analysis of oral microbiota in children with severe early childhood dental caries.

    Science.gov (United States)

    Jiang, Wen; Zhang, Jie; Chen, Hui

    2013-11-01

    Severe early childhood caries are a prevalent public health problem among preschool children throughout the world. However, little is known about the microbiota found in association with severe early childhood caries. Our study aimed to explore the bacterial microbiota of dental plaques to study the etiology of severe early childhood caries through pyrosequencing analysis based on 16S rRNA gene V1-V3 hypervariable regions. Forty participants were enrolled in the study, and we obtained twenty samples of supragingival plaque from caries-free subjects and twenty samples from subjects with severe early childhood caries. A total of 175,918 reads met the quality control standards, and the bacteria found belonged to fourteen phyla and sixty-three genera. Our results show the overall structure and microbial composition of oral bacterial communities, and they suggest that these bacteria may present a core microbiome in the dental plaque microbiota. Three genera, Streptococcus, Granulicatella, and Actinomyces, were increased significantly in children with severe dental cavities. These data may facilitate improvements in the prevention and treatment of severe early childhood caries.

  14. Relationship of children's salivary microbiota with their caries status: a pyrosequencing study.

    Science.gov (United States)

    Gomar-Vercher, S; Cabrera-Rubio, R; Mira, A; Montiel-Company, J M; Almerich-Silla, J M

    2014-12-01

    Different dental caries status could be related with alterations in oral microbiota. Previous studies have collected saliva as a representative medium of the oral ecosystem. The purpose of this study was to assess the composition of oral microbiota and its relation to the presence of dental caries at different degrees of severity. One hundred ten saliva samples from 12-year-old children were taken and divided into six groups defined in strict accordance with their dental caries prevalence according to the International Caries Detection and Assessment System II criteria. These samples were studied by pyrosequencing PCR products of the 16S ribosomal RNA gene. The results showed statistically significant intergroup differences at the class and genus taxonomic levels. Streptococcus is the most frequent genus in all groups; although it did not show intergroup statistical differences. In patients with cavities, Porphyromonas and Prevotella showed an increasing percentage compared to healthy individuals. Bacterial diversity diminished as the severity of the disease increased, so those patients with more advanced stages of caries presented less bacterial diversity than healthy subjects. Although microbial composition tended to be different, the intragroup variation is large, as evidenced by the lack of clear intragroup clustering in principal component analyses. Thus, no clear differences were found, indicating that using bacterial composition as the sole source of biomarkers for dental caries may not be reliable in the unstimulated saliva samples used in the current study.

  15. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

    Directory of Open Access Journals (Sweden)

    Asker Noomi

    2009-07-01

    Full Text Available Abstract Background The teleost Zoarces viviparus (eelpout lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this species genome has however restrained the use of efficient molecular-level assays, such as gene expression microarrays. Results In the present study we present the first comprehensive characterization of the Zoarces viviparus liver transcriptome. From 400,000 reads generated by massively parallel pyrosequencing, more than 50,000 pieces of putative transcripts were assembled, annotated and functionally classified. The data was estimated to cover roughly 40% of the total transcriptome and homologues for about half of the genes of Gasterosteus aculeatus (stickleback were identified. The sequence data was consequently used to design an oligonucleotide microarray for large-scale gene expression analysis. Conclusion Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates enough genomic information for adequate de novo assembly of a large number of genes in a higher vertebrate. The generated sequence data, including the validated microarray probes, are publicly available to promote genome-wide research in Zoarces viviparus.

  16. Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing.

    Science.gov (United States)

    Smith, Drake M; Snow, David E; Rees, Eric; Zischkau, Ann M; Hanson, J Delton; Wolcott, Randall D; Sun, Yan; White, Jennifer; Kumar, Shashi; Dowd, Scot E

    2010-09-21

    Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities. Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics. Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.

  17. Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Randall D

    2010-09-01

    Full Text Available Abstract Background Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories. Methods Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP, a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities. Results Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics. Conclusions Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.

  18. Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Eiko E Kuramae

    Full Text Available We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age in pots associated with four maize cultivars, including two genetically modified (GM cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA. The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most "active" fungi (as recovered via RNA. Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production. Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.

  19. Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere.

    Science.gov (United States)

    Yousaf, Sohail; Bulgari, Daniela; Bergna, Alessandro; Pancher, Michael; Quaglino, Fabio; Casati, Paola; Campisano, Andrea

    2014-01-01

    Generally, plants are not considered as hosts for human and animal pathogens (HAP). The recent produce-associated outbreaks of food-borne diseases have drawn attention toward significant deficiencies in our understanding of the ecology of HAP, and their potential for interkingdom transfer. To examine the association of microorganisms classified as HAP with plants, we surveyed the presence and distribution of HAP bacterial taxa (henceforth HAPT, for brevity's sake) in the endosphere of grapevine (Vitis vinifera L.) both in the plant stems and leaves. An enrichment protocol was used on leaves to detect taxa with very low abundance in undisturbed tissues. We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). The majority of the bacterial sequences in the genus Propionibacterium, from grapevine leaf and stem, were identified as P. acnes. Clostridia were detected in leaves and stems, but their number was much higher in leaves after enrichment. HAPT were indentified both in leaves and wood of grapevines. This depicts the ability of these taxa to be internalized within plant tissues and maintain their population levels in a variety of environments. Our analysis highlighted the presence of HAPT in the grapevine endosphere and unexpected occurrence of these bacterial taxa in this atypical environment.

  20. Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes.

    Directory of Open Access Journals (Sweden)

    Meng Zhang

    Full Text Available Despite recent successes in the control of dental caries, the mechanism of caries development remains unclear. To investigate the causes of dental decay, especially in early childhood caries, the supragingival microflora composition of 20 twins with discordant caries phenotypes were analyzed using high-throughput pyrosequencing. In addition, the parents completed a lifestyle questionnaire. A total of 228,789 sequencing reads revealed 10 phyla, 84 genera, and 155 species of microflora, the relative abundances of these strains varied dramatically among the children, Comparative analysis between groups revealed that Veillonella, Corynebacterium and Actinomyces were presumed to be caries-related genera, Fusobacterium, Kingella and Leptotrichia were presumed to be healthy-related genus, yet this six genera were not statistically significant (P>0.05. Moreover, a cluster analysis revealed that the microbial composition of samples in the same group was often dissimilar but that the microbial composition observed in twins was usually similar. Although the genetic and environmental factors that strongly influence the microbial composition of dental caries remains unknown, we speculate that genetic factors primarily influence the individual's susceptibility to dental caries and that environmental factors primarily regulate the microbial composition of the dental plaque and the progression to caries. By using improved twins models and increased sample sizes, our study can be extended to analyze the specific genetic and environmental factors that affect the development of caries.

  1. Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing

    Science.gov (United States)

    Jing, H.; Rocke, E.; Kong, L.; Xia, X.; Liu, H.; Landry, M. R.

    2015-08-01

    Marine planktonic protists, including microalgae and protistan grazers, are an important contributor to global primary production and carbon and mineral cycles, however, little is known about their population shifts along the oxic-anoxic gradient in the water column. We used 454 pyrosequencing of the 18S rRNA gene and gene transcripts to study the community composition of whole and active protists throughout a water column in the Costa Rica Dome, where a stable oxygen minimum zone (OMZ) exists at a depth of 400~700 m. A clear shift of protist composition from photosynthetic Dinoflagellates in the surface to potential parasitic Dinoflagellates and Ciliates in the deeper water was revealed along the vertical profile at both rRNA and rDNA levels. Those protist groups recovered only at the rDNA level represent either lysed aggregates sinking from the upper waters or potential hosts for parasitic groups. UPGMA clustering demonstrated that total and active protists in the anoxic core of OMZ (550 m) were distinct from those in other water depths. The reduced community diversity and presence of a parasitic/symbiotic trophic lifestyle in the OMZ, especially the anoxic core, suggests that OMZs can exert a selective pressure on protist communities. Such changes in community structure and a shift in trophic lifestyle could result in a modulation of the microbial loop and associated biogeochemical cycling.

  2. Rhizosphere bacteriome of the medicinal plant Sapindus saponaria L. revealed by pyrosequencing.

    Science.gov (United States)

    Garcia, A; Polonio, J C; Polli, A D; Santos, C M; Rhoden, S A; Quecine, M C; Azevedo, J L; Pamphile, J A

    2016-11-03

    Sapindus saponaria L. of Sapindaceae family is popularly known as soldier soap and is found in Central and South America. A study of such medicinal plants might reveal a more complex diversity of microorganisms as compared to non-medicinal plants, considering their metabolic potential and the chemical communication between their natural microbiota. Rhizosphere is a highly diverse microbial habitat with respect to both the diversity of species and the size of the community. Rhizosphere bacteriome associated with medicinal plant S. saponaria is still poorly known. The objective of this study was to assess the rhizosphere microbiome of the medicinal plant S. saponaria using pyrosequencing, a culture-independent approach that is increasingly being used to estimate the number of bacterial species present in different environments. In their rhizosphere microbiome, 26 phyla were identified from 5089 sequences of 16S rRNA gene, with a predominance of Actinobacteria (33.54%), Acidobacteria (22.62%), and Proteobacteria (24.72%). The rarefaction curve showed a linear increase, with 2660 operational taxonomic units at 3% distance sequence dissimilarity, indicating that the rhizosphere microbiome associated with S. saponaria was highly diverse with groups of bacteria important for soil management, which could be further exploited for agricultural and biotechnological purposes.

  3. Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing.

    Science.gov (United States)

    Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin; Zhou, Zhi; Wu, Chen; Nagarajan, Sanjay

    2015-01-01

    Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere.

  4. Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Lisa-Maree Gulino

    Full Text Available Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering. Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales. These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

  5. A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis.

    Science.gov (United States)

    Harris, Stephen; Croft, Julie; O'Flynn, Ciaran; Deusch, Oliver; Colyer, Alison; Allsopp, Judi; Milella, Lisa; Davis, Ian J

    2015-01-01

    Periodontitis is the most frequently diagnosed health problem in cats yet little is known about the bacterial species important for the disease. The objective of this study was to identify bacterial species associated with health, gingivitis or mild periodontitis (gingivitis or mild periodontitis. Pyrosequencing of the V1-V3 region of the 16S rDNA from these plaque samples generated more than one million reads and identified a total of 267 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all gingival health categories, particularly in health along with Moraxella and Fusobacteria. The Peptostreptococcaceae were the most abundant family in gingivitis and mild periodontitis. Logistic regression analysis identified species from various genera that were significantly associated with health, gingivitis or mild periodontitis. The species identified were very similar to those observed in canine plaque in the corresponding health and disease states. Such similarities were not observed between cat and human at the bacterial species level but with disease progression similarities did emerge at the phylum level. This suggests that interventions targeted at human pathogenic species will not be effective for use in cats but there is more potential for commonalities in interventions for cats and dogs.

  6. Comparative transcriptomic analysis of two closely related ground beetle species with marked genital divergence using pyrosequencing.

    Science.gov (United States)

    Fujimaki, Kotaro; Fujisawa, Tomochika; Yazawa, Shigenobu; Nishimura, Osamu; Sota, Teiji

    2014-09-01

    Ground beetles of the subgenus Ohomopterus (genus Carabus) show marked divergence in species-specific male and female genital morphologies, which contributes to reproductive isolation among species. Characterizing the genetic basis of species-specific genital morphology is essential for understanding their diversification, but genomic information on Ohomopterus is not yet available. We analyzed mRNA extracted from abdominal sections of the last instar larvae and pupae of two sister species, Carabus (Ohomopterus) iwawakianus and C. (O.) uenoi, which show marked differences in genital morphology, to compare transcriptomic profiles using Roche 454 pyrosequencing. We obtained 1,608,572 high-quality reads and assembled them into 176,278 unique sequences, of which 66,049 sequences were combined into 12,662 clusters. Differential expression analyses for sexed pupae suggested that four and five clusters were differentially expressed between species for males and females, respectively. We also identified orthologous sequences of genes involved in genital development in Drosophila, which potentially affect genital development and species-specific genital morphology in Ohomopterus. This study provides the first large transcriptomic data set for a morphologically diversified beetle group, which can facilitate future studies on the genetic basis of species-specific genitalia.

  7. [The quantitative testing of V617F mutation in gen JAK2 using pyrosequencing technique].

    Science.gov (United States)

    Dunaeva, E A; Mironov, K O; Dribnokhodova, T E; Subbotina, E E; Bashmakova; Ol'hovskiĭ, I A; Shipulin, G A

    2014-11-01

    The somatic mutation V617F in gen JAK2 is a frequent cause of chronic myeloprolific diseases not conditioned by BCR/ABL mutation. The quantitative testing of relative percentage of mutant allele can be used in establishing severity of disease and its prognosis and in prescription of remedy inhibiting activity of JAK2. To quantitatively test mutation the pyrosequencing technique was applied. The developed technique permits detecting and quantitatively, testing percentage of mutation fraction since 7%. The "gray zone" is presented by samples with percentage of mutant allele from 4% to 7%. The dependence of expected percentage of mutant fraction in analyzed sample from observed value of signal is described by equation of line with regression coefficients y = - 0.97, x = -1.32 and at that measurement uncertainty consists ± 0.7. The developed technique is approved officially on clinical material from 192 patients with main forms of myeloprolific diseases not conditioned by BCR/ABL mutation. It was detected 64 samples with mautant fraction percentage from 13% to 91%. The developed technique permits implementing monitoring of therapy of myeloprolific diseases and facilitates to optimize tactics of treatment.

  8. Multifocal fibrosing thyroiditis and its association with papillary thyroid carcinoma using BRAF pyrosequencing.

    Science.gov (United States)

    Frank, Renee; Baloch, Zubair W; Gentile, Caren; Watt, Christopher D; LiVolsi, Virginia A

    2014-09-01

    Multifocal fibrosing thyroiditis (MFT) is characterized by numerous foci of fibrosis in a stellate configuration with fibroelastotic and fibroblastic centers entrapping epithelial structures. MFT has been proposed as a risk factor for papillary thyroid carcinoma (PTC) development. We attempted to identify whether MFT showed such molecular changes and could possibly be related to PTC. We identified seven cases of PTC with MFT in our institutional pathology database and personal consult service of one of the authors (VAL) for the years 1999 to 2012. Areas of PTC, MFT, and normal tissue were selected for BRAF analysis. Macro-dissection, DNA extraction and PCR amplification, and pyrosequencing were performed to detect BRAF mutations in codon 600. All of the MFT lesions and normal thyroid tissue were negative for BRAF mutations. Of the seven PTCs analyzed, five (71 %) were negative for BRAF mutations, while two cases were positive. In our study, none of the MFT lesions harbored BRAF mutations, whereas 29 % (two of seven) PTCs in the same gland were positive. Hence, in this small study, we found no evidence that the MFT lesion is a direct precursor to PTC. It is likely an incidental bystander in the process and a reflection of the background thyroiditis.

  9. The Prognostic Value of Pyrosequencing-Detected MGMT Promoter Hypermethylation in Newly Diagnosed Patients with Glioblastoma

    Directory of Open Access Journals (Sweden)

    Veronica Villani

    2015-01-01

    Full Text Available O6-methylguanine-DNA-methyltransferase (MGMT has emerged as a relevant predictor of therapeutic response and good prognosis in patients with glioblastoma (GBM. Transcriptionally active MGMT rapidly removes the alkyl adducts, preventing the formation of cross-links and thereby causing resistance to alkylating drugs. Studies with pyrosequencing (PSQ showed that this technique has a higher reproducibility and sensitivity than other techniques. However, the definition of a prognostically relevant threshold for the percentage of MGMT methylation remains one of the most critical issues in the use of PSQ analysis. The aim of this study was to define the cut-off value correlated with good favourable prognostic outcomes. We retrospectively analyzed 51 patients (33 males, 18 females with GBM who underwent surgery or biopsy. The Receiver Operating Characteristics analysis showed that the best possible criteria for PSQ-detected percentage of MGMT methylation that predicted progression-free survival (PFS and overall survival (OS were 19% and 13%, respectively. Patients with ≤19% of PSQ-detected MGMT had a shorter PFS (HR: 0.24, p<0.01; those ones with ≤13% had a shorter OS (HR: 0.33, p<0.05. Our study reinforces the importance of MGMT in the management of GBM patients, but future studies with larger sample sizes are warranted to confirm our findings.

  10. Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

    Science.gov (United States)

    Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y H; Maguire, Anita J; Kienzle, Marco; Klieve, Athol V

    2013-01-01

    Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

  11. Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae.

    Science.gov (United States)

    Castro-Carrera, T; Toral, P G; Frutos, P; McEwan, N R; Hervás, G; Abecia, L; Pinloche, E; Girdwood, S E; Belenguer, A

    2014-03-01

    Developing novel strategies to increase the content of bioactive unsaturated fatty acids (FA) in ruminant-derived products requires a deeper understanding of rumen biohydrogenation and bacteria involved in this process. Although high-throughput pyrosequencing may allow for a great coverage of bacterial diversity, it has hardly been used to investigate the microbiology of ruminal FA metabolism. In this experiment, 454 pyrosequencing and a molecular fingerprinting technique (terminal restriction fragment length polymorphism; T-RFLP) were used concurrently to assess the effect of diet supplementation with marine algae (MA) on the rumen bacterial community of dairy sheep. Eleven lactating ewes were divided in 2 lots and offered a total mixed ration based on alfalfa hay and concentrate (40:60), supplemented with 0 (control) or 8 (MA) g of MA/kg of dry matter. After 54 d on treatments, animals were slaughtered and samples of rumen content and fluid were collected separately for microbial analysis. Pyrosequencing yielded a greater coverage of bacterial diversity than T-RFLP and allowed the identification of low abundant populations. Conversely, both molecular approaches pointed to similar conclusions and showed that relevant changes due to MA addition were observed within the major ruminal phyla, namely Bacteroidetes, Firmicutes, and Proteobacteria. Decreases in the abundance of unclassified Bacteroidales, Porphyromonadaceae, and Ruminococcaceae and increases in as-yet uncultured species of the family Succinivibrionaceae, might be related to a potential role of these groups in different pathways of rumen FA metabolism. Diet supplementation with MA, however, had no effect on the relative abundance of Butyrivibrio and Pseudobutyrivibrio genera. In addition, results from both 454 pyrosequencing and T-RFLP indicate that the effect of MA was rather consistent in rumen content or fluid samples, despite inherent differences between these fractions in their bacterial composition

  12. MGMT promoter methylation determined by HRM in comparison to MSP and pyrosequencing for predicting high-grade glioma response.

    Science.gov (United States)

    Switzeny, Olivier J; Christmann, Markus; Renovanz, Mirjam; Giese, Alf; Sommer, Clemens; Kaina, Bernd

    2016-01-01

    The DNA repair protein O(6)-methylguanine-DNA methyltransferase (MGMT) causes resistance of cancer cells to alkylating agents and, therefore, is a well-established predictive marker for high-grade gliomas that are routinely treated with alkylating drugs. Since MGMT is highly epigenetically regulated, the MGMT promoter methylation status is taken as an indicator of MGMT silencing, predicting the outcome of glioma therapy. MGMT promoter methylation is usually determined by methylation specific PCR (MSP), which is a labor intensive and error-prone method often used semi-quantitatively. Searching for alternatives, we used closed-tube high resolution melt (HRM) analysis, which is a quantitative method, and compared it with MSP and pyrosequencing regarding its predictive value. We analyzed glioblastoma cell lines with known MGMT activity and formalin-fixed samples from IDH1 wild-type high-grade glioma patients (WHO grade III/IV) treated with radiation and temozolomide by HRM, MSP, and pyrosequencing. The data were compared as to progression-free survival (PFS) and overall survival (OS) of patients exhibiting the methylated and unmethylated MGMT status. A promoter methylation cut-off level relevant for PFS and OS was determined. In a multivariate Cox regression model, methylation of MGMT promoter of high-grade gliomas analyzed by HRM, but not MSP, was found to be an independent predictive marker for OS. Univariate Kaplan-Meier analyses revealed for PFS and OS a significant and better discrimination between methylated and unmethylated tumors when quantitative HRM was used instead of MSP. Compared to MSP and pyrosequencing, the HRM method is simple, cost effective, highly accurate and fast. HRM is at least equivalent to pyrosequencing in quantifying the methylation level. It is superior in predicting PFS and OS of high-grade glioma patients compared to MSP and, therefore, can be recommended being used routinely for determination of the MGMT status of gliomas.

  13. Microplanktonic community structure in a coastal system relative to a Phaeocystis bloom inferred from morphological and tag pyrosequencing methods.

    Directory of Open Access Journals (Sweden)

    Sébastien Monchy

    Full Text Available BACKGROUND: Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC, have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. METHODOLOGY AND PRINCIPAL FINDINGS: The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. CONCLUSIONS: Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the

  14. Microbial Diversity of Bovine Mastitic Milk as Described by Pyrosequencing of Metagenomic 16s rDNA

    OpenAIRE

    Oikonomou, Georgios; Machado, Vinicius Silva; Santisteban, Carlos; Schukken, Ynte Hein; Bicalho, Rodrigo Carvalho

    2012-01-01

    Dairy cow mastitis is an important disease in the dairy industry. Different microbial species have been identified as causative agents in mastitis, and are traditionally diagnosed by bacterial culture. The objective of this study was to use metagenomic pyrosequencing of bacterial 16S rRNA genes to investigate bacterial DNA diversity in milk samples of mastitic and healthy dairy cows and compare the results with those obtained by classical bacterial culture. One hundred and thirty-six milk sam...

  15. Pyrosequencing Analysis of the Microbial Diversity of Airag, Khoormog and Tarag, Traditional Fermented Dairy Products of Mongolia

    OpenAIRE

    OKI, Kaihei; DUGERSUREN, Jamyan; DEMBEREL, Shirchin; WATANABE, Koichi

    2014-01-01

    Here, we used pyrosequencing to obtain a detailed analysis of the microbial diversities of traditional fermented dairy products of Mongolia. From 22 Airag (fermented mare’s milk), 5 Khoormog (fermented camel’s milk) and 26 Tarag (fermented milk of cows, goats and yaks) samples collected in the Mongolian provinces of Arhangai, Bulgan, Dundgobi, Tov, Uburhangai and Umnugobi, we obtained a total of 81 operational taxonomic units, which were assigned to 15 families, 21 genera and 41 species in 3 ...

  16. Self-consistent approach for neutral community models with speciation

    Science.gov (United States)

    Haegeman, Bart; Etienne, Rampal S.

    2010-03-01

    Hubbell’s neutral model provides a rich theoretical framework to study ecological communities. By incorporating both ecological and evolutionary time scales, it allows us to investigate how communities are shaped by speciation processes. The speciation model in the basic neutral model is particularly simple, describing speciation as a point-mutation event in a birth of a single individual. The stationary species abundance distribution of the basic model, which can be solved exactly, fits empirical data of distributions of species’ abundances surprisingly well. More realistic speciation models have been proposed such as the random-fission model in which new species appear by splitting up existing species. However, no analytical solution is available for these models, impeding quantitative comparison with data. Here, we present a self-consistent approximation method for neutral community models with various speciation modes, including random fission. We derive explicit formulas for the stationary species abundance distribution, which agree very well with simulations. We expect that our approximation method will be useful to study other speciation processes in neutral community models as well.

  17. Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology

    Directory of Open Access Journals (Sweden)

    Elie Jami

    2014-01-01

    Full Text Available The mammalian gut houses a complex microbial community which is believed to play a significant role in host physiology. In recent years, several microbial community analysis methods have been implemented to study the whole gut microbial environment, in contrast to classical microbiological methods focusing on bacteria which can be cultivated. One of these is automated ribosomal intergenic spacer analysis (ARISA, an inexpensive and popular way of analyzing bacterial diversity and community fingerprinting in ecological samples. ARISA uses the natural variability in length of the DNA fragment found between the 16S and 23S genes in different bacterial lineages to infer diversity. This method is now being supplanted by affordable next-generation sequencing technologies that can also simultaneously annotate operational taxonomic units for taxonomic identification. We compared ARISA and pyrosequencing of samples from the rumen microbiome of cows, previously sampled at different stages of development and varying in microbial complexity using several ecological parameters. We revealed close agreement between ARISA and pyrosequencing outputs, especially in their ability to discriminate samples from different ecological niches. In contrast, the ARISA method seemed to underestimate sample richness. The good performance of the relatively inexpensive ARISA makes it relevant for straightforward use in bacterial fingerprinting analysis as well as for quick cross-validation of pyrosequencing data.

  18. Identification and genotyping of molluscum contagiosum virus from genital swab samples by real-time PCR and Pyrosequencing.

    Science.gov (United States)

    Trama, Jason P; Adelson, Martin E; Mordechai, Eli

    2007-12-01

    Laboratory diagnosis of molluscum contagiosum virus (MCV) is important as lesions can be confused with those caused by Cryptococcus neoformans, herpes simplex virus, human papillomavirus, and varicella-zoster virus. To develop a rapid method for identifying patients infected with MCV via swab sampling. Two dual-labeled probe real-time PCR assays, one homologous to the p43K gene and one to the MC080R gene, were designed. The p43K PCR was designed to be used in conjunction with Pyrosequencing for confirmation of PCR products and discrimination between MCV1 and MCV2. Both PCR assays were optimized with respect to reaction components, thermocycling parameters, and primer and probe concentrations. The specificities of both PCR assays were confirmed by non-amplification of 38 known human pathogens. Sensitivity assays demonstrated detection of as few as 10 copies per reaction. Testing 703 swabs, concordance between the two real-time PCR assays was 99.9%. Under the developed conditions, Pyrosequencing of the p43K PCR product was capable of providing enough nucleotide sequence to definitively differentiate MCV1 and MCV2. These real-time PCR assays can be used for the rapid, sensitive, and specific detection of MCV and, when combined with Pyrosequencing, can further discriminate between MCV1 and MCV2.

  19. Uranium Speciation and Bioavailability in Aquatic Systems: An Overview

    Directory of Open Access Journals (Sweden)

    Scott J. Markich

    2002-01-01

    Full Text Available The speciation of uranium (U in relation to its bioavailability is reviewed for surface waters (fresh- and seawater and their sediments. A summary of available analytical and modeling techniques for determining U speciation is also presented. U(VI is the major form of U in oxic surface waters, while U(IV is the major form in anoxic waters. The bioavailability of U (i.e., its ability to bind to or traverse the cell surface of an organism is dependent on its speciation, or physicochemical form. U occurs in surface waters in a variety of physicochemical forms, including the free metal ion (U4+ or UO22+ and complexes with inorganic ligands (e.g., uranyl carbonate or uranyl phosphate, and humic substances (HS (e.g., uranyl fulvate in dissolved, colloidal, and/or particulate forms. Although the relationship between U speciation and bioavailability is complex, there is reasonable evidence to indicate that UO22+ and UO2OH+ are the major forms of U(VI available to organisms, rather than U in strong complexes (e.g., uranyl fulvate or adsorbed to colloidal and/or particulate matter. U(VI complexes with inorganic ligands (e.g., carbonate or phosphate and HS apparently reduce the bioavailability of U by reducing the activity of UO22+ and UO2OH+. The majority of studies have used the results from thermodynamic speciation modeling to support these conclusions. Time-resolved laser-induced fluorescence spectroscopy is the only analytical technique able to directly determine specific U species, but is limited in use to freshwaters of low pH and ionic strength. Nearly all of the available information relating the speciation of U to its bioavailability has been derived using simple, chemically defined experimental freshwaters, rather than natural waters. No data are available for estuarine or seawater. Furthermore, there are no available data on the relationship between U speciation and bioavailability in sediments. An understanding of this relationship has been

  20. Behavioural divergence, interfertility and speciation: a review.

    Science.gov (United States)

    Pillay, Neville; Rymer, Tasmin L

    2012-11-01

    Behavioural compatibility between mates is fundamental for maintaining species boundaries and is achieved through appropriate communication between males and females. A breakdown in communication will lead to behavioural divergence and reduced interfertility. In this review, we summarise the current knowledge on male signals and female perception of these signals, integrating the literature from several taxa. We advocate that signaller-perceiver coevolution, which is usually under strong stabilising selection to enable mating, forms the basis of species-specific mate recognition systems. The mechanisms (phylogeny, geography, ecology, biology) shaping signaller-perceiver systems are briefly discussed to demonstrate the factors underpinning the evolution of signaller-perceiver couplings. Since divergence and diversification of communication systems is driven by changes in the mechanical properties of sensory pathways and morphology of sensory organs, we highlight signal modalities (auditory, olfactory, visual, tactile) and their importance in communication, particularly in mate selection. Next, using available examples and generating a stylised model, we suggest how disruption (biological, ecological, stochastic) of signaller-perceiver systems drives behavioural divergence and consequently results in reduced interfertility and speciation. Future studies should adopt an integrative approach, combining multiple parameters (phylogeny, adaptive utility of communication systems, genetics and biomechanical/biochemical properties of signals and perception) to explore how disruption of signaller-perceiver systems results in behavioural divergence and reduced interfertility. Finally, we question the impact that rapid environmental change will have on disruption of communication systems, potentially interfering with signaller-perceiver couplings. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Molecular activation analysis for chemical speciation studies

    International Nuclear Information System (INIS)

    Chai-Chifang

    1998-01-01

    The term of Molecular Activation Analysis (MAA) refers to an activation analysis method that is able to provide information about the chemical species of elements in system of interests, though its definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the total concentrations are often without any meaning when assessing health or environmental risks of trace elements.In practice, the MAA is a combination of conventional instrumental or radiochemical activation analysis and physical, chemical or biochemical separation techniques. The MAA is able to play a particular role in speciation studies. However, the critical point in the MAA is that it is not permitted to change the primitive chemical species of elements in systems, or the change has to be under control; in the meantime it is not allowed to form the 'new artifact' originally not present in systems. Some practical examples of MAA for chemical species research performed recently in our laboratory will be presented as follows: Chemical species of platinum group elements in sediment; Chemical species of iodine in marine algae; Chemical species of mercury in human tissues; Chemical species of selenium in corn; Chemical species of rare earth elements in natural plant, etc. The merits and limitations of MAA will be described as well. (author)

  2. Speciation needs in relation with environmental and biological purposes

    International Nuclear Information System (INIS)

    Moulin, V.; Ansoborlo, E.; Bion, L.; Doizi, D.; Moulin, C.; Cote, G.; Madic, C.; Van Der Lee, J.

