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

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.

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.

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.

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.

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...

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...

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.

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.

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.

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.

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.

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

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

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...

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...

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...

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...

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.

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

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....

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.

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)

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.

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.

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

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)

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.

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.

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

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.

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

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.)

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.

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.

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.

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

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.

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...

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

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

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.

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.

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.

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...

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...

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:...

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.

Removing Noise From Pyrosequenced Amplicons

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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

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.

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.

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...

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.

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.

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.

Efficient alignment of pyrosequencing reads for re-sequencing applications

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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.

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)

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)

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

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.

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)

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.

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.

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].

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

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

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

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.

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.

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.

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.

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)

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.

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)

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)

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

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

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...

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.

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.

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.

Review: Speciation in the myrtle family (Myrtaceae: rapid and slow models

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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

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

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

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

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.

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

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...

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...

Speciation environments and centres of diversity in southern Africa. I. Conceptual framework

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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.

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

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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.

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.

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

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.

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

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.

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.

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.

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)

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.

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.

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

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

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.

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)

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

Pollinator-driven ecological speciation in plants: new evidence and future perspectives.

Science.gov (United States)

Van der Niet, Timotheüs; Peakall, Rod; Johnson, Steven D

2014-01-01

The hypothesis that pollinators have been important drivers of angiosperm diversity dates back to Darwin, and remains an important research topic today. Mounting evidence indicates that pollinators have the potential to drive diversification at several different stages of the evolutionary process. Microevolutionary studies have provided evidence for pollinator-mediated floral adaptation, while macroevolutionary evidence supports a general pattern of pollinator-driven diversification of angiosperms. However, the overarching issue of whether, and how, shifts in pollination system drive plant speciation represents a critical gap in knowledge. Bridging this gap is crucial to fully understand whether pollinator-driven microevolution accounts for the observed macroevolutionary patterns. Testable predictions about pollinator-driven speciation can be derived from the theory of ecological speciation, according to which adaptation (microevolution) and speciation (macroevolution) are directly linked. This theory is a particularly suitable framework for evaluating evidence for the processes underlying shifts in pollination systems and their potential consequences for the evolution of reproductive isolation and speciation. This Viewpoint paper focuses on evidence for the four components of ecological speciation in the context of plant-pollinator interactions, namely (1) the role of pollinators as selective agents, (2) floral trait divergence, including the evolution of 'pollination ecotypes', (3) the geographical context of selection on floral traits, and (4) the role of pollinators in the evolution of reproductive isolation. This Viewpoint also serves as the introduction to a Special Issue on Pollinator-Driven Speciation in Plants. The 13 papers in this Special Issue range from microevolutionary studies of ecotypes to macroevolutionary studies of historical ecological shifts, and span a wide range of geographical areas and plant families. These studies further illustrate

Pollinator-driven ecological speciation in plants: new evidence and future perspectives

Science.gov (United States)

Van der Niet, Timotheüs; Peakall, Rod; Johnson, Steven D.

2014-01-01

Background The hypothesis that pollinators have been important drivers of angiosperm diversity dates back to Darwin, and remains an important research topic today. Mounting evidence indicates that pollinators have the potential to drive diversification at several different stages of the evolutionary process. Microevolutionary studies have provided evidence for pollinator-mediated floral adaptation, while macroevolutionary evidence supports a general pattern of pollinator-driven diversification of angiosperms. However, the overarching issue of whether, and how, shifts in pollination system drive plant speciation represents a critical gap in knowledge. Bridging this gap is crucial to fully understand whether pollinator-driven microevolution accounts for the observed macroevolutionary patterns. Testable predictions about pollinator-driven speciation can be derived from the theory of ecological speciation, according to which adaptation (microevolution) and speciation (macroevolution) are directly linked. This theory is a particularly suitable framework for evaluating evidence for the processes underlying shifts in pollination systems and their potential consequences for the evolution of reproductive isolation and speciation. Scope This Viewpoint paper focuses on evidence for the four components of ecological speciation in the context of plant-pollinator interactions, namely (1) the role of pollinators as selective agents, (2) floral trait divergence, including the evolution of ‘pollination ecotypes‘, (3) the geographical context of selection on floral traits, and (4) the role of pollinators in the evolution of reproductive isolation. This Viewpoint also serves as the introduction to a Special Issue on Pollinator-Driven Speciation in Plants. The 13 papers in this Special Issue range from microevolutionary studies of ecotypes to macroevolutionary studies of historical ecological shifts, and span a wide range of geographical areas and plant families. These studies

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.

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.

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.

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

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

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...

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.)

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

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....

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.

Science.gov (United States)

Pigot, Alex L; Phillimore, Albert B; Owens, Ian P F; Orme, C David L

2010-12-01

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of

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....

Influence of natural organic matter on the speciation of radionuclides in a geochemistry context; Influence de la matiere organique naturelle sur la speciation des radionucleides en contexte geochimique

Energy Technology Data Exchange (ETDEWEB)

Marang, L

2007-09-15

The principal aim of this work is the study of the influence of natural organic matter, in particularly humic substances (HS), on the speciation of radionuclides (RN). The studied radionuclides are cobalt (II), europium (III) and uranium (VI). It has been shown that mobility and bioavailability of a metal are related to its speciation. The NICA-Donnan model describes metal ion binding to NOM: it accounts for NOM chemical heterogeneity, competition during binding and ionic strength effects. However the model has been calibrated with a limited number of experimental data for the RN. Indeed there is only a few speciation technique available for the study of the interactions RN-HS. Within the framework of this study, we have developed and optimised speciation technique (Flux Donnan Membrane Technique and the use of an un-solubilized humic acid) in order to acquire new experimental data, we have also studied the effect of the competition on RN speciation and finally we have tested the model capacity to predict the RN behavior in laboratory or in situ. (author)

Speciation and solubility of neptunium in underground environments by paper electrophoresis

International Nuclear Information System (INIS)

Nagasaki, S.; Tanaka, Satoru; Takahashi, Yoichi

1988-01-01

Speciation and solubility of neptunium were studied using paper electrophoresis, ion exchange and ultrafiltration. Among these methods, the paper electrophoresis was found to be suitable for measuring speciation and solubility of neptunium of low concentration, if chemical species had opposite charge to each other or dissolved species had a charge. Using paper electrophoresis, hydrolysis constants of NpO 2 OH 0 and NpO 2 - (OH) 2 - and solubility product of NpO 2 were obtained and ionic-strength dependence of speciation was observed. (author) 9 refs.; 3 figs.; 2 tabs

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:...

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

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.

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.

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.

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.

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.)

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 ...

Interaction between Digestive Strategy and Niche Specialization Predicts Speciation Rates across Herbivorous Mammals.

Science.gov (United States)

Tran, Lucy A P

2016-04-01

Biotic and abiotic factors often are treated as mutually exclusive drivers of diversification processes. In this framework, ecological specialists are expected to have higher speciation rates than generalists if abiotic factors are the primary controls on species diversity but lower rates if biotic interactions are more important. Speciation rate is therefore predicted to positively correlate with ecological specialization in the purely abiotic model but negatively correlate in the biotic model. In this study, I show that the positive relationship between ecological specialization and speciation expected from the purely abiotic model is recovered only when a species-specific trait, digestive strategy, is modeled in the terrestrial, herbivorous mammals (Mammalia). This result suggests a more nuanced model in which the response of specialized lineages to abiotic factors is dependent on a biological trait. I also demonstrate that the effect of digestive strategy on the ecological specialization-speciation rate relationship is not due to a difference in either the degree of ecological specialization or the speciation rate between foregut- and hindgut-fermenting mammals. Together, these findings suggest that a biological trait, alongside historical abiotic events, played an important role in shaping mammal speciation at long temporal and large geographic scales.

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.

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.

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

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.)

Progress report on SYVAC chemical speciation modelling studies during 1983/4

International Nuclear Information System (INIS)

Cross, J.; Smith, G.L.; Williams, D.R.

1984-01-01

This report summarises progress made on the SYVAC (System Variability Analysis program) chemical speciation project during 1983-4. Chemical speciation is defined and its importance in the SYVAC approach to Radioactive Waste Management is discussed. Computer modelling of chemical equilibria is described and the two programs presently operational at UWIST - SOLMNQ and MINEQL - are compared and discussed in detail. In view of the shortcomings of the databases supplied with these programs, a new database of equilibrium constants has been compiled containing 483 aqueous species and 329 solid phases, including data for the radionuclides uranium, plutonium, americium, neptunium and thorium. The collaborative work with AERE, Harwell, is reported. A leaching experiment carried out at Harwell has been modelled using the chemical speciation programs. The results for uranium, plutonium, americium and neptunium, are presented. However, the experimental data provided by AERE is insufficient for accurate simulations. Chemical speciation studies relating to specific sites require accurate characterisation of the groundwater, i.e. chemical composition, Eh and pH. In the absence of such information, preliminary studies have been made using an average granite groundwater. The results of these studies are presented and include solubility and speciation plots for uranium, plutonium, thorium and neptunium. The future aims of the project are discussed. (author)

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

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

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.

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

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)

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...