    2004-01-01

    Radionuclides can occur in the environment either through chronic releases of nuclear facilities, or due to incidents or accidents. In order to study their behaviour in the environment (migration, retention, transfer, and in human organisms (metabolism, retention, excretion), it is of prime importance to know their solution chemistry, and more particularly thermodynamic constants, which will allow to determine their speciation. In fact, speciation governs the migration, the bioavailability and the toxicity of elements. Moreover, this knowledge is also of great interest for decorporation or decontamination purposes. In this framework, a CEA working group on speciation has been created in order to share data both on thermodynamic constants and on speciation analytical methods, interesting chemists, environmentalists and biologists. It has been focused, in a first time, on actinides, namely Th, U, Pu, Am, Np, taking into account their most important oxidation states occurring in environmental or biological environments: Th(IV), U(IV, VI), Pu(III, IV, VI), Am(III), Np(IV, V). A particular attention was devoted to the choice of ligands (inorganic and organic) for being the most representative of environmental and biological media. The thermodynamic database used is BASSIST for Base Applied to Speciation in Solution and at Interfaces and Solubility (developed by CEA), in interaction with the code JCHESS. Different examples will be then presented on the selection of data (thermodynamic constants, ligands of interest) through benchmark exercises (case of U(VI), Am(III), Pu(IV)) which will show the lacks or weakness of knowledge. Speciation diagrams will support these discussions. Moreover, analytical methods to determine thermodynamic constants or direct speciation will also be presented and discussed. (author)

  3. Guidelines for terms related to chemical speciations and fractionation of elements : definitions, structural aspects, and methodological approaches (IUPAC Recommendations 2000)

    NARCIS (Netherlands)

    Templeton, D.M.; Ariese, F.; Cornelis, R.; Danielsson, L.G.; Muntau, H.; Leeuwen, van H.P.; Lobínski, R.

    2000-01-01

    This paper presents definitions of concepts related to speciation of elements, more particularly speciation analysis and chemical species. Fractionation is distinguished from speciation analysis, and a general outline of fractionation procedures is given. We propose a categorization of species

  4. Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture.

    Directory of Open Access Journals (Sweden)

    Marcela S Montecchia

    Full Text Available The Southern Andean Yungas in Northwest Argentina constitute one of the main biodiversity hotspots in the world. Considerable changes in land use have taken place in this ecoregion, predominantly related to forest conversion to croplands, inducing losses in above-ground biodiversity and with potential impact on soil microbial communities. In this study, we used high-throughput pyrosequencing of the 16S ribosomal RNA gene to assess whether land-use change and time under agriculture affect the composition and diversity of soil bacterial communities. We selected two areas dedicated to sugarcane and soybean production, comprising both short- and long-term agricultural sites, and used the adjacent native forest soils as a reference. Land-use change altered the composition of bacterial communities, with differences between productive areas despite the similarities between both forests. At the phylum level, only Verrucomicrobia and Firmicutes changed in abundance after deforestation for sugarcane and soybean cropping, respectively. In cultivated soils, Verrucomicrobia decreased sharply (~80%, while Firmicutes were more abundant. Despite the fact that local diversity was increased in sugarcane systems and was not altered by soybean cropping, phylogenetic beta diversity declined along both chronosequences, evidencing a homogenization of soil bacterial communities over time. In spite of the detected alteration in composition and diversity, we found a core microbiome resistant to the disturbances caused by the conversion of forests to cultivated lands and few or none exclusive OTUs for each land-use type. The overall changes in the relative abundance of copiotrophic and oligotrophic taxa may have an impact in soil ecosystem functionality. However, communities with many taxa in common may also share many functional attributes, allowing to maintain at least some soil ecosystem services after forest conversion to croplands.

  5. Pyrosequencing-based analysis of the microbiome associated with the horn fly, Haematobia irritans.

    Directory of Open Access Journals (Sweden)

    Azhahianambi Palavesam

    Full Text Available The horn fly, Haematobia irritans, is one of the most economically important pests of cattle. Insecticides have been a major element of horn fly management programs. Growing concerns with insecticide resistance, insecticide residues on farm products, and non-availability of new generation insecticides, are serious issues for the livestock industry. Alternative horn fly control methods offer the promise to decrease the use of insecticides and reduce the amount of insecticide residues on livestock products and give an impetus to the organic livestock farming segment. The horn fly, an obligatory blood feeder, requires the help of microflora to supply additional nutrients and metabolize the blood meal. Recent advancements in DNA sequencing methodologies enable researchers to examine the microflora diversity independent of culture methods. We used the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP method to carry out the classification analysis of bacterial flora in adult female and male horn flies and horn fly eggs. The bTEFAP method identified 16S rDNA sequences in our samples which allowed the identification of various prokaryotic taxa associated with the life stage examined. This is the first comprehensive report of bacterial flora associated with the horn fly using a culture-independent method. Several rumen, environmental, symbiotic and pathogenic bacteria associated with the horn fly were identified and quantified. This is the first report of the presence of Wolbachia in horn flies of USA origin and is the first report of the presence of Rikenella in an obligatory blood feeding insect.

  6. Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing.

    Science.gov (United States)

    Li, Tongtong; Long, Meng; Gatesoupe, François-Joël; Zhang, Qianqian; Li, Aihua; Gong, Xiaoning

    2015-01-01

    Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29 ± 0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filter-feeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune

  7. Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.

    Directory of Open Access Journals (Sweden)

    James R White

    Full Text Available BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs. Approximately 65,550 rRNA sequences (24% could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa, and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa

  8. Cyanobacterial composition and spatial distribution based on pyrosequencing data in the Gurbantunggut Desert, Northwestern China.

    Science.gov (United States)

    Zhang, Bingchang; Li, Renhui; Xiao, Peng; Su, Yangui; Zhang, Yuanming

    2016-03-01

    Cyanobacteria are the primary colonizers and form a dominant component of soil photosynthetic communities in biological soil crusts. They are crucial in improving soil environments, namely accumulating soil carbon and nitrogen. Many classical studies have examined cyanobacterial diversity in desert crusts, but relatively few comprehensive molecular surveys have been conducted. We used 454 pyrosequencing of 16S rRNA to investigate cyanobacterial composition and distribution on regional scales in the Gurbantunggut Desert. The relationship between cyanobacterial distribution and environmental factors was also explored. A total of 24,973 cyanobacteria partial 16S rRNA gene sequences were obtained, and 507OTUs were selected, as most OTUs had very few reads. Among these, 347 OTU sequences were of cyanobacteria origin, belonging to Oscillatoriales, Nostocales, Chroococcales, and uncultured cyanobacterium clone, respectively. Microcoleus vaginatus, Chroococcidiopsis spp. and M. steenstrupii were the dominant species in most areas of the Gurbantunggut Desert. Compared with other desert, the Gurbantunggut Desert differed in the prominence of Chroococcidiopsis spp. and lack of Pseudanabaenales. Species composition and abundance of cyanobacteria also showed distinct variations. Soil texture, precipitation, and nutrients and salt levels affected cyanobacterial distribution. Increased precipitation was helpful in improving cyanobacterial diversity. A higher content of coarse sand promoted the colonization and growth of Oscillatoriales and some phylotypes of Chroococcales. The fine-textured soil with higher nutrients and salts supported more varied populations of cyanobacteria, namely some heterocystous cyanobacteria. The results suggested that the Gurbantunggut Desert was rich in cyanobacteria and that precipitation was a primary regulating factor for cyanobacterial composition on a regional scale. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

    Directory of Open Access Journals (Sweden)

    Hahn Daniel A

    2009-05-01

    Full Text Available Abstract Background Flesh flies in the genus Sarcophaga are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of Sarcophaga flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly Sarcophaga crassipalpis. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription. Results We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (ES. crassipalpis unigenes among GO Biological Process functional groups with that of the Drosophila melanogaster transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among S. crassipalpis, D. melanogaster, and Anopheles gambiae. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs. Conclusion Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential microsatellite and SNP markers that could be used in population and systematic

  10. Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing.

    Science.gov (United States)

    Li, Ou; Xiao, Rong; Sun, Lihua; Guan, Chenglin; Kong, Dedong; Hu, Xiufang

    2017-01-01

    As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ) to 96.08% (YN), and Delftia (10.39-38.42%), Burkholderia (2.71-15.98%), Escherichia/Shigella (4.90-25.12%), Pseudomonas (2.68-30.72%) and Sphingomonas (1.83-2.05%) dominated in four planting bases. Pseudomonas (17.94-22.06%), Escherichia/Shigella (6.59-11.59%), Delftia (9.65-22.14%) and Burkholderia (3.12-11.05%) dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples.

  11. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Özgül Inceoğlu

    Full Text Available BACKGROUND: Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process. METHODOLOGY/PRINCIPAL FINDINGS: DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample. Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria. Principal components analyses revealed that rhizosphere samples were significantly different from corresponding bulk soil in each growth stage. Furthermore, cultivar effects were found in the young plant stage, whereas these became insignificant in the flowering and senescence stages. Besides, an effect of time of season was observed for both rhizosphere and bulk soils. The analyzed rhizosphere samples of the potato cultivars were grouped into two groups, in accordance with the allocation of carbon to starch in their tubers, i.e. Aveka, Aventra and Karnico (high versus Premiere and Desiree (low and thus replicates per group were established. CONCLUSIONS: Across all potato cultivars, the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages. Furthermore, Pseudomonas, Beta-, Alpha- and

  12. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Benjamin M

    2008-03-01

    Full Text Available Abstract Background Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications followed by pyrosequencing, shotgun Sanger sequencing, and denaturing gradient gel electrophoresis were utilized to survey the major populations of bacteria that occur in the pathogenic biofilms of three types of chronic wound types: diabetic foot ulcers (D, venous leg ulcers (V, and pressure ulcers (P. Results There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, including Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia spp. Each of the wound types reveals marked differences in bacterial populations, such as pressure ulcers in which 62% of the populations were identified as obligate anaerobes. There were also populations of bacteria that were identified but not recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also compared to those obtained using traditional culture-based diagnostics. Only in one wound type did culture methods correctly identify the primary bacterial population indicating the need for improved diagnostic methods. Conclusion If clinicians can gain a better understanding of the wound's microbiota, it will give them a greater understanding of the wound's ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in

  13. Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Ou Li

    Full Text Available As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ to 96.08% (YN, and Delftia (10.39-38.42%, Burkholderia (2.71-15.98%, Escherichia/Shigella (4.90-25.12%, Pseudomonas (2.68-30.72% and Sphingomonas (1.83-2.05% dominated in four planting bases. Pseudomonas (17.94-22.06%, Escherichia/Shigella (6.59-11.59%, Delftia (9.65-22.14% and Burkholderia (3.12-11.05% dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples.

  14. Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing

    Science.gov (United States)

    Li, Ou; Sun, Lihua; Guan, Chenglin; Kong, Dedong

    2017-01-01

    As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ) to 96.08% (YN), and Delftia (10.39–38.42%), Burkholderia (2.71–15.98%), Escherichia/Shigella (4.90–25.12%), Pseudomonas (2.68–30.72%) and Sphingomonas (1.83–2.05%) dominated in four planting bases. Pseudomonas (17.94–22.06%), Escherichia/Shigella (6.59–11.59%), Delftia (9.65–22.14%) and Burkholderia (3.12–11.05%) dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples. PMID:28931073

  15. Prerequisites for Amplicon Pyrosequencing of Microbial Methanol Utilizers in the Environment

    Directory of Open Access Journals (Sweden)

    Steffen eKolb

    2013-09-01

    Full Text Available The commercial availability of next generation sequencing (NGS technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of PQQ-dependent methanol dehydrogenase (mxaF has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2, of the NAD-dependent MDH (mdh, of the methanol oxidoreductase of Actinobacteria (mdo, of the fungal FAD-dependent alcohol oxidase (mod1, mod2, and homologues, and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

  16. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  17. Insight into protist diversity in Arctic sea ice and melt-pond aggregate obtained by pyrosequencing

    Directory of Open Access Journals (Sweden)

    Estelle Silvia Kilias

    2014-11-01

    Full Text Available Protists in the central Arctic Ocean are adapted to the harsh environmental conditions of its various habitats. During the Polarstern cruise ARK-XXVI/3 in 2011, at one sea-ice station, large aggregates accumulated at the bottom of the melt ponds. In this study, the protist assemblages of the bottom layer of the sea-ice and melt-pond aggregate were investigated using flow cytometry and 454-pyrosequencing. The objective is to provide a first molecular overview of protist biodiversity in these habitats and to consider the overlaps and/or differences in the community compositions. Results of flow cytometry pointed to a cell size distribution that was dominated by 3–10 µm nanoflagellates. The phylogenetic classification of all sequences was conducted at a high taxonomic level, while a selection of abundant (≥1% of total reads sequences was further classified at a lower level. At a high taxonomic level, both habitats showed very similar community structures, dominated by chrysophytes and chlorophytes. At a lower taxonomic level, dissimilarities in the diversity of both groups were encountered in the abundant biosphere. While sea-ice chlorophytes and chrysophytes were dominated by Chlamydomonas/Chloromonas spp. and Ochromonas spp., the melt-pond aggregate was dominated by Carteria sp., Ochromonas spp. and Dinobryon faculiferum. We suppose that the similarities in richness and community structure are a consequence of melt-pond freshwater seeping through porous sea ice in late summer. Differences in the abundant biosphere nevertheless indicate that environmental conditions in both habitats vary enough to select for different dominant species.

  18. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback.

    Directory of Open Access Journals (Sweden)

    David A Marques

    2016-02-01

    Full Text Available Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this.

  19. Pollinator-Driven Speciation in Sexually Deceptive Orchids

    Directory of Open Access Journals (Sweden)

    Shuqing Xu

    2012-01-01

    Full Text Available Pollinator-mediated selection has been suggested to play a major role for the origin and maintenance of the species diversity in orchids. Sexually deceptive orchids are one of the prime examples for rapid, pollinator-mediated plant radiations, with many species showing little genetic differentiation, lack of postzygotic barriers, but strong prezygotic reproductive isolation. These orchids mimic mating signals of female insects and employ male insects as pollinators. This kind of sexual mimicry leads to highly specialised pollination and provides a good system for investigating the process of pollinator-driven speciation. Here, we summarise the knowledge of key processes of speciation in this group of orchids and conduct a meta-analysis on traits that contribute to species differentiation, and thus potentially to speciation. Our study suggests that pollinator shift through changes in floral scent is predominant among closely related species in sexually deceptive orchids. Such shifts can provide a mechanism for pollinator-driven speciation in plants, if the resulting floral isolation is strong. Furthermore, changes in floral scent in these orchids are likely controlled by few genes. Together these factors suggest speciation in sexually deceptive orchids may happen rapidly and even in sympatry, which may explain the remarkable species diversity observed in this plant group.

  20. Speciation and Health Risks of Atmospheric Nanoparticulates

    Science.gov (United States)

    Nguyen, Kennedy

    Exposure to air pollution causes several adverse health effects such as asthma, respiratory disease, cardiovascular disease, cancer, and premature death; and the San Joaquin Valley is one of the most heavily polluted regions in the US. The mountains that surround the valley allow air pollution, including particulate matter, to remain stagnant, prolonging the exposure of valley populations to it. The primary sources of particulate matter for this region are aluminosilicate dust from agricultural activities, and soot emissions from diesel trucks and vehicular traffic. A substantial fraction of emitted material is nanoparticulate matter (testing in cell culture studies, and correlation of particulate properties and sources with their negative health impacts. These results can help identify the sources of air pollution to prioritize for mitigation for the greatest health benefit. In addition, further chemical speciation can help monitor the results of such mitigation efforts. Here, natural particulate matter samples from Merced and Fresno, two cities in the San Joaquin Valley, were analyzed. Ultrafine particles present were 40 to 50 nm in diameter and mostly composed of aluminum, silicon, oxygen, and iron hydroxide. XAS data confirmed the presence of the aluminosilicate as smectite clay and the iron hydroxide as ferrihydrite. Furthermore, a chemical speciation study investigated industrial emissions of air particulate matter. Samples were analyzed using electron microscopy for elemental composition and size distribution, and found to contain fine metal particulates (lead and iron) that can lead to lung inflammation. From characterization data, in order to create a simplified proxy particle system for cell culture studies, amorphous silica particles were synthesized using a modified Stober Synthesis and coated with iron hydroxide. A range of iron hydroxide concentrations (0.06 to 1.63 mmol of iron per gram of silica) were used to test the effect of iron contamination on

  1. Study of Np speciation in citrate medium

    Energy Technology Data Exchange (ETDEWEB)

    Bonin, L.; Den Auwer, C.; Ansoborlo, E.; Moisy, P. [CEA Valrho - DEN/DRCP/SCPS, Bagnols sur Ceze (France); Cote, G. [ENSP - LECA, UMR 7575, Paris (France)

    2007-07-01

    In the framework of the French Environmental Nuclear Toxicology program, additional experiments related to the decorporation of actinides are planned. Decorporation is the removal or release from target organs (bones, liver, kidney..), tissues or cells of radioactive material previously incorporated in them, using chelating agents or other administrated pharmaceutical agents. The contradictory data on the neptunium complexation behaviour within blood and its transfer to target organs, as well as the inefficiency of therapeutic treatments, led us to study the complexation of this element with biological constituents. Within this purpose, the in vitro behaviour of Np(IV) and Np(V) in simple media simulating biological fluids was studied. This study was more specifically focused on the behaviour of neptunium with citrate ion, which is an essential component in a number of metalloenzyme active sites. In order to determine the speciation of this system, spectrophotometry was more particularly used. Concerning the complexation phenomenon, the existence of several complexes of Np(V) with various acido-basic forms of the citrate anion was observed; regarding Np(IV), complexes with Cit{sup 3-} have been observed. From the quantitative study of these equilibria, the values of the absolute constants for the complexation of Np(IV) and Np(V) with citrate were determined. Concerning the stability of neptunium towards oxydo-reduction, it was confirmed that Np(VI) was very quickly reduced to Np(V) by the citrate anions, whereas Np(IV) was stable. In the case of Np(V), it was observed that, depending on the pH and the citrate concentration, Np(V) was unstable and was reduced to Np(IV). The E-pH diagrams, constructed using the stability constants determined in this study, showed that this instability was due to the Np(V) disproportionation. (orig.)

  2. Voltammetric Investigation Of Hydrothermal Iron Speciation

    Directory of Open Access Journals (Sweden)

    Charlotte eKleint

    2016-05-01

    Full Text Available Hydrothermal vent fluids are highly enriched in iron (Fe compared to ambient seawater, and organic ligands may play a role in facilitating the transport of some hydrothermal Fe into the open ocean. This is important since Fe is a limiting micronutrient for primary production in large parts of the world`s surface ocean. We have investigated the concentration and speciation of Fe in several vent fluid and plume samples from the Nifonea vent field, Coriolis Troughs, New Hebrides Island Arc, South Pacific Ocean using competitive ligand exchange - adsorptive cathodic stripping voltammetry (CLE - AdCSV with salicylaldoxime (SA as the artificial ligand. Our results for total dissolved Fe (dFe in the buoyant hydrothermal plume samples showed concentrations up to 3.86 µM dFe with only a small fraction between 1.1% and 11.8% being chemically labile. Iron binding ligand concentrations ([L] were found in µM level with strong conditional stability constants up to log K[L],Fe3+ of 22.9. Within the non-buoyant hydrothermal plume above the Nifonea vent field, up to 84.7% of the available Fe is chemically labile and [L] concentrations up to 97 nM were measured. [L] was consistently in excess of Felab, indicating that all available Fe is being complexed, which in combination with high Felab values in the non-buoyant plume, signifies that a high fraction of hydrothermal dFe is potentially being transported away from the plume into the surrounding waters, contributing to the global oceanic Fe budget.

  3. Microimaging and tomography with chemical speciation

    Energy Technology Data Exchange (ETDEWEB)

    Rau, C. E-mail: rau@esrf.fr; Somogyi, A.; Simionovici, A

    2003-01-01

    Materials science deals with the study of the morphology of samples, their chemical composition and the relation between both. One general problem is the preservation of the sample throughout the different analyses, like it is often the case for classical chemical analysis. Destruction-free chemical speciation in three dimensions with micrometer resolution can be achieved by combining X-ray spectroscopy and imaging techniques. Highly brilliant radiation is needed for this purpose available at 3rd generation synchrotrons such as the ESRF. X-ray absorption near-edge spectroscopy (XANES) is a non-destructive well-known and established technique in chemistry. By scanning the X-ray energy in the vicinity (50-100 eV) of the absorption edge of an element, information can be obtained about the oxidation state of the probed atoms. The (conventional) technique mainly employed until now applies to homogeneous, specifically prepared flat samples where the measured signal can be considered as the average over the whole irradiated volume. This restriction for samples is partially released when the XANES method is combined with imaging techniques. 2D resolved data is acquired using area detectors or by scanning with a focussed beam. X-ray absorption tomography is a method of choice for investigating the 3D structure of objects and its dual energy version is used for getting information about the 3D distribution of a given element within the sample. Although the combination of XANES and tomography seems to be a natural extension of dual-energy tomography, in practice several experimental problems have to be overcome in order to obtain useable data. In the following we describe the results of XANES imaging and tomography obtained measuring a phantom sample of pure molybdenum compounds using a FreLoN 2000 camera system at the ESRF undulator beamline ID22. This system allowed making volume resolved distinctions between different oxidation states with spatial resolution in the

  4. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

    Directory of Open Access Journals (Sweden)

    Binhua Liang

    Full Text Available BACKGROUND: Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS: HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE: Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.

  5. Investigating ecological speciation in non-model organisms

    DEFF Research Database (Denmark)

    Foote, Andrew David

    2012-01-01

    Background: Studies of ecological speciation tend to focus on a few model biological systems. In contrast, few studies on non-model organisms have been able to infer ecological speciation as the underlying mechanism of evolutionary divergence. Questions: What are the pitfalls in studying ecological...... speciation in non-model organisms that lead to this bias? What alternative approaches might redress the balance? Organism: Genetically differentiated types of the killer whale (Orcinus orca) exhibiting differences in prey preference, habitat use, morphology, and behaviour. Methods: Review of the literature...... on killer whale evolutionary ecology in search of any difficulty in demonstrating causal links between variation in phenotype, ecology, and reproductive isolation in this non-model organism. Results: At present, we do not have enough evidence to conclude that adaptive phenotype traits linked to ecological...

  6. Simultaneous speciation of trace elements using chemical separation and neutron activation

    International Nuclear Information System (INIS)

    Chatt, A.

    2003-01-01

    Speciation neutron activation analysis (SNAA) is a sophisticated analytical technique which can be developed for studying the simultaneous speciation of a number of elements in a variety of matrices. The advantages of SNAA are demonstrated with typical examples such as (i) arsenic speciation in sea foods and water, and simultaneous speciation of (ii) arsenic, antimony and selenium in water, (iii) chlorine, bromine and iodine in fish, (iv) lanthanides in simulated vitrified waste, and (v) trace elements bound to proteins. (author)

  7. ISSEBETS 2009. 7. International Symposium on Speciation of Elements in Biological, Environmental and Toxicological Sciences

    International Nuclear Information System (INIS)

    2009-01-01

    The 7th ISSEBETS was held in August 2009 in city of Eger, Hungary. The main topics were: speciation of essential and toxic elements in food, in traditional drugs, designing functional foods through applied speciation, metallomics and metalloproteomics, metal species in health and disease, cycling of elemental species in the environment, speciation related regulations and legislation, metal environmental, bioremediation, quality assurance of speciation analysis. (S.I.)

  8. Meeting Disorders.

    Science.gov (United States)

    Yager, Joel; Katzman, Jeffrey W

    2017-12-01

    Although meetings are central to organizational work, considerable time devoted to meetings in Academic Health Centers appears to be unproductively spent. The primary purposes of this article are to delineate and describe Meeting Disorders, pathological processes resulting in these inefficient and ineffective scenarios, and Meeting Fatigue Disorder (MFD), a clinical syndrome. The paper also offers preliminary approaches to remedies. The authors integrate observations made during tens of thousands of hours in administrative meetings in academic medical settings with information in the literature regarding the nature, causes and potential interventions for dysfunctional groups and meetings. Meeting Disorders, resulting from distinct pathologies of leadership and organization, constitute prevalent subgroups of the bureaucrapathologies, pathological conditions caused by dysfunctional bureaucratic processes that generate excesses of wasted time, effort, and other resources. These disorders also generate frustration and demoralization among participants, contributing to professional burnout. Meeting Fatigue Disorder (MFD) is a subjective condition that develops in individuals who overdose on these experiences and may reflect one manifestation of burnout. Meeting disorders and Meeting Fatigue Disorder occur commonly in bureaucratic life. Resources and potential remedies are available to help ameliorate their more deleterious effects.

  9. Evaluation of persistence of resistant variants with ultra-deep pyrosequencing in chronic hepatitis C patients treated with telaprevir.

    Directory of Open Access Journals (Sweden)

    Xiomara V Thomas

    Full Text Available BACKGROUND & AIMS: Telaprevir, a hepatitis C virus NS3/4A protease inhibitor has significantly improved sustained viral response rates when given in combination with pegylated interferon alfa-2a and ribavirin, compared with current standard of care in hepatitis C virus genotype 1 infected patients. In patients with a failed sustained response, the emergence of drug-resistant variants during treatment has been reported. It is unclear to what extent these variants persist in untreated patients. The aim of this study was to assess using ultra-deep pyrosequencing, whether after 4 years follow-up, the frequency of resistant variants is increased compared to pre-treatment frequencies following 14 days of telaprevir treatment. METHODS: Fifteen patients from 2 previous telaprevir phase 1 clinical studies (VX04-950-101 and VX05-950-103 were included. These patients all received telaprevir monotherapy for 14 days, and 2 patients subsequently received standard of care. Variants at previously well-characterized NS3 protease positions V36, T54, R155 and A156 were assessed at baseline and after a follow-up of 4±1.2 years by ultra-deep pyrosequencing. The prevalence of resistant variants at follow-up was compared to baseline. RESULTS: Resistance associated mutations were detectable at low frequency at baseline. In general, prevalence of resistance mutations at follow-up was not increased compared to baseline. Only one patient had a small, but statistically significant, increase in the number of V36M and T54S variants 4 years after telaprevir-dosing. CONCLUSION: In patients treated for 14 days with telaprevir monotherapy, ultra-deep pyrosequencing indicates that long-term persistence of resistant variants is rare.

  10. A molecular gram stain using broad range PCR and pyrosequencing technology: a potentially useful tool for diagnosing orthopaedic infections.

    Science.gov (United States)

    Kobayashi, Naomi; Bauer, Thomas W; Togawa, Daisuke; Lieberman, Isador H; Sakai, Hiroshige; Fujishiro, Takaaki; Tuohy, Marion J; Procop, Gary W

    2005-06-01

    The bacteria associated with orthopaedic infections are usually common gram-positive and gram-negative bacteria. This fundamental grouping of bacteria is a necessary first step in the selection of appropriate antibiotics. Since polymerase chain reaction (PCR) is more rapid and may be more sensitive than culture, we developed a postamplification pyrosequencing method to subcategorize bacteria based on a few nucleotide polymorphisms in the 16S rRNA gene. We validated this method using well-characterized strains of bacteria and applied it to specimens from spinal surgery cases with suspected infections. Lysates of 114 bacteria including 75 species were created following standard cultivation to obtain DNA. The DNA was amplified by a broad-range real-time PCR. The amplicons were evaluated by pyrosequencing and were classified as gram-positive, gram-negative, or acid-fast bacilli based on the first three to five nucleotides sequenced. In addition, clinical cases of suspected infection were obtained from spinal surgery. The results of the "molecular Gram stain" were compared with the results of traditional Gram stain and culture. The lysates of 107 (93.9%) of the bacteria extracts tested were appropriately categorized as gram-positive and gram-negative or as acid-fast bacilli on the basis of this assay. The sensitivity and specificity of this assay were 100% and 97.4% for gram-positive and 88.3% and 100% for gram-negative isolates. All of the five clinical samples were appropriately categorized as containing gram-positive or gram-negative bacteria with this assay. This study demonstrates that high sensitivity and specificity of a molecular gram stain may be achieved using broad-range real-time PCR and pyrosequencing.

  11. Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Ingmar S Middelbos

    Full Text Available BACKGROUND: Dogs suffer from many of the same maladies as humans that may be affected by the gut microbiome, but knowledge of the canine microbiome is incomplete. This work aimed to use 16S rDNA tag pyrosequencing to phylogenetically characterize hindgut microbiome in dogs and determine how consumption of dietary fiber affects community structure. PRINCIPAL FINDINGS: Six healthy adult dogs were used in a crossover design. A control diet without supplemental fiber and a beet pulp-supplemented (7.5% diet were fed. Fecal DNA was extracted and the V3 hypervariable region of the microbial 16S rDNA gene amplified using primers suitable for 454-pyrosequencing. Microbial diversity was assessed on random 2000-sequence subsamples of individual and pooled DNA samples by diet. Our dataset comprised 77,771 reads with an average length of 141 nt. Individual samples contained approximately 129 OTU, with Fusobacteria (23-40% of reads, Firmicutes (14-28% of reads and Bacteroidetes (31-34% of reads being co-dominant phyla. Feeding dietary fiber generally decreased Fusobacteria and increased Firmicutes, but these changes were not equally apparent in all dogs. UniFrac analysis revealed that structure of the gut microbiome was affected by diet and Firmicutes appeared to play a strong role in by-diet clustering. CONCLUSIONS: Our data suggest three co-dominant bacterial phyla in the canine hindgut. Furthermore, a relatively small amount of dietary fiber changed the structure of the gut microbiome detectably. Our data are among the first to characterize the healthy canine gut microbiome using pyrosequencing and provide a basis for studies focused on devising dietary interventions for microbiome-associated diseases.