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

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)

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

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

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)

How common is ecological speciation in plant-feeding insects? A 'Higher' Nematinae perspective

Directory of Open Access Journals (Sweden)

Nyman Tommi

2010-09-01

Full Text Available Abstract Background Ecological speciation is a process in which a transiently resource-polymorphic species divides into two specialized sister lineages as a result of divergent selection pressures caused by the use of multiple niches or environments. Ecology-based speciation has been studied intensively in plant-feeding insects, in which both sympatric and allopatric shifts onto novel host plants could speed up diversification. However, while numerous examples of species pairs likely to have originated by resource shifts have been found, the overall importance of ecological speciation in relation to other, non-ecological speciation modes remains unknown. Here, we apply phylogenetic information on sawflies belonging to the 'Higher' Nematinae (Hymenoptera: Tenthredinidae to infer the frequency of niche shifts in relation to speciation events. Results Phylogenetic trees reconstructed on the basis of DNA sequence data show that the diversification of higher nematines has involved frequent shifts in larval feeding habits and in the use of plant taxa. However, the inferred number of resource shifts is considerably lower than the number of past speciation events, indicating that the majority of divergences have occurred by non-ecological allopatric speciation; based on a time-corrected analysis of sister species, we estimate that a maximum of c. 20% of lineage splits have been triggered by a change in resource use. In addition, we find that postspeciational changes in geographic distributions have led to broad sympatry in many species having identical host-plant ranges. Conclusion Our analysis indicates that the importance of niche shifts for the diversification of herbivorous insects is at present implicitly and explicitly overestimated. In the case of the Higher Nematinae, employing a time correction for sister-species comparisons lowered the proportion of apparent ecology-based speciation events from c. 50-60% to around 20%, but such corrections are

Modeling Non-Steady Isotopologue and Isotopomer Speciation and Fractionation during Denitrification in Soils

Science.gov (United States)

Maggi, F.; Riley, W. J.

2009-12-01

The composition and location of 15N atoms on N2O isotopomers and isotopologues during isotope speciation has been used to characterize soil biological N cycling and N2O surface emissions. Although there exist few experimental observations, no attempt has been made to model N2O isotopomer speciation. The mathematical treatment of biological kinetic reactions in isotopic applications normally makes use of first-order and quasi steady-state complexation assumptions without taking into account changes in enzyme concentration, reaction stoichiometry, and isotopologue and isotopomer speciation. When multiatomic isotopically-labeled reactants are used in a multi-molecurar reaction, these assumptions may fail since they always lead to a constant fractionation factor and cannot describe speciation of isotopologues and isotopomers. We have developed a mathematical framework that is capable of describing isotopologue and isotopmer speciation and fractionation under the assumption of non-steady complexation during biological kinetic reactions that overcome the limitations mentioned above. This framework was applied to a case study of non-steady (variable and inverse) isotopic effects observed during N2O production and consumption in soils. Our mathematical treatment has led to generalized kinetic equations which replicate experimental observations with high accuracy and help interpret non-steady isotopic effects and isotopologue and isotopomer speciation. The kinetic equations introduced and applied here have general validity in describing isotopic effects in any biochemical reactions by considering: changing enzyme concentrations, mass and isotope conservation, and reaction stoichiometry. The equations also describe speciation of any isotopologue and isotopomer product from any isotopologue and isotopmer reactant.

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.

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...

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

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.

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

Sample preparation and storage can change arsenic speciation in human urine.

Science.gov (United States)

Feldmann, J; Lai, V W; Cullen, W R; Ma, M; Lu, X; Le, X C

1999-11-01

Stability of chemical speciation during sample handling and storage is a prerequisite to obtaining reliable results of trace element speciation analysis. There is no comprehensive information on the stability of common arsenic species, such as inorganic arsenite [As(III)], arsenate [As(V)], monomethylarsonic acid, dimethylarsinic acid, and arsenobetaine, in human urine. We compared the effects of the following storage conditions on the stability of these arsenic species: temperature (25, 4, and -20 degrees C), storage time (1, 2, 4, and 8 months), and the use of additives (HCl, sodium azide, benzoic acid, benzyltrimethylammonium chloride, and cetylpyridinium chloride). HPLC with both inductively coupled plasma mass spectrometry and hydride generation atomic fluorescence detection techniques were used for the speciation of arsenic. We found that all five of the arsenic species were stable for up to 2 months when urine samples were stored at 4 and -20 degrees C without any additives. For longer period of storage (4 and 8 months), the stability of arsenic species was dependent on urine matrices. Whereas the arsenic speciation in some urine samples was stable for the entire 8 months at both 4 and -20 degrees C, other urine samples stored under identical conditions showed substantial changes in the concentration of As(III), As(V), monomethylarsonic acid, and dimethylarsinic acid. The use of additives did not improve the stability of arsenic speciation in urine. The addition of 0.1 mol/L HCl (final concentration) to urine samples produced relative changes in inorganic As(III) and As(V) concentrations. Low temperature (4 and -20 degrees C) conditions are suitable for the storage of urine samples for up to 2 months. Untreated samples maintain their concentration of arsenic species, and additives have no particular benefit. Strong acidification is not appropriate for speciation analysis.

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 ...

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.

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

Science.gov (United States)

Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Otwinowski, Zbyszek; Grishin, Nick V

2016-04-28

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.

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...

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.

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

Effects of pH on the speciation of radionuclides in groundwater of beishan area, gansu province, China

International Nuclear Information System (INIS)

Zhanshi, Zhang; Wenbin, Zhou; Xianhua, Fan

2002-01-01

Speciation of radioactive nuclides is one of the most important factors in the study of migration and precipitation of the nuclides related to deep geological disposal of high level radwastes (HLW). Theoretical speciation analysis with thermodynamic equilibrium codes is an effective method. The authors have employed the EQ3NR, a computer program for geochemical aqueous speciation-solubility calculation, to evaluate the speciation of the key nuclides in the groundwater of Beishan Area, a potential area for hosting the HLW Repository of China. The calculated results showed that pH value as well as chemical composition of the water had a great impact on the speciation of key nuclides, such as Np, Pu, Am, U and Th, which would be released from HLW to the groundwater of Beishan Area. In addition, it was found that the speciation of nuclides varied from one to another. However, under alkaline conditions, the speciations were relatively simpler and hydroxyl complexes and carbonate complexes were dominant. (author)

Geography, assortative mating, and the effects of sexual selection on speciation with gene flow.

Science.gov (United States)

Servedio, Maria R

2016-01-01

Theoretical and empirical research on the evolution of reproductive isolation have both indicated that the effects of sexual selection on speciation with gene flow are quite complex. As part of this special issue on the contributions of women to basic and applied evolutionary biology, I discuss my work on this question in the context of a broader assessment of the patterns of sexual selection that lead to, versus inhibit, the speciation process, as derived from theoretical research. In particular, I focus on how two factors, the geographic context of speciation and the mechanism leading to assortative mating, interact to alter the effect that sexual selection through mate choice has on speciation. I concentrate on two geographic contexts: sympatry and secondary contact between two geographically separated populations that are exchanging migrants and two mechanisms of assortative mating: phenotype matching and separate preferences and traits. I show that both of these factors must be considered for the effects of sexual selection on speciation to be inferred.

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.

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 ...

Multielemental speciation analysis by advanced hyphenated technique - HPLC/ICP-MS: A review.

Science.gov (United States)

Marcinkowska, Monika; Barałkiewicz, Danuta

2016-12-01

Speciation analysis has become an invaluable tool in human health risk assessment, environmental monitoring or food quality control. Another step is to develop reliable multielemental speciation methodologies, to reduce costs, waste and time needed for the analysis. Separation and detection of species of several elements in a single analytical run can be accomplished by high performance liquid chromatography hyphenated to inductively coupled plasma mass spectrometry (HPLC/ICP-MS). Our review assembles articles concerning multielemental speciation determination of: As, Se, Cr, Sb, I, Br, Pb, Hg, V, Mo, Te, Tl, Cd and W in environmental, biological, food and clinical samples analyzed with HPLC/ICP-MS. It addresses the procedures in terms of following issues: sample collection and pretreatment, selection of optimal conditions for elements species separation by HPLC and determination using ICP-MS as well as metrological approach. The presented work is the first review article concerning multielemental speciation analysis by advanced hyphenated technique HPLC/ICP-MS. Copyright © 2016 Elsevier B.V. All rights reserved.

Status of determining transuranic nuclides speciation in aqueous solution with laser spectrometry

International Nuclear Information System (INIS)

Wang Bo; Liu Dejun; Yao Jun; Chen Xi; Long Haoqi; Zeng Jishu; Su Xiguang; Fan Xianhua

2007-01-01

The knowledge about speciation of transuranic nuclides in aqueous solution is a basis for understanding the chemical and migration behavior of transuranic nuclides in aqueous solution. The speciation of transuranic nuclides with trace concentration is complicated in near neutral aqueous solutions, including change of oxidation state, complexation and colloid generation, etc. The concentrations of transuranium in near neutral aqueous solution usually below the sensitivity range of method such as conventional absorption spectroscopy. The radioactive analysis method has a very low detection limits for radionuclides, however, it wouldn' t allow the direct measurement of the transuranic species. In contrast with these methods, laser spectroscopy is an ideal method with high sensitivity, and non-contact and non-destructive for determining the speciation of transuranic nuclides. This paper summarizes the status and application of LIPAS (Laser-induced Photoacoustic Spectrometry), LIBD (Laser-induced Breakdown Detection) and TRLFS (Time-resolved Laser Fluorescence Spectrometry) to determine the speciation of transuranic nuclides with trace concentration in aqueous solutions. (authors)

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.

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies.

Science.gov (United States)

Potter, Sally; Bragg, Jason G; Blom, Mozes P K; Deakin, Janine E; Kirkpatrick, Mark; Eldridge, Mark D B; Moritz, Craig

2017-01-01

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale . We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

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.

Current mass spectrometry strategies for selenium speciation in dietary sources of high-selenium

Energy Technology Data Exchange (ETDEWEB)

Infante, Heidi Goenaga; Hearn, Ruth; Catterick, Tim [LGC Limited, Teddington, Middlesex (United Kingdom)

2005-06-01

This document reviews the most relevant mass spectrometry approaches to selenium (Se) speciation in high-Se food supplements in terms of qualitative and quantitative Se speciation and Se-containing species identification, with special reference to high-Se yeast, garlic, onions and Brazil nuts. Important topics such as complexity of Se speciation in these materials and the importance of combining Se-specific detection and molecule-specific determination of the particular species of this element in parallel with chromatography, to understand their nutritional role and cancer preventive properties are critically discussed throughout. The versatility and potential of mass spectrometric detection in this field are clearly demonstrated. Although great advances have been achieved, further developments are required, especially if ''speciated''certified reference materials (CRMs) are to be produced for validation of measurements of target Se-containing species in Se-food supplements. (orig.)