  12. Patterns of plant speciation in the Cape floristic region.

    Science.gov (United States)

    van der Niet, Timotheüs; Johnson, Steven D

    2009-04-01

    Plant species have accumulated in the Cape region of southern Africa to a much greater degree than in areas of equivalent size in the rest of the subcontinent. Although this could be a consequence simply of lower extinction rates in the Cape, most researchers have invoked high rates of ecological speciation, driven by unique aspects of the Cape environment, as the primary explanation for this richness. To assess these ideas, we analyzed the frequencies of ecological shifts among 188 sister species pairs obtained from molecular phylogenies of eight Cape clades. Ecological shifts were evident in 80% of sister species pairs, with general habitat, pollinator, and fire-survival strategy shifts being especially frequent. Contrary to an established idea that shifts in soil type are frequently associated with speciation of Cape taxa, these shifts were relatively rare, occurring in just 17% of species pairs. More cases of sister species divergence are accompanied solely by floral than by vegetative diversification, suggesting an important role for pollinator-driven speciation. In an analysis of two large orchid genera that have radiated in both the Cape and the rest of southern Africa, the frequency of ecological shifts (general habitat, soil type, altitude and flowering time), did not differ between sister species pairs in the Cape region and those outside it. Despite suggestions that Cape plants tend to have small range sizes and show fine-scale patterns of speciation, range size did not differ significantly between species in the Cape and those outside it. We conclude that ecological speciation is likely to have been important for radiation of the Cape flora, but there is no evidence as yet for special "Cape" patterns of ecological speciation.

  13. Towards accounting for dissolved iron speciation in global ocean models

    Directory of Open Access Journals (Sweden)

    A. Tagliabue

    2011-10-01

    Full Text Available The trace metal iron (Fe is now routinely included in state-of-the-art ocean general circulation and biogeochemistry models (OGCBMs because of its key role as a limiting nutrient in regions of the world ocean important for carbon cycling and air-sea CO2 exchange. However, the complexities of the seawater Fe cycle, which impact its speciation and bioavailability, are simplified in such OGCBMs due to gaps in understanding and to avoid high computational costs. In a similar fashion to inorganic carbon speciation, we outline a means by which the complex speciation of Fe can be included in global OGCBMs in a reasonably cost-effective manner. We construct an Fe speciation model based on hypothesised relationships between rate constants and environmental variables (temperature, light, oxygen, pH, salinity and assumptions regarding the binding strengths of Fe complexing organic ligands and test hypotheses regarding their distributions. As a result, we find that the global distribution of different Fe species is tightly controlled by spatio-temporal environmental variability and the distribution of Fe binding ligands. Impacts on bioavailable Fe are highly sensitive to assumptions regarding which Fe species are bioavailable and how those species vary in space and time. When forced by representations of future ocean circulation and climate we find large changes to the speciation of Fe governed by pH mediated changes to redox kinetics. We speculate that these changes may exert selective pressure on phytoplankton Fe uptake strategies in the future ocean. In future work, more information on the sources and sinks of ocean Fe ligands, their bioavailability, the cycling of colloidal Fe species and kinetics of Fe-surface coordination reactions would be invaluable. We hope our modeling approach can provide a means by which new observations of Fe speciation can be tested against hypotheses of the processes present in governing the ocean Fe cycle in an

  14. Pyrosequencing Reveals the Predominance of Pseudomonadaceae in Gut Microbiome of a Gall Midge

    Directory of Open Access Journals (Sweden)

    Raman Bansal

    2014-06-01

    Full Text Available Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654 high quality sequences of the V3 hypervariable region of the 16S rRNA gene were obtained through 454-pyrosequencing. From these sequences, 311 operational taxonomic units (OTUs were obtained at the >97% similarity cutoff. In the gut of 1st instar, otu01, a member of Pseudomonas, was predominant, representing 90.2% of total sequences. otu13, an unidentified genus in the Pseudomonadaceae family, represented 1.9% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 2nd instar, otu01 and otu13 decreased to 85.5% and 1.5%, respectively. otu04, a member of Buttiauxella, represented 9.7% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 3rd instar, otu01 and otu13 further decreased to 29.0% and 0%, respectively. otu06, otu08, and otu16, also three members of the Pseudomonadaceae family were 13.2%, 8.6%, and 2.3%, respectively. In addition, otu04 and otu14, two members of the Enterobacteriaceae family, were 4.7% and 2.5%; otu18 and otu20, two members of the Xanthomonadaceae family, were 1.3% and 1.2%, respectively; otu12, a member of Achromobacter, was 4.2%; otu19, a member of Undibacterium, was 1.4%; and otu9, otu10, and otu15, members of various families, were 6.1%, 6.3%, and 1.9%, respectively. The investigation into dynamics of Pseudomonas, the most abundant genera, revealed that its population level was at peak in freshly hatched or 1 day larvae as well as in later developmental stages, thus suggesting a prominent role for this bacterium in Hessian fly development and in its interaction with host plants. This study is the first comprehensive survey on bacteria associated with the gut of a gall

  15. Ultra-deep pyrosequencing (UDPS data treatment to study amplicon HCV minor variants.

    Directory of Open Access Journals (Sweden)

    Josep Gregori

    Full Text Available We have investigated the reliability and reproducibility of HCV viral quasispecies quantification by ultra-deep pyrosequencing (UDPS methods. Our study has been divided in two parts. First of all, by UDPS sequencing of clone mixes samples we have established the global noise level of UDPS and fine tuned a data treatment workflow previously optimized for HBV sequence analysis. Secondly, we have studied the reproducibility of the methodology by comparing 5 amplicons from two patient samples on three massive sequencing platforms (FLX+, FLX and Junior after applying the error filters developed from the clonal/control study. After noise filtering the UDPS results, the three replicates showed the same 12 polymorphic sites above 0.7%, with a mean CV of 4.86%. Two polymorphic sites below 0.6% were identified by two replicates and one replicate respectively. A total of 25, 23 and 26 haplotypes were detected by GS-Junior, GS-FLX and GS-FLX+. The observed CVs for the normalized Shannon entropy (Sn, the mutation frequency (Mf, and the nucleotidic diversity (Pi were 1.46%, 3.96% and 3.78%. The mean absolute difference in the two patients (5 amplicons each, in the GS-FLX and GS-FLX+, were 1.46%, 3.96% and 3.78% for Sn, Mf and Pi. No false polymorphic site was observed above 0.5%. Our results indicate that UDPS is an optimal alternative to molecular cloning for quantitative study of HCV viral quasispecies populations, both in complexity and composition. We propose an UDPS data treatment workflow for amplicons from the RNA viral quasispecies which, at a sequencing depth of at least 10,000 reads per strand, enables to obtain sequences and frequencies of consensus haplotypes above 0.5% abundance with no erroneous mutations, with high confidence, resistant mutants as minor variants at the level of 1%, with high confidence that variants are not missed, and highly confident measures of quasispecies complexity.

  16. Bacterial communities in the rhizosphere of amilaceous maize (Zea mays L. as assessed by pyrosequencing

    Directory of Open Access Journals (Sweden)

    David Correa-Galeote

    2016-07-01

    Full Text Available Maize (Zea mays L. is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere

  17. Pyrosequencing Reveals Soil Enzyme Activities and Bacterial Communities Impacted by Graphene and Its Oxides.

    Science.gov (United States)

    Rong, Yan; Wang, Yi; Guan, Yina; Ma, Jiangtao; Cai, Zhiqiang; Yang, Guanghua; Zhao, Xiyue

    2017-10-25

    Graphene (GN) and graphene oxides (GOs) are novel carbon nanomaterial; they have been attracting much attention because of their excellent properties and are widely applied in many areas, including energy, electronics, biomedicine, environmental science, etc. With industrial production and consumption of GN/GO, they will inevitably enter the soil and water environments. GN/GO may directly cause certain harm to microorganisms and lead to ecological and environmental risks. GOs are GN derivatives with abundant oxygen-containing functional groups in their graphitic backbone. The structure and chemistry of GN show obvious differences compared to those of GO, which lead to the different environmental behaviors. In this study, four different types of soil (S1-S4) were employed to investigate the effect of GN and GO on soil enzymatic activity, microbial population, and bacterial community through pyrosequencing of 16S rRNA gene amplicons. The results showed that soil enzyme activity (invertase, protease, catalase, and urease) and microbial population (bacteria, actinomycetes, and fungi) changed after GN/GO release into soils. Soil microbial community species are more rich, and the diversity also increases after GO/GN application. The phylum of Proteobacteria increased at 90 days after treatment (DAT) after GN/GO application. The phylum of Chloroflexi occurred after GN application at 90 DAT in S1 soil and reached 4.6%. Proteobacteria was the most abundant phylum in S2, S3, and S4 soils; it ranged from 43.6 to 71.4% in S2 soil, from 45.6 to 73.7% in S3 soil, and from 38.1 to 56.7% in S4 soil. The most abundant genera were Bacillus (37.5-47.0%) and Lactococcus (28.0-39.0%) in S1 soil, Lysobacter and Flavobacterium in S2 soil, Pedobacter in S3 soil, and Massilia in S4 soil. The effect of GN and GO on the soil microbial community is time-dependent, and there are no significant differences between the samples at 10 and 90 DAT.

  18. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

    Directory of Open Access Journals (Sweden)

    Sanz Libia

    2011-05-01

    Full Text Available Abstract Background A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects. Results The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27% were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements and class II (DNA transposons mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large

  19. The EU network on trace element speciation in full swing

    DEFF Research Database (Denmark)

    Cornelis, R.; Camara, C.; Ebdon, L.

    2000-01-01

    health and hygiene. The network covers a number of important issues including organotin compounds, chromium and nickel species, chemical characterisation of environmental and industrial particulate samples, risk assessment, selenium and a series of other essential and toxic elements in food, as well......The EC-funded thematic network 'Speciation 21' links scientists in analytical chemistry working in method development for the chemical speciation of trace elements, and potential users from industry and representatives of legislative agencies, in the field of environment, food and occupational...

  20. Speciation of Long-Lived Radionuclides in the Environment

    DEFF Research Database (Denmark)

    Hou, Xiaolin

    , isotopes of Pu, and 237Np in seawater, fresh water, soil, sediment, vegetations, and concrete. The developed methods are used for the investigation of the chemical speciation of these radionuclides as well as their environmental behaviours, especially in Danish environment. In addition the speciation of Pu...... isotopes in waste samples from the decommissioning of Danish nuclear facilities is also investigated. The report summarizes these works completed in this project. Through this research project, a number of research papers have been published in the scientific journals, the research results has also been...

  1. Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans

    Directory of Open Access Journals (Sweden)

    Raoult Didier

    2008-12-01

    Full Text Available Abstract Background Recent studies of 16S rRNA genes in the mammalian gut microbiota distinguished a higher Firmicutes/Bacteroidetes ratio in obese individuals compared to lean individuals. This ratio was estimated using a clonal Sanger sequencing approach which is time-consuming and requires laborious data analysis. In contrast, new high-throughput pyrosequencing technology offers an inexpensive alternative to clonal Sanger sequencing and would significantly advance our understanding of obesity via the development of a clinical diagnostic method. Here we present a cost-effective method that combines 16S rRNA pyrosequencing and DNA barcodes of the Firmicutes and Bacteroidetes 16S rRNA genes to determine the Firmicutes/Bacteroidetes ratio in the gut microbiota of obese humans. Results The main result was the identification of DNA barcodes targeting the Firmicutes and Bacteroidetes phyla. These barcodes were validated using previously published 16S rRNA gut microbiota clone libraries. In addition, an accurate F/B ratio was found when the DNA barcodes were applied to short pyrosequencing reads of published gut metagenomes. Finally, the barcodes were utilized to define the F/B ratio of 16S rRNA pyrosequencing data generated from brain abscess pus and cystic fibrosis sputum. Conclusion Using DNA barcodes of Bacteroidetes and Firmicutes 16S rRNA genes combined with pyrosequencing is a cost-effective method for monitoring relevant changes in the relative abundance of Firmicutes and Bacteroidetes bacterial communities in microbial ecosystems.

  2. STAFF MEETING

    CERN Document Server

    2003-01-01

    I should like to invite all members of the CERN Personnel to a meeting on Wednesday 25th June 2003 at 11.00 hrs - Auditorium, bldg. 500 to give a report on the outcome of the June Meetings of Council and its Committees. Closed-circuit transmission of the meeting will be available in the AB Auditorium (Prévessin), the AB Auditorium (Meyrin - bldg. 6), the IT Auditorium (bldg. 31) and the AT Auditorium (bldg. 30). Luciano Maiani Director General

  3. 454-Pyrosequencing Analysis of Bacterial Communities from Autotrophic Nitrogen Removal Bioreactors Utilizing Universal Primers: Effect of Annealing Temperature.

    Science.gov (United States)

    Gonzalez-Martinez, Alejandro; Rodriguez-Sanchez, Alejandro; Rodelas, Belén; Abbas, Ben A; Martinez-Toledo, Maria Victoria; van Loosdrecht, Mark C M; Osorio, F; Gonzalez-Lopez, Jesus

    2015-01-01

    Identification of anaerobic ammonium oxidizing (anammox) bacteria by molecular tools aimed at the evaluation of bacterial diversity in autotrophic nitrogen removal systems is limited by the difficulty to design universal primers for the Bacteria domain able to amplify the anammox 16S rRNA genes. A metagenomic analysis (pyrosequencing) of total bacterial diversity including anammox population in five autotrophic nitrogen removal technologies, two bench-scale models (MBR and Low Temperature CANON) and three full-scale bioreactors (anammox, CANON, and DEMON), was successfully carried out by optimization of primer selection and PCR conditions (annealing temperature). The universal primer 530F was identified as the best candidate for total bacteria and anammox bacteria diversity coverage. Salt-adjusted optimum annealing temperature of primer 530F was calculated (47°C) and hence a range of annealing temperatures of 44-49°C was tested. Pyrosequencing data showed that annealing temperature of 45°C yielded the best results in terms of species richness and diversity for all bioreactors analyzed.

  4. 16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease.

    Science.gov (United States)

    Suchodolski, Jan S; Dowd, Scot E; Wilke, Vicky; Steiner, Jörg M; Jergens, Albert E

    2012-01-01

    Canine idiopathic inflammatory bowel disease (IBD) is believed to be caused by a complex interaction of genetic, immunologic, and microbial factors. While mucosa-associated bacteria have been implicated in the pathogenesis of canine IBD, detailed studies investigating the enteric microbiota using deep sequencing techniques are lacking. The objective of this study was to evaluate mucosa-adherent microbiota in the duodenum of dogs with spontaneous idiopathic IBD using 16 S rRNA gene pyrosequencing. Biopsy samples of small intestinal mucosa were collected endoscopically from healthy dogs (n = 6) and dogs with moderate IBD (n = 7) or severe IBD (n = 7) as assessed by a clinical disease activity index. Total RNA was extracted from biopsy specimens and 454-pyrosequencing of the 16 S rRNA gene was performed on aliquots of cDNA from each dog. Intestinal inflammation was associated with significant differences in the composition of the intestinal microbiota when compared to healthy dogs. PCoA plots based on the unweighted UniFrac distance metric indicated clustering of samples between healthy dogs and dogs with IBD (ANOSIM, pmicrobial groups, which bear resemblance to dysbiosis reported in humans with chronic intestinal inflammation. These bacterial groups may serve as useful targets for monitoring intestinal inflammation.

  5. Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors.

    Science.gov (United States)

    Ontiveros-Valencia, Aura; Tang, Youneng; Zhao, He-Ping; Friese, David; Overstreet, Ryan; Smith, Jennifer; Evans, Patrick; Rittmann, Bruce E; Krajmalnik-Brown, Rosa

    2014-07-01

    We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO3(-)) and perchlorate (ClO4(-)) in contaminated groundwater. The groundwater also contained oxygen (O2) and sulfate (SO4(2-)), which became important electron sinks that affected the NO3(-) and ClO4(-) removal rates. Using pyrosequencing, we elucidated how important phylotypes of each "primary" microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO4(2-) reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the "primary" groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.

  6. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

    Science.gov (United States)

    Pires, Ana C C; Cleary, Daniel F R; Almeida, Adelaide; Cunha, Angela; Dealtry, Simone; Mendonça-Hagler, Leda C S; Smalla, Kornelia; Gomes, Newton C M

    2012-08-01

    Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.

  7. Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica as revealed by 454 pyrosequencing

    Directory of Open Access Journals (Sweden)

    Neng Fei eWang

    2015-10-01

    Full Text Available This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil in the Fildes Region (King George Island, Antarctica using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01, phosphate phosphorus (p < 0.01, organic carbon (p < 0.05, and organic nitrogen (p < 0.05 were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.

  8. 454-Pyrosequencing Analysis of Bacterial Communities from Autotrophic Nitrogen Removal Bioreactors Utilizing Universal Primers: Effect of Annealing Temperature

    Directory of Open Access Journals (Sweden)

    Alejandro Gonzalez-Martinez

    2015-01-01

    Full Text Available Identification of anaerobic ammonium oxidizing (anammox bacteria by molecular tools aimed at the evaluation of bacterial diversity in autotrophic nitrogen removal systems is limited by the difficulty to design universal primers for the Bacteria domain able to amplify the anammox 16S rRNA genes. A metagenomic analysis (pyrosequencing of total bacterial diversity including anammox population in five autotrophic nitrogen removal technologies, two bench-scale models (MBR and Low Temperature CANON and three full-scale bioreactors (anammox, CANON, and DEMON, was successfully carried out by optimization of primer selection and PCR conditions (annealing temperature. The universal primer 530F was identified as the best candidate for total bacteria and anammox bacteria diversity coverage. Salt-adjusted optimum annealing temperature of primer 530F was calculated (47°C and hence a range of annealing temperatures of 44–49°C was tested. Pyrosequencing data showed that annealing temperature of 45°C yielded the best results in terms of species richness and diversity for all bioreactors analyzed.

  9. Pyrosequencing, a method approved to detect the two major EGFR mutations for anti EGFR therapy in NSCLC

    Directory of Open Access Journals (Sweden)

    Richard Marie-Jeanne

    2011-05-01

    Full Text Available Abstract Background Epidermal Growth Factor Receptor (EGFR mutations, especially in-frame deletions in exon 19 (ΔLRE and a point mutation in exon 21 (L858R predict gefitinib sensitivity in patients with non-small cell lung cancer. Several methods are currently described for their detection but the gold standard for tissue samples remains direct DNA sequencing, which requires samples containing at least 50% of tumor cells. Methods We designed a pyrosequencing assay based on nested PCR for the characterization of theses mutations on formalin-fixed and paraffin-embedded tumor tissue. Results This method is highly specific and permits precise characterization of all the exon 19 deletions. Its sensitivity is higher than that of "BigDye terminator" sequencing and enabled detection of 3 additional mutations in the 58 NSCLC tested. The concordance between the two methods was very good (97.4%. In the prospective analysis of 213 samples, 7 (3.3% samples were not analyzed and EGFR mutations were detected in 18 (8.7% patients. However, we observed a deficit of mutation detection when the samples were very poor in tumor cells. Conclusions pyrosequencing is then a highly accurate method for detecting ΔLRE and L858R EGFR mutations in patients with NSCLC when the samples contain at least 20% of tumor cells.

  10. Pyrosequencing analysis of the microbial diversity of airag, khoormog and tarag, traditional fermented dairy products of mongolia.

    Science.gov (United States)

    Oki, Kaihei; Dugersuren, Jamyan; Demberel, Shirchin; Watanabe, Koichi

    2014-01-01

    Here, we used pyrosequencing to obtain a detailed analysis of the microbial diversities of traditional fermented dairy products of Mongolia. From 22 Airag (fermented mare's milk), 5 Khoormog (fermented camel's milk) and 26 Tarag (fermented milk of cows, goats and yaks) samples collected in the Mongolian provinces of Arhangai, Bulgan, Dundgobi, Tov, Uburhangai and Umnugobi, we obtained a total of 81 operational taxonomic units, which were assigned to 15 families, 21 genera and 41 species in 3 phyla. The genus Lactobacillus is a core bacterial component of Mongolian fermented milks, and Lactobacillus helveticus, Lactobacillus kefiranofaciens and Lactobacillus delbrueckii were the predominant species of lactic acid bacteria (LAB) in the Airag, Khoormog and Tarag samples, respectively. By using this pyrosequencing approach, we successfully detected most LAB species that have been isolated as well as seven LAB species that have not been found in our previous culture-based study. A subsequent analysis of the principal components of the samples revealed that L. delbrueckii, L. helveticus, L. kefiranofaciens and Streptococcus thermophilus were the main factors influencing the microbial diversity of these Mongolian traditional fermented dairy products and that this diversity correlated with the animal species from which the milk was sourced.

  11. Logic Meeting

    CERN Document Server

    Tugué, Tosiyuki; Slaman, Theodore

    1989-01-01

    These proceedings include the papers presented at the logic meeting held at the Research Institute for Mathematical Sciences, Kyoto University, in the summer of 1987. The meeting mainly covered the current research in various areas of mathematical logic and its applications in Japan. Several lectures were also presented by logicians from other countries, who visited Japan in the summer of 1987.

  12. Electrochemical metal speciation in natural and model polyelectrolyte systems

    NARCIS (Netherlands)

    Hoop, van den M.A.G.T.

    1994-01-01

    The purpose of the research described in this thesis was to examine the applicability of electro-analytical techniques in obtaining information on the speciation of metals, i.e. their distribution over different physico-chemical forms, in aquatic systems containing charged macromolecules.

  13. Speciation and determination of priority metals in sediments of Oyun ...

    African Journals Online (AJOL)

    This work was carried out to determine the concentrations, bioavailability and mobility of priority metals in sediments of Oyun River, Sango, Ilorin, Nigeria. The river sediments were sampled at six selected locations and the samples were analyzed for some certain priority metals to determine the concentration, speciation and ...

  14. Speciation and phase separation of water in quartz (A review ...

    African Journals Online (AJOL)

    By sp3-hybridization of electron bonds, the water molecule exhibits a tetrahedral charged structure, leading to various water point defects in the form of substitution of ... The formation of combined defect [SiO4]-H2O-M+ [M3+O4] upon water speciation (M+ is metallic ion), is an indication of the presence of hydrous species.

  15. Heavy metal speciation and their accumulation in sediments of Lake ...

    African Journals Online (AJOL)

    UFUOMA

    Key words: Heavy metals, chemical speciation, sediments, Burullus, Lake. INTRODUCTION ..... fuel for use in internal combustion engines and in making batteries. ..... (Tuner, 1989). According to this model, human risk assessment was .... 593 - 594. Hökanson L (1980). "Ecological Risk Index for Aquatic Pollution. Control.

  16. Comparative Studies of the Speciation Patterns of Nickel and ...

    African Journals Online (AJOL)

    Results of speciation stdies of nickel and chromium in wastewater, surface and groundwater systems using flame atomic absorption spectrometry (FAAS), graphite furnace atomic absorption spectrometry (GFAAS) and differential pulse adsorptive cathodic stripping voltammetry (DPAdCSV) are presented. Dimethylglyoxime ...

  17. Fractionation, characterization and speciation of heavy metals in ...

    African Journals Online (AJOL)

    Speciation of heavy metals in soils determines the availability for metals for plant uptake and potential for contamination of groundwater following application of composts to agricultural lands. Methods used to characterize heavy metals in solid phase of composts and compost amended soils include physical fractionation ...

  18. Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish

    NARCIS (Netherlands)

    Selz, O. M.; Thommen, R.; Maan, M. E.; Seehausen, O.

    Hybrid speciation is constrained by the homogenizing effects of gene flow from the parental species. In the absence of post-mating isolation due to structural changes in the genome, or temporal or spatial premating isolation, another form of reproductive isolation would be needed for homoploid

  19. The molecular basis of speciation: from patterns to processes, rules ...

    Indian Academy of Sciences (India)

    male; large X-effect; meiotic drive; genomic conflict. Abstract. The empirical study of speciation has brought us closer to unlocking the origins of life's vast diversity. By examining recently formed species, a number of general patterns, or rules, ...

  20. Mitochondrial Recombination and Introgression during Speciation by Hybridization.

    Science.gov (United States)

    Leducq, Jean-Baptiste; Henault, Mathieu; Charron, Guillaume; Nielly-Thibault, Lou; Terrat, Yves; Fiumera, Heather L; Shapiro, B Jesse; Landry, Christian R

    2017-08-01

    Genome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Heavy metal speciation and their accumulation in sediments of Lake ...

    African Journals Online (AJOL)

    Several sediment samples in Lake Burullus have been affected by the discharges of heavy metals through different drains. The study aimed to analyze the chemical speciation of these metals. In particular, the chemical forms of Cd, Cu, Fe, Mn, Pb and Zn in sediments collected in spring season were studied using a ...

  2. Mercury speciation with fluorescent gold nanocluster as a probe.

    Science.gov (United States)

    Yang, Jian-Yu; Yang, Ting; Wang, Xiao-Yan; Chen, Ming-Li; Yu, Yong-Liang; Wang, Jian-Hua

    2018-05-11

    Fluorescent nanoparticles are widely used for sensing biologically significant species. However, it is rarely reported for the discrimination or speciation of metal species. In this work, we report for the first time the speciation of mercury (Hg 2+ ) and methylmercury (CH 3 Hg + ) by taking advantage of the fluorescence feature of folic acid-capped gold nanoclusters (FA-AuNCs). FA-Au NCs exhibit an average size of 2.08±0.15 nm and a maximum emission at λ ex /λ em = 280/440 nm with a quantum yield of 27.3%. It is interesting that Hg 2+ causes a significant quench on the fluorescence of FA-Au NCs, whereas CH 3 Hg + leads to a remarkable fluorescence enhancement. Based on this discriminative fluorescent response between Hg 2+ and CH 3 Hg + , a novel nanosensor for the speciation of CH 3 Hg + and Hg 2+ was developed, providing limits of detection (LOD) of 28 nM for Hg 2+ and 25 nM for CH 3 Hg + within 100-1000 nM. This sensing system is highly selective to mercury. Its practical applications were further demonstrated by the analysis of CH 3 Hg + and the speciation of mercury (CH 3 Hg + and Hg 2+ ) in environmental water and fish samples.

  3. Geometry, charge distribution, and surface speciation of phosphate on goethite.

    NARCIS (Netherlands)

    Rahnemaie, R.; Hiemstra, T.; Riemsdijk, van W.H.

    2007-01-01

    The surface speciation of phosphate has been evaluated with surface complexation modeling using an interfacial charge distribution (CD) approach based on ion adsorption and ordering of interfacial water. In the CD model, the charge of adsorbed ions is distributed over two electrostatic potentials in

  4. Speciation of Fe in Fe-modified zeolite catalysts

    Czech Academy of Sciences Publication Activity Database

    Smoláková, L.; Grygar, Tomáš; Čapek, L.; Schneeweiss, Oldřich; Zbořil, R.

    2010-01-01

    Roč. 647, č. 1 (2010), s. 8-19 ISSN 1572-6657 Institutional research plan: CEZ:AV0Z40320502; CEZ:AV0Z20410507 Keywords : solid state speciation * Fe2O3 * heterogeneous catalysts Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.732, year: 2010

  5. Speciation Studies of Some Toxic Metal Complexes of Glycylglycine ...

    African Journals Online (AJOL)

    NICO

    mixtures apart from its established utility in understanding ... Chemical speciation of metals is important for an understand- ... Titrations with differ- ent ratios (1:2.5, 1:3.5 and 1:5) of metal-ligand were performed with 0.4 mol L–1 sodium hydroxide solution. The mixtures obtained from PG and water are non-ideal due.

  6. Speciation of Candida isolates obtained from diarrheal stool

    Directory of Open Access Journals (Sweden)

    Beena Uppal

    2016-01-01

    Conclusion Candida diarrhea was mostly seen in individuals younger than 12 years, most commonly caused by C. krusei. Resistance to fluconazole was high. A rising resistance to amphotericin B is alarming. Speciation of Candida is important to see the difference in antifungal susceptibility in different species.

  7. FINE PARTICULATE MATTER (PM) AND ORGANIC SPECIATION OF FIREPLACE EMISSIONS

    Science.gov (United States)

    This paper presents a summary of fireplace particle size and organic speciation data gathered to date in an on-going project. Tests are being conducted in a residential wood combustion (RWC) laboratory on three factory-built fireplaces. RWC wood smoke particles <10?m (PM10) con...

  8. Speciation of Zinc Mixed Ligand Complexes in Salt Water Systems ...

    African Journals Online (AJOL)

    Speciation of Zinc Mixed Ligand Complexes in Salt Water Systems. ... method has been used to study heavy metal interaction in model lake water in KNO3 ... is of no consequential effect because in its normal state, the [OH-] of the lake water is ...

  9. Speciation and bioavailability of copper in Lake Tjeukemeer

    NARCIS (Netherlands)

    Verweij, W.

    1991-01-01

    Chapter 1: introduction

    In this thesis an account is given of a research project dealing with the chemical speciation and bioavailability of copper in Lake Tjeukemeer, a lake in the north of the Netherlands. The reason for the initiation of this project was a lack of

  10. Distribution and Speciation of Mercury in Mine Waste Dumps

    Czech Academy of Sciences Publication Activity Database

    Hojdová, Maria; Navrátil, Tomáš; Rohovec, Jan

    2008-01-01

    Roč. 80, č. 3 (2008), s. 237-241 ISSN 0007-4861 R&D Projects: GA AV ČR(CZ) KJB300130615 Institutional research plan: CEZ:AV0Z30130516 Keywords : mercury * mine waste * mercury speciation * thermo-desorption analysis Subject RIV: DD - Geochemistry Impact factor: 0.609, year: 2008

  11. Speciation and migration of 129I in soil profiles

    DEFF Research Database (Denmark)

    Luo, Maoyi; Hou, Xiaolin; Zhou, Weijian

    2013-01-01

    A method has been developed for speciation analysis of ultra low level 129I in soil using sequential extraction combined with coprecipitation for separation of carrier free iodine and AMS measurement of 129I. Two loess profiles collected from northwest China were analyzed for species of 129I...

  12. Phytotoxicity and bioavailablity of nickel: chemical speciation and bioaccumulation

    NARCIS (Netherlands)

    Weng, L.P.; Lexmond, T.M.; Wolthoorn, A.; Temminghoff, E.J.M.; Riemsdijk, van W.H.

    2003-01-01

    The effect of pH on the bioaccumulation of nickel (Ni) by plants is opposite when using a nutrient solution or a soil as a growing medium. This paradox can be understood if the pH effect on the bioaccumulation, on the chemical speciation in the soil solution, and on the binding to the soil of Ni are

  13. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    Science.gov (United States)

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.

  14. Speciation of trace elements in the environmental studies

    International Nuclear Information System (INIS)

    Reddy, A.V.R.

    2012-01-01

    Elements present at trace levels, often referred as trace elements, play an important role in the environment and in the functioning of life on our planet. Trace elements in environment present as free metal ions or incorporated into colloids or attached to particulate matter or exist in different physical and chemical forms. It is well established that some elements are highly toxic and some are essential, but can become toxic at higher doses. It is also now known that the forms of elements (speciation) and their amounts are more important than the chemical dose of the elements as their interaction depends on different species. For example, Cr(VI) ions are considered far more toxic than Cr(III), whereas As(III) is more toxic than As(V). Similarly, in the case of mercury, both methylmercury and inorganic mercury are toxic but they show different levels of toxicity. Thus the adverse effects depend on the nature of species of the elements and therefore speciation studies are of paramount importance in many areas like toxicology, environmental chemistry and geochemisty. In view of this, speciation studies is a challenge to analytical chemists as the measurement methodologies have to be carefully developed, validated and applied. The grand challenge is to obtain quality data ensuring traceability, as the data obtained will be used in modeling for predicting the environmental impacts. In this talk importance of speciation and challenges to environmental analytical chemists will be discussed along with the following three speciation studies on Cr, U and Hg which were carried out in our laboratories

  15. Purex process modelling - do we really need speciation data?

    International Nuclear Information System (INIS)

    Taylor, R.J.; May, I.

    2001-01-01

    The design of reprocessing flowsheets has become a complex process requiring sophisticated simulation models, containing both chemical and engineering features. Probably the most basic chemical data needed is the distribution of process species between solvent and aqueous phases at equilibrium, which is described by mathematical algorithms. These algorithms have been constructed from experimentally determined distribution coefficients over a wide range of conditions. Distribution algorithms can either be empirical fits of the data or semi-empirical equations, which describe extraction as functions of process variables such as temperature, activity coefficients, uranium loading, etc. Speciation data is not strictly needed in the accumulation of distribution coefficients, which are simple ratios of analyte concentration in the solvent phase to that in the aqueous phase. However, as we construct process models of increasing complexity, speciation data becomes much more important both to raise confidence in the model and to understand the process chemistry at a more fundamental level. UV/vis/NIR spectrophotometry has been our most commonly used speciation method since it is a well-established method for the analysis of actinide ion oxidation states in solution at typical process concentrations. However, with the increasing availability to actinide science of more sophisticated techniques (e.g. NMR; EXAFS) complementary structural information can often be obtained. This paper will, through examples, show how we have used spectrophotometry as a primary tool in distribution and kinetic experiments to obtain data for process models, which are then validated through counter-current flowsheet trials. It will also discuss how spectrophotometry and other speciation methods are allowing us to study the link between molecular structure and extraction behaviour, showing how speciation data really is important in PUREX process modelling. (authors)

  16. Sex chromosomes and speciation in birds and other ZW systems.

    Science.gov (United States)

    Irwin, Darren E

    2018-02-14

    Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation. Focusing on ZW sex determination (females ZW, males ZZ; the system in birds, many snakes, and lepidopterans), I review how evolutionary dynamics are expected to differ between the Z, W and the autosomes, discuss how these differences may lead to a greater role of the sex chromosomes in speciation and use data from birds to compare relative evolutionary rates of sex chromosomes and autosomes. Neutral mutations, partially or completely recessive beneficial mutations, and deleterious mutations under many conditions are expected to accumulate faster on the Z than on autosomes. Sexually antagonistic polymorphisms are expected to arise on the Z, raising the possibility of the spread of preference alleles. The faster accumulation of many types of mutations and the potential for complex evolutionary dynamics of sexually antagonistic traits and preferences contribute to a role for the Z chromosome in speciation. A quantitative comparison among a wide variety of bird species shows that the Z tends to have less within-population diversity and greater between-species differentiation than the autosomes, likely due to both adaptive evolution and a greater rate of fixation of deleterious alleles. The W chromosome also shows strong potential to be involved in speciation, in part because of its co-inheritance with the mitochondrial genome. While theory and empirical evidence suggest a disproportionate role for sex chromosomes in speciation, the importance of sex chromosomes is moderated by their small size compared to the whole genome. © 2018 John Wiley & Sons Ltd.

  17. Simultaneous speciation neutron activation analysis for trace elements

    International Nuclear Information System (INIS)

    Chatt, A.; Kiceniuk, J.W.; Menendez Sanchez, W.; Bottaro, C.

    2006-01-01

    Among the various forms of neutron activation technique being developed in our laboratory, much emphasis has been placed over the last ten years or so on the development of simultaneous speciation neutron activation analysis (SSNAA). This technique can now be used for the simultaneous determination of various species of a number of elements. Almost all speciation techniques consist of two steps. The first step involves the separation of species from the sample followed by the second step of element-specific detection. A number of characteristic features of NAA, which other techniques normally do not possess, can be advantageously exploited in SSNAA. For example, SSNAA can be used for: (i) multielement speciation with high specificity, (ii) speciation of chemically dissimilar elements such as Cd, Mn and Se, (iii) speciation of elements such as Cl, Br and I which are rather difficult to determine by most other techniques, etc. We have developed SSNAA methods for assaying various arsenic species, namely As(III), As(V), dimethyl arsonic acid (DMA), monomethylarsinic acid (MMA), arsenobetaine (AsB), organically bound arsenic (OBAs), and lipid-soluble arsenic (LSAs) in marine fish samples. We have extended these methods to include simultaneous determination of various species of As, Sb and Se in water. We have also developed SSNAA methods employing biochemical techniques for the simultaneous separation, preconcentration and characterization of metalloproteins and protein-bound trace element species of As, Br, Cd, Cu, Mn, Se, and Zn. We have developed methods for the simultaneous separation and characterization of organohalogen compounds in fish. An overview of the SSNAA methods being developed in our laboratory will be presented. (author)

  18. August Meeting

    African Journals Online (AJOL)

    chifaou.amzat

    2011-10-19

    Oct 19, 2011 ... rural hometowns, where they unite with their rural-based colleagues for ... extent have they empowered the women-folk in the public sphere? ...... It would be safe, therefore, for one to conceptualise the 'August Meeting'.

  19. Public meetings

    CERN Multimedia

    Staff Association

    2014-01-01

    You were hundreds of persons to participate in our information meetings of October 3 and 6 2014, and we thank you for your participation! The full presentation is available here. A summary of the topics is available here (in french).

  20. Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance.

    Directory of Open Access Journals (Sweden)

    Wen Xie

    Full Text Available BACKGROUND: Bemisia tabaci (Gennadius is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. METHODOLOGY AND PRINCIPAL FINDINGS: Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45% unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10-5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. CONCLUSIONS: This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the

  1. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.

    Directory of Open Access Journals (Sweden)

    Marcus J Claesson

    Full Text Available BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. METHODS AND FINDINGS: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400-1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. CONCLUSIONS: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genus-level with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate

  2. Public meetings

    CERN Multimedia

    Staff Association

    2017-01-01

    Do you have questions about the elections to the Staff Council, 2017 MERIT exercise, EVE and School, LD to IC exercise, CHIS, the Pension Fund… Come get informed and ask your questions at our public meetings. These public meetings are also an opportunity to get the more information on current issues. Benefit from this occasion to get the latest news and to discuss with the representatives of the statutory body that is the Staff Association!

  3. Evaluation of feed grade sodium bisulfate impact on gastrointestinal tract microbiota ecology in broilers via a pyrosequencing platform.

    Science.gov (United States)

    Park, Si Hong; Dowd, Scot E; McReynolds, Jack L; Byrd, James A; Nisbet, David J; Ricke, Steven C

    2015-12-01

    The gastrointestinal microbial community in broiler chickens consists of many different species of bacteria, and the overall microbiota can vary from bird to bird. To control pathogenic bacteria in broilers and improve gut health, numerous potential dietary amendments have been used. In this study, we used a pyrosequencing platform to evaluate the effect of sodium bisulfate on microbiota of the crop, cecum, and ileum of broiler chickens grown over several weeks. The diversity information in each digestive organ sample exhibited considerable variation and was clearly separable, suggesting distinct bacterial populations. Although no apparent microbial clustering occurred between the control and the dietary treatments, we did observe shifts in overall microbiota populations in the crop, ileum, and ceca as well as changes in specific microorganisms such as Bacteroides, Clostridium, and Lactobacillus species that were identified as birds became older. © 2015 Poultry Science Association Inc.

  4. Meeting Mid-Year Meeting

    Indian Academy of Sciences (India)

    23 Newsletter of the Indian Academy of ScienCE. 57th Annual. Meeting ... Srinivas, Institute for Social and Economic. Change ... "Quantum mechanics and statistical mechanics of anyons" .... Special Issue on Geomagnetic Methods and.

  5. Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes

    DEFF Research Database (Denmark)

    Holmsgaard, Peter Nikolai; Sørensen, Søren Johannes; Hansen, Lars H.

    2013-01-01

    The use of amplicon pyrosequencing makes it possible to produce thousands of sequences of the same gene at relatively low costs. Here we show that it is possible to simultaneously sequence the 16S rRNA gene, IncP-1 trfA gene and mercury reductase gene (merA) as a way for screening the diversity...

  6. 454-Pyrosequencing survey of microbiota in adult Spotted Wing Drosophila (SWD) corroborates a core microbiome and additional symbiotic and entomopathogenic bacterial associates

    Science.gov (United States)

    Complete surveys of insect endosymbionts including species of economic importance have until recently been hampered by a lack of high-throughput genetic assays. We used 454-pyrosequencing of the 16S rRNA gene amplicon of adult spotted wing Drosophila (SWD) Drosophila suzukii (Matsumura) from souther...

  7. Field efficacy of four anthelmintics and confirmation of drug-resistant nematodes by controlled efficacy test and pyrosequencing on a sheep and goat farm in Denmark

    DEFF Research Database (Denmark)

    Pena-Espinoza, Miguel Angel; Thamsborg, Stig M.; Demeler, Janina

    2014-01-01

    and Trichostrongylus colubriformis isolated from adult goats on the farm. Recovered specimens of H. contortus were subjected to pyrosequencing for detection of single nucleotide polymorphisms (SNPs) related to benzimidazole (BZ) resistance. During the FECRT, FECs in untreated lambs dropped significantly by 47%. No FEC...

  8. Somatic populations of PGT135-137 HIV-1-neutralizing antibodies identified by 454 pyrosequencing and bioinformatics

    Directory of Open Access Journals (Sweden)

    Jiang eZhu

    2012-09-01

    Full Text Available Select HIV-1-infected individuals develop sera capable of neutralizing diverse viral strains. The molecular basis of this neutralization is currently being deciphered by the isolation of HIV-1-neutralizing antibodies. In one infected donor, three neutralizing antibodies, PGT135-137, were identified by assessment of neutralization from individually sorted B cells and found to recognize an epitope containing an N-linked glycan at residue 332 on HIV-1 gp120. Here we use deep sequencing and bioinformatics methods to interrogate the B cell record of this donor to gain a more complete understanding of the humoral immune response. PGT135-137-gene family-specific primers were used to amplify heavy and light chain-variable domain sequences. 454 pyrosequencing produced 141,298 heavy-chain sequences of IGHV4-39 origin and 87,229 light-chain sequences of IGKV3-15 origin. A number of heavy and light chain sequences of ~90% identity to PGT137, several to PGT136, and none of high identity to PGT135 were identified. After expansion of these sequences to include close phylogenetic relatives, a total of 202 heavy-chain sequences and 72 light-chain sequences were identified. These sequences were clustered into populations of 95% identity comprising 15 for heavy chain and 10 for light chain, and a select sequence from each population was synthesized and reconstituted with a PGT137-partner chain. Reconstituted antibodies showed varied neutralization phenotypes for HIV-1 clade A and D isolates. Sequence diversity of the antibody population represented by these tested sequences was notably higher than observed with a 454 pyrosequencing-control analysis on 10 antibodies of defined sequence, suggesting that this diversity results primarily from somatic maturation. Our results thus provide an example of how pathogens like HIV-1 are opposed by a varied humoral immune response, derived from intrinsic mechanisms of antibody development, and embodied by somatic populations

  9. 16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease.

    Directory of Open Access Journals (Sweden)

    Jan S Suchodolski

    Full Text Available BACKGROUND: Canine idiopathic inflammatory bowel disease (IBD is believed to be caused by a complex interaction of genetic, immunologic, and microbial factors. While mucosa-associated bacteria have been implicated in the pathogenesis of canine IBD, detailed studies investigating the enteric microbiota using deep sequencing techniques are lacking. The objective of this study was to evaluate mucosa-adherent microbiota in the duodenum of dogs with spontaneous idiopathic IBD using 16 S rRNA gene pyrosequencing. METHODOLOGY/PRINCIPAL FINDINGS: Biopsy samples of small intestinal mucosa were collected endoscopically from healthy dogs (n = 6 and dogs with moderate IBD (n = 7 or severe IBD (n = 7 as assessed by a clinical disease activity index. Total RNA was extracted from biopsy specimens and 454-pyrosequencing of the 16 S rRNA gene was performed on aliquots of cDNA from each dog. Intestinal inflammation was associated with significant differences in the composition of the intestinal microbiota when compared to healthy dogs. PCoA plots based on the unweighted UniFrac distance metric indicated clustering of samples between healthy dogs and dogs with IBD (ANOSIM, p<0.001. Proportions of Fusobacteria (p = 0.010, Bacteroidaceae (p = 0.015, Prevotellaceae (p = 0.022, and Clostridiales (p = 0.019 were significantly more abundant in healthy dogs. In contrast, specific bacterial genera within Proteobacteria, including Diaphorobacter (p = 0.044 and Acinetobacter (p = 0.040, were either more abundant or more frequently identified in IBD dogs. CONCLUSIONS/SIGNIFICANCE: In conclusion, dogs with spontaneous IBD exhibit alterations in microbial groups, which bear resemblance to dysbiosis reported in humans with chronic intestinal inflammation. These bacterial groups may serve as useful targets for monitoring intestinal inflammation.

  10. Pyrosequencing the transcriptome of the greenhouse whitefly, Trialeurodes vaporariorum reveals multiple transcripts encoding insecticide targets and detoxifying enzymes

    Directory of Open Access Journals (Sweden)

    Gorman Kevin

    2011-01-01

    Full Text Available Abstract Background The whitefly Trialeurodes vaporariorum is an economically important crop pest in temperate regions that has developed resistance to most classes of insecticides. However, the molecular mechanisms underlying resistance have not been characterised and, to date, progress has been hampered by a lack of nucleotide sequence data for this species. Here, we use pyrosequencing on the Roche 454-FLX platform to produce a substantial and annotated EST dataset. This 'unigene set' will form a critical reference point for quantitation of over-expressed messages via digital transcriptomics. Results Pyrosequencing produced around a million sequencing reads that assembled into 54,748 contigs, with an average length of 965 bp, representing a dramatic expansion of existing cDNA sequences available for T. vaporariorum (only 43 entries in GenBank at the time of this publication. BLAST searching of non-redundant databases returned 20,333 significant matches and those gene families potentially encoding gene products involved in insecticide resistance were manually curated and annotated. These include, enzymes potentially involved in the detoxification of xenobiotics and those encoding the targets of the major chemical classes of insecticides. A total of 57 P450s, 17 GSTs and 27 CCEs were identified along with 30 contigs encoding the target proteins of six different insecticide classes. Conclusion Here, we have developed new transcriptomic resources for T. vaporariorum. These include a substantial and annotated EST dataset that will serve the community studying this important crop pest and will elucidate further the molecular mechanisms underlying insecticide resistance.

  11. Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Kimberly D Cephas

    Full Text Available Bacterial contribution to oral disease has been studied in young children, but there is a lack of data addressing the developmental perspective in edentulous infants. Our primary objectives were to use pyrosequencing to phylogenetically characterize the salivary bacterial microbiome of edentulous infants and to make comparisons against their mothers. Saliva samples were collected from 5 edentulous infants (mean age = 4.6±1.2 mo old and their mothers or primary care givers (mean age = 30.8±9.5 y old. Salivary DNA was extracted, used to generate DNA amplicons of the V4-V6 hypervariable region of the bacterial 16S rDNA gene, and subjected to 454-pyrosequencing. On average, over 80,000 sequences per sample were generated. High bacterial diversity was noted in the saliva of adults [1012 operational taxonomical units (OTU at 3% divergence] and infants (578 OTU at 3% divergence. Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria were predominant bacterial phyla present in all samples. A total of 397 bacterial genera were present in our dataset. Of the 28 genera different (P<0.05 between infants and adults, 27 had a greater prevalence in adults. The exception was Streptococcus, which was the predominant genera in infant saliva (62.2% in infants vs. 20.4% in adults; P<0.05. Veillonella, Neisseria, Rothia, Haemophilus, Gemella, Granulicatella, Leptotrichia, and Fusobacterium were also predominant genera in infant samples, while Haemophilus, Neisseria, Veillonella, Fusobacterium, Oribacterium, Rothia, Treponema, and Actinomyces were predominant in adults. Our data demonstrate that although the adult saliva bacterial microbiome had a greater OTU count than infants, a rich bacterial community exists in the infant oral cavity prior to tooth eruption. Streptococcus, Veillonella, and Neisseria are the predominant bacterial genera present in infants. Further research is required to characterize the development of oral microbiota early in life

  12. Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Arfken, Ann M; Song, Bongkeun; Mallin, Michael A

    2015-09-01

    Hog lagoons can be major sources of waste and nutrient contamination to watersheds adjacent to pig farms. Fecal source tracking methods targeting Bacteroidetes 16S rRNA genes in pig fecal matter may underestimate or fail to detect hog lagoon contamination in riverine environments. In order to detect hog lagoon wastewater contamination in the Cape Fear Watershed, where a large number of hog farms are present, we conducted pyrosequencing analyses of Bacteroidetes 16S rRNA genes in hog lagoon waste and identified new hog lagoon-specific marker sequences. Additional pyrosequencing analyses of Bacteroidetes 16S rRNA genes were conducted with surface water samples collected at 4 sites during 5 months in the Cape Fear Watershed. Using an operational taxonomic unit (OTU) identity cutoff value of 97 %, these newly identified hog lagoon markers were found in 3 of the river samples, while only 1 sample contained the pig fecal marker. In the sample containing the pig fecal marker, there was a relatively high percentage (14.1 %) of the hog lagoon markers and a low pig fecal marker relative abundance of 0.4 % in the Bacteroidetes 16S rRNA gene sequences. This suggests that hog lagoon contamination must be somewhat significant in order for pig fecal markers to be detected, and low levels of hog lagoon contamination cannot be detected targeting only pig-specific fecal markers. Thus, new hog lagoon markers have a better detection capacity for lagoon waste contamination, and in conjunction with a pig fecal marker, provide a more comprehensive and accurate detection of hog lagoon waste contamination in susceptible watersheds.

  13. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

    Directory of Open Access Journals (Sweden)

    Elianne Egge

    Full Text Available Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.

  14. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  15. Pyrosequencing for classification of human FcγRIIIA allotypes: a comparison with PCR-based techniques.

    Science.gov (United States)

    Matlawska-Wasowska, Ksenia; Gale, James M; Nickl, Christian K; Khalili, Parisa; Shirley, Brian; Wilson, Bridget S; Vasef, Mohammad A; Winter, Stuart S

    2014-12-01

    Surface-specific antigens expressed by hematopoietic cells are attractive targets for antibody-mediated immunotherapy. Monoclonal antibodies (mAbs) involve various mechanisms to eliminate target cells, including antibody-dependent cellular cytotoxicity (ADCC)- and phagocytosis (ADCP)-mediated killing through natural killer (NK) and macrophage effector cells bearing FcγRIIIA (CD16). The clinical efficacy of ADCC is particularly impacted by a single nucleotide polymorphism (SNP) found in the gene encoding FcγRIIIA (FCGR3A), which generates a variable distribution of the 158 V/V, F/V or F/F CD16 allotypes (F = phenylalanine, V = valine) in the normal human population. Currently, most patients are not screened for CD16 allotypes, creating the potential to include in their treatment a mAb-based therapy that may have limited benefit. Therefore, it is important to identify CD16 allotypes when considering mAb therapies that require ADCC/ADCP. The objective of this study was to develop a reliable PCR-based assay for classification of human FcγRIIIA allotypes. We studied 42 normal human subjects for the incidence of FcγRIIIA-158 polymorphisms using comparative molecular approaches. The results of our study showed 100% accuracy in genotyping by pyrosequencing. In contrast, nested PCR-based allele-specific restriction assay and quantitative PCR techniques proved to be relatively less sensitive and less specific in distinguishing variant genotypes. Since the efficacy of the mAb-based targeted immunotherapy may be highly dependent upon the CD16 polymorphism in a given individual, we recommend pyrosequencing for CD16 allotype testing.

  16. U(IV) fluorescence spectroscopy. A new speciation tool

    Energy Technology Data Exchange (ETDEWEB)

    Lehmann, Susanne; Brendler, Vinzenz [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Surface Processes; Steudtner, Robin [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Inst. of Resource Ecology

    2017-06-01

    We combined absorption and fluorescence spectroscopy to study the speciation of U(IV) in solution in concentrations down to 10{sup -6} M uranium. With our time-resolved laser-induced fluorescence setup we could determine the fluorescence decay time of U(IV) in perchloric as well as in chloric acid with 2.6 ± 0.3 ns at room temperature and 148.4 ± 6.5 ns at liquid nitrogen temperature. For the U(IV) sulfate system, we observed a bathochromic shift and a peak shape modification in the fluorescence spectra with increasing sulfate concentration in solution. Thus, the potential of U(IV) fluorescence for speciation analysis could be proven.

  17. Synergy between Allopatry and Ecology in Population Differentiation and Speciation

    Directory of Open Access Journals (Sweden)

    Yann Surget-Groba

    2012-01-01

    Full Text Available The general diversity pattern of the Caribbean anole radiation has been described in detail; however, the actual mechanisms at the origin of their diversification remain controversial. In particular, the role of ecological speciation, and the relative importance of divergence in allopatry and in parapatry, is debated. We describe the genetic structure of anole populations across lineage contact zones and ecotones to investigate the effect of allopatric divergence, natural selection, and the combination of both factors on population differentiation. Allopatric divergence had no significant impact on differentiation across the lineage boundary, while a clear bimodality in genetic and morphological characters was observed across an ecotone within a single lineage. Critically, the strongest differentiation was observed when allopatry and ecology act together, leading to a sharp reduction in gene flow between two lineages inhabiting different habitats. We suggest that, for Caribbean anoles to reach full speciation, a synergistic combination of several historical and ecological factors may be requisite.

  18. Determining uranium speciation in Fernald soils by molecular spectroscopic methods

    International Nuclear Information System (INIS)

    Allen, P.G.; Berg, J.M.; Crisholm-Brause, C.J.; Conradson, S.D.; Donohoe, R.J.; Morris, D.E.; Musgrave, J.A.; Tait, C.D.

    1994-07-01

    This progress report describes new experimental results and interpretations for data collected from October 1, 1992, through September 30, 1993, as part of the Characterization Task of the Uranium in Soils Integrated Demonstration of the Office of Technology Development, Office of Environmental Restoration and Waste Management of the US Department of Energy. X-ray absorption, optical luminescence, and Raman vibrational spectroscopies were used to determine uranium speciation in contaminated soils from the US DOE's former uranium production facility at Fernald, Ohio. These analyses were carried out both before and after application of one of the various decontamination technologies being developed within the Integrated Demonstration. This year the program focused on characterization of the uranium speciation remaining in the soils after decontamination treatment. X-ray absorption and optical luminescence spectroscopic data were collected for approximately 40 Fernald soil samples, which were treated by one or more of the decontamination technologies

  19. Speciation of Fe in ambient aerosol and cloudwater

    Energy Technology Data Exchange (ETDEWEB)

    Siefert, Ronald Lyn [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    1996-08-15

    Atmospheric iron (Fe) is thought to play an important role in cloudwater chemistry (e.g., S(IV) oxidation, oxidant production, etc.), and is also an important source of Fe to certain regions of the worlds oceans where Fe is believed to be a rate-limiting nutrient for primary productivity. This thesis focuses on understanding the chemistry, speciation and abundance of Fe in cloudwater and aerosol in the troposphere, through observations of Fe speciation in the cloudwater and aerosol samples collected over the continental United States and the Arabian Sea. Different chemical species of atmospheric Fe were measured in aerosol and cloudwater samples to help assess the role of Fe in cloudwater chemistry.

  20. Pu speciation in actual and simulated aged wastes

    Energy Technology Data Exchange (ETDEWEB)

    Lezama-pacheco, Juan S [Los Alamos National Laboratory; Conradson, Steven D [Los Alamos National Laboratory

    2008-01-01

    X-ray Absorption Fine Structure Spectroscopy (XAFS) at the Pu L{sub II/III} edge was used to determine the speciation of this element in (1) Hanford Z-9 Pu crib samples, (2) deteriorated waste resins from a chloride process ion-exchange purification line, and (3) the sediments from two Waste Isolation Pilot Plant Liter Scale simulant brine systems. The Pu speciation in all of these samples except one is within the range previously displayed by PuO{sub 2+x-2y}(OH){sub y}{center_dot}zH{sub 2}O compounds, which is expected based on the putative thermodynamic stability of this system for Pu equilibrated with excess H{sub 2}O and O{sub 2} under environmental conditions. The primary exception was a near neutral brine experiment that displayed evidence for partial substitution of the normal O-based ligands with Cl{sup -} and a concomitant expansion of the Pu-Pu distance relative to the much more highly ordered Pu near neighbor shell in PuO{sub 2}. However, although the Pu speciation was not necessarily unusual, the Pu chemistry identified via the history of these samples did exhibit unexpected patterns, the most significant of which may be that the presence of the Pu(V)-oxo species may decrease rather than increase the overall solubility of these compounds. Several additional aspects of the Pu speciation have also not been previously observed in laboratory-based samples. The molecular environmental chemistry of Pu is therefore likely to be more complicated than would be predicted based solely on the behavior of PuO{sub 2} under laboratory conditions.

  1. Speciation and gene flow between snails of opposite chirality.

    Directory of Open Access Journals (Sweden)

    Angus Davison

    2005-09-01

    Full Text Available Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent "single-gene speciation" or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be

  2. SOME SPECIATION STUDIES IN FOODSTUFF BY ATOMIC ABSORPTION SPECTROMETRY

    OpenAIRE

    Gücer, S

    2000-01-01

    There has been increasing interest in speciation studies of essentialelements in foods. The main limitation of this studies, their levels in foodsamples and the difficulties for the determination in their own differentforms without any changes in their original forms.Atomic Absorption Spectrometry (AAS) coupled with separation methodswould be outline in this presentation. Analytical scheme was given for tea, olive and garlic samples forManganese, Magnesium and Selenium respectively. Activated...

  3. Speciation of cadmium mixed ligand complexes in salt water lakes ...

    African Journals Online (AJOL)

    The experimentally determined shifts in half-wave potentials are used to compute several formation constants. At the natural [CO32-] of 0.5 M in the lake, the main contributor to the speciation of cadmium is [Cd(CO3Cl2)]2-. At high [Cd2+], the DPASV detects the presence of free Cd2+ ions, hence, potential polluting effect, ...

  4. Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers.

    Science.gov (United States)

    Al-Sadi, A M; Al-Mazroui, S S; Phillips, A J L

    2015-08-01

    Potting media and organic fertilizers (OFs) are commonly used in agricultural systems. However, there is a lack of studies on the efficiency of culture-based techniques in assessing the level of fungal diversity in these products. A study was conducted to investigate the efficiency of seven culture-based techniques and pyrosequencing for characterizing fungal diversity in potting media and OFs. Fungal diversity was evaluated using serial dilution, direct plating and baiting with carrot slices, potato slices, radish seeds, cucumber seeds and cucumber cotyledons. Identity of all the isolates was confirmed on the basis of the internal transcribed spacer region of the ribosomal RNA (ITS rRNA) sequence data. The direct plating technique was found to be superior over other culture-based techniques in the number of fungal species detected. It was also found to be simple and the least time consuming technique. Comparing the efficiency of direct plating with 454 pyrosequencing revealed that pyrosequencing detected 12 and 15 times more fungal species from potting media and OFs respectively. Analysis revealed that there were differences between potting media and OFs in the dominant phyla, classes, orders, families, genera and species detected. Zygomycota (52%) and Chytridiomycota (60%) were the predominant phyla in potting media and OFs respectively. The superiority of pyrosequencing over cultural methods could be related to the ability to detect obligate fungi, slow growing fungi and fungi that exist at low population densities. The evaluated methods in this study, especially direct plating and pyrosequencing, may be used as tools to help detect and reduce movement of unwanted fungi between countries and regions. © 2015 The Society for Applied Microbiology.

  5. Detection by real-time PCR and pyrosequencing of the cry1Ab and cry1Ac genes introduced in genetically modified (GM) constructs.