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....

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.

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.

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.

Influence of natural organic matter on the speciation of radionuclides in a geochemistry context

International Nuclear Information System (INIS)

Marang, L.

2007-09-01

The principal aim of this work is the study of the influence of natural organic matter, in particularly humic substances (HS), on the speciation of radionuclides (RN). The studied radionuclides are cobalt (II), europium (III) and uranium (VI). It has been shown that mobility and bioavailability of a metal are related to its speciation. The NICA-Donnan model describes metal ion binding to NOM: it accounts for NOM chemical heterogeneity, competition during binding and ionic strength effects. However the model has been calibrated with a limited number of experimental data for the RN. Indeed there is only a few speciation technique available for the study of the interactions RN-HS. Within the framework of this study, we have developed and optimised speciation technique (Flux Donnan Membrane Technique and the use of an un-solubilized humic acid) in order to acquire new experimental data, we have also studied the effect of the competition on RN speciation and finally we have tested the model capacity to predict the RN behavior in laboratory or in situ. (author)

Influence of natural organic matter on the speciation of radionuclides in a geochemistry context

International Nuclear Information System (INIS)

Marang, L.

2007-09-01

The principal aim of this work is the study of the influence of natural organic matter, in particularly humic substances (HS), on the speciation of radionuclides (RN). The studied radionuclides are cobalt (II), europium (III) and uranium (VI). It has been shown that mobility and bioavailability of a metal are related to its speciation. The NICA-Donnan model describes metal ion binding to NOM: it accounts for NOM chemical heterogeneity, competition during binding and ionic strength effects. However the model has been calibrated with a limited number of experimental data for the RN. Indeed there is only a few speciation techniques available for the study of the interactions RN-HS. Within the framework of this study, we have developed and optimised speciation technique (Flux Donnan Membrane Technique and the use of an insolubilized humic acid) in order to acquire new experimental data, we have also studied the effect of the competition on RN speciation and finally we have tested the model capacity to predict the RN behavior in laboratory or in situ. (author)

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.

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...

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana.

Science.gov (United States)

MacLeod, Amy; Rodríguez, Ariel; Vences, Miguel; Orozco-terWengel, Pablo; García, Carolina; Trillmich, Fritz; Gentile, Gabriele; Caccone, Adalgisa; Quezada, Galo; Steinfartz, Sebastian

2015-06-22

The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes--are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within--island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50,000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island--ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

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.

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.

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...

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.

Science.gov (United States)

Beaulieu, Jeremy M; O'Meara, Brian C

2016-07-01

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved

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.

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...

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.

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...

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)

Early events in speciation: Cryptic species of Drosophila aldrichi.

Science.gov (United States)

Castro Vargas, Cynthia; Richmond, Maxi Polihronakis; Ramirez Loustalot Laclette, Mariana; Markow, Therese Ann

2017-06-01

Understanding the earliest events in speciation remains a major challenge in evolutionary biology. Thus identifying species whose populations are beginning to diverge can provide useful systems to study the process of speciation. Drosophila aldrichi , a cactophilic fruit fly species with a broad distribution in North America, has long been assumed to be a single species owing to its morphological uniformity. While previous reports either of genetic divergence or reproductive isolation among different D. aldrichi strains have hinted at the existence of cryptic species, the evolutionary relationships of this species across its range have not been thoroughly investigated. Here we show that D. aldrichi actually is paraphyletic with respect to its closest relative, Drosophila wheeleri , and that divergent D. aldrichi lineages show complete hybrid male sterility when crossed. Our data support the interpretation that there are at least two species of D. aldrichi, making these flies particularly attractive for studies of speciation in an ecological and geographical context.

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

Genomic islands of divergence are not affected by geography of speciation in sunflowers.

Science.gov (United States)

Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

2013-01-01

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

Iron solubility driven by speciation in dust sources to the ocean

Science.gov (United States)

Schroth, A.W.; Crusius, John; Sholkovitz, E.R.; Bostick, B.C.

2009-01-01

Although abundant in the Earths crust, iron is present at trace concentrations in sea water and is a limiting nutrient for phytoplankton in approximately 40% of the ocean. Current literature suggests that aerosols are the primary external source of iron to offshore waters, yet controls on iron aerosol solubility remain unclear. Here we demonstrate that iron speciation (oxidation state and bonding environment) drives iron solubility in arid region soils, glacial weathering products (flour) and oil combustion products (oil fly ash). Iron speciation varies by aerosol source, with soils in arid regions dominated by ferric (oxy)hydroxides, glacial flour by primary and secondary ferrous silicates and oil fly ash by ferric sulphate salts. Variation in iron speciation produces systematic differences in iron solubility: less than 1% of the iron in arid soils was soluble, compared with 2-3% in glacial products and 77-81% in oil combustion products, which is directly linked to fractions of more soluble phases. We conclude that spatial and temporal variations in aerosol iron speciation, driven by the distribution of deserts, glaciers and fossil-fuel combustion, could have a pronounced effect on aerosol iron solubility and therefore on biological productivity and the carbon cycle in the ocean. ?? 2009 Macmillan Publishers Limited.

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

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.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

KAUST Repository

Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh

2014-01-01

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris).

Science.gov (United States)

Lemmon, Emily Moriarty; Lemmon, Alan R; Cannatella, David C

2007-09-01

Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with divergence times among species in the continentally distributed trilling chorus frogs (Pseudacris). In particular, we ask whether marine inundation of the Mississippi Embayment, uplift of the Appalachian Mountains, or modification of the ancient Teays-Mahomet River system contributed to speciation. To examine the plausibility of ancient rivers causing divergence, we tested whether modern river systems inhibit gene flow. Additionally, we compared the effects of Quaternary climatic factors (glaciation and aridification) on levels of genetic variation. Divergence time estimates using penalized likelihood and coalescent approaches indicate that the major lineages of chorus frogs diversified during the Tertiary, and also exclude Quaternary climate change as a factor in speciation of chorus frogs. We show the first evidence that inundation of the Mississippi Embayment contributed to speciation. We reject the hypotheses that Cenozoic uplift of the Appalachians and that diversion of the Teays-Mahomet River contributed to speciation in this clade. We find that by reducing gene flow, rivers have the potential to cause divergence of lineages. Finally, we demonstrate that populations in areas affected by Quaternary glaciation and aridification have reduced levels of genetic variation compared to those from more equable regions, suggesting recent colonization.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

KAUST Repository

Huang, Chao-Li

2014-11-11

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Proceedings of the DAE-BRNS theme meeting on ion chromatography separations - state of art and perspectives

International Nuclear Information System (INIS)

Jeyakumar, S.; Ramakumar, K.L.

2012-01-01

Ion Chromatography (IC) plays a vital role in all disciplines of science and technology. In the field of trace separations and speciation studies, use of IC techniques becomes indispensable. In nuclear technology, IC plays a pivotal role in the reactor water chemistry, in the front end of fuel cycle especially in the characterization of nuclear materials including the reactor fuels, post irradiation examination, actinide speciation studies and in understanding the interaction and migration of actinide species in the geo environment. Ion chromatography is also useful in the studies related to waste management particularly for the separation and determination of fission products. The aim of this meeting is to provide a forum to all the researchers in the area of ion chromatography to discuss their recent findings and information, to learn from the mutual experiences and interests, and to promote cooperation both nationally and internationally. Ion chromatography techniques including Ion Chromatography Separations and Nuclear Materials, Speciation Studies by Ion chromatography, Hyphenated -IC Techniques, Reactor Water Chemistry and Ion Chromatography, Solid Phase Extraction and Sample Preparations for IC and Separation of Bio-molecules and Environmental aspects etc are discussed. Papers relevant to INIS are indexed separately

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.

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.

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)

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.

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

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.

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.

Speciation, diversification, and coexistence of sessile species that compete for space

DEFF Research Database (Denmark)

Mitarai, Namiko; Heinsalu, Els; Sneppen, Kim

2014-01-01

Speciation, diversification, and competition between species challenge the stability of complex ecosystems. Laboratory experiments often focus on one or two species competing under conditions where they may grow exponentially. Field studies, in contrast, emphasize multi-species communities...... appear due to immigration from outside of the considered ecosystem. The species self-organize their spatial distribution through competitive interactions to create many patches, implicitly protecting each other from competitively superior species, and speciation in each patch leads the system to high...

Arsenic speciation by liquid chromatography coupled with ionspray tandem mass spectrometry

DEFF Research Database (Denmark)

Corr, J. J.; Larsen, Erik Huusfeldt

1996-01-01

Ionspray mass spectrometry, a well established organic analysis technique, has been coupled to high-performance liquid chromatography for speciation of organic arsenic compounds, The ionspray source and differentially pumped interface of the mass spectrometer were operated in dual modes...... fragmentation patterns showing molecular dissociation through an expected common product ion were obtained for the four arsenosugars, Molecular mode detection was utilized for qualitative verification of speciation analysis by high-performance liquid chromatography coupled to inductively coupled plasma mass...

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).

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

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.