    Science.gov (United States)

    Debode, Frederic; Janssen, Eric; Bragard, Claude; Berben, Gilbert

    2017-08-01

    The presence of genetically modified organisms (GMOs) in food and feed is mainly detected by the use of targets focusing on promoters and terminators. As some genes are frequently used in genetically modified (GM) construction, they also constitute excellent screening elements and their use is increasing. In this paper we propose a new target for the detection of cry1Ab and cry1Ac genes by real-time polymerase chain reaction (PCR) and pyrosequencing. The specificity, sensitivity and robustness of the real-time PCR method were tested following the recommendations of international guidelines and the method met the expected performance criteria. This paper also shows how the robustness testing was assessed. This new cry1Ab/Ac method can provide a positive signal with a larger number of GM events than do the other existing methods using double dye-probes. The method permits the analysis of results with less ambiguity than the SYBRGreen method recommended by the European Reference Laboratory (EURL) GM Food and Feed (GMFF). A pyrosequencing method was also developed to gain additional information thanks to the sequence of the amplicon. This method of sequencing-by-synthesis can determine the sequence between the primers used for PCR. Pyrosequencing showed that the sequences internal to the primers present differences following the GM events considered and three different sequences were observed. The sensitivity of the pyrosequencing was tested on reference flours with a low percentage GM content and different copy numbers. Improvements in the pyrosequencing protocol provided correct sequences with 50 copies of the target. Below this copy number, the quality of the sequence was more random.

  6. Public meeting

    CERN Multimedia

    HR Department

    2010-01-01

    Dear Colleagues, I am pleased to invite you to a public meeting which will be held on Thursday 11 November 2010 at 2:30 p.m., in the Main Auditorium (welcome coffee from 2 p.m.) In this meeting Sigurd Lettow, Director for Administration and General Infrastructure will present the Management’s proposals towards restoring full funding of the Pension Fund. The meeting will follow discussions which took place with the Staff Association, at the Standing Concertation Committee (CCP) of 1 November 2010 and will be held with the Members States, at the Tripartite Employment Conditions Forum (TREF) of 4 November 2010. You will be able to attend this presentation in the Main Auditorium or via the webcast. The Management will also be available to reply to your questions on this subject. Best regards, Anne-Sylvie Catherin

  7. ACCU Meeting

    CERN Multimedia

    PH Department

    2010-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 December 2010 at 9:15 a.m. in room 60-6-002 Chairperson's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on services from GS department The CERN Ombuds The new account management system Crèche progress + Restaurants Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairperson in writing or by e-mail to Michael.Hauschild@cern.ch   Michael Hauschild (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): ...

  8. ACCU Meeting

    CERN Multimedia

    PH Department

    2011-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 March 2011 At 9:15 a.m. in room 60-6-002   Chairperson's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on services from GS department Update on Safety at CERN The new account management system Users’ Office news Any Other Business Agenda for the next meeting   Anyone wishing to raise any points under item 10 is invited to send them to the Chairperson in writing or by e-mail to Michael.Hauschild@cern.ch Michael Hauschild (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel (76592) Belgium ...

  9. ACCU MEETING

    CERN Multimedia

    PH Department

    2010-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 September 2010 at 9:15 a.m. in Room 60-6-002 Chairperson’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on services from GS Department An update on Safety at CERN The CERN Summer Student program Bringing Library services to users Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairperson in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): ...

  10. ACCU Meeting

    CERN Multimedia

    PH Department

    2010-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 June 2010 At 9:15 a.m. in room 60-6-002 Chairperson’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on services from GS department CERN Global Network An update on Safety at CERN Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairperson in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel (76592) ...

  11. Speciation, in the nuclear fuel cycle by spectroscopic techniques

    International Nuclear Information System (INIS)

    Colette, S.; Plancque, G.; Allain, F.; Lamouroux, C.; Steiner, V.; Amekraz, B.; Moulin, C.

    2000-01-01

    New analytical techniques allowing to perform speciation in the framework of the nuclear fuel cycle are more and more needed. They have to be selective (since matrix encountered are very complex), sensitive (in order to work at representative concentration and below solubility limit), as well as non intrusive (in order to keep the image of the real solution). Among them, laser-based analytical techniques present these advantages together with the possibility to perform remote measurements via fiber optics. Hence, Time-Resolved Laser-Induced Fluorescence (TRLIF) has been used for actinides/lanthanides interaction and speciation studies in inorganic and organic matrices from the reprocessing to waste storage. Moreover, new ion detection methods such as Electro-Spray - Mass Spectrometry (ES-MS) seems promising for speciation studies. Hence, it is the first time that it is possible to directly couple a liquid at atmospheric pressure to a mass detection working at reduced pressure with a soft mode of ionisation that should allow to give informations on chemical species present. Principle, advantages and limitations as well as results obtained with the use of TRLIF and ES-MS on different systems of interest including actinides, lanthanides, fission products in interaction with simple organic molecules to very complex structure will be presented and discussed. (authors)

  12. Speciation, in the nuclear fuel cycle by spectroscopic techniques

    Energy Technology Data Exchange (ETDEWEB)

    Colette, S.; Plancque, G.; Allain, F.; Lamouroux, C.; Steiner, V.; Amekraz, B.; Moulin, C. [CEA/Saclay, Dept, des Procedes d' Enrichissement (DPE), 91 - Gif-sur-Yvette (France)

    2000-07-01

    New analytical techniques allowing to perform speciation in the framework of the nuclear fuel cycle are more and more needed. They have to be selective (since matrix encountered are very complex), sensitive (in order to work at representative concentration and below solubility limit), as well as non intrusive (in order to keep the image of the real solution). Among them, laser-based analytical techniques present these advantages together with the possibility to perform remote measurements via fiber optics. Hence, Time-Resolved Laser-Induced Fluorescence (TRLIF) has been used for actinides/lanthanides interaction and speciation studies in inorganic and organic matrices from the reprocessing to waste storage. Moreover, new ion detection methods such as Electro-Spray - Mass Spectrometry (ES-MS) seems promising for speciation studies. Hence, it is the first time that it is possible to directly couple a liquid at atmospheric pressure to a mass detection working at reduced pressure with a soft mode of ionisation that should allow to give informations on chemical species present. Principle, advantages and limitations as well as results obtained with the use of TRLIF and ES-MS on different systems of interest including actinides, lanthanides, fission products in interaction with simple organic molecules to very complex structure will be presented and discussed. (authors)

  13. Metal accumulation by stream bryophytes, related to chemical speciation

    Energy Technology Data Exchange (ETDEWEB)

    Tipping, E. [Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP (United Kingdom)], E-mail: et@ceh.ac.uk; Vincent, C.D.; Lawlor, A.J.; Lofts, S. [Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP (United Kingdom)

    2008-12-15

    Metal accumulation by aquatic bryophytes was investigated using data for headwater streams of differing chemistry. The Windermere Humic Aqueous Model (WHAM) was applied to calculate chemical speciation, including competitive proton and metal interactions with external binding sites on the plants. The speciation modelling approach gives smaller deviations between observed and predicted bryophyte contents of Cu, Zn, Cd and Pb than regressions based on total filtered metal concentrations. If all four metals, and Ni, are considered together, the WHAM predictions are superior at the 1% level. Optimised constants for bryophyte binding by the trace metals are similar to those for humic substances and simple carboxylate ligands. Bryophyte contents of Na, Mg and Ca are approximately explained by binding at external sites, while most of the K is intracellular. Oxide phases account for some of the Al, and most of the Mn, Fe and Co. - Speciation modelling can be used to interpret the accumulation of Ni, Cu, Zn, Cd and Pb by bryophytes, supporting its use to quantify trace metal bioavailability in the field.

  14. The role of male contest competition over mates in speciation

    Directory of Open Access Journals (Sweden)

    Anna QVARNSTRÖM, Niclas VALLIN, Andreas RUDH

    2012-06-01

    Full Text Available Research on the role of sexual selection in the speciation process largely focuses on the diversifying role of mate choice. In particular, much attention has been drawn to the fact that population divergence in mate choice and in the male traits subject to choice directly can lead to assortative mating. However, male contest competition over mates also constitutes an important mechanism of sexual selection. We review recent empirical studies and argue that sexual selection through male contest competition can affect speciation in ways other than mate choice. For example, biases in aggression towards similar competitors can lead to disruptive and negative frequency-dependent selection on the traits used in contest competition in a similar way as competition for other types of limited resources. Moreover, male contest abilities often trade-off against other abilities such as parasite resistance, protection against predators and general stress tolerance. Populations experiencing different ecological conditions should therefore quickly diverge non-randomly in a number of traits including male contest abilities. In resource based breeding systems, a feedback loop between competitive ability and habitat use may lead to further population divergence. We discuss how population divergence in traits used in male contest competition can lead to the build up of reproductive isolation through a number of different pathways. Our main conclusion is that the role of male contest competition in speciation remains largely scientifically unexplored [Current Zoology 58 (3: 490–506, 2012].

  15. Staff meeting

    CERN Document Server

    2006-01-01

    I would like to invite all members of the CERN Personnel to a meeting on Thursday 18 January 2007 at 3:00 p.m. Main Auditorium (bldg.. 500) to convey my best wishes for the new year, to review CERN's activities during 2006 and to present the perspectives for this special year of the LHC start-up. Closed-circuit transmission of the meeting will be available in the Council Chamber and in the AB Auditorium (Meyrin), the AB Auditorium (Prévessin), the IT Auditorium (bldg.. 31) and the AT Auditorium (bldg.. 30). Simultaneous translation into English will be available in the main Auditorium. Robert AYMAR

  16. Scientific meetings

    International Nuclear Information System (INIS)

    1973-01-01

    One of the main aims of the IAEA is to foster the exchange of scientific and technical information and one of the main ways of doing this is to convene international scientific meetings. They range from large international conferences bringing together several hundred scientists, smaller symposia attended by an average of 150 to 250 participants and seminars designed to instruct rather than inform, to smaller panels and study groups of 10 to 30 experts brought together to advise on a particular programme or to develop a set of regulations. The topics of these meetings cover every part of the Agency's activities and form a backbone of many of its programmes. (author)

  17. STAFF MEETING

    CERN Multimedia

    Robert Aymar

    2005-01-01

    I would like to invite all members of the CERN Personnel to a meeting on Thursday 12 January 2006 at 4:00 p.m. - Main Auditorium (bldg. 500) to convey my best wishes for the new year, to review CERN's activities during 2005 and to present the perspectives for this coming year. Closed-circuit transmission of the meeting will be available in the Council Chamber and in the AB Auditorium (Meyrin), the AB Auditorium (Prévessin), the IT Auditorium (bldg. 31) and the AT Auditorium (bldg. 30). A simultaneous translation into English will be available in the main Auditorium. Best wishes for the festive season Robert AYMAR

  18. STAFF MEETING

    CERN Multimedia

    2004-01-01

    I would like to invite all members of the CERN Personnel to a meeting on Tuesday 13 January 2004 at 4:00 p.m. - Main Auditorium (bldg. 500) to convey my best wishes for the new year and to present a perspective of CERN's future activities. Closed-circuit transmission of the meeting will be available in the Council Chamber and in the AB Auditorium (Meyrin), the AB Auditorium (Prévessin), the IT Auditorium (bldg. 31) and the AT Auditorium (bldg. 30). A simultaneous translation into English will be available in the main Auditorium. Robert AYMAR

  19. Public meetings

    CERN Multimedia

    Staff Association

    2014-01-01

      Public meetings : Come and talk about your future employment conditions !   The Staff Association will come and present the results of our survey on the 2015 five-yearly review. Following the survey, the topics discussed, will be contract policy, recognition of merit (MARS), working time arrangements and family policy. After each meeting and around a cup of coffee or tea you will be able to continue the discussions. Do not hesitate to join us, the five-yearly review, it is with YOU!

  20. Atmospheric speciation of mercury in two contrasting Southeastern US airsheds

    Science.gov (United States)

    Gabriel, Mark C.; Williamson, Derek G.; Brooks, Steve; Lindberg, Steve

    Simultaneous measurement of gaseous elemental, reactive gaseous, and fine particulate mercury took place in Tuscaloosa AL, (urban airshed) and Cove Mountain, TN (non-urban airshed) during the summers of 2002 and 2003. The objective of this research was to (1) summarize the temporal distribution of each mercury specie at each site and compare to other speciation data sets developed by other researchers and (2) provide insight into urban and non-urban mercury speciation effects using various statistical methods. Average specie concentrations were as follows: 4.05 ng m -3 (GEM), 13.6 pg m -3 (RGM), 16.4 pg m -3 (Hg-p) for Tuscaloosa; 3.20 ng m -3 (GEM), 13.6 pg m -3 (RGM), 9.73 pg m -3 (Hg-p) for Cove Mountain. As a result of urban airshed impacts, short periods of high concentration for all mercury species was common in Tuscaloosa. At Cove Mountain a consistent mid-day rise and evening drop for mercury species was found. This pattern was primarily the result of un-impacted physical boundary layer movement, although, other potential impacts were ambient photochemistry and air-surface exchange of mercury. Meteorological parameters that are known to heavily impact mercury speciation were similar for the study period for Tuscaloosa and Cove Mountain except for wind speed (m s -1), which was higher at Cove Mountain. For both sites statistically significant ( p<0.0001), inverse relationships existed between wind speed and Hg 0 concentration. A weaker windspeed-Hg 0 correlation existed for Tuscaloosa. By analyzing Hg concentration—wind speed magnitude change at both sites it was found that wind speed at Cove Mountain had a greater influence on Hg 0 concentration variability than Tuscaloosa by a factor of 3. Using various statistical tests, we concluded that the nature of Tuscaloosa's atmospheric mercury speciation was the result of typical urban airshed impacts. Cove Mountain showed atmospheric mercury speciation characteristics indicative of a non-urban area along with

  1. Crisis meeting

    CERN Multimedia

    Staff Association

    2014-01-01

      To all CERN staff: your rights are at risk ! We invite you to come to a crisis meeting on Wednesday 2nd April at 10:30 a.m., Auditorium, Main Building, Meyrin site. Your presence is crucial, we are ALL concerned !

  2. Crisis meeting

    CERN Multimedia

    Staff Association

    2015-01-01

    To all CERN staff: your rights are at risk! We invite you to come to a crisis meeting on Thursday 7th May 2015 at 9 a.m., Auditorium, Main Building, Meyrin site. Your presence is crucial, we are ALL concerned!

  3. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2002-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 4 December 2002 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Fellows, Associates and Summer Student Programmes Particle Data Book distribution Revoking Computer accounts Equipment insurance on site Reports from ACCU representatives on other committees Users' Office news Any Other Business Dates for meetings in 2003 Agenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch   ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (74837...

  4. ACCU MEETING

    CERN Multimedia

    Chris Onions (Secretary)

    2001-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 5 December 2001 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 2. Adoption of the agenda 3. Minutes of the previous meeting 4. Matters arising 5. News from the CERN Management 6. Housing 7. Restaurant Surveillance Committee 8. Users' Office news 9. Election of ACCU chairman 10. Any Other Business 11. Dates for meetings in 2002 12. Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria  W. Adam  (71661) Belgium  G. Wilquet  (74664) Bulgaria  R. Tzenov  (77958) Czech Republic  P. Závada&am...

  5. ACCU MEETING

    CERN Multimedia

    Chris Onions (Secretary)

    2001-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 5 December 2001 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 2. Adoption of the agenda 3. Minutes of the previous meeting 4. Matters arising 5. News from the CERN Management 6. Housing 7. Restaurant Surveillance Committee 8. Users' Office news 9. Election of ACCU chairman 10. Any Other Business 11. Dates for meetings in 2002 12. Agenda for the next meetingAnyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland A. Kiiskinen (79387) Fr...

  6. ACCU MEETING

    CERN Multimedia

    2000-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 December 2000 At 10 a.m. in the 6th floor Conference Room, Main Building Chairman's remarks Adoption of the agenda News from the CERN Management Minutes of the previous meeting Matters arising Equal Opportunities at CERN The Summer Student programme CERN Programme for Physics High School Teachers Users' Office News Any Other Business Dates for Meetings in 2001 Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets) :   Austria G. Neuhofer (74094) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958)...

  7. ACCU MEETING

    CERN Multimedia

    Chris Onions (Secretary)

    2000-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 December 2000 At 10 a.m. in the 6th floor Conference Room, Main Building Chairman's remarks Adoption of the agenda News from the CERN Management Minutes of the previous meeting Matters arising Equal Opportunities at CERN The Summer Student programme CERN Programme for Physics High School Teachers Users' Office News Any Other Business Dates for Meetings in 2001 Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets) : Austria G. Neuhofer (74094) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Re...

  8. ACCU Meeting

    CERN Multimedia

    PH Department

    2011-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 15 June 2011 At 9:15 a.m. in room 60-6-002 Chairperson’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on services from GS department Update on Safety at CERN Reports from ACCU representatives on other Committees a. Scientific Information Policy Board (SIPB) b. IT Service Review Meeting (ITSRM) c. GS User Commission Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairperson in writing or by e-mail to Michael.Hauschild@cern.ch Michael Hauschild (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in bra...

  9. The importance of element speciation in water analysis - a plea for further investigations

    International Nuclear Information System (INIS)

    Frimmel, F.H.; Gremm, T.

    1994-01-01

    Water analysis is dominated by parameters given in laws and recommendations concerning water quality. Speciation has been broadly neglected. This might be due to the difficulties in defining speciation and in determining species at low concentrations. This paper addresses the physical, chemical and biological approaches to speciation and gives examples for methods which are suited for species determination in aquatic systems. Metals and non-metallic elements are covered as well. It is obvious that speciation is a key for understanding the function of aquatic ecosystems and their technical utilization. (orig.)

  10. The Secondary Contact Zone of Phylogenetic Lineages of the Philaenus spumarius (Hemiptera: Aphrophoridae): An Example of Incomplete Allopatric Speciation

    Science.gov (United States)

    Lis, Agata; Maryańska-Nadachowska, Anna; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz

    2014-01-01

    Abstract Previous studies on the phylogeography of the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) suggest the existence of a contact zone of its main phylogenetic lineages along mountain chains in Europe and western Asia. This study presents a detailed examination of the population genetics of P. spumarius within the Carpathian Mountains. The main objective was to determine whether the populations inhabiting that area consist of individuals belonging to different genetic units and whether the observed pattern could be an example of secondary contact zone which formed after incomplete allopatric speciation. Specimens from six transects across the Carpathian arc were examined. The mitochondrial phylogeography of the meadow spittlebug in the examined area clearly shows that individuals from both main clades meet and mix there. Representatives of all three main EF1-α clades were also found. The present distribution of the main clades with a zone of overlap along the mountain ranges may suggest that these phylogenetic lineages form a young hybrid zone. Moreover, a limited number of individuals were shown to possess heteroplasmic mitochondrial DNA, which gives additional support to intraspecific hybridization. P. spumarius could be used in future work as an excellent model species in investigating population genetics, intraspecific hybridization, and speciation in progress. PMID:25500280

  11. The secondary contact zone of phylogenetic lineages of the Philaenus spumarius (Hemiptera: Aphrophoridae): an example of incomplete allopatric speciation.

    Science.gov (United States)

    Lis, Agata; Maryańska-Nadachowska, Anna; Lachowska-Cierlik, Dorota; Kajtoch, Lukasz

    2014-01-01

    Previous studies on the phylogeography of the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) suggest the existence of a contact zone of its main phylogenetic lineages along mountain chains in Europe and western Asia. This study presents a detailed examination of the population genetics of P. spumarius within the Carpathian Mountains. The main objective was to determine whether the populations inhabiting that area consist of individuals belonging to different genetic units and whether the observed pattern could be an example of secondary contact zone which formed after incomplete allopatric speciation. Specimens from six transects across the Carpathian arc were examined. The mitochondrial phylogeography of the meadow spittlebug in the examined area clearly shows that individuals from both main clades meet and mix there. Representatives of all three main EF1-α clades were also found. The present distribution of the main clades with a zone of overlap along the mountain ranges may suggest that these phylogenetic lineages form a young hybrid zone. Moreover, a limited number of individuals were shown to possess heteroplasmic mitochondrial DNA, which gives additional support to intraspecific hybridization. P. spumarius could be used in future work as an excellent model species in investigating population genetics, intraspecific hybridization, and speciation in progress. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

  12. The secondary contact zone of phylogenetic lineages of the Philaenus spumarius (Hemiptera: Aphrophoridae: Cercopidae): an example of incomplete allopatric speciation.

    Science.gov (United States)

    Lis, Agata; Maryańska-Nadachowska, Anna; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz

    2014-01-01

    Previous studies on the phylogeography of the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae: Cercopidae) suggest the existence of a contact zone of its main phylogenetic lineages along mountain chains in Europe and western Asia. This study presents a detailed examination of the population genetics of P. spumarius within the Carpathian Mountains. The main objective was to determine whether the populations inhabiting that area consist of individuals belonging to different genetic units and whether the observed pattern could be an example of secondary contact zone which formed after incomplete allopatric speciation. Specimens from six transects across the Carpathian arc were examined. The mitochondrial phylogeography of the meadow spittlebug in the examined area clearly shows that individuals from both main clades meet and mix there. Representatives of all three main EF1-α clades were also found. The present distribution of the main clades with a zone of overlap along the mountain ranges may suggest that these phylogenetic lineages form a young hybrid zone. Moreover, a limited number of individuals were shown to possess heteroplasmic mitochondrial DNA, which gives additional support to intraspecific hybridization. P. spumarius could be used in future work as an excellent model species in investigating population genetics, intraspecific hybridization, and speciation in progress. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

  13. Public meetings

    CERN Multimedia

    Staff Association

    2012-01-01

    MARS PENSIONS CONTRACT POLICY GENERAL INFORMATION   PUBLIC MEETINGS COME AND BE INFORMED! Public meetings Monday 15 Oct. 2 pm Amphi IT, 31-3-004 Meyrin Wednesday 17 Oct. 10 am Amphi BE, 864-1-D02 Prévessin Thursday 18 Oct. 10 am Salle du Conseil/ Council Chamber 503-1-001 Meyrin Thursday 18 Oct. 2 pm Filtration Plant, 222-R-001(in English) Meyrin   Overview of the topics to be discussed Recognition of Merit – MARS Outcome of last exercise 2007 to 2012 : lessons learned Pension Fund Capital preservation policy : what is it ? Contract policy LC2IC statistics SA proposal General information CVI 2013 Voluntary programmes (PRP, SLS)  

  14. Staff meeting

    CERN Multimedia

    2007-01-01

    I would like to invite all members of the CERN Personnel to a meeting on Wednesday 16 January 2008 at 3:00 p.m. Main Auditorium (bldg 500) to convey my best wishes for the new year, to review CERN’s activities during 2007 and to present the perspectives for 2008, the year of the LHC start-up. Closed-circuit transmission of the meeting will be available in the Council Chamber and in the AB Auditorium (Meyrin), the AB Auditorium (Prévessin), the IT Auditorium (Bldg. 31) and the AT Auditorium (Bldg. 30). Simultaneous translation into English will be available in the main Auditorium. Best wishes for the festive season! Robert AYMAR

  15. Meeting information

    Science.gov (United States)

    The 1986 Ocean Sciences Meeting of the American Geophysical Union and the American Society of Limnology and Oceanography (ASLO) will be held January 13-17, 1986, in New Orleans, La., at the Fairmont Hotel. Co-sponsoring societies are the Acoustical Society of America (ASA), the American Meteorological Society (AMS), the Marine Technology Society (MTS), and the Institute of Electrical and Electronics Engineers, Oceanic Engineering Society (OES).

  16. ACCU Meeting

    CERN Multimedia

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 March 2004 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 6. The PH Department 2. Adoption of the agenda 7. Reports from ACCU representatives on other committees 3. Minutes of the previous meeting 8. Users' Office news 4. News from the CERN Management 9. Any Other Business 5. Matters arising 10. Agenda for the next meeting Anyone wishing to raise any points under item 9 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Norway H. Helstrup (73601) Belgium G. Wilquet (74664) Poland Z. Hajduk (75917) Bulgaria R. Tsenov (79573) Portugal P. Bordalo (74704) Czech Republic P. Závada ...

  17. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 March 2004 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting News from the CERN Management Matters arising The PH Department Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 9 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark P. Hansen (75941) Finland E. Tuominen (71534) France F. Bauer (71247) L. Serin...

  18. ACCU MEETING

    CERN Multimedia

    Chris Onions/EP (Secretary)

    2001-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 June 2001 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda News from the CERN Management Minutes of the previous meeting Matters arising EP Space management Cars Housing EDH from the User's point of view VRVS Users' Office News Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland A. Kiiskinen (79387) France M. Déj...

  19. ACCU Meeting

    CERN Document Server

    Chris Onions

    2006-01-01

    DRAFT Agenda of the meeting to be held on Wednesday 8 March 2006 At 9:15 a.m. in Room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Proposal for a centralised access control service Report from PH Space Management Policy Board Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under Item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives on ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) ...

  20. ACCU MEETING

    CERN Document Server

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 5 December 2007 at 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks7.\tEmergency Services at CERN 2.\tAdoption of the agenda\t8.\tThe Meyrin Tram project 3.\tMinutes of the previous meeting9.\tReports from ACCU representatives on other committees 4.\tMatters arising10.\tUsers’ Office news 5.\tNews from the CERN Management11.\tElection of ACCU Chair 6. LHC 2008 start-up events 6.\tLogistics and transport at CERN 12.\tAny Other Business 13.\tAgenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Aust...

  1. ACCU MEETING

    CERN Multimedia

    PH Department

    2008-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 11 June 2008 At 9:15 a.m. in Room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tAn update on safety at CERN 7.\tChildcare initiative 8.\tReports from ACCU representatives on other committees 9.\tUsers’ Office news 10.\tAny Other Business 11.\tAgenda for the next meeting Anyone wishing to raise any points under Item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium C. Vander Velde (71539) Bulgaria Czech Republic P. Závada (75...

  2. ACCU meeting

    CERN Document Server

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 5 December 2007 At 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tLHC 2008 start-up events 7.\tEmergency Services at CERN 8.\tThe Meyrin Tram project 9.\tReports from ACCU representatives on other committees 10.\tUsers’ Office news 11.\tElection of ACCU Chair 12.\tAny Other Business 13.\tAgenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilq...

  3. ACCU MEETING

    CERN Document Server

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 June 2004 at 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Update on CERN's 50th anniversary celebrations Report from the EPOG (European Particle Physics Outreach Group) Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark P. Hansen (75941...

  4. ACCU Meeting

    CERN Document Server

    Chris Onions

    2005-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 7 September 2005 At 9:15 a.m. in room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Logistics at CERN Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K. Lassila-Perini (79354) France F. Bauer S. Laplace...

  5. ACCU Meeting

    CERN Document Server

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 September 2004 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management The Visits Service Lifetime of Computer Accounts Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark P. Hansen (75941) Finland K. Lassila-Perini (79354) France F. Bauer (7...

  6. ACCU MEETING

    CERN Document Server

    2006-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 September 2006 at 9:15 a.m. in room 60-6-002 1.     Chairman's remarks 2.     Adoption of the agenda 3.     Minutes of the previous meeting 4.     Matters arising 5.     News from the CERN Management 6.     Report on Fellows and Associates programme 7.     Overview of safety at CERN 8.     Reports from ACCU representatives on other committees 9.     Users' Office news 10.  Any Other Business 11.  Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets):Austria W. Adam  (71661) Belgium G. Wilquet (74664) Bulgaria ...

  7. ACCU Meeting

    CERN Document Server

    Chris Onions

    2005-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 7 December 2005 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Closure of computer accounts upon CERN contract expiry Reports from ACCU representatives on other committees Users' Office news Election of ACCU Chair Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets). Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) ...

  8. ACCU Meeting

    CERN Multimedia

    Chris Onions

    2005-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 June 2005 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Logistics at CERN Open Access Publishing Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K. Lassila-Perini ...

  9. ACCU Meeting

    CERN Document Server

    Chris Onions

    2006-01-01

    DRAFT Agendafor the meeting to be held on Wednesday 8 March 2006At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Proposal for a centralised access control service Report from PH Space Management Policy Board Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Fin...

  10. ACCU Meeting

    CERN Multimedia

    Chris Onions

    2005-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 March 2005 At 9:15 a.m. in room 160-1-009 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Purchasing procedures at CERN Reports from ACCU representatives on other committees Users' Office news CERN Clubs Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K. Las...

  11. ACCU MEETING

    CERN Document Server

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 12 September 2007 at 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks7.\tCar sharing pilot project 2.\tAdoption of the agenda\t8.\tReports from ACCU representatives on other committees 3.\tMinutes of the previous meeting9.\tUsers’ Office newss 4.\tMatters arising10.\tAny Other Business 5.\tNews from the CERN Management11.\tAgenda for the next meeting 6.\tLogistics and transport at CERN Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria\tW. Adam (71661)NorwayG. Løvhøiden (73176)Belgium\tG. Wilquet (74664)PolandM. Witek (78967)...

  12. ACCU MEETING

    CERN Multimedia

    PH Department

    2008-01-01

    DRAFT Agenda for the meeting to be heldon Wednesday 5 March 2008 At 9:15 a.m. in room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management An update on Safety at CERN The CERN Ombudsperson proposal Childcare initiative Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) BelgiumnC. Vander Velde (71539) Bulgaria Czech Republic P. Závada (75877) Denm...

  13. ACCU MEETING

    CERN Document Server

    2006-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 December 2006 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Safety at CERN Car sharing pilot project CERN Public Web Sites and Intranet Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria   Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finl...

  14. ACCU Meeting

    CERN Multimedia

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 December 2004 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting The effects of the reorganization of CERN's structure, one year on Matters arising News from the CERN Management Computer Security The new CERN Dosimeter Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark P. Hansen (7594...

  15. ACCU MEETING

    CERN Multimedia

    2006-01-01

    DRAFT Agenda of the meeting to be held on Wednesday 6 September 2006 at 9:15 a.m. in Room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on Fellows and Associates Programme Overview of safety at CERN Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under Item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K....

  16. ACCU meeting

    CERN Document Server

    PH Department

    2008-01-01

    DRAFT Agenda for the meeting to be heldon Wednesday 5 March 2008 At 9:15 a.m. in room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management An update on Safety at CERN The CERN Ombudsperson proposal Childcare initiative Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) BelgiumnC. Vander Velde (71539) Bulgaria Czech Republic P. Závada (75877) Denm...

  17. ACCU MEETING

    CERN Document Server

    PH Department

    2008-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 September 2008 At 9:15 a.m. in Room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management An update on Safety at CERN Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 9 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria, W. Adam (71661) Belgium, C. Vander Velde (71539) Bulgaria Czech Republic, P. Závada (75877) Denmark, J.B. Hansen (...