Role of natural nanoparticles on the speciation of Ni in andosols of la Reunion

Science.gov (United States)

Levard, Clément; Doelsch, Emmanuel; Rose, Jérôme; Masion, Armand; Basile-Doelsch, Isabelle; Proux, Olivier; Hazemann, Jean-Louis; Borschneck, Daniel; Bottero, Jean-Yves

2009-08-01

Andosols on the island of Réunion have high nickel (Ni) concentrations due to the natural pedo-geochemical background. Enhanced knowledge of Ni speciation is necessary to predict the bioavailability and potential toxicity of this element. Ni speciation in these andosols, marked by the presence of high amounts of natural aluminosilicate nanoparticles, was investigated in two complementary systems: (i) In a soil sample—densimetric fractionation was first performed in order to separate the potential bearing phases, prior to Ni speciation characterization. (ii) In a synthetic sample—Ni reactivity with synthetic aluminosilicate nanoparticle analogs were studied. In both cases, Ni speciation was determined using X-ray absorption spectroscopy (XAS). The results revealed that Ni had the same local environment in both systems (natural and synthetic systems), and Ni was chemically linked to natural short-range ordered aluminosilicates or analogs. This complex represented about 75% of the total Ni in the studied soil.

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.

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

Recent trends in nanomaterial-based microanalytical systems for the speciation of trace elements: A critical review.

Science.gov (United States)

Tseng, Wei-Chang; Hsu, Keng-Chang; Shiea, Christopher Stephen; Huang, Yeou-Lih

2015-07-16

Trace element speciation in biomedical and environmental science has gained increasing attention over the past decade as researchers have begun to realize its importance in toxicological studies. Several nanomaterials, including titanium dioxide nanoparticles (nano-TiO2), carbon nanotubes (CNTs), and magnetic nanoparticles (MNPs), have been used as sorbents to separate and preconcentrate trace element species prior to detection through mass spectrometry or optical spectroscopy. Recently, these nanomaterial-based speciation techniques have been integrated with microfluidics to minimize sample and reagent consumption and simplify analyses. This review provides a critical look into the present state and recent applications of nanomaterial-based microanalytical systems in the speciation of trace elements. The adsorption and preconcentration efficiencies, sample volume requirements, and detection limits of these nanomaterial-based speciation techniques are detailed, and their applications in environmental and biological analyses are discussed. Current perspectives and future trends into the increasing use of nanomaterial-based microfluidic techniques for trace element speciation are highlighted. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Genetic tests for ecological and allopatric speciation in anoles on an island archipelago.

Science.gov (United States)

Thorpe, Roger S; Surget-Groba, Yann; Johansson, Helena

2010-04-29

From Darwin's study of the Galapagos and Wallace's study of Indonesia, islands have played an important role in evolutionary investigations, and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation. Even during the ongoing paradigm shift towards other modes of speciation, island radiations, such as the Lesser Antillean anoles, are thought to exemplify this process. Geological and molecular phylogenetic evidence show that, in this archipelago, Martinique anoles provide several examples of secondary contact of island species. Four precursor island species, with up to 8 mybp divergence, met when their islands coalesced to form the current island of Martinique. Moreover, adjacent anole populations also show marked adaptation to distinct habitat zonation, allowing both allopatric and ecological speciation to be tested in this system. We take advantage of this opportunity of replicated island coalescence and independent ecological adaptation to carry out an extensive population genetic study of hypervariable neutral nuclear markers to show that even after these very substantial periods of spatial isolation these putative allospecies show less reproductive isolation than conspecific populations in adjacent habitats in all three cases of subsequent island coalescence. The degree of genetic interchange shows that while there is always a significant genetic signature of past allopatry, and this may be quite strong if the selection regime allows, there is no case of complete allopatric speciation, in spite of the strong primae facie case for it. Importantly there is greater genetic isolation across the xeric/rainforest ecotone than is associated with any secondary contact. This rejects the development of reproductive isolation in allopatric divergence, but supports the potential for ecological speciation, even though full speciation has not been achieved in this case. It also explains the paucity of anole species

Analytical methodologies for aluminium speciation in environmental and biological samples--a review.

Science.gov (United States)

Bi, S P; Yang, X D; Zhang, F P; Wang, X L; Zou, G W

2001-08-01

It is recognized that aluminium (Al) is a potential environmental hazard. Acidic deposition has been linked to increased Al concentrations in natural waters. Elevated levels of Al might have serious consequences for biological communities. Of particular interest is the speciation of Al in aquatic environments, because Al toxicity depends on its forms and concentrations. In this paper, advances in analytical methodologies for Al speciation in environmental and biological samples during the past five years are reviewed. Concerns about the specific problems of Al speciation and highlights of some important methods are elucidated in sections devoted to hybrid techniques (HPLC or FPLC coupled with ET-AAS, ICP-AES, or ICP-MS), flow-injection analysis (FIA), nuclear magnetic resonance (27Al NMR), electrochemical analysis, and computer simulation. More than 130 references are cited.

Mechanisms by Which Phenotypic Plasticity Affects Adaptive Divergence and Ecological Speciation.

Science.gov (United States)

Nonaka, Etsuko; Svanbäck, Richard; Thibert-Plante, Xavier; Englund, Göran; Brännström, Åke

2015-11-01

Phenotypic plasticity is the ability of one genotype to produce different phenotypes depending on environmental conditions. Several conceptual models emphasize the role of plasticity in promoting reproductive isolation and, ultimately, speciation in populations that forage on two or more resources. These models predict that plasticity plays a critical role in the early stages of speciation, prior to genetic divergence, by facilitating fast phenotypic divergence. The ability to plastically express alternative phenotypes may, however, interfere with the early phase of the formation of reproductive barriers, especially in the absence of geographic barriers. Here, we quantitatively investigate mechanisms under which plasticity can influence progress toward adaptive genetic diversification and ecological speciation. We use a stochastic, individual-based model of a predator-prey system incorporating sexual reproduction and mate choice in the predator. Our results show that evolving plasticity promotes the evolution of reproductive isolation under diversifying environments when individuals are able to correctly select a more profitable habitat with respect to their phenotypes (i.e., adaptive habitat choice) and to assortatively mate with relatively similar phenotypes. On the other hand, plasticity facilitates the evolution of plastic generalists when individuals have a limited capacity for adaptive habitat choice. We conclude that plasticity can accelerate the evolution of a reproductive barrier toward adaptive diversification and ecological speciation through enhanced phenotypic differentiation between diverging phenotypes.

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

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

Characterization of iron speciation in urban and rural single particles using XANES spectroscopy and micro X-ray fluorescence measurements: investigating the relationship between speciation and fractional iron solubility

OpenAIRE

Oakes, M.; Weber, R. J.; Lai, B.; Russell, A.; Ingall, E. D.

2012-01-01

Soluble iron in fine atmospheric particles has been identified as a public health concern by participating in reactions that generate reactive oxygen species (ROS). The mineralogy and oxidation state (speciation) of iron have been shown to influence fractional iron solubility (soluble iron/total iron). In this study, iron speciation was determined in single particles at urban and rural sites in Georgia USA using synchrotron-based techniques, such as X-ray Absorption Near-Edge Structure (XANES...

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.

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

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

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.

Speciation of Mercury in Selected Areas of the Petroleum Value Chain.

Science.gov (United States)

Avellan, Astrid; Stegemeier, John P; Gai, Ke; Dale, James; Hsu-Kim, Heileen; Levard, Clément; O'Rear, Dennis; Hoelen, Thomas P; Lowry, Gregory V

2018-02-06

Petroleum, natural gas, and natural gas condensate can contain low levels of mercury (Hg). The speciation of Hg can affect its behavior during processing, transport, and storage so efficient and safe management of Hg requires an understanding of its chemical form in oil, gas and byproducts. Here, X-ray absorption spectroscopy was used to determine the Hg speciation in samples of solid residues collected throughout the petroleum value chain including stabilized crude oil residues, sediments from separation tanks and condensate glycol dehydrators, distillation column pipe scale, and biosludge from wastewater treatment. In all samples except glycol dehydrators, metacinnabar (β-HgS) was the primary form of Hg. Electron microscopy on particles from a crude sediment showed nanosized (crude oil being processed, i.e. sweet (low sulfur crudes) vs sour (higher sulfur crudes). This information on Hg speciation in the petroleum value chain will inform development of better engineering controls and management practices for Hg.

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)

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)

Contribution of neutron activation analysis and radioanalytical techniques to trace element speciation in environmental analysis

International Nuclear Information System (INIS)

Gallorini, M.; Orvini, E.; Sabbioni, E.; Pietra, R.

1984-01-01

The feasibility of the NAA in contributing to trace element speciation in environmental and biological samples is shown by a few selected applications. They are: (i) the determination of different species of vanadium, arsenic and selenium in freshwater. The pre-irradiation treatments in which the different chemical species are selectively isolated are critically evaluated. Problems arising from possible contaminations or losses and from blanks are discussed; (ii) the use of NAA in metallobiochemical speciation once biochemical methods of cellular fractionation for the isolation of metallobiocomplexes are developed. Examples concern the biochemical speciation of vanadium in human blood and the development of a method for speciation of inorganic and organic arsenic compounds in biological samples. The use of radioanalytical techniques in developing the separation procedures of different trace metal chemical and biochemical species is also briefly discussed. 24 references, 5 figures, 4 tables

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

Effects of pH and Competing Anions on the Solution Speciation of Arsenic by Ion Exchange Resins

Energy Technology Data Exchange (ETDEWEB)

Impellitteri, Christopher A.; Ryan, JAmes A.; Al-Abed, Souhail R.; Scheckel, Kirk G.; Randall, Paul M.; Richardson, Collin A.

2003-03-26

Anion-exchange resins (AER) are used to differentiate As(V) and As(III) by retaining As(V) and allowing As(III) to pass through. AERs allow rapid speciation of As in the field which precludes the effects of sample preservation on As speciation. Aqueous environmental samples contain anions that may interfere with the speciation of As. This study compares the speciation of As by two commercially available AERs. A silica-based AER was selected for further study. As(V) and As(III) were passed through the AER in the presence of NO3 -, SO4 2-, HPO4 2-, Cl- and HCO3 - at pH 4, 6 and 8. Recoveries of As species in mixed systems range between 90 to 100%. Breakthrough curves for As(V) are presented which allow calculation of loading rates. HPO4 2- has the greatest effect on the speciation of As by AER.