  18. ACCU MEETING

    CERN Document Server

    Chris Onions

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 13 June 2007 at 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Dosimetry at CERN Status of collaborative tools at CERN Reports from ACCU representatives on other committees Users' Office newss Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K. Lassila-Perini (7935...

  19. ACCU Meeting

    CERN Document Server

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 7 March 2007 at 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Car-sharing pilot project Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 9 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K. Lassila-Perini (79354) France F. Kunne S. ...

  20. ACCU MEETING

    CERN Multimedia

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 13 June 2007 at 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks 6.\tDosimetry at CERN 2.\tAdoption of the agenda 7.\tStatus of collaborative tools at CERN 3.\tMinutes of the previous meeting 8.\tReports from ACCU representatives on other committees 4.\tMatters arising 9.\tUsers’ Office newss 5.\tNews from the CERN Management 10.\tAny Other Business 11.\tAgenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Norway G. Løvhøiden (73176) Belgium G. Wilquet (74664) Poland M. Witek (78967) Bulgaria Portugal...

  1. ACCU Meeting

    CERN Document Server

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 September 2004 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management The Visits Service Lifetime of Computer Accounts Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark P. Hansen (75941) Finland K. Lassila-Perini (79354) France F. Bauer (...

  2. ACCU Meeting

    CERN Multimedia

    2006-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 December 2006 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Safety at CERN Car sharing pilot project CERN Public Web Sites and Intranet Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria   Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finl...

  3. ACCU Meeting

    CERN Multimedia

    PH Department

    2008-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 11 June 2008 At 9:15 a.m. in room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management An update on Safety at CERN Childcare initiative Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria - W. Adam (71661) Belgium - C. Vander Velde (71539) Bulgaria Czech Republic - P. Závada (75877) Denmark - J.B. Hansen...

  4. ACCU Meeting

    CERN Multimedia

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 8 December 2004 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting The effects of the reorganization of CERN's structure, one year on Matters arising News from the CERN Management Computer Security The new CERN Dosimeter Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark P. Hansen (75941) Finl...

  5. ACCU Meeting

    CERN Multimedia

    Chris Onions

    2004-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 June 2004 at 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Update on CERN's 50th anniversary celebrations Report from the EPOG (European Particle Physics Outreach Group) Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tsenov (79573) Czech Republic P. Závada (75877) Denmark P. Hansen (75941) Finlan...

  6. ACCU MEETING

    CERN Document Server

    PH Department

    2008-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 3 December 2008 at 9:15 a.m. in Room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tReport from the new Director-General 7.\tReport on the Fellows and Associates programme 8.\tAn update on Safety at CERN 9.\tReports from ACCU representatives on other committees 10.\tUsers’ Office news 11.\tAny Other Business 12.\tAgenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium C. ...

  7. ACCU MEETING

    CERN Document Server

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 12 September 2007 at 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks6.\tLogistics and transport at CERN2.\tAdoption of the agenda\t7.\tCar sharing pilot project3.\tMinutes of the previous meeting8.\tReports from ACCU representatives on other committees4.\tMatters arising9.\tUsers’ Office newss5.\tNews from the CERN Management10.\tAny Other Business11.\tAgenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria\tW. Adam (71661)NorwayG. Løvhøiden (73176)Belgium\tG. Wilquet (74664)PolandM. Witek (78967)Bulgaria\tPortugalP...

  8. ACCU Meeting

    CERN Document Server

    2007-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 7 March 2007 at 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Car-sharing pilot project Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 9 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) Denmark J.B. Hansen (75941) Finland K. Lassila-Perini (79354) France F. Kunne S. La...

  9. ACCU MEETING

    CERN Multimedia

    Chris Onions (Secretary)

    2001-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 June 2001 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda News from the CERN Management Minutes of the previous meeting Matters arising Logistics and Self-service stores EP Space management follow-up How to improve IT User Support? Users' Office News Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Roger.Jones@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland A. Kiis...

  10. ACCU MEETING

    CERN Multimedia

    Chris Onions (Secretary)

    2001-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 12 September 2001 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda News from the CERN Management Minutes of the previous meeting Matters arising Logistics and Self-service stores EP Space management follow-up How to improve IT User Support? Users' Office News Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Roger.Jones@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland A. Kiiskin...

  11. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2001-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 7 March 2001 At 9:15 a.m. in the 6th floor Conference Room, Main Building Chairman's remarks Adoption of the agenda News from the CERN Management Minutes of the previous meeting Matters arising Video-conferencing/recording Fellows programme Operational Circular No. 6 EP Space management Update on Computing Issues Users' Office News Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary)  ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic...

  12. ACCU Meeting

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 September 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 7. Equal Opportunities Commission 2. Adoption of the agenda 8. Registration plans for portables 3. Minutes of the previous meeting 9. Reports from ACCU representatives on other committees 4. Matters arising 10. Users' Office news 5. News from the CERN Management 11. Any Other Business 6. The Press Office 12. Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Norway H. Helstrup (73601) Belgium G. Wilquet (74664) Poland Z. Hajduk (75917) Bulgar...

  13. ACCU MEETING

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 5 March 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 7. Equipment insurance on site 2. Adoption of the agenda,8. ACCU reporting mechanisms in the different countries 3. Minutes of the previous meeting9. Reports from ACCU representatives on other committees 4. Matters arising10. Users' Office news 5. News from the CERN Management11. Any Other Business 6. CHIS news and follow-up of survey12. Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661)NorwayH. Helstrup (73601) Belgium G. Wilquet (74664) Poland Z. Hajduk (7591...

  14. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2002-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 11 September 2002 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Health Insurance Questionnaire Host States Relations Service Update on EP Space management Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland E. Tuominen (71534) France F. Bauer (71247) L. Serin (...

  15. ACCU MEETING

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 December 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 8. Report from IT division on Computing matters 2. Adoption of the agenda 9. Young Particle Physicists Association 3. Minutes of the previous meeting 10. Reports from ACCU representatives on other committees 4. Matters arising 11. Users' Office news 5. News from the CERN Management 12. Election of the ACCU Chair 6. Report from the new Director-General 13. Any Other Business 7. CERN's 50th anniversary 14. Agenda for the next meeting Anyone wishing to raise any points under item 13 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Ada...

  16. ACCU MEETING

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 5 March 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 7. Equipment insurance on site 2. Adoption of the agenda 8. ACCU reporting mechanisms in the different countries 3. Minutes of the previous meeting 9. Reports from ACCU representatives on other committees 4. Matters arising 10. Users' Office news 5. News from the CERN Management 11. Any Other Business 6. Health Insurance news and follow-up of survey 12. Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Norway H. Helstrup (73601) Belgium G. Wil...

  17. ACCU MEETING

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 11 June 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 7. Reports from ACCU representatives 2. Adoption of the agenda on other committees 3. Minutes of the previous meeting 8. Users' Office news 4. Matters arising 9. Any Other Business 5. News from the CERN Management 10. Agenda for the next meeting 6. Property Protection at CERN Anyone wishing to raise any points under item 9 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Norway H. Helstrup (73601) Belgium G. Wilquet (74664) Poland Z. Hajduk (75917) Bulgaria R. Tsenov (74837) Portugal P. Bordalo (74704) Czech Republic ...

  18. ACCU Meeting

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 September 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 8. Registration plans for portables 2. Adoption of the agenda 9. Reports from ACCU representatives 3. Minutes of the previous meeting on other committees 4. Matters arising 10. Users' Office news 5. News from the CERN Management 11. Any Other Business 6. The Press Office 12. Agenda for the next meeting 7. Equal Opportunities Commission Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): AustriaW. Adam (71661) Norway H. Helstrup (73601) Belgium G. Wilquet (74664) Poland Z. Hajduk (75917) Bulgari...

  19. ACCU MEETING

    CERN Multimedia

    2003-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 December 2003 At 9:15 a.m. in room 60-6-002 1. Chairman's remarks 8. Report from IT division on Computing matters 2. Adoption of the agenda 9. Young Particle Physicists Association 3. Minutes of the previous meeting 10. Reports from ACCU representatives on other committees 4. Matters arising 11. Users' Office news 5. News from the CERN Management 12. Election of the ACCU Chair 6. Report from the new Director-General 13. Any Other Business 7. CERN's 50th anniversary 14. Agenda for the next meeting Anyone wishing to raise any points under item 13 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (716...

  20. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2002-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 6 March 2002 At 9:15 a.m. in the Council Chamber Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Follow-up on Space Management Users' Desktop needs PIE procedures Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland E. Tuominen (71534) France F. Bauer L. Serin (712...

  1. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2002-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 12 June 2002 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management PIE procedures CERN Cars EP Electronics Advisory Board Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch   ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland E. Tuominen (71534) France F. Bauer (71247) L. Serin (71143) Germany H. Kroha...

  2. ACCU MEETING

    CERN Multimedia

    2000-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 13 September 2000 At 10 a.m. in the 6th floor Conference Room, Main Building 1. Chairman's remarks 2. Adoption of the agenda 3. News from the CERN Management 4. Minutes of the previous meeting 5. Matters arising 6. Report from the Scientific Information Policy Board 7. Report from ETT Division: The Press Office 8. Update on Computing Issues 9. Users' Office News 10. Any Other Business 11. Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail to Bryan Pattison (Secretary). ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets) : Austria G. Neuhofer (74094) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Z vada (75...

  3. ACCU MEETING

    CERN Multimedia

    Bryan Pattison

    2000-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 13 September 2000 At 10 a.m. in the 6th floor Conference Room, Main Building1. Chairman's remarks2. Adoption of the agenda3. News from the CERN Management4. Minutes of the previous meeting5. Matters arising6. Report from the Scientific Information Policy Board7. Report from ETT Division: The Press Office8. Update on Computing Issues9. Users' Office News10. Any Other Business11. Agenda for the next meetingAnyone wishing to raise any points under item 10 is invited to send them to the Secretary in writing via the CERN Users' Office or by e-mail toBryan Pattison(Secretary).ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets) :Austria G. Neuhofer (74094)Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958)Czech Republic P. Závada (75877)Den...

  4. ACCU MEETING

    CERN Multimedia

    Chris Onions

    2002-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 12 June 2002 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management PIE procedures CERN Cars EP Electronics Advisory Board Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch   ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria R. Tzenov (77958) Czech Republic P. Závada (75877) Denmark A. Waananen (75941) Finland E. Tuominen (71534) France F. Bauer (71247) L. Serin (71143) Germany H. Kroha ...

  5. ACCU MEETING

    CERN Multimedia

    PH Department

    2009-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 11 March 2009 At 9:15 a.m. in room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management The CERN Press Office An update on Safety at CERN The Burotel project Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel () Belgium C. Vander Velde (71539) Bulgaria Czech Republic P. Závada (75877) Denmark...

  6. ACCU MEETING

    CERN Multimedia

    PH Department

    2010-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 March 2010 At 9:15 a.m. in room 60-6-002 Chairperson’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Report on services from GS department An update on Safety at CERN Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 10 is invited to send them to the Chairman in writing or by e-mail to Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives on ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel (76592) Belgium C. Vander Velde (Chairperson) (71539) Bulgaria Czech Republic S. Nemecek (71144) ...

  7. ACCU MEETING

    CERN Multimedia

    PH Department

    2011-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 7 September 2011 at 9:15 a.m. in room 60-6-002   Chairperson's remarks Adoption of the agenda      Minutes of the previous meeting Matters arising       News from the CERN Management Report on services from GS department Report on new CHIS rules Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 9 is invited to send them to the Chairperson in writing or by e-mail to Michael.Hauschild@cern.ch Michael Hauschild (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria M. Jeitler (76307) Belgium C. Vander Velde (Chairperson)...

  8. ACCU MEETING

    CERN Multimedia

    PH Department

    2009-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 September 2009 At 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tCode of conduct 7.\tEqual Opportunities at CERN 8.\tAn update on safety at CERN 9.\tThe CERN shuttle service 10.\tReports from ACCU representatives on other committees 11.\tUsers’ Office news 12.\tOther business 13.\tAgenda of the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives on ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel (76592) Belgium C. Vander Velde (71539) Bulgaria Czech Re...

  9. ACCU MEETING

    CERN Multimedia

    PH Department

    2009-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 10 June 2009At 9:15 a.m. in room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management CERN Social Services User services in GS Department An update on Safety at CERN Reports from ACCU representatives on other committees Users’ Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria - G. Walzel (76592) Belgium - C. Vander Velde (71539) Bulgaria Czech Republic - P. Závada (7587...

  10. ACCU Meeting

    CERN Multimedia

    Chris Onions

    DRAFT Agenda for the meeting to be held on Wednesday 9 December 2009 At 9:15 a.m. in Room 60-6-002 Chairman’s remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Restaurant No. 1 extension An update on Safety at CERN Reports from ACCU representatives on other committees Users’ Office news Election of the ACCU Chair Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel (76592) Belgium C. Vander Velde (71539) Bulgaria Czech Republic P. Záv...

  11. ACCU MEETING

    CERN Multimedia

    PH Department

    2009-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 9 September 2009 At 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tCode of Conduct 7.\tEqual Opportunities at CERN 8.\tAn update on Safety at CERN 9.\tThe CERN shuttle service 10.\tReports from ACCU representatives on other committees 11.\tUsers’ Office news 12.\tAny Other Business 13.\tAgenda for the next meeting Anyone wishing to raise any points under item 12 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel (76592) Belgium C. Vander Velde (71539) Bulgaria Cze...

  12. ACCU MEETING

    CERN Multimedia

    PH Department

    2009-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 11 March 2009 At 9:15 a.m. in room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tThe CERN Press Office 7.\tAn update on Safety at CERN 8.\tThe Burotel project 9.\tReports from ACCU representatives on other committees 10.\tUsers’ Office news 11.\tAny Other Business 12.\tAgenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to mailto:Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria G. Walzel () Belgium C. Vander Velde (71539) Bulgaria C...

  13. ACCU Meeting

    CERN Document Server

    Chris Onions

    2006-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 14 June 2006 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Car sharing pilot project The CERN Document Server : the portal to Open Access Videoconferencing and collaborative tools at CERN Reports from ACCU representatives on other committees Users' Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (7...

  14. ACCU Meeting

    CERN Document Server

    Chris Onions

    2006-01-01

    DRAFT Agenda for the meeting to be held on Wednesday 14 June 2006 At 9:15 a.m. in room 60-6-002 Chairman's remarks Adoption of the agenda Minutes of the previous meeting Matters arising News from the CERN Management Car sharing pilot project The CERN Document Server : the portal to Open Access Videoconferencing and collaborative tools at CERN Reports from ACCU representatives on other committees Users'Office news Any Other Business Agenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium G. Wilquet (74664) Bulgaria Czech Republic P. Závada (75877) ...

  15. 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides.

    Science.gov (United States)

    Zagrobelny, Mika; Scheibye-Alsing, Karsten; Jensen, Niels Bjerg; Møller, Birger Lindberg; Gorodkin, Jan; Bak, Søren

    2009-12-02

    An essential driving component in the co-evolution of plants and insects is the ability to produce and handle bioactive compounds. Plants produce bioactive natural products for defense, but some insects detoxify and/or sequester the compounds, opening up for new niches with fewer competitors. To study the molecular mechanism behind the co-adaption in plant-insect interactions, we have investigated the interactions between Lotus corniculatus and Zygaena filipendulae. They both contain cyanogenic glucosides which liberate toxic hydrogen cyanide upon breakdown. Moths belonging to the Zygaena family are the only insects known, able to carry out both de novo biosynthesis and sequestration of the same cyanogenic glucosides as those from their feed plants. The biosynthetic pathway for cyanogenic glucoside biosynthesis in Z. filipendulae proceeds using the same intermediates as in the well known pathway from plants, but none of the enzymes responsible have been identified. A genomics strategy founded on 454 pyrosequencing of the Z. filipendulae transcriptome was undertaken to identify some of these enzymes in Z. filipendulae. Comparisons of the Z. filipendulae transcriptome with the sequenced genomes of Bombyx mori, Drosophila melanogaster, Tribolium castaneum, Apis mellifera and Anopheles gambiae indicate a high coverage of the Z. filipendulae transcriptome. 11% of the Z. filipendulae transcriptome sequences were assigned to Gene Ontology categories. Candidate genes for enzymes functioning in the biosynthesis of cyanogenic glucosides (cytochrome P450 and family 1 glycosyltransferases) were identified based on sequence length, number of copies and presence/absence of close homologs in D. melanogaster, B. mori and the cyanogenic butterfly Heliconius. Examination of biased codon usage, GC content and selection on gene candidates support the notion of cyanogenesis as an "old" trait within Ditrysia, as well as its origins being convergent between plants and insects

  16. 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

    Directory of Open Access Journals (Sweden)

    Jensen Niels

    2009-12-01

    Full Text Available Abstract Background An essential driving component in the co-evolution of plants and insects is the ability to produce and handle bioactive compounds. Plants produce bioactive natural products for defense, but some insects detoxify and/or sequester the compounds, opening up for new niches with fewer competitors. To study the molecular mechanism behind the co-adaption in plant-insect interactions, we have investigated the interactions between Lotus corniculatus and Zygaena filipendulae. They both contain cyanogenic glucosides which liberate toxic hydrogen cyanide upon breakdown. Moths belonging to the Zygaena family are the only insects known, able to carry out both de novo biosynthesis and sequestration of the same cyanogenic glucosides as those from their feed plants. The biosynthetic pathway for cyanogenic glucoside biosynthesis in Z. filipendulae proceeds using the same intermediates as in the well known pathway from plants, but none of the enzymes responsible have been identified. A genomics strategy founded on 454 pyrosequencing of the Z. filipendulae transcriptome was undertaken to identify some of these enzymes in Z. filipendulae. Results Comparisons of the Z. filipendulae transcriptome with the sequenced genomes of Bombyx mori, Drosophila melanogaster, Tribolium castaneum, Apis mellifera and Anopheles gambiae indicate a high coverage of the Z. filipendulae transcriptome. 11% of the Z. filipendulae transcriptome sequences were assigned to Gene Ontology categories. Candidate genes for enzymes functioning in the biosynthesis of cyanogenic glucosides (cytochrome P450 and family 1 glycosyltransferases were identified based on sequence length, number of copies and presence/absence of close homologs in D. melanogaster, B. mori and the cyanogenic butterfly Heliconius. Examination of biased codon usage, GC content and selection on gene candidates support the notion of cyanogenesis as an "old" trait within Ditrysia, as well as its origins being

  17. Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?

    Science.gov (United States)

    Rosser, Neil; Kozak, Krzysztof M; Phillimore, Albert B; Mallet, James

    2015-06-30

    Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two

  18. Potential application of SERS for arsenic speciation in biological matrices.

    Science.gov (United States)

    Yang, Mingwei; Matulis, Shannon; Boise, Lawrence H; McGoron, Anthony J; Cai, Yong

    2017-08-01

    Speciation of arsenic is usually carried out using chromatography-based methods coupled with spectroscopic determination; however, the inevitable procedures involving sample preparation and separation could potentially alter the integrity of the arsenic metabolites present in biological samples. Surface-enhanced Raman spectroscopy (SERS) could be a promising alternative for providing a reliable arsenic analysis under the influence of a cellular matrix. A method for arsenic speciation using SERS in cellular matrix was developed in this study and four arsenicals were selected, including arsenite (As III ), arsenate (As V ), monomethylarsonic acid (MMA V ) and dimethylarsinic acid (DMA V ). Silver nanoparticles in the form of colliodal suspension with different surface charges, i.e., coated with citrate (AgNPs-Citrate) and spermine (AgNPs-Spermine) were employed as SERS substrates. Adsorption of arsenicals on nanoparticles in colloidal suspensions and the cellular matrix and the pH, size, and zeta potential of the colloidal suspensions were investigated for a better understanding of the SERS signal response of arsenicals in the colloidal suspensions or under the influence of cellular matrix. Arsenicals showed substantially different SERS responses in the two colloidal suspensions, mainly because of the distinct difference in the interaction between the arsenicals and the nanoparticles. Arsenic speciation in cell lysate could be successfully carried out in AgNPs-Spermine suspension, while AgNPs-Citrate could not yield significant SERS signals under the experimental conditions. This study proved that AgNPs-Spermine colloidal suspension could be a promising SERS substrate for studying arsenic metabolism in a biological matrix, reducing the bias caused by traditional techniques that involve sample extraction and pretreatment.

  19. Nickel speciation in cement-stabilized/solidified metal treatment filtercakes

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Amitava, E-mail: reroy@lsu.edu [J. Bennett Johnston, Sr., Center for Advanced Microstructures and Devices, Louisiana State University, Baton Rouge, LA 70806, USA (United States); Stegemann, Julia A., E-mail: j.stegemann@ucl.ac.uk [Centre for Resource Efficiency & the Environment, Department of Civil, Environmental & Geomatic Engineering, University College London, Chadwick Building, Gower Street, London WC1E 6BT, UK (United Kingdom)

    2017-01-05

    Highlights: • XAS shows the same Ni speciation in untreated and stabilized/solidified filtercake. • Ni solubility is the same for untreated and stabilized/solidified filtercake. • Leaching is controlled by pH and physical encapsulation for all binders. - Abstract: Cement-based stabilization/solidification (S/S) is used to decrease environmental leaching of contaminants from industrial wastes. In this study, two industrial metal treatment filtercakes were characterized by X-ray diffractometry (XRD), thermogravimetric and differential thermogravimetric analysis (TG/DTG) and Fourier transform infrared (FTIR); speciation of nickel was examined by X-ray absorption (XAS) spectroscopy. Although the degree of carbonation and crystallinity of the two untreated filtercakes differed, α-nickel hydroxide was identified as the primary nickel-containing phase by XRD and nickel K edge XAS. XAS showed that the speciation of nickel in the filtercake was unaltered by treatment with any of five different S/S binder systems. Nickel leaching from the untreated filtercakes and all their stabilized/solidified products, as a function of pH in the acid neutralization capacity test, was essentially complete below pH ∼5, but was 3–4 orders of magnitude lower at pH 8–12. S/S does not respeciate nickel from metal treatment filtercakes and any reduction of nickel leaching by S/S is attributable to pH control and physical mechanisms only. pH-dependent leaching of Cr, Cu and Ni is similar for the wastes and s/s products, except that availability of Cr, Cu and Zn at decreased pH is reduced in matrices containing ground granulated blast furnace slag.

  20. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

    Science.gov (United States)

    Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

    2015-11-01

    Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

  1. Miscibility and Speciation in the Water/carbon Dioxide System

    Science.gov (United States)

    Abramson, E.; Bollengier, O.; Brown, J. M.

    2017-12-01

    We have been exploring fluid-fluid solubilities and speciation in mixed systems of CO2-H2O. Fluid-fluid immiscibility extends to the highest pressures and temperatures yet explored (7 GPa, 700K). In this region, commonly used COH fluid models agree neither with the data nor among themselves. The range of immiscibility is extended by addition of NaCl, but miscibility limits determined in preliminary experiments are not as expected from extrapolation of lower pressure (linked to an observed change in speciation as CO2(aq) reacts with water. The identity of the newly formed species is, as of the writing of this abstract, unknown, but presumed to be either H2CO3 or HCO3-. A reasonable match between the observed equilibria and an application of HKF theory suggests that the new species is, indeed, HCO3-, but with a Raman frequency shifted from that found in the dilute aqueous solution. Application of HKF theory to the CO2(f)-CO2(aq) equilibrium suffers from an incompatibility of the usual formulation of the theory with known molar volumes of CO2(f) at higher pressures. On the basis of these studies we conclude that models of CO2-H2O fluids must take into account major changes in speciation, and that simple equations-of-state, of a few fitted parameters, will not afford an adequate description of such fluids. "First principles" models, tested against real data, seem more likely to yield the desired results. This statement extends as well to the calculation of the dielectric constants of these mixed fluids, the basis of ionic solution chemistry. Further, semi-empirical formulations of solution thermodynamics, which function well at pressures of kbars, ought to be re-worked for use over larger pressure ranges.

  2. Genetic evidence for hybrid trait speciation in heliconius butterflies.

    Directory of Open Access Journals (Sweden)

    Camilo Salazar

    2010-04-01

    Full Text Available Homoploid hybrid speciation is the formation of a new hybrid species without change in chromosome number. So far, there has been a lack of direct molecular evidence for hybridization generating novel traits directly involved in animal speciation. Heliconius butterflies exhibit bright aposematic color patterns that also act as cues in assortative mating. Heliconius heurippa has been proposed as a hybrid species, and its color pattern can be recreated by introgression of the H. m. melpomene red band into the genetic background of the yellow banded H. cydno cordula. This hybrid color pattern is also involved in mate choice and leads to reproductive isolation between H. heurippa and its close relatives. Here, we provide molecular evidence for adaptive introgression by sequencing genes across the Heliconius red band locus and comparing them to unlinked wing patterning genes in H. melpomene, H. cydno, and H. heurippa. 670 SNPs distributed among 29 unlinked coding genes (25,847bp showed H. heurippa was related to H. c. cordula or the three species were intermixed. In contrast, among 344 SNPs distributed among 13 genes in the red band region (18,629bp, most showed H. heurippa related with H. c. cordula, but a block of around 6,5kb located in the 3' of a putative kinesin gene grouped H. heurippa with H. m. melpomene, supporting the hybrid introgression hypothesis. Genealogical reconstruction showed that this introgression occurred after divergence of the parental species, perhaps around 0.43Mya. Expression of the kinesin gene is spatially restricted to the distal region of the forewing, suggesting a mechanism for pattern regulation. This gene therefore constitutes the first molecular evidence for adaptive introgression during hybrid speciation and is the first clear candidate for a Heliconius wing patterning locus.

  3. Modelling interaction of deep groundwaters with bentonite and radionuclide speciation

    International Nuclear Information System (INIS)

    Wanner, H.

    1986-04-01

    In the safety analysis recently reported for a potential Swiss high-level waste repository, radionuclide speciation and solubility limits are calculated for expected granitic groundwater conditions. With the objective of deriving a more realistic description of radionuclide release from the near-field, an investigation has been initiated to quantitatively specify the chemistry of the near-field. In the Swiss case, the main components of the near-field are the glass waste-matrix, a thick steel canister horizontally emplaced in a drift, and a backfill of highly compacted sodium bentonite. This report describes a thermodynamic model which is used to estimate the chemical composition of the pore water in compacted sodium bentonite. Solubility limits and speciation of important actinides and the fission product technetium in the bentonite pore water are then calculated. The model is based on available experimental data on the interaction of sodium bentonite and groundwater and represents means of extrapolation from laboratory data to repository conditions. The modelled composition of the pore water of compacted sodium bentonite, as well as the various compositions resulting from the long-term extrapolation, are used to estimate radionuclide solubilities in the near-field of a deep repository. From the chemical point of view, calcium bentonite seems to be more stable than sodium bentonite in the presence of Swiss Reference Groundwater. Since the effect of calcium bentonite on the groundwater chemical composition will be considerably less marked than that of sodium bentonite, especially with respect to key parameters for the nuclide speciation like carbonate concentration and pH, the use of calcium bentonite instead of sodium bentonite will improve the reliability in the prediction of source terms for radionuclide transport in the geosphere. (author)

  4. Trace metal speciation: Finally, correctly addressing trace metal issues

    International Nuclear Information System (INIS)

    Donard, O.F.X.

    2001-01-01

    The history of the development of trace metal speciation was discussed and the reasons behind the relatively slow widespread acceptance of its importance were presented. Partially, this was due to the lack of availability of commercial instrumentation and partly to the drive towards improving sensitivity in analytical chemistry which had focused attention on total concentration determinations. The sophistication and control of analytical instrumentation is now such that the spotlight must be turned onto the chemical species of an element present in a sample since this is what governs its behaviour in the biosphere. Indeed, several companies are currently considering the introduction of instrumentation specifically designed for metal species determination

  5. WHATIF-AQ, Geochem Speciation and Saturation of Aqueous Solution

    International Nuclear Information System (INIS)

    Nielsen, Ole John; Jensen, Bror Skytte

    1988-01-01

    1 - Description of program or function: WHATIF-AQ is part of a family of programs for calculations of geochemistry in the near-field of radioactive waste with temperature gradients. The program calculates speciation and saturation indices for an aqueous solution at temperatures in the range 0 - 125 degrees C. The chemical equilibrium is determined by solving a set of nonlinear equations consisting of the equilibrium constant and mass balance constraints. 2 - Method of solution: The set of equations is solved using a generalized Newton-Raphson technique

  6. Chemical speciation and transformation of mercury in contaminated sediments

    OpenAIRE

    Drott, Andreas

    2009-01-01

    Biomagnification of mercury (Hg) in aquatic food webs occurs almost exclusively as mono-methyl Hg (MeHg). In this thesis, the influence of chemical speciation and environmental conditions on transformations of inorganic Hg (HgII) and MeHg was studied at eight sites in Sweden with Hg contaminated sediments. The source of contamination was either Hg0(l) or phenyl-Hg, and total Hg concentrations ranged between 1.0-1100 nmol g-1. The environmental conditions, e.g. salinity, temperature climate, p...

  7. Evolution of blind beetles in isolated aquifers: a test of alternative modes of speciation

    NARCIS (Netherlands)

    Leys, R.; Nes, van E.H.; Watts, C.H.; Cooper, S.J.B.; Humphreys, W.F.; Hogendoorn, K.

    2012-01-01

    Evidence is growing that not only allopatric but also sympatric speciation can be important in the evolution of species. Sympatric speciation has most convincingly been demonstrated in laboratory experiments with bacteria, but field-based evidence is limited to a few cases. The recently discovered

  8. Comparison of analytical charge-form and equilibrium thermodynamic speciation of certain radionuclides

    International Nuclear Information System (INIS)

    Jenne, E.A.; Cowan, C.E.; Robertson, D.E.