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.

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...

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

Science.gov (United States)

MacLeod, Amy; Rodríguez, Ariel; Vences, Miguel; Orozco-terWengel, Pablo; García, Carolina; Trillmich, Fritz; Gentile, Gabriele; Caccone, Adalgisa; Quezada, Galo; Steinfartz, Sebastian

2015-01-01

The effects of the direct interaction between hybridization and speciation—two major contrasting evolutionary processes—are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50 000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island—ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole. PMID:26041359

Moran model as a dynamical process on networks and its implications for neutral speciation

Science.gov (United States)

de Aguiar, Marcus A. M.; Bar-Yam, Yaneer

2011-03-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert.

Science.gov (United States)

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-02-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (F ST = 0.35), and F ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.

Assessment of uranium and selenium speciation in human and bacterial biological models to probe changes in their structural environment

International Nuclear Information System (INIS)

Avoscan, L.; Milgram, S.; Untereiner, G.; Collins, R.; Khodja, H.; Carriere, M.; Gouget, B.; Coves, J.; Hazemann, J.L.

2009-01-01

This study illustrates the potential of physicochemical techniques to speciate uranium (U) and selenium (Se) in biological samples. Speciation, defined he0re as the study of structural environment, of both toxic elements, was characterized at several levels in biological media and directly in human cells or bacteria once the metal(loid)s were internalized. External speciation that is extracellular speciation in culture media was predicted by thermodynamic equilibrium computer modelling using the JChess software and validated by spectroscopic measurements (XANES and EXAFS). Internal speciation that is intracellular speciation in eukaryotic and prokaryotic cells was studied in vitro with a soil bacterium Cupriavidus metallidurans CH34 and ROS 17/2.8 osteoblasts, human cells responsible for bone formation. XANES, EXAFS, HPLC-ICP-MS and SDS-PAGE coupled to particle induced X-ray emission (PIXE) permitted the identification and quantification of complexes formed with organic or inorganic molecules and/or larger proteins. (orig.)

Assessment of uranium and selenium speciation in human and bacterial biological models to probe changes in their structural environment

Energy Technology Data Exchange (ETDEWEB)

Avoscan, L.; Milgram, S.; Untereiner, G.; Collins, R.; Khodja, H.; Carriere, M.; Gouget, B. [Lab. Pierre Sue, CEA-CNRS UMR 9956, CEA/Saclay, Gif-sur-Yvette (France); Coves, J. [Inst. de Biologie Structurale - J.-P. Ebel, Lab. des Proteines Membranaires, Grenoble (France); Hazemann, J.L. [Lab. de Geophysique Interne et Tectonopbysique, UMR CNRS/Univ. Joseph Fourier, Saint-Martin-D' Heres (France)

2009-07-01

This study illustrates the potential of physicochemical techniques to speciate uranium (U) and selenium (Se) in biological samples. Speciation, defined he0re as the study of structural environment, of both toxic elements, was characterized at several levels in biological media and directly in human cells or bacteria once the metal(loid)s were internalized. External speciation that is extracellular speciation in culture media was predicted by thermodynamic equilibrium computer modelling using the JChess software and validated by spectroscopic measurements (XANES and EXAFS). Internal speciation that is intracellular speciation in eukaryotic and prokaryotic cells was studied in vitro with a soil bacterium Cupriavidus metallidurans CH34 and ROS 17/2.8 osteoblasts, human cells responsible for bone formation. XANES, EXAFS, HPLC-ICP-MS and SDS-PAGE coupled to particle induced X-ray emission (PIXE) permitted the identification and quantification of complexes formed with organic or inorganic molecules and/or larger proteins. (orig.)

Speciation, phenotypic variation and plasticity: what can endocrine disruptors tell us?

Science.gov (United States)

Ayala-García, Braulio; López-Santibáñez Guevara, Marta; Marcos-Camacho, Lluvia I; Fuentes-Farías, Alma L; Meléndez-Herrera, Esperanza; Gutiérrez-Ospina, Gabriel

2013-01-01

Phenotype variability, phenotypic plasticity, and the inheritance of phenotypic traits constitute the fundamental ground of processes such as individuation, individual and species adaptation and ultimately speciation. Even though traditional evolutionary thinking relies on genetic mutations as the main source of intra- and interspecies phenotypic variability, recent studies suggest that the epigenetic modulation of gene transcription and translation, epigenetic memory, and epigenetic inheritance are by far the most frequent reliable sources of transgenerational variability among viable individuals within and across organismal species. Therefore, individuation and speciation should be considered as nonmutational epigenetic phenomena.

Speciation, Phenotypic Variation and Plasticity: What Can Endocrine Disruptors Tell Us?

Directory of Open Access Journals (Sweden)

Braulio Ayala-García

2013-01-01

Full Text Available Phenotype variability, phenotypic plasticity, and the inheritance of phenotypic traits constitute the fundamental ground of processes such as individuation, individual and species adaptation and ultimately speciation. Even though traditional evolutionary thinking relies on genetic mutations as the main source of intra- and interspecies phenotypic variability, recent studies suggest that the epigenetic modulation of gene transcription and translation, epigenetic memory, and epigenetic inheritance are by far the most frequent reliable sources of transgenerational variability among viable individuals within and across organismal species. Therefore, individuation and speciation should be considered as nonmutational epigenetic phenomena.

A role for a neo-sex chromosome in stickleback speciation

Science.gov (United States)

Kitano, Jun; Ross, Joseph A.; Mori, Seiichi; Kume, Manabu; Jones, Felicity C.; Chan, Yingguang F.; Absher, Devin M.; Grimwood, Jane; Schmutz, Jeremy; Myers, Richard M.; Kingsley, David M.; Peichel, Catherine L.

2009-01-01

Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex chromosome turnover and speciation. Although closely related species often have different sex chromosome systems, it is unknown whether sex chromosome turnover contributes to the evolution of reproductive isolation between species. In this study, we show that a newly evolved sex chromosome harbours genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome harbours loci for male courtship display traits that contribute to behavioural isolation, while the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large-X effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data suggest that sex chromosome turnover might play a greater role in speciation than previously appreciated. PMID:19783981

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.

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.

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...

Transuranium element behavior in the environment: What speciation studies can tell us

International Nuclear Information System (INIS)

Cleveland, J.M.

1989-01-01

Some of the transuranium elements - especially plutonium - can exist in the environment in several different oxidation states which differ chemically from one another as much as if they were different elements. Hence an understanding of the environmental chemistry of these elements requires knowledge of their oxidation-state distribution, or speciation, under a variety of realistic conditions. Such studies are in their infancy, but already several chemical speciation methods have yielded results indicating the uniqueness of transuranic environment chemistry; for example, dioxoplutonium(V), which is unstable in the acid solutions employed in laboratory and processing plant, is often the most prevalent plutonium oxidation state in natural waters. More sensitive and less invasive physical speciation methods under development will hopefully permit the extension of these studies to a wider variety of environmental conditions and to determinations of sorbed species necessary for an understanding of sorption processes

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

Characterizing Zinc Speciation in Soils from a Smelter-Affected Boreal Forest Ecosystem.

Science.gov (United States)

Hamilton, Jordan G; Farrell, Richard E; Chen, Ning; Feng, Renfei; Reid, Joel; Peak, Derek

2016-03-01

HudBay Minerals, Inc., has mined and/or processed Zn and Cu ore in Flin Flon, MB, Canada, since the 1930s. The boreal forest ecosystem and soil surrounding these facilities have been severely impacted by mixed metal contamination and HSO deposition. Zinc is one of the most prevalent smelter-derived contaminants and has been identified as a key factor that may be limiting revegetation. Metal toxicity is related to both total concentrations and speciation; therefore, X-ray absorption spectroscopy and X-ray fluorescence mapping were used to characterize Zn speciation in soils throughout the most heavily contaminated areas of the landscape. Zinc speciation was linked to two distinct soil types. Group I soils consist of exposed soils in weathered positions of bedrock outcrops with Zn present primarily as franklinite, a (ZnFeO) spinel mineral. Group II soils are stabilized by an invasive metal-tolerant grass species, with Zn found as a mixture of octahedral (Fe oxides) and tetrahedral Mn oxides) adsorption complexes with a franklinite component. Soil erosion influences Zn speciation through the redistribution of Zn and soil particulates from Group I landscape positions to Group II soils. Despite Group II soils having the highest concentrations of CaCl-extractable Zn, they support metal-tolerant plant growth. The metal-tolerant plants are probably preferentially colonizing these areas due to better soil and nutrient conditions as a result of soil deposition from upslope Group I areas. Zinc concentration and speciation appears to not influence the colonization by metal-tolerant grasses, but the overall soil properties and erosion effects prevent the revegetation by native boreal forest species. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

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.

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

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

Biogeography of speciation in Cenozoic marine ostracoda: the role of climatic change

Energy Technology Data Exchange (ETDEWEB)

Cronin, T.M.

1985-01-01

Evolutionary theory holds that geographic isolation of populations with its resultant reproductive isolation is an important factor in the origin of new species. Climatic change alters species' biogeography by creating and eliminating barriers that affect gene flow between populations. For benthic organisms such as shallow marine ostracodes, thermal gradients at biogeographic province boundaries and the area of continental shelf are factors affected by climatic and associated sea level changes. Studies of Cenozoic marine ostracodes show that allopatric speciation does not account for paleobiogeographic patterns of species subjected to climatic change. Studies of 127 endemic species from middle latitudes of the western Atlantic show that most speciation events in temperature and subtropical taxa are, in the zoogeographic sense, sympatric or parapatric-clinal and are induced by oceanographic changes related to climatic events rather than geographic isolation of populations. Most ostracode species in middle latitudes are adapted to frequent, cyclical climatic changes typical of these regions and originated during rare periods of major climatic transition. High-latitude arctic-subarctic genera such as Finmarchinella have circumpolar distributions. A parapatric-clinal model accounts for speciation patterns observed in some high-latitude and tropical taxa. However the dynamic nature of thermal gradients and species' biogeography during climatic change renders questionable the controversial distinction between parapatric and allopatric-peripatric speciation models.