    1984-01-01

    Calculating trace element speciation with a thermodynamic model is often challenged on the basis that the existing thermodynamic data are not sufficiently reliable. Water quality data and corresponding analytical charge-form speciation analysis were available for radionuclides occurring in a low-level radioactive groundwater. This offered an opportunity for comparing the results of an equilibrium thermodynamic model with the results of analytical charge-form speciation. The charge-form speciation was determined using the Battelle Large Volume Water Sampler, which contains consecutive layers of cation resin, anion resin and activated aluminum oxide for retention of cationic, anionic and non-ionic dissolved chemical species, respectively. The thermodynamic speciation of Cs, Cr, Fe, I, Mn, Mo, Na, and Zn was calculated using the MINTEQ geochemical model. Ce, Co, Tc, Np, Pm, and Sb were speciated by hand calculation. Excellent agreement between the analytically determined charge-form and the thermodynamic speciation was observed for 54 Mn, 144 Ce, 131 I, 24 Na, 137 Cs, 99 Mo, 99 Tc, 151 Pm, 239 Np. Organic complexation by natural and/or synthetic organics in the waters may be important in the speciation of 65 An, 60 Co, 131 I, 59 Fe and possibly 51 Cr. Both 124 Sb and 125 Sb appeared to be in redox disequilibria with the groundwater. 29 references, 2 tables

  9. Differential survival between visual environments supports a role of divergent sensory drive in cichlid fish speciation

    NARCIS (Netherlands)

    Maan, Martine E.; Seehausen, Ole; Groothuis, Ton G. G.

    Identifying the selective forces that initiate ecological speciation is a major challenge in evolutionary biology. Sensory drive has been implicated in speciation in various taxa, largely based on phenotype-environment correlations and signatures of selection in sensory genes. Here, we present a

  10. Recent Developments in the Speciation and Determination of Mercury Using Various Analytical Techniques

    Directory of Open Access Journals (Sweden)

    Lakshmi Narayana Suvarapu

    2015-01-01

    Full Text Available This paper reviews the speciation and determination of mercury by various analytical techniques such as atomic absorption spectrometry, voltammetry, inductively coupled plasma techniques, spectrophotometry, spectrofluorometry, high performance liquid chromatography, and gas chromatography. Approximately 126 research papers on the speciation and determination of mercury by various analytical techniques published in international journals since 2013 are reviewed.

  11. Mimetic Divergence and the Speciation Continuum in the Mimic Poison Frog Ranitomeya imitator

    DEFF Research Database (Denmark)

    Twomey, Evan; Vestergaard, Jacob Schack; Venegas, Pablo J.

    2016-01-01

    While divergent ecological adaptation can drive speciation, understanding the factors that facilitate or constrain this process remains a major goal in speciation research. Here, we study two mimetic transition zones in the poison frog Ranitomeya imitator, a species that has undergone a Mullerian...

  12. Influence of EDDS on metal speciation in soil extracts: Measurement and mechanistic multicomponent modeling

    NARCIS (Netherlands)

    Koopmans, G.F.; Schenkeveld, W.D.C.; Song, J.; Luo, Y.; Japenga, J.; Temminghoff, E.J.M.

    2008-01-01

    The use of the [S,S]-isomer of EDDS to enhance phytoextraction has been proposed for the remediation of heavy metal contaminated soils. Speciation of metals in soil solution in the presence of EDDS and dissolved organic matter (DOM) received, however, almost no attention, whereas metal speciation

  13. Chemical speciation of L-glutamine complexes with Co(II), Ni(II) and ...

    African Journals Online (AJOL)

    The trend in the variation of stability constants of the complexes with mole fraction of the surfactant is attributed to the compartmentalization of complexation equilibria. Distribution of species and effect of influential parameters on chemical speciation have also been presented. KEY WORDS: Chemical speciation, complex ...

  14. EPA’s SPECIATE 4.4 Database - Development and Uses

    Science.gov (United States)

    SPECIATE is the EPA's repository of TOG, PM, and Other Gases speciation profiles of air pollution sources. It includes weight fractions of both organic species and PM and provides data in consistent units. Species include metals, ions, elements, and organic and inorganic compound...

  15. Overview of receptor-based source apportionment studies for speciated atmospheric mercury

    OpenAIRE

    Cheng, I.; Xu, X.; Zhang, L.

    2015-01-01

    Receptor-based source apportionment studies of speciated atmospheric mercury are not only concerned with source contributions but also with the influence of transport, transformation, and deposition processes on speciated atmospheric mercury concentrations at receptor locations. Previous studies applied multivariate receptor models including principal components analysis and positive matrix factorization, and back trajectory receptor models including potential source contri...

  16. HPLC inorganic arsenic speciation analysis of samples containing high sulfuric acid and iron levels

    NARCIS (Netherlands)

    Gonzalez-Contreras, P.A.; Gerrits, I.P.A.M.; Weijma, J.; Buisman, C.J.N.

    2011-01-01

    To monitor the oxidation of arsenite to arsenate in oxidizing and bioleaching reactors, speciation analysis of the inorganic arsenic compounds is required. Existing arsenic speciation analysis techniques are based on the use of liquid chromatography columns coupled to detector equipment such as

  17. Speciation analysis of 129I in seawater using coprecipitation and accelerator mass spectrometry and its applications

    DEFF Research Database (Denmark)

    Xing, Shan; Hou, Xiaolin; Aldahan, Ala

    2017-01-01

    Speciation analysis of long-lived 129I in seawater can provide useful information on the source of water masses. This paper presents an improved method for speciation analysis of 129I based on coprecipitation of iodide as AgI with Ag2SO3 and AgCl. By adding a small amount of 127I carrier...

  18. Comparison between cultivated and total bacterial communities associated with Cucurbita pepo using cultivation-dependent techniques and 454 pyrosequencing.

    Science.gov (United States)

    Eevers, N; Beckers, B; Op de Beeck, M; White, J C; Vangronsveld, J; Weyens, N

    2016-02-01

    Endophytic bacteria often have beneficial effects on their host plants that can be exploited for bioremediation applications but, according to the literature, only 0.001-1% of all endophytic microbes should be cultivable. This study compared the cultivated endophytic communities of the roots and shoots of Cucurbita pepo with the total endophytic communities as determined by cultivation-dependent techniques and 454 pyrosequencing. The ten most abundant taxa of the total communities aligned well with the cultivated taxa; however, the abundance of these taxa in the two communities differed greatly. Enterobacter showed very low presence in the total communities, whereas they were dominantly present in the cultivated communities. Although Rhizobium dominated in total root and shoot communities, it was poorly cultivable and even then only in growth media containing plant extract. Since endophytes likely contribute to plant-growth promotion, cultivated bacterial strains were tested for their plant-growth promoting capabilities, and the results were correlated with their abundance in the total community. Bacillus and Pseudomonas showed promising results when considering cultivability, abundance in the total community and plant-growth promoting capability. This study demonstrated that, although a limited number of bacterial genera were cultivable, current cultivation-dependent techniques may be sufficient for further isolation and inoculation experiments that aim to improve phytoremediation efficiency. Copyright © 2015 Elsevier GmbH. All rights reserved.

  19. Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

    Science.gov (United States)

    Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

    2014-03-01

    Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  20. Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Edward Alain B. Pajarillo

    2015-04-01

    Full Text Available This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level. Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

  1. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    Science.gov (United States)

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

    2013-01-01

    Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  2. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Science.gov (United States)

    Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

    2015-01-01

    The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

  3. Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar (Coleoptera: Curculionidae Reveals Multiple Protease-Like Transcripts.

    Directory of Open Access Journals (Sweden)

    Arnubio Valencia

    Full Text Available The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.

  4. Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora

    KAUST Repository

    Gao, Zhao-Ming

    2015-06-11

    Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study.

  5. The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

    Science.gov (United States)

    Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

    2015-01-01

    In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

  6. Insight into the bacterial diversity of fermentation woad dye vats as revealed by PCR-DGGE and pyrosequencing.

    Science.gov (United States)

    Milanović, Vesna; Osimani, Andrea; Taccari, Manuela; Garofalo, Cristiana; Butta, Alessandro; Clementi, Francesca; Aquilanti, Lucia

    2017-07-01

    The bacterial diversity in fermenting dye vats with woad (Isatis tinctoria L.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent PCR-DGGE analyses and next-generation sequencing of 16S rRNA amplicons. An extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. PCR-DGGE analyses revealed the presence of Paenibacillus lactis, Sporosarcina koreensis, Bacillus licheniformis, and Bacillus thermoamylovorans, while Bacillus thermolactis, Bacillus pumilus and Bacillus megaterium were also identified but with sequence identities lower than 97%. Dominant operational taxonomic units (OTUs) identified by pyrosequencing included Clostridium ultunense, Tissierella spp., Alcaligenes faecalis, Erysipelothrix spp., Enterococcus spp., Virgibacillus spp. and Virgibacillus panthothenicus, while sub-dominant OTUs included clostridia, alkaliphiles, halophiles, bacilli, moderately thermophilic bacteria, lactic acid bacteria, Enterobacteriaceae, aerobes, and even photosynthetic bacteria. Based on the current knowledge of indigo-reducing bacteria, it is considered that indigo-reducing bacteria constituted only a small fraction in the unique microcosm detected in the natural indigo dye vats.

  7. Assessment of bacterial diversity in Hyalomma aegyptium, H. marginatum and H. excavatum ticks through tag-encoded pyrosequencing.

    Science.gov (United States)

    Keskin, Adem; Bursali, Ahmet; Snow, David E; Dowd, Scot E; Tekin, Saban

    2017-12-01

    Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination of microbial diversity with tag-encoded pyrosequencing indicates that H. marginatum and H. excavatum were more diversity rich than H. aegyptium. Although numerous pathogenic and non-pathogenic bacterial genera were detected, including Acidovorax, Bacillus, Bacteroides, Bdellovibrio, Clostridium, Curvibacter, Escherichia, Flavobacterium, Limnohabitans, Paenibacillus, Ralstonia, Sarcina, Sediminibacterium, Segetibacter Stenotrophomonas and Variovorax, the predominant zoonotic bacteria represented in these ticks were genera Borrelia, Francisella, and Rickettsia. To the authors' knowledge, this work represents the first detection of Yersinia enterocolitica in the tick H. excavatum, raising questions regarding the vector competency of this tick, as well as associations of different disease representations perhaps through previously unforeseen routes of pathogen introduction. Likewise, similar questions are related to the presence of Legionella pneumophila in one H. excavatum sample.

  8. Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach.

    Science.gov (United States)

    Takeshita, Toru; Yasui, Masaki; Shibata, Yukie; Furuta, Michiko; Saeki, Yoji; Eshima, Nobuoki; Yamashita, Yoshihisa

    2015-01-30

    Dental plaque is a dynamic microbial biofilm ecosystem that comprises hundreds of species including difficult-to-cultivate bacteria. We observed the assembly of a plaque bacterial community through 16S rRNA gene analysis. Plaque samples that accumulated on a hydroxyapatite disk for 1, 2, 3, 4, 5, and 7 days with saliva on day 0 were collected from 19 young adults using a removable resin splint. Quantitative PCR analysis showed that the total bacterial amount gradually increased and reached a plateau on day 4. Barcoded pyrosequencing analysis revealed that the microbial richness and diversity particularly increased between days 5 and 7. A principal coordinate analysis plot based on unweighted UniFrac showed the community assembly in a time-related manner, which became increasingly similar to the salivary microbiota. Facultative anaerobic bacteria such as Streptococcus, Neisseria, Abiotrophia, Gemella, and Rothia were predominant in the plaque bacterial community in the earlier days, whereas obligate anaerobes, such as Porphyromonas, Fusobacterium, Prevotella, and Capnocytophaga showed increased dominance on later days. UniFrac analysis also demonstrated that dental caries experience had a significant effect on the assembly process. Our results reveal the development pattern of the plaque bacterial community as well as the inter-individual differences associated with dental caries experience.

  9. Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) Reveals Multiple Protease-Like Transcripts.

    Science.gov (United States)

    Valencia, Arnubio; Wang, Haichuan; Soto, Alberto; Aristizabal, Manuel; Arboleda, Jorge W; Eyun, Seong-Il; Noriega, Daniel D; Siegfried, Blair

    2016-01-01

    The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.

  10. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.

    Science.gov (United States)

    Pagenkopp Lohan, K M; Fleischer, R C; Carney, K J; Holzer, K K; Ruiz, G M

    2016-04-01

    Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

  11. Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra

    Science.gov (United States)

    Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

    2012-01-01

    The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species. PMID:22837688

  12. Exploring the variation of oral microbiota in supragingival plaque during and after head-and-neck radiotherapy using pyrosequencing.

    Science.gov (United States)

    Gao, Li; Hu, Yuejian; Wang, Yuxia; Jiang, Wenxin; He, Zhiyan; Zhu, Cailian; Ma, Rui; Huang, Zhengwei

    2015-09-01

    The aim of this article was to study the variation in oral microflora of the subgingival plaque during and after radiotherapy. During and after radiotherapy, microbial samples were collected at seven time points (early stage, medium stage, and later stage of radiotherapy, and 1 month, 3 months, 6 months, and 1 year after radiotherapy) in three subjects for a total of 21 samples. Polymerase chain reaction (PCR) amplification was carried out on the 16S rDNA hypervariable V1-V3 region, and then the PCR products were determined by high-throughput pyrosequencing. The rarefaction curve indicating the richness of the microflora demonstrated that the number of operational taxonomic units (OTUs) was in decline from the early stage of radiotherapy to the time point 1 month after radiotherapy and then trended upward. The Shannon diversity index declined during radiotherapy (ranging from 4.59 to 3.73), and generally rose after radiotherapy, with the lowest value of 3.5 (1 month after radiotherapy) and highest value of 4.75 (6 months after radiotherapy). A total of 120 genera were found; five genera (Actinomyces, Veillonella, Prevotella, Streptococcus, Campylobacter) were found in all subjects across all time points. The richness and diversity of oral ecology decreased with increased radiation dose, and it was gradually restored with time. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    Directory of Open Access Journals (Sweden)

    Daochen Zhu

    Full Text Available BACKGROUND: Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. METHODOLOGY/PRINCIPAL FINDINGS: Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. CONCLUSIONS: This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  14. Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, Raja pulchra.

    Science.gov (United States)

    Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

    2012-01-01

    The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1-10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni's correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.

  15. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

    KAUST Repository

    Qian, Peiyuan

    2010-07-29

    The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea. © 2011 International Society for Microbial Ecology All rights reserved.

  16. Bar-coded pyrosequencing reveals the responses of PBDE-degrading microbial communities to electron donor amendments.

    Directory of Open Access Journals (Sweden)

    Meiying Xu

    Full Text Available Polybrominated diphenyl ethers (PBDEs can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32 and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters.

  17. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

    KAUST Repository

    Qian, Peiyuan; Wang, Yong; Lee, Onon; Lau, Chunkwan; Yang, Jiangke; Lafi, Feras Fawzi; Al-Suwailem, Abdulaziz M.; Wong, Tim

    2010-01-01

    The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea. © 2011 International Society for Microbial Ecology All rights reserved.

  18. Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

    Energy Technology Data Exchange (ETDEWEB)

    Lladó, S., E-mail: llado@biomed.cas.cz [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Covino, S., E-mail: covino@biomed.cas.cz [Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Solanas, A.M., E-mail: asolanas@ub.edu [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Petruccioli, M., E-mail: petrucci@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); D’annibale, A., E-mail: dannib@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); Viñas, M., E-mail: marc.vinas@irta.cat [GIRO Joint Research Unit IRTA-UPC, Institute of Research and Technology Food and Agriculture [IRTA], Torre Marimon, E-08140 Caldes de Montbui (Spain)

    2015-02-11

    Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success.

  19. Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed Eimeria infection.

    Science.gov (United States)

    Hume, Michael E; Barbosa, Nei A; Dowd, Scot E; Sakomura, Nilva K; Nalian, Armen G; Martynova-Van Kley, Alexandra; Oviedo-Rondón, Edgar O

    2011-11-01

    A protective digestive microflora helps prevent and reduce broiler infection and colonization by enteropathogens. In the current experiment, broilers fed diets supplemented with probiotics and essential oil (EO) blends were infected with a standard mixed Eimeria spp. to determine effects of performance enhancers on ileal and cecal microbial communities (MCs). Eight treatment groups included four controls (uninfected-unmedicated [UU], unmedicated-infected, the antibiotic BMD plus the ionophore Coban as positive control, and the ionophore as negative control), and four treatments (probiotics BC-30 and Calsporin; and EO, Crina Poultry Plus, and Crina PoultryAF). Day-old broilers were raised to 14 days in floor pens on used litter and then were moved to Petersime batteries and inoculated at 15 days with mixed Eimeria spp. Ileal and cecal samples were collected at 14 days and 7 days postinfection. Digesta DNA was subjected to pyrosequencing for sequencing of individual cecal bacteria and denaturing gradient gel electrophoresis (DGGE) for determination of changes in ileal and cecal MC according to percentage similarity coefficient (%SC). Pyrosequencing is very sensitive detecting shifts in individual bacterial sequences, whereas DGGE is able to detect gross shifts in entire MC. These combined techniques offer versatility toward identifying feed additive and mild Eimeria infection modulation of broiler MC. Pyrosequencing detected 147 bacterial species sequences. Additionally, pyrosequencing revealed the presence of relatively low levels of the potential human enteropathogens Campylobacter sp. and four Shigella spp. as well as the potential poultry pathogen Clostridiun perfringens. Pre- and postinfection changes in ileal (56%SC) and cecal (78.5%SC) DGGE profiles resulted from the coccidia infection and with increased broiler age. Probiotics and EO changed MC from those seen in UU ilea and ceca. Results potentially reflect the performance enhancement above expectations in

  20. Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

    International Nuclear Information System (INIS)

    Lladó, S.; Covino, S.; Solanas, A.M.; Petruccioli, M.; D’annibale, A.; Viñas, M.

    2015-01-01

    Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success

  1. Staff meeting

    CERN Multimedia

    2007-01-01

    Dear Colleagues, 2007 is a very special year for CERN. I would like to review the status of our activities with you, and I invite you to a presentation on Wednesday 27 June 2007 at 3:00 p.m. Main Auditorium (bldg. 500) Closed-circuit transmission of the meeting will be available in the Council Chamber and in the AB Auditorium (Meyrin), the AB Auditorium (Prévessin), the IT Auditorium (bldg. 31) and the AT Auditorium (bldg. 30). Simultaneous translation into English will be available in the Main Auditorium. Robert AYMAR

  2. Public meetings

    CERN Multimedia

    Staff Association

    2014-01-01

      MARS 2015 FIVE YEARLY REVIEW CONTRACT POLICY PENSION FUND GENERAL INFORMATION   COME AND BE INFORMED! PUBLIC MEETINGS Friday 3rd October at 10 am Amphi BE, 864-1-D02 Prévessin Friday 3rd October at 2 pm Salle du Conseil / Council Chamber, 503-1-001 (in English) Meyrin Monday 6th October at 10 am Kjell Johnsen Auditorium, 30-7-018 Meyrin Monday 6th October at 2 pm Salle du Conseil / Council Chamber, 503-1-001 Meyrin  

  3. Speciation driven by hybridization and chromosomal plasticity in a wild yeast.

    Science.gov (United States)

    Leducq, Jean-Baptiste; Nielly-Thibault, Lou; Charron, Guillaume; Eberlein, Chris; Verta, Jukka-Pekka; Samani, Pedram; Sylvester, Kayla; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R

    2016-01-11

    Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.

  4. Speciation environments and centres of diversity in southern Africa. I. Conceptual framework

    Directory of Open Access Journals (Sweden)

    E. R. Robinson

    1982-10-01

    Full Text Available A knowledge of the nature and distribution of the environments where speciation (micro-evolution is or has been rapid would help explain plant distributions and give insight into the mechanisms of plant evolution. Before southern African speciation environments can be identified and described, a number of basic theoretical concepts have to be clarified. In this paper the major taxonomic, systematic, floristic, ecological and evolutionary ideas pertinent to speciation environments are reviewed and discussed. Despite many publications about species concepts, species diversity, modes of speciation and the relationship between environments and genetic variability within taxa, it is still not possible to make predictions about the kinds of environments that favour speciation.

  5. Review: Speciation in the myrtle family (Myrtaceae: rapid and slow models

    Directory of Open Access Journals (Sweden)

    PUDJI WIDODO

    2007-01-01

    Full Text Available Speciation or formation of new species is a process which may take very long time. When a new species is really formed from a previous species is still unknown exactly. However, sometimes when populations no longer interbreed, they are thought to be separate species. As natural selection, if populations adapt the occupying different environments, they will diverge into races, subspecies, and finally separate species. There are some models of speciation such as geographical, polyploidy, chromosomal, and ecological speciation. However, in the myrtle family (Myrtaceae they can be grouped into two big models of speciation namely the rapid and slow speciation. This review points out that hybridization is a major factor affecting Myrtaceae, although evolution activities were also approved by the fact that some fossil pollens have been found in Antartica

  6. Review of speciation and solubility of radionuclides in the near and far field. Pt. 2

    International Nuclear Information System (INIS)

    Smith-Briggs, J.L.

    1992-01-01

    This report represents Part 2 in a series of three reports which review the speciation and solubility of radionuclides in the near and far field. Part 2 is a general bibliography from 1978 to 1991. This report contains the bibliography for the review of speciation and solubility radionuclides in the near and far field from 1978 to 1991. The importance of the solubility and speciation of radionuclides in relation to the safety assessment of the repository is discussed. Solubility is defined, both theoretically and pragmatically, and the factors which influence solubility and speciation are discussed. The literature search was performed using the INIS database. The UKAEA RECAP database, the NIREX report bibliography and a list of DOE reports provided by the DOE were also used. The bibliography is divided into five sections, solubility and speciation experimental data, basic thermodynamic data, solubility limiting solid phases, experimental design and review and overview articles. Some references appear in more than one section. (Author)

  7. ACCU MEETING

    CERN Document Server

    PH Department

    2008-01-01

    DRAFT Agenda for the meetingto be held on Wednesday 3 December 2008 at 9:15 a.m.in Room 60-6-002 1.\tChairman’s remarks 2.\tAdoption of the agenda 3.\tMinutes of the previous meeting 4.\tMatters arising 5.\tNews from the CERN Management 6.\tReport from the new Director-General 7.\tReport on the Fellows and Associates programme 8.\tAn update on Safety at CERN 9.\tReports from ACCU representatives on other committees 10.\tUsers’ Office news 11.\tAny Other Business 12.\tAgenda for the next meeting Anyone wishing to raise any points under item 11 is invited to send them to the Chairman in writing or by e-mail to Christopher.Onions@cern.ch Chris Onions (Secretary) ACCU is the forum for discussion between the CERN Management and the representatives of CERN Users to review the practical means taken by CERN for the work of Users of the Laboratory. The User Representatives to ACCU are (CERN internal telephone numbers in brackets): Austria W. Adam (71661) Belgium C. Va...

  8. Divergence with gene flow across a speciation continuum of Heliconius butterflies.

    Science.gov (United States)

    Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

    2015-09-24

    A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

  9. Uranium speciation in biofilms studies by laser fluorescence techniques

    International Nuclear Information System (INIS)

    Arnold, Thuro; Grossmann, Kay; Baumann, Nils

    2010-01-01

    Biofilms may immobilize toxic heavy metals in the environment and thereby influence their migration behaviour. The mechanisms of these processes are currently not understood, because the complexity of such biofilms creates many discrete geochemical microenvironments which may differ from the surrounding bulk solution in their bacterial diversity, their prevailing geochemical properties, e.g. pH and dissolved oxygen concentration, the presence of organic molecules, e.g. metabolites, and many more, all of which may affect metal speciation. To obtain such information, which is necessary for performance assessment studies or the development of new cost-effective strategies for cleaning waste waters, it is very important to develop new non-invasive methods applicable to study the interactions of metals within biofilm systems. Laser fluorescence techniques have some superior features, above all very high sensitivity for fluorescent heavy metals. An approach combining confocal laser scanning microscopy and laser-induced fluorescence spectroscopy for study of the interactions of biofilms with uranium is presented. It was found that coupling these techniques furnishes a promising tool for in-situ non-invasive study of fluorescent heavy metals within biofilm systems. Information on uranium speciation and uranium redox states can be obtained.

  10. Quantifying variation in speciation and extinction rates with clade data.

    Science.gov (United States)

    Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

    2013-12-01

    High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  11. Iron(III) citrate speciation in aqueous solution.

    Science.gov (United States)

    Silva, Andre M N; Kong, XiaoLe; Parkin, Mark C; Cammack, Richard; Hider, Robert C

    2009-10-28

    Citrate is an iron chelator and it has been shown to be the major iron ligand in the xylem sap of plants. Furthermore, citrate has been demonstrated to be an important ligand for the non-transferrin bound iron (NTBI) pool occurring in the plasma of individuals suffering from iron-overload. However, ferric citrate chemistry is complicated and a definitive description of its aqueous speciation at neutral pH remains elusive. X-Ray crystallography data indicates that the alcohol function of citrate (Cit4-) is involved in Fe(III) coordination and that deprotonation of this functional group occurs upon complex formation. The inability to include this deprotonation in the affinity constant calculations has been a major source of divergence between various reports of iron(III)-citrate affinity constants. However the recent determination of the alcoholic pKa of citric acid (H4Cit) renders the reassessment of the ferric citrate system possible. The aqueous speciation of ferric citrate has been investigated by mass spectrometry and EPR spectroscopy. It was observed that the most relevant species are a monoiron dicitrate species and dinuclear and trinuclear oligomeric complexes, the relative concentration of which depends on the solution pH value and the iron : citric acid molar ratio. Spectrophotometric titration was utilized for affinity constant determination and the formation constant for the biologically relevant [Fe(Cit)2]5- is reported for the first time.

  12. Metal speciation: survey of environmental methods of analysis

    Energy Technology Data Exchange (ETDEWEB)

    Mach, M.H.; Nott, B.; Scott, J.W.; Maddalone, R.F.; Whiddon, N.T. [TRW, Redondo Beach, CA (United States). Chemistry Technology Dept.

    1996-07-01

    As part of a recent task under the EPRI Analytical Methods Qualification Program (RP 1851), TRW has surveyed the methods available for monitoring metal species in typical utility aqueous discharge streams. Methods for determining the individual species of these metals can become important in a regulatory sense as the EPA transitions to assessment of environmental risk based on bioavailability. For example, EPA considers methyl mercury and Cr(VI) much more toxic to the aquatic environment than inorganic mercury or Cr(III). The species of a given element can also differ in their transport and bioaccumulation. Methods for speciation generally include a selective separation step followed by standard metals analysis. Speciation, therefore, is mainly derived from the separation step and not from the method of final quantisation. Examples of separation/analysis include: selective extraction followed by graphite furnace atomic absorption or ICP-MS; separation by GC followed by metals detection; chelation and/or direct separation by LC followed by UV measurement or metals detection; and ion chromatography with conductivity, UV, or metals detection. There are a number of sampling issues associated with metal species such as stabilization (maintaining oxidation state), absorption, and filtration that need to be addressed in order to obtain and maintain a representative sample for analysis. 45 refs., 1 tab.

  13. Selenium speciation from food source to metabolites: a critical review

    Energy Technology Data Exchange (ETDEWEB)

    Dumont, Emmie; Vanhaecke, Frank; Cornelis, Rita [Ghent University, Department of Analytical Chemistry, Ghent (Belgium)

    2006-08-15

    Especially in the last decade, a vast number of papers on Se and its role in health issues have been published. This review gives a brief, critical overview of the main analytical findings reported in these papers. Of particular interest is the Se content in different food sources worldwide and the extent to which their consumption is reflected in the Se content of human tissues and body fluids. Several food sources, both natural (Brazil nuts, garlic, Brassica juncea) and Se-enriched (yeast-based supplements), are discussed as to origin, characteristics, Se metabolism and impact of their consumption on the human body. The continuous development of new and improvement of existing analytical techniques has provided different powerful tools to unravel the Se species and their function. An up-to-date literature study on Se speciation analysis is given, illustrating how analytical chemistry in its different facets aids in the identification of Se compounds and provides insight into the complete metabolic pathway of Se throughout the human body. This review includes a detailed image of the current state-of-the-art of Se speciation analysis in these food sources and in human tissues and body fluids. (orig.)

  14. Allopatric speciation within a cryptic species complex of Australasian octopuses.

    Science.gov (United States)

    Amor, Michael D; Norman, Mark D; Cameron, Hayley E; Strugnell, Jan M

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the 'tetricus complex'. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide.

  15. Speciation and migration of 129I in soil profiles

    International Nuclear Information System (INIS)

    Luo, Maoyi; Hou, Xiaolin; Zhou, Weijian; He, Chaohui; Chen, Ning; Liu, Qi; Zhang, Luoyuan

    2013-01-01

    A method has been developed for speciation analysis of ultra low level 129 I in soil using sequential extraction combined with coprecipitation for separation of carrier free iodine and AMS measurement of 129 I. Two loess profiles collected from northwest China were analyzed for species of 129 I and 127 I. Similar partitioning of 129 I and 127 I was observed in the loess profiles, the distribution of iodine isotopes followed an order of organic > leachable > reducible > residue. The 129 I concentrations and 129 I/ 127 I ratios decreased exponentially with the depth, and 2 orders of magnitude lower in the deepest layer (60 and 90 cm) compared with the top layer, indicating a significant contribution of anthropogenic input in the upper layer, and high retention of 129 I in soil. The mobility of 129 I in different fractions decreased in an order of leachable > organic > oxides > residue. The results suggest that migration of iodine downwards in the soil profile is a slow process; the oxides and residue are the less mobile fractions of iodine. Highlights: ► 129 I concentration decreases exponentially with the depth of soil profile. ► The mobility of 129 I in fractions decreases: leachable > organic > oxides > residue. ► Iodine shows less mobility in oxides and residue fractions. ► High organic soil content can effectively reduce the migration of 129 I in the environment. ► Carrier free iodine AMS is an effective method for natural 129 I speciation analysis in the environment

  16. Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses

    Science.gov (United States)

    Amor, Michael D.; Norman, Mark D.; Cameron, Hayley E.; Strugnell, Jan M.