Arsenic Speciation and Cadmium Determination in Tobacco Leaves, Ash and Smoke.

Science.gov (United States)

Iwai, Takahiro; Chiba, Koichi; Narukawa, Tomohiro

2016-01-01

The concentrations of arsenic (As) and cadmium (Cd) in the tobacco leaves, ash and smoke of 10 kinds of cigarettes collected from different countries worldwide were determined by ICP-MS after microwave-assisted digestion. Total As and Cd concentrations in the tobacco leaves ranged from 0.20 to 0.63 and 1.8 to 9.9 mg kg(-1), respectively. By the speciation analysis of As in tobacco leaves and ash by HPLC-ICP-MS following acid extraction, arsenite [As(III)] and arsenate [As(V)] were determined and trace amounts of monomethylarsonic acid (MMAA), dimethylarsinic acid (DMAA), trimethylarsine oxide (TMAO), tetramethylarsonium (TeMA) and some unidentified As species were also found. Arsenic speciation for smoke absorbed in an aqueous solution was carried out. The sum of the As species in tobacco leaves, ash and smoke was in good agreement with the result of total As determination in each sample, and the recoveries of speciation were 100 ± 10%. The distributions and the behaviors of As species were clarified.

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

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.

Speciation in the Derrida-Higgs model with finite genomes and spatial populations

Science.gov (United States)

de Aguiar, Marcus A. M.

2017-02-01

The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it for finite genomes, focusing on the question of how many genes it actually takes to trigger neutral sympatric speciation. We find that, for typical parameters used in the original model, it takes the order of 105 genes. We compare the results with a similar spatially explicit model where about 100 genes suffice for speciation. We show that when the number of genes is small the species that emerge are strongly segregated in space. For a larger number of genes, on the other hand, the spatial structure of the population is less important and the species distribution overlap considerably.

Trace metal characterization and speciation in geothermal effluent by multiple scanning anodic stripping voltammetry and atomic absorption analysis

Energy Technology Data Exchange (ETDEWEB)

Kowalski, B.R.

1979-05-25

Recent studies have shown geothermal power plants to have a significant environmental impact on the ground water of the area. The heavy metals arsenic and mercury are special problems, as both are concentrated by flora and fauna exposed to the effluent waters. Because the toxicity of these and other metallic pollutants present in geothermal effluent depends on the chemical form, or speciation, of the particular metal, any serious study of the environmental impact of a geothermal development should include studies of trace metal speciation, in addition to trace metal concentration. This proposal details a method for determining metal speciation in dilute waters. The method is based on ion-exchange and backed by atomic absorption spectrometry and multiple scanning anodic stripping voltammetry. Special laboratory studies will be performed on mercury, arsenic and selenium speciation in synthetic geothermal water. The method will be applied to three known geothermal areas in Washington and Oregon, with emphasis on the speciation of mercury, arsenic and selenium in these waters. The computer controlled electrochemical instrumentation was built and tested. Using this instrumentation, a new experimental procedure was developed to determine the chemical form (speciation) of metal ions in very dilute solutions (ng/ml). This method was tested on model systems including Pb, Cd, and As with C1/sup -/, CO/sub 3//sup 2 -/ and glycine ligands. Finally, the speciation of lead in a geothermal water was examined and the PbC1/sup +/ complex was observed and quantified.

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

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.

Analysis of RET promoter CpG island methylation using methylation-specific PCR (MSP), pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM): impact on stage II colon cancer patient outcome.

Science.gov (United States)

Draht, Muriel X G; Smits, Kim M; Jooste, Valérie; Tournier, Benjamin; Vervoort, Martijn; Ramaekers, Chantal; Chapusot, Caroline; Weijenberg, Matty P; van Engeland, Manon; Melotte, Veerle

2016-01-01

Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylation markers have been introduced into clinical practice. One reason why the vast majority of methylation markers do not translate into clinical applications is lack of independent validation of methylation markers, often caused by differences in methylation analysis techniques. We recently described RET promoter CpG island methylation as a potential prognostic marker in stage II colorectal cancer (CRC) patients of two independent series. In the current study, we analyzed the RET promoter CpG island methylation of 241 stage II colon cancer patients by direct methylation-specific PCR (MSP), nested-MSP, pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM). All primers were designed as close as possible to the same genomic region. In order to investigate the effect of different DNA methylation assays on patient outcome, we assessed the clinical sensitivity and specificity as well as the association of RET methylation with overall survival for three and five years of follow-up. Using direct-MSP and nested-MSP, 12.0 % (25/209) and 29.6 % (71/240) of the patients showed RET promoter CpG island methylation. Methylation frequencies detected by pyrosequencing were related to the threshold for positivity that defined RET methylation. Methylation frequencies obtained by pyrosequencing (threshold for positivity at 20 %) and MS-HRM were 13.3 % (32/240) and 13.8 % (33/239), respectively. The pyrosequencing threshold for positivity of 20 % showed the best correlation with MS-HRM and direct-MSP results. Nested-MSP detected RET promoter CpG island methylation in deceased patients with a higher sensitivity (33.1 %) compared to direct-MSP (10.7 %), pyrosequencing (14.4 %), and MS-HRM (15.4 %). While RET methylation frequencies detected by nested

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.

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 ...

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

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 ...

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

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.

Differential Survival between Visual Environments Supports a Role of Divergent Sensory Drive in Cichlid Fish Speciation.

Science.gov (United States)

Maan, Martine E; Seehausen, Ole; Groothuis, Ton G G

2017-01-01

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 reciprocal transplant experiment revealing species differences in performance in alternative visual environments, consistent with speciation by divergent sensory drive. The closely related cichlids Pundamilia pundamilia and Pundamilia nyererei inhabit different visual environments in Lake Victoria and show associated differences in visual system properties. Mimicking the two light environments in the laboratory, we find a substantial reduction in survival of both species when reared in the other species' visual environment. This implies that the observed differences in Pundamilia color vision are indeed adaptive and substantiates the implicit assumption in sensory drive speciation models that divergent environmental selection is strong enough to drive divergence in sensory properties.

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.

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.

Laser-induced photoacoustic spectroscopy for the speciation of transuranic elements in natural aquatic systems

International Nuclear Information System (INIS)

Kim, J.I.; Stumpe, R.; Klenze, R.

1990-08-01

Laser-induced Photoacoustic Spectroscopy (LPAS) is a new elegant instrumentation for the chemical speciation of acoustic transuranium (TRU) ions in very dilute concentrations (> 10 -8 mol L -1 ). The paper describes the principle of LPAS and its application to the study of the chemical behaviour of TRU ions in natural aquatic systems, the knowledge of which has become increasingly in demand in connection with the safety analysis of nuclear waste disposal in the geosphere. The first part of the paper describes the principle, instrumentation and characteristics of LPAS in aqueous solution, taking particular examples from our own experience. The theoretical estimation of the speciation sensitivity is demonstrated and the result is compared with experiment. The second part deals with the spectral work in aqueous solution and then with the aplication of LPAS for the speciation of TRU ions in groundwater. Some examples demonstrated are hydrolysis reaction, complexation and colloid generation of the Am 3+ ion. Speciation sensitivities of U, Np, Pu and Am of different oxidation states in a variety of aqueous solutions are summarized. The application is of course open to a broad field of microchemistry in which the conventional spectrophotometric method has difficulty with sensitivity. (orig.)

Laser-induced photoacoustic spectroscopy for the speciation of transuranic elements in natural aquatic systems

International Nuclear Information System (INIS)

Kim, J.I.; Stumpe, R.; Klenze, R.

1991-01-01

Laser-induced photoacoustic spectroscopy (LPAS) is a new elegant instrumentation for the chemical speciation of aquatic transuranium (TRU) ions in very dilute concentrations (>10 -8 mol L -1 ). The paper describes the principle of LPAS and its application to the study of the chemical behaviour of TRU ions in natural aquatic systems, the knowledge of which has become increasingly in demand in connection with the safety analysis of nuclear waste disposal in the geosphere. The first part of the paper describes the principle, instrumentation and characteristics of LPAS in aqueous solution, taking particular examples from our own experience. The theoretical estimation of the speciation sensitivity is demonstrated and the result is compared with experiment. The second part deals with the spectral work in aqueous solution and then with the application of LPAS for the speciation of TRU ions in groundwater. Some examples demonstrated are hydrolysis reaction, complexation and colloid generation of the Am 3+ ion. Speciation sensitivities of U, Np, Pu and Am of different oxidation states in a variety of aqueous solutions are summarized. The application is of course open to a broad field of microchemistry in which the conventional spectrophotometric method has difficulty with sensitivity

LJUNGSKILE 1.0 A Computer Program for Investigation of Uncertainties in Chemical Speciation

International Nuclear Information System (INIS)

Ekberg, Christian; Oedegaard-Jensen, Arvid

2002-11-01

In analysing the long-term safety of nuclear waste disposal, there is a need to investigate uncertainties in chemical speciation calculations. Chemical speciation is of importance in evaluating the solubility of radionuclides, the chemical degradation of engineering materials, and chemical processes controlling groundwater composition. The uncertainties in chemical speciation may for instance be related to uncertainties in thermodynamic data, the groundwater composition, or the extrapolation to the actual temperature and ionic strength. The magnitude of such uncertainties and its implications are seldom explicitly evaluated in any detail. Commonly available chemical speciation programmes normally do not have a build-in option to include uncertainty ranges. The program developed within this project has the capability of incorporating uncertainty ranges in speciation calculations and can be used for graphical presentation of uncertainty ranges for dominant species. The program should be regarded as a starting point for assessing uncertainties in chemical speciation, since it is not yet comprehensive in its capabilities. There may be limitations in its usefulness to address various geochemical problems. The LJUNGSKILE code allows the user to select two approaches: the Monte Carlo (MC) approach and the Latin Hypercube Sampling (LHS). LHS allows to produce a satisfactory statistics with a minimum of CPU time. It is, in general, possible to do a simple theoretical speciation calculation within seconds. There are, admittedly, alternatives to LHS and there is criticism towards the uncritical use of LHS output because commonly correlation between some of the input variables exists. LHS, like MC, is not capable to take these correlations into account. Such a correlation can, i.e. exist between the pH of a solution and the partial pressure of CO 2 : higher pH solutions may absorb larger amounts of CO 2 and can reduce the CO 2 partial pressure. It is therefore of advantage to

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.