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ‘tetricus complex’. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. PMID:24964133

  17. Evaluation of mercury speciation by EPA (Draft) Method 29

    Energy Technology Data Exchange (ETDEWEB)

    Laudal, D.L.; Heidt, M.K. [Energy & Environmental Research Center, Grand Forks, ND (United States); Nott, B. [Electric Power Research Institute, Palo Alto, CA (United States)

    1995-11-01

    The 1990 Clean Air Act Amendments require that the U.S. Environmental protection Agency (EPA) assess the health risks associated with mercury emissions. Also, the law requires a separate assessment of health risks posed by the emission of 189 tract chemicals (including mercury) for electric utility steam-generating units. In order to conduct a meaningful assessment of health and environmental effects, we must have, among other things, a reliable and accurate method to measure mercury emissions. In addition, the rate of mercury deposition and the type of control strategies used may depend upon the type of mercury emitted (i.e., whether it is in the oxidized or elemental form). It has been speculated that EPA (Draft) Method 29 can speciate mercury by selective absorption; however, this claim has yet to be proven. The Electric Power Research Institute (EPRI) and the U.S. Department of Energy (DOE) have contracted with the Energy & Environmental Research Center (EERC) at University of North Dakota to evaluate EPA (Draft) Method 29 at the pilot-scale level. The objective of the work is to determine whether EPA (Draft) Method 29 can reliably quantify and speciate mercury in the flue gas from coal-fired boilers.

  18. Assortative flocking in crossbills and implications for ecological speciation.

    Science.gov (United States)

    Smith, Julie W; Sjoberg, Stephanie M; Mueller, Matthew C; Benkman, Craig W

    2012-10-22

    How reproductive isolation is related to divergent natural selection is a central question in speciation. Here, we focus on several ecologically specialized taxa or 'call types' of red crossbills (Loxia curvirostra complex), one of the few groups of birds providing much evidence for ecological speciation. Call types differ in bill sizes and feeding capabilities, and also differ in vocalizations, such that contact calls provide information on crossbill phenotype. We found that two call types of red crossbills were more likely to approach playbacks of their own call type than those of heterotypics, and that their propensity to approach heterotypics decreased with increasing divergence in bill size. Although call similarity also decreased with increasing divergence in bill size, comparisons of responses to familiar versus unfamiliar call types indicate that the decrease in the propensity to approach heterotypics with increasing divergence in bill size was a learned response, and not a by-product of calls diverging pleiotropically as bill size diverged. Because crossbills choose mates while in flocks, assortative flocking could lead indirectly to assortative mating as a by-product. These patterns of association therefore provide a mechanism by which increasing divergent selection can lead to increasing reproductive isolation.

  19. AN ANALYTICAL METHOD FOR CHEMICAL SPECIATION OF SELENIUM IN SOIL

    Directory of Open Access Journals (Sweden)

    Constantin Luca

    2010-10-01

    Full Text Available Selenium is an essential microelement, sometimes redoubtable, through its beneficial role - risk depending on its concentration in the food chain, at low dose is an important nutrient in the life of humans and animals, contrary at high doses, it becomes toxic. Selenium may be find itself in the environment (soil, sediment, water in many forms (oxidized, reduced, organometallic which determine their mobility and toxicity. Determination of chemical speciation (identification of different chemical forms provides much more complete information for a better understanding of the behavior and the potential impact on the environment. In this work we present the results of methodological research on the extraction of sequential forms of selenium in the soil and the coupling of analytical methods capable of identifying very small amounts of selenium in soils An efficient scheme of sequential extractions forms of selenium (SES consisting in atomic absorption spectrometry coupled with hydride generation (HGAAS has been developed into five experimental steps, detailed in the paper. This operational scheme has been applied to the analysis of chemical speciation in the following areas: the Bărăgan Plain and Central Dobrogea of Romania.

  20. Technetium Inventory, Distribution, and Speciation in Hanford Tanks

    Energy Technology Data Exchange (ETDEWEB)

    Serne, R. Jeffrey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rapko, Brian M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Pegg, Ian L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-11-13

    The purpose of this report is three fold: 1) assemble the available information regarding Tc inventory, distribution between phases, and speciation in Hanford’s 177 storage tanks into a single, detailed, comprehensive assessment; 2) discuss the fate (distribution/speciation) of Tc once retrieved from the storage tanks and processed into final waste forms; and 3) discuss/document in less detail the available data on the inventory of Tc in other “pools” such as the vadose zone below inactive cribs and trenches, below single-shell tanks (SSTs) that have leaked, and in the groundwater below the Hanford Site. This report was revised in September 2014 to add detail and correct inaccuracies in Section 5.0 on the fate of technetium (Tc) recycle from the off-gas systems downstream of the low-activity waste (LAW) melters back to the melters, based on several reports that were not found in the original literature search on the topic. The newly provided reports, from experts active in the Hanford Tank Waste Treatment and Immobilization Plant (WTP) glass studies, the Vitreous State Laboratory at The Catholic University of America (VSL) melter and off-gas system demonstrations and overall WTP systems analysis, were not originally found on electronic databases commonly searched. The major revisions to Section 5.0 also required changes to Section 7.0 (Summary and Conclusions) and this executive summary.

  1. Triassic-Jurassic pteridosperms of Australasia: speciation, diversity and decline

    Energy Technology Data Exchange (ETDEWEB)

    Pattemore, G. A.; Rigby, J. F.; Playford, G.

    2015-07-01

    Pteridosperms are preserved abundantly in the Gondwanan Triassic, with many species exhibiting consider- able morphological variation that has been attributed to a hybridization model of speciation. This is an improbable explanation given that hybridization is very rare in gymnosperms. Allopatric speciation resulting from geographic and climatic provincialism is a more likely explanation for the morphological diversity which is well represented in Anisian Norian (Middle and Upper Triassic) floras of Australasia and elsewhere in Gondwana. Most specimens are distributed among three families: Umkomasiaceae, Peltaspermaceae and Matatiellaceae. These families, together with other possibly pteridospermous genera, are reviewed herein. Diversity in these families apparently declined by the Rhaetian and they did not persist into the Gondwanan post-Triassic. Australasian post-Triassic strata contain remarkably different floral assemblages to those of the Triassic. No fructifications are clearly pteridospermous and no remains show any obvious relationship with pteridosperms of the Gondwanan Triassic. Caytonialean fructifications are not known in Australasian strata; however, associated foliage has been reported from the Eastern Gondwanan Upper Triassic through Middle Jurassic including Australia. Much fern-like foliage, claimed to be pteridospermous from the Lower Jurassic through Eocene of Eastern Gondwana, lacks supporting evidence of such affiliation. (Author)

  2. Meeting Venus

    Science.gov (United States)

    Sterken, Christiaan; Aspaas, Per Pippin

    2013-06-01

    On 2-3 June 2012, the University of Tromsoe hosted a conference about the cultural and scientific history of the transits of Venus. The conference took place in Tromsoe for two very specific reasons. First and foremost, the last transit of Venus of this century lent itself to be observed on the disc of the Midnight Sun in this part of Europe during the night of 5 to 6 June 2012. Second, several Venus transit expeditions in this region were central in the global enterprise of measuring the scale of the solar system in the eighteenth century. The site of the conference was the Nordnorsk Vitensenter (Science Centre of Northern Norway), which is located at the campus of the University of Tromsoe. After the conference, participants were invited to either stay in Tromsoe until the midnight of 5-6 June, or take part in a Venus transit voyage in Finnmark, during which the historical sites Vardoe, Hammerfest, and the North Cape were to be visited. The post-conference program culminated with the participants observing the transit of Venus in or near Tromsoe, Vardoe and even from a plane near Alta. These Proceedings contain a selection of the lectures delivered on 2-3 June 2012, and also a narrative description of the transit viewing from Tromsoe, Vardoe and Alta. The title of the book, Meeting Venus, refers the title of a play by the Hungarian film director, screenwriter and opera director Istvan Szabo (1938-). The autobiographical movie Meeting Venus (1991) directed by him is based on his experience directing Tannhauser at the Paris Opera in 1984. The movie brings the story of an imaginary international opera company that encounters a never ending series of difficulties and pitfalls that symbolise the challenges of any multicultural and international endeavour. As is evident from the many papers presented in this book, Meeting Venus not only contains the epic tales of the transits of the seventeenth, eighteenth and nineteenth centuries, it also covers the conference

  3. Multiplex pyrosequencing assay using AdvISER-MH-PYRO algorithm: a case for rapid and cost-effective genotyping analysis of prostate cancer risk-associated SNPs.

    Science.gov (United States)

    Ambroise, Jérôme; Butoescu, Valentina; Robert, Annie; Tombal, Bertrand; Gala, Jean-Luc

    2015-06-25

    Single Nucleotide Polymorphisms (SNPs) identified in Genome Wide Association Studies (GWAS) have generally moderate association with related complex diseases. Accordingly, Multilocus Genetic Risk Scores (MGRSs) have been computed in previous studies in order to assess the cumulative association of multiple SNPs. When several SNPs have to be genotyped for each patient, using successive uniplex pyrosequencing reactions increases analytical reagent expenses and Turnaround Time (TAT). While a set of several pyrosequencing primers could theoretically be used to analyze multiplex amplicons, this would generate overlapping primer-specific pyro-signals that are visually uninterpretable. In the current study, two multiplex assays were developed consisting of a quadruplex (n=4) and a quintuplex (n=5) polymerase chain reaction (PCR) each followed by multiplex pyrosequencing analysis. The aim was to reliably but rapidly genotype a set of prostate cancer-related SNPs (n=9). The nucleotide dispensation order was selected using SENATOR software. Multiplex pyro-signals were analyzed using the new AdvISER-MH-PYRO software based on a sparse representation of the signal. Using uniplex assays as gold standard, the concordance between multiplex and uniplex assays was assessed on DNA extracted from patient blood samples (n = 10). All genotypes (n=90) generated with the quadruplex and the quintuplex pyroquencing assays were perfectly (100 %) concordant with uniplex pyrosequencing. Using multiplex genotyping approach for analyzing a set of 90 patients allowed reducing TAT by approximately 75 % (i.e., from 2025 to 470 min) while reducing reagent consumption and cost by approximately 70 % (i.e., from ~229 US$ /patient to ~64 US$ /patient). This combination of quadruplex and quintuplex pyrosequencing and PCR assays enabled to reduce the amount of DNA required for multi-SNP analysis, and to lower the global TAT and costs of SNP genotyping while providing results as reliable as uniplex

  4. Public meetings

    CERN Multimedia

    Staff Association

    2013-01-01

    MARS SURVEY 5YR 2015 GENERAL INFORMATION ELECTIONS 2013   COME AND BE INFORMED! Public meetings Tuesday 1st Oct. 10 am Amphi IT, 31-3-004 Meyrin Tuesday 1st Oct. 2 pm Council Chamber, 503-1-001 Meyrin Friday 4 Oct. 10 am Amphi BE, 864-1-D02 Prévessin Monday 7 Oct. 2 pm Council Chamber, 503-1-001 (in English) Meyrin Tuesday 8 Oct. 10 am Amphi Kjell Johnsen, 30-7-018 Meyrin   Overview of the topics to be discussed Recognition of Merit – MARS Outcome of last exercise 2007 to 2013: lessons learned Survey: five-yearly review, give us your opinion General information CVI 2014 Voluntary programmes (PRP, SLS) Elections 2013 Renewal of the Staff Council 2014 - 2015  

  5. Meetings and Meeting Modeling in Smart Environments

    NARCIS (Netherlands)

    Nijholt, Antinus; op den Akker, Hendrikus J.A.; Heylen, Dirk K.J.

    In this paper we survey our research on smart meeting rooms and its relevance for augmented reality meeting support and virtual reality generation of meetings in real time or off-line. The research reported here forms part of the European 5th and 6th framework programme projects multi-modal meeting

  6. Meetings and meeting modeling in smart surroundings

    NARCIS (Netherlands)

    op den Akker, Hendrikus J.A.; Heylen, Dirk K.J.; Nijholt, Antinus; Nishida, T.

    2004-01-01

    In this paper we survey our research on smart meeting rooms and its relevance for augmented reality meeting support and virtual reality generation of meetings in real-time or off-line. Intelligent real-time and off-line generation requires understanding of what is going on during a meeting. The

  7. Pyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study

    Directory of Open Access Journals (Sweden)

    Guillaume eMinard

    2014-05-01

    Full Text Available The Asian tiger mosquito Aedes (Stegomya albopictus is an invasive species that has spread across the world in the last two decades, showing a great capacity to adapt to contrasting climates and environments. While demonstrated in many insects, the contribution of bacterial symbionts in Aedes ecology is a challenging aspect that needs to be investigated however. Some bacterial species have already been identified in Ae. albopictus using classical methods, but a more accurate survey of mosquito-associated bacterial diversity is needed to decipher the potential biological functions of bacterial symbionts in mediating or constraining insect adaptation. We surveyed the bacteria associated with field populations of Ae. albopictus from Madagascar by pyrosequencing 16S rRNA gene amplicons. Different aspects of amplicon preparation and sequencing depth were tested to optimise the breadth of bacterial diversity identified. The results revealed that all mosquitoes collected from different sites have a bacterial microbiota dominated by a single taxon, Wolbachia pipientis, which accounted for about 99% of all 98,520 sequences obtained. Ae. albopictus is known to harbour two Wolbachia strains, wAlbA and wAlbB, and quantitative PCR was used to estimate the relative densities, i.e. the bacteria-to-host gene ratios, of the strains in individual mosquitoes. Relative densities were between 6.25 × 100.01 and 5.47 × 100.1 for wAlbA and between 2.03 × 100.1 and 1.4 × 101 for wAlbB. Apart from Wolbachia, a total of 32 bacterial taxa were identified at the genus level using the different in method variations. Diversity index values were low and probably underestimated the true diversity due to the high abundance of Wolbachia sequences vastly outnumbering sequences from other taxa. Further studies should implement alternative strategies to specifically discard from analysis any sequences from Wolbachia, the dominant endosymbiotic bacterium in Ae. albopictus from

  8. Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing

    Directory of Open Access Journals (Sweden)

    Cuicui Xiao

    2016-07-01

    Full Text Available Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700 clustered into 10,365 operational taxonomic units (OTUs; 97% identity, representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. Smooth rarefaction curves were suggestive of plaque microbial diversity. α diversity analysis showed that healthy plaque microbial diversity exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups and that group members were relatively constant, only showing differences in abundance. Analysis of composition differences identified 10 health-related and 21 caries-related genera. Key genera (27 that potentially contributed to plaque microbiota distributions between groups were identified. Finally, co-occurrence network analysis and function prediction were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed.

  9. Investigation of ruminal bacterial diversity in dairy cattle fed supplementary monensin alone and in combination with fat, using pyrosequencing analysis.

    Science.gov (United States)

    Kim, M; Eastridge, M L; Yu, Z

    2014-02-01

    The objective of this study was to examine and compare the effects of monensin, both alone and together with dietary fat, on ruminal bacterial communities in dairy cattle fed the following 3 diets: a control diet, the control diet supplemented with monensin, and the control diet supplemented with both monensin and fat. Bacterial communities in the liquid and the adherent fractions of rumen content were analyzed using 454 pyrosequencing analysis of 16S rRNA gene amplicons. Most sequences were assigned to phyla Firmicutes and Bacteroidetes, irrespective of diets and fractions. Prevotella was the most dominant genus, but most sequences could not be classified at the genus level. The proportion of Gram-positive Firmicutes was reduced by 4.5% in response to monensin but increased by 12.8% by combination of monensin and fat, compared with the control diet. Some of the operational taxonomic units in Firmicutes and Bacteroidetes were also affected by monensin or by the combination of monensin with fat. The proportion of numerous bacteria potentially involved in lipolysis and (or) biohydrogenation was increased by both monensin and fat. The Shannon diversity index was decreased in the control diet supplemented with both monensin and fat, compared with the other 2 diet groups. Supplementary fats hinder bacterial attachment to plant particles and then result in decreased bacterial diversity in the rumen. The finding of this study may help in understanding the effect of monensin and fat on ruminant nutrition and the adverse effect of monensin and fat, such as milk fat depression and decreased feed digestibility.

  10. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

    Directory of Open Access Journals (Sweden)

    Lank Simon M

    2012-08-01

    Full Text Available Abstract Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.

  11. Analysis of Gastric Body Microbiota by Pyrosequencing: Possible Role of Bacteria Other Than Helicobacter pylori in the Gastric Carcinogenesis.

    Science.gov (United States)

    Sohn, Sung-Hwa; Kim, Nayoung; Jo, Hyun Jin; Kim, Jaeyeon; Park, Ji Hyun; Nam, Ryoung Hee; Seok, Yeong-Jae; Kim, Yeon-Ran; Lee, Dong Ho

    2017-06-01

    Gastric microbiota along with Helicobacter pylori (HP) plays a key role in gastric disease. The aim of our study is to investigate the difference of human gastric microbiota between antrum and body according to disease (control vs. gastric cancer) and HP status. Each antrum and body biopsy was collected from 12 subjects at Seoul National University Bundang Hospital. Gastric microbiota was analyzed by bar-coded 454 pyrosequencing of the 16S rRNA gene. Twelve subjects consisted of HP-negative control (n = 2), HP-negative cancer (n = 2), HP-positive control (n = 3), and HP-positive cancer (n = 5). The analysis was focused on non-HP urease-producing bacteria (UB) and non-HP nitrosating or nitroreducing bacteria (NB) between antrum and body. Gastric body samples showed higher diversity compared to gastric antrum mucosa samples but there was no significant difference. The mean of operational taxonomic units was higher in HP(-) cancer than HP(+) cancer (antrum, 273.5 vs. 228.2, P = 0.439; body, 585.5 vs. 183.2, P = 0.053). The number of non-HP UB and non-HP NB was higher in HP(-) cancer groups than the others. These differences were more pronounced in the body ( P = 0.051 and P = 0.081, respectively). Analysis of overlap of non-HP UB and non-HP NB revealed the higher composition of Streptococcus pseudopneumoniae, S. parasanguinis , and S. oralis in HP(-) cancer groups than the others, only in the body ( P = 0.030) but not in the antrum ( P = 0.123). Higher diversity and higher composition of S. pseudopneumoniae, S. parasanguinis , and S. oralis in HP(-) cancer group than the other groups in the body suggest that analysis of microbiota from body mucosa could be beneficial to identify a role of non-HP bacteria in the gastric carcinogenesis.

  12. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

    Directory of Open Access Journals (Sweden)

    Bonten Marc JM

    2010-04-01

    Full Text Available Abstract Background The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. Results We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI, which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner. Conclusions Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.

  13. A multi-technique investigation of copper and zinc distribution, speciation and potential bioavailability in biosolids

    International Nuclear Information System (INIS)

    Donner, E.; Ryan, C.G.; Howard, D.L.; Zarcinas, B.; Scheckel, K.G.; McGrath, S.P.; Jonge, M.D. de; Paterson, D.; Naidu, R.; Lombi, E.

    2012-01-01

    The use of biosolids in agriculture continues to be debated, largely in relation to their metal contents. Our knowledge regarding the speciation and bioavailability of biosolids metals is still far from complete. In this study, a multi-technique approach was used to investigate copper and zinc speciation and partitioning in one contemporary and two historical biosolids used extensively in previous research and field trials. Using wet chemistry and synchrotron spectroscopy techniques it was shown that copper/zinc speciation in the biosolids was largely equivalent despite the biosolids being derived from different countries over a 50 year period. Furthermore, copper speciation was consistently dominated by sorption to organic matter whereas Zn partitioned mainly to iron oxides. These data suggest that the results of historical field trials are still relevant for modern biosolids and that further risk assessment studies should concentrate particularly on Cu as this metal is associated with the mineralisable biosolids fraction. - Highlights: ► Complementary techniques were used to investigate Cu and Zn speciation in biosolids. ► Historic and contemporary biosolids with differing metal contents were examined. ► Similarities in Cu/Zn speciation were observed irrespective of biosolids provenance. ► Key binding environments identified were organic matter for Cu and Fe oxides for Zn. ► Similarities show historic field trial results are still relevant for biosolids management. - Historic and contemporary biosolids show similarities in Cu/Zn speciation despite having very different total Zn/Cu contents.

  14. Airborne Vertical Profiling of Mercury Speciation near Tullahoma, TN, USA

    Directory of Open Access Journals (Sweden)

    Steve Brooks

    2014-08-01

    Full Text Available Atmospheric transport and in situ oxidation are important factors influencing mercury concentrations at the surface and wet and dry deposition rates. Contributions of both natural and anthropogenic processes can significantly impact burdens of mercury on local, regional and global scales. To address these key issues in atmospheric mercury research, airborne measurements of mercury speciation and ancillary parameters were conducted over a region near Tullahoma, Tennessee, USA, from August 2012 to June 2013. Here, for the first time, we present vertical profiles of Hg speciation from aircraft for an annual cycle over the same location. These airborne measurements included gaseous elemental mercury (GEM, gaseous oxidized mercury (GOM and particulate bound mercury (PBM, as well as ozone (O3, sulfur dioxide (SO2, condensation nuclei (CN and meteorological parameters. The flights, each lasting ~3 h, were conducted typically one week out of each month to characterize seasonality in mercury concentrations. Data obtained from 0 to 6 km altitudes show that GEM exhibited a relatively constant vertical profile for all seasons with an average concentration of 1.38 ± 0.17 ng∙m−3. A pronounced seasonality of GOM was observed, with the highest GOM concentrations up to 120 pg∙m−3 in the summer flights and lowest (0–20 pg∙m−3 in the winter flights. Vertical profiles of GOM show the maximum levels at altitudes between 2 and 4 km. Limited PBM measurements exhibit similar levels to GOM at all altitudes. HYSPLIT back trajectories showed that the trajectories for elevated GOM (>70 pg∙m−3 or PBM concentrations (>30 pg∙m−3 were largely associated with air masses coming from west/northwest, while events with low GOM (<20 pg∙m−3 or PBM concentrations (<5 pg∙m−3 were generally associated with winds from a wider range of wind directions. This is the first set of speciated mercury vertical profiles collected in a single location over the course

  15. Speciated Elemental and Isotopic Characterization of Atmospheric Aerosols - Recent Advances

    Science.gov (United States)

    Shafer, M.; Majestic, B.; Schauer, J.

    2007-12-01

    Detailed elemental, isotopic, and chemical speciation analysis of aerosol particulate matter (PM) can provide valuable information on PM sources, atmospheric processing, and climate forcing. Certain PM sources may best be resolved using trace metal signatures, and elemental and isotopic fingerprints can supplement and enhance molecular maker analysis of PM for source apportionment modeling. In the search for toxicologically relevant components of PM, health studies are increasingly demanding more comprehensive characterization schemes. It is also clear that total metal analysis is at best a poor surrogate for the bioavailable component, and analytical techniques that address the labile component or specific chemical species are needed. Recent sampling and analytical developments advanced by the project team have facilitated comprehensive characterization of even very small masses of atmospheric PM. Historically; this level of detail was rarely achieved due to limitations in analytical sensitivity and a lack of awareness concerning the potential for contamination. These advances have enabled the coupling of advanced chemical characterization to vital field sampling approaches that typically supply only very limited PM mass; e.g. (1) particle size-resolved sampling; (2) personal sampler collections; and (3) fine temporal scale sampling. The analytical tools that our research group is applying include: (1) sector field (high-resolution-HR) ICP-MS, (2) liquid waveguide long-path spectrophotometry (LWG-LPS), and (3) synchrotron x-ray absorption spectroscopy (sXAS). When coupled with an efficient and validated solubilization method, the HR-ICP-MS can provide quantitative elemental information on over 50 elements in microgram quantities of PM. The high mass resolution and enhanced signal-to-noise of HR-ICP-MS significantly advance data quality and quantity over that possible with traditional quadrupole ICP-MS. The LWG-LPS system enables an assessment of the soluble

  16. Selenium speciation influences bioaccumulation in Limnodynastes peronii tadpoles

    Energy Technology Data Exchange (ETDEWEB)

    Lanctôt, C.M., E-mail: c.lanctot@griffith.edu.au [Central Queensland University, School of Medical and Applied Sciences, Gladstone, QLD 4680 (Australia); Australian Rivers Institute, School of Environment, Griffith University, Southport, QLD 4215 (Australia); Melvin, S.D., E-mail: s.melvin@griffith.edu.au [Australian Rivers Institute, School of Environment, Griffith University, Southport, QLD 4215 (Australia); Cresswell, T., E-mail: tom.cresswell@ansto.gov.au [Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia)

    2017-06-15

    Highlights: • Differences in SeIV and SeVI bioaccumulation and biodistribution were assessed. • Limnodynastes peronii tadpoles accumulated more selenite than selenate. • Selenium depuration kinetics was similar for both forms. • Tadpoles accumulated Se predominantly in the digestive and excretory organs. - Abstract: Despite being essential for animal health and fitness, Se has a relatively narrow range between deficiency and toxicity, and excess Se can cause a variety of adverse effects in aquatic organisms. Amphibians are particularly vulnerable to contaminants during larval aquatic life stage, because they can accumulate toxic ions through various routes including skin, gills, lungs and digestive tract. Few attempts have been made to understand the tissue-specific accumulation of trace elements, including the impacts of chemical speciation in developing amphibian larvae. We used radiolabelled {sup 75}Se to explore the biokinetics and tissue distributions of the two dominant forms occurring in surface waters, selenite (SeIV) and selenate (SeVI). Tadpoles of the native Australian frog Limnodynastes peronii were exposed to Se in both forms, and live-animal gamma spectroscopy was used to track accumulation and retention over time. Tissue biodistributions were also quantified at the end of the uptake and depuration phases. Results showed the bioconcentration of SeIV to be 3 times greater compared to SeVI, but rates of elimination were similar for both forms. This suggests a change of Se speciation within the organism prior to excretion. Depuration kinetics were best described by a one-phase exponential decay model, and tadpoles retained approximately 19% of the accumulated Se after 12 days of depuration in clean water. Selenium bioaccumulation was greatest in digestive and excretory organs, as well as the eye, which may directly relate to previously reported Se-induced impairments. Results demonstrate how the use of radiotracing techniques can significantly

  17. Speciation and bioavailability of lead in complementary medicines

    International Nuclear Information System (INIS)

    Bolan, S.; Naidu, R.; Kunhikrishnan, A.; Seshadri, B.; Ok, Y.S.; Palanisami, T.; Dong, M.; Clark, I.

    2016-01-01

    Complementary medicines have associated risks which include toxic heavy metal(loid) and pesticide contamination. The objective of this study was to examine the speciation and bioavailability of lead (Pb) in selected complementary medicines. Six herbal and six ayurvedic medicines were analysed for: (i) total heavy metal(loid) contents including arsenic (As), cadmium (Cd), Pb and mercury (Hg); (ii) speciation of Pb using sequential fractionation and extended x-ray absorption fine structure (EXAFS) techniques; and (iii) bioavailability of Pb using a physiologically-based in vitro extraction test (PBET). The daily intake of Pb through the uptake of these medicines was compared with the safety guidelines for Pb. The results indicated that generally ayurvedic medicines contained higher levels of heavy metal(loid)s than herbal medicines with the amount of Pb much higher than the other metal(loid)s. Sequential fractionation indicated that while organic-bound Pb species dominated the herbal medicines, inorganic-bound Pb species dominated the ayurvedic medicines. EXAFS data indicated the presence of various Pb species in ayurvedic medicines. This implies that Pb is derived from plant uptake and inorganic mineral input in herbal and ayurvedic medicines, respectively. Bioavailability of Pb was higher in ayurvedic than herbal medicines, indicating that Pb added as a mineral therapeutic input is more bioavailable than that derived from plant uptake. There was a positive relationship between soluble Pb fraction and bioavailability indicating that solubility is an important factor controlling bioavailability. The daily intake values for Pb as estimated by total and bioavailable metal(loid) contents are likely to exceed the safe threshold level in certain ayurvedic medicines. This research demonstrated that Pb toxicity is likely to result from the regular intake of these medicines which requires further investigation. - Highlights: • Pb species in complementary medicines was

  18. Public meeting

    CERN Multimedia

    Staff Association

    2015-01-01

    Last Monday at 9 a.m. the Council Chamber was full, with several people standing, for the public meeting of the Staff Association. Simultaneously, many of our colleagues followed the presentations in the Amphitheatre in Prévessin. We would like to thank all of you for the interest you have shown and for your feedback. In the introduction we explained how the Staff Association represents the staff in its discussions with Management and Member States, and how the staff itself defined, by its participation in the 2013 staff survey, the priority assigned to various points related to the employment conditions. The position of the Staff Association regarding the new contract policy, to be implemented as of 31 March 2015 after approval by Council, was stated. Then, in the framework of the 2015 five-yearly review, the general approach that we would like to see for the new career structure, was explained. Concerning diversity, based on what we know about the situation in other international organiza...

  19. Fruitful meeting

    CERN Multimedia

    Mike Lamont

    2010-01-01

    The annual meeting for the LHC Performance Workshop was held in Chamonix from 25 to 29 January 2010 in the Centre de Congrès Le Majestic. The Workshop focused on how to reach the maximum operating energy.   The LHC Performance Workshop took place between 25 and 29 January 2010 in a rather chilly Chamonix. Following the successful start of beam commissioning last year, there remain a number of important questions about the near future of the machine. Topics discussed included the maximum operational energy that will be possible in 2010 and the steps need to go above the planned 2010 start-up energy of 3.5 TeV. Of particular importance were the required splice and magnet consolidation measures that would be demanded by an increase above this energy.  The energy in the magnets and beams will always represent a considerable threat, and the possible impact of an incident and the potential measures required to speed up a recovery were put on the table. Safety is critical and there were...

  20. The speciation of dissolved elements in aquatic solution. Radium and actinides

    International Nuclear Information System (INIS)

    Haesaenen, E.

    1994-01-01

    In the publication, the chemistry and speciation of radium, thorium, protactinium, uranium, neptunium, lutonium, americium and curium in ground-water environment is reviewed. Special attention is given to the transuranium elements, which have a central role in the repository of nuclear wastes. The most important methods used in the speciation of these elements is presented. The laser-induced methods, developed in the 1980's, are especially discussed. These have made it possible, e.g., to speciate the transuranium elements in their very low, actual repository ground-water concentrations (10-100 ng/l). (54 refs., 10 figs., 3 tabs.)