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...

Speciation on a local geographic scale: the evolution of a rare rock outcrop specialist in Mimulus.

Science.gov (United States)

Ferris, Kathleen G; Sexton, Jason P; Willis, John H

2014-08-05

Speciation can occur on both large and small geographical scales. In plants, local speciation, where small populations split off from a large-ranged progenitor species, is thought to be the dominant mode, yet there are still few examples to verify speciation has occurred in this manner. A recently described morphological species in the yellow monkey flowers, Mimulus filicifolius, is an excellent candidate for local speciation because of its highly restricted geographical range. Mimulus filicifolius was formerly identified as a population of M. laciniatus due to similar lobed leaf morphology and rocky outcrop habitat. To investigate whether M. filicifolius is genetically divergent and reproductively isolated from M. laciniatus, we examined patterns of genetic diversity in ten nuclear and eight microsatellite loci, and hybrid fertility in M. filicifolius and its purported close relatives: M. laciniatus, M. guttatus and M. nasutus. We found that M. filicifolius is genetically divergent from the other species and strongly reproductively isolated from M. laciniatus. We conclude that M. filicifolius is an independent rock outcrop specialist despite being morphologically and ecologically similar to M. laciniatus, and that its small geographical range nested within other wide-ranging members of the M. guttatus species complex is consistent with local speciation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

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

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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.

Contribution of analytical techniques coupled to the knowledge of the uranium speciation in natural conditions

International Nuclear Information System (INIS)

Petit, J.

2009-06-01

To understand the transport mechanisms and the radionuclides behaviour in the bio-geosphere is necessary to evaluate healthy and environmental risks of nuclear industry. These mechanisms are monitored by radioelements speciation, namely the distribution between their different physico-chemical forms in the environment. From this perspective, this PhD thesis deals with uranium speciation in a natural background. A detailed summary of uranium biogeochemistry has been written, which enables to restrict the PhD issue to uranium complexation with oxalic acid, a hydrophilic organic acid with good binding properties, ubiquitous in soil waters. Analytical conditions have been established by means of speciation diagrams. The speciation diagrams building by means of literature stability constants has allowed to define the analytical conditions of complex formation. The chosen analytical technique is the hyphenation of a separative technique (liquid chromatography LC or capillary electrophoresis CE) with mass spectrometry (ICPMS). The studied complexes presence in the synthetic samples has been confirmed with UV/visible spectrophotometry. LC-ICPMS analyses have proved the lability of the uranyl-organic acid complexes, namely their tendency to dissociate during analysis, which prevents from studying uranium speciation. CE-ICPMS study of labile complexes from a metal-ligand system has been made possible by employing affinity capillary electrophoresis, which enables to determine stability constants and electrophoretic mobilities. This PhD thesis has allowed to compare the different mathematical treatments of binding isotherm and to take into account ionic strength and real ligand concentration. Affinity CE has been applied successfully to lanthanum-oxalate (model system) and uranium-oxalate systems. The obtained results have been applied to a real system (situated in Le Bouchet). This shows the contribution of the developed method to the modelling of uranium speciation. (author)

Pyrosequencing-Based Assays for Rapid Detection of HER2 and HER3 Mutations in Clinical Samples Uncover an E332E Mutation Affecting HER3 in Retroperitoneal Leiomyosarcoma

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Paula González-Alonso

2015-08-01

Full Text Available Mutations in Human Epidermal Growth Factor Receptors (HER are associated with poor prognosis of several types of solid tumors. Although HER-mutation detection methods are currently available, such as Next-Generation Sequencing (NGS, alternative pyrosequencing allow the rapid characterization of specific mutations. We developed specific PCR-based pyrosequencing assays for identification of most prevalent HER2 and HER3 mutations, including S310F/Y, R678Q, L755M/P/S/W, V777A/L/M, 774-776 insertion, and V842I mutations in HER2, as well as M91I, V104M/L, D297N/V/Y, and E332E/K mutations in HER3. We tested 85 Formalin Fixed and Paraffin Embbeded (FFPE samples and we detected three HER2-V842I mutations in colorectal carcinoma (CRC, ovarian carcinoma, and pancreatic carcinoma patients, respectively, and a HER2-L755M mutation in a CRC specimen. We also determined the presence of a HER3-E332K mutation in an urothelial carcinoma sample, and two HER3-D297Y mutations, in both gastric adenocarcinoma and CRC specimens. The D297Y mutation was previously detected in breast and gastric tumors, but not in CRC. Moreover, we found a not-previously-described HER3-E332E synonymous mutation in a retroperitoneal leiomyosarcoma patient. The pyrosequencing assays presented here allow the detection and characterization of specific HER2 and HER3 mutations. These pyrosequencing assays might be implemented in routine diagnosis for molecular characterization of HER2/HER3 receptors as an alternative to complex NGS approaches.

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

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

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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.

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

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 ...

Biodegradation and speciation of residual SS-ethylenediaminedisuccinic acid (EDDS) in soil solution left after soil washing.

Science.gov (United States)

Tandy, Susan; Ammann, Adrian; Schulin, Rainer; Nowack, Bernd

2006-07-01

This paper aims to investigate the degradation and speciation of EDDS-complexes (SS-ethylenediaminedisuccinic acid) in soil following soil washing. The changes in soil solution metal and EDDS concentrations were investigated for three polluted soils. EDDS was degraded after a lag phase of 7-11 days with a half-life of 4.18-5.60 days. No influence of EDDS-speciation on the reaction was observed. The decrease in EDDS resulted in a corresponding decrease in solubilized metals. Changes in EDDS speciation can be related to (1) initial composition of the soil, (2) temporarily anoxic conditions in the soil slurry after soil washing, (3) exchange of EDDS complexes with Cu even in soils without elevated Cu and (4) formation of NiEDDS. Dissolved organic matter is important for metal speciation at low EDDS concentrations. Our results show that even in polluted soils EDDS is degraded from a level of several hundred micromoles to below 1 microM within 50 days.

Trace-element speciation and partitioning in environmental geochemistry and health

Energy Technology Data Exchange (ETDEWEB)

Farmer, J.G.; Gibson, M.J.; Lovell, M.A.

1983-09-01

Establishment of the chemical form and associations of trace elements is important in the scientifc and medical fields related to environmental geochemistry and health. Fundamental understanding of trace-element behavior, the realistic formulation of historical perspectives of trace-element contamination, an assessment of environmental transformation processes and a thorough appraisal of environment-related ill health and disease all depend on knowledge of the chemical speciation and partitioning of trace elements. These topics and the development of analytical speciation techniques and procedures are discussed with reference to trace-element studies in the Department of Forensic Medicine and Science, University of Glasgow, on lacustrine sediments and water, the atmosphere, soil and street dirt of an urban environment, and human biological fluids. 206 references, 4 figures.

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.

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

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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

Speciation of uranium in minerals by Sem, Tem, μ-PIXE, XPS and XAFS

International Nuclear Information System (INIS)

Toshihiko Ohnuki; Hiroshi Isobe; Tomihiro Kamiya; Takuro Sakai; Takashi Murakami

2001-01-01

Many kinds of electromagnetic waves and particle beams are used as analytical probes for the investigation of uranium-mineralogy and speciation. The representatives of the probes are SEM, TEM, μ-PIRE, XPS and XAFS. Each of these analytical probes has its own advantages and disadvantages. We have performed studies to compare the advantages and disadvantages on the basis of the analysis of the distribution and speciation of U containing rock samples collected at the Koongarra uranium deposit, Australia. The spatial resolutions of the probes are in the order of TEM>SEM, μ-PIXE>XFAS, XPS. The lower detection limits of the probes are in the order of μ-PIXE< TEM, SEM< XFAS, XPS. Oxidation state of U was determined by XFAS and XPS. These results indicate that combination of the above probes can give us sufficient data on U speciation not only in natural rock samples but in solid samples obtained in the laboratory. (authors)

Lead Speciation and In Vitro Bioaccessibility of Compost-Amended Urban Garden Soils

Energy Technology Data Exchange (ETDEWEB)

Attanayake, Chammi P.; Hettiarachchi, Ganga M.; Ma, Qing; Pierzynski, Gary M.; Ransom, Michel D. (NWU); (KSU)

2017-01-01

In situ soil amendments can modify the Pb bioavailability by changing soil Pb speciation. Urban soils from three vegetable gardens containing different total Pb concentrations were used. The study evaluated how compost amendment and aging of soil-compost mixture in situ affected the following: (i) soil Pb speciation in the field and (ii) change of soil Pb speciation during an in vitro bioaccessibility extraction mimicking gastric phase dissolution at pH 2.5. X-ray absorption fine structure spectroscopy was used to determine Pb speciation in amended and nonamended soils and residues left after in vitro bioaccessibility extraction of those soils. Compost amendment and aging of compost in the field had a negligible effect on Pb bioaccessibility in the soils. Major Pb species in the soils were Pb sorbed to Fe oxy(hydr)oxide (Pb-Fh) and to soil organic C (Pb-Org). The fraction of Pb-Org was increased as soil-compost mixture aged in the field. During the in vitro extraction, the fraction of Pb-Fh was decreased, the fraction of Pb-Org was increased, and hydroxypyromorphite was formed in both amended and nonamended soils. Freshly incorporated compost enhanced the dissolution of Pb-Fh during the extraction. As soil-compost mixture aged in the field, the dissolution of Pb-Fh was low, demonstrating more stability of the Pb-Fh during the extraction. Compost amendment showed potential to contribute to reduced bioaccessibility of Pb as compost aged in the soil by increasing Pb-Org fraction in the field and stability of Pb-Fh during the in vitro bioaccessibility extraction.

Mathematical modeling of the effects of aerobic and anaerobic chelate biodegradation on actinide speciation

International Nuclear Information System (INIS)

Banaszak, J.E.; VanBriesen, J.; Rittmann, B.E.; Reed, D.T.

1998-01-01

Biodegradation of natural and anthropogenic chelating agents directly and indirectly affects the speciation, and, hence, the mobility of actinides in subsurface environments. We combined mathematical modeling with laboratory experimentation to investigate the effects of aerobic and anaerobic chelate biodegradation on actinide [Np(IV/V), Pu(IV)] speciation. Under aerobic conditions, nitrilotriacetic acid (NTA) biodegradation rates were strongly influenced by the actinide concentration. Actinide-chelate complexation reduced the relative abundance of available growth substrate in solution and actinide species present or released during chelate degradation were toxic to the organisms. Aerobic bio-utilization of the chelates as electron-donor substrates directly affected actinide speciation by releasing the radionuclides from complexed form into solution, where their fate was controlled by inorganic ligands in the system. Actinide speciation was also indirectly affected by pH changes caused by organic biodegradation. The two concurrent processes of organic biodegradation and actinide aqueous chemistry were accurately linked and described using CCBATCH, a computer model developed at Northwestern University to investigate the dynamics of coupled biological and chemical reactions in mixed waste subsurface environments. CCBATCH was then used to simulate the fate of Np during anaerobic citrate biodegradation. The modeling studies suggested that, under some conditions, chelate degradation can increase Np(IV) solubility due to carbonate complexation in closed aqueous systems

Chromosomal Speciation Revisited: Modes of Diversification in Australian Morabine Grasshoppers (Vandiemenella, viatica Species Group

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Steven J. B. Cooper

2011-03-01

Full Text Available Chromosomal rearrangements can alter the rate and patterns of gene flow within or between species through a reduction in the fitness of chromosomal hybrids or by reducing recombination rates in rearranged areas of the genome. This concept, together with the observation that many species have structural variation in chromosomes, has led to the theory that the rearrangements may play a direct role in promoting speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group are an excellent model for studying the role of chromosomal rearrangement in speciation because they show extensive chromosomal variation, parapatric distribution patterns, and narrow hybrid zones at their boundaries. This species group stimulated development of one of the classic chromosomal speciation models, the stasipatric speciation model proposed by White in 1968. Our population genetic and phylogeographic analyses revealed extensive non-monophyly of chromosomal races along with historical and on-going gene introgression between them. These findings suggest that geographical isolation leading to the fixation of chromosomal variants in different geographic regions, followed by secondary contact, resulted in the present day parapatric distributions of chromosomal races. The significance of chromosomal rearrangements in the diversification of the viatica species group can be explored by comparing patterns of genetic differentiation between rearranged and co-linear parts of the genome.

Mathematical modelling of the effects of aerobic and anaerobic chelate biodegradation on actinide speciation

International Nuclear Information System (INIS)

Banaszak, J.E.; VanBriesen, J.M.; Rittmann, B.E.; Reed, D.T.

1998-01-01

Biodegradation of natural and anthropogenic chelating agents directly and indirectly affects the speciation, and hence, the mobility of actinides in subsurface environments. We combined mathematical modelling with laboratory experimentation to investigate the effects of aerobic and anaerobic chelate biodegradation on actinide [Np(IV/V), Pu(IV)] speciation. Under aerobic conditions, nitrilotriacetic acid (NTA) biodegradation rates were strongly influenced by the actinide concentration. Actinide-chelate complexation reduced the relative abundance of available growth substrate in solution and actinide species present or released during chelate degradation were toxic to the organisms. Aerobic bioutilization of the chelates as electron-donor substrates directly affected actinide speciation by releasing the radionuclides from complexed form into solution, where their fate was controlled by inorganic ligands in the system. Actinide speciation was also indirectly affected by pH changes caused by organic biodegradation. The two concurrent processes of organic biodegradation and actinide aqueous chemistry were accurately linked and described using CCBATCH, a computer model developed at Northwestern University to investigate the dynamics of coupled biological and chemical reactions in mixed waste subsurface environments. CCBATCH was then used to simulate the fate of Np during anaerobic citrate biodegradation. The modelling studies suggested that, under some conditions, chelate degradation can increase Np(IV) solubility due to carbonate complexation in closed aqueous systems. (orig.)

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.

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

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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.

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.

Analytical developments in ICP-MS for arsenic and selenium speciation. Application to granitic waters

International Nuclear Information System (INIS)

Garraud, Herve

1999-01-01

Nuclear waste storage in geological areas needs the understanding of the physico-chemistry of groundwaters interactions with surrounding rocks. Redox potential measurements and speciation, calculated from geochemical modelling are not significant for the determination of water reactivity. We have thus chosen to carry out experimental speciation by developing sensitive analytical tools with respect of specie chemical identity. We have studied two redox indicators from reference sites (thermal waters from Pyrenees, France): arsenic and selenium. At first, we have determined the concentrations in major ions (sulphide, sulphate, chloride, fluoride, carbonate, Na, K, Ca). Speciation was conducted by HPLC hyphenated to quadrupole ICP-MS and high resolution ICP-MS. These analyses have shown the presence of two new arsenic species in solution, in addition of a great reactivity of these waters during stability studies. A sampling, storage and analysis method is described. (author) [fr

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

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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.

Fourth natural analogue working group meeting and Pocos de Caldas project final workshop

International Nuclear Information System (INIS)

Come, B.; Chapman, N.A.

1991-01-01

The fourth meeting of the CEC-sponsored natural analogue working group (NAWG) was held in Pitlochry, Scotland, from 18 to 22 June 1990, and also included the final workshop of the Pocos de Caldas (Brazil) natural analogue project, sponsored by Nagra (CH), SKB (S) UK-DOE and US-DOE. About 80 specialists attended this meeting, originating from EC Member States and also Australia, Brazil, Canada, Finland, Japan, Sweden, Switzerland and the USA. The IAEA and OCDE-NEA were also represented. This plenary meeting was the opportunity to review and discuss five years of progress and activities of natural analogues in central areas of performance assessment: waste forms and engineered barriers, geochemistry and radionuclide speciation, radionuclide migration and the overall geological context of radwaste disposal. In addition, a feedback session provided the opportunity for regulators and those individuals who had advisory roles to give their views and impressions on the significance of natural analogue research. These proceedings, divided into two sessions, contain 32 technical papers and 14 abstracts of published papers

Speciation evolution of zinc and copper during pyrolysis and hydrothermal carbonization treatments of sewage sludges.

Science.gov (United States)

Huang, Rixiang; Zhang, Bei; Saad, Emily M; Ingall, Ellery D; Tang, Yuanzhi

2018-04-01

Thermal and hydrothermal treatments are promising techniques for sewage sludge management that can potentially facilitate safe waste disposal, energy recovery, and nutrient recovery/recycling. Content and speciation of heavy metals in the treatment products affect the potential environmental risks upon sludge disposal and/or application of the treatment products. Therefore, it is important to study the speciation transformation of heavy metals and the effects of treatment conditions. By combining synchrotron X-ray spectroscopy/microscopy analysis and sequential chemical extraction, this study systematically characterized the speciation of Zn and Cu in municipal sewage sludges and their chars derived from pyrolysis (a representative thermal treatment technique) and hydrothermal carbonization (HTC; a representative hydrothermal treatment technique). Spectroscopy analysis revealed enhanced sulfidation of Zn and Cu by anaerobic digestion and HTC treatments, as compared to desulfidation by pyrolysis. Overall, changes in the chemical speciation and matrix properties led to reduced mobility of Zn and Cu in the treatment products. These results provide insights into the reaction mechanisms during pyrolysis and HTC treatments of sludges and can help evaluate the environmental/health risks associated with the metals in the treatment products. Copyright © 2018 Elsevier Ltd. All rights reserved.

Speciation evolution of zinc and copper during pyrolysis and hydrothermal carbonization treatments of sewage sludges

Energy Technology Data Exchange (ETDEWEB)

Huang, Rixiang; Zhang, Bei; Saad, Emily M.; Ingall, Ellery D.; Tang, Yuanzhi

2018-04-01

Thermal and hydrothermal treatments are promising techniques for sewage sludge management that can potentially facilitate safe waste disposal, energy recovery, and nutrient recovery/recycling. Content and speciation of heavy metals in the treatment products affect the potential environmental risks upon sludge disposal and/or application of the treatment products. Therefore, it is important to study the speciation transformation of heavy metals and the effects of treatment conditions. By combining synchrotron X-ray spectroscopy/microscopy analysis and sequential chemical extraction, this study systematically characterized the speciation of Zn and Cu in municipal sewage sludges and their chars derived from pyrolysis (a representative thermal treatment technique) and hydrothermal carbonization (HTC; a representative hydrothermal treatment technique). Spectroscopy analysis revealed enhanced sulfidation of Zn and Cu by anaerobic digestion and HTC treatments, as compared to desulfidation by pyrolysis. Overall, changes in the chemical speciation and matrix properties led to reduced mobility of Zn and Cu in the treatment products. These results provide insights into the reaction mechanisms during pyrolysis and HTC treatments of sludges and can help evaluate the environmental/health risks associated with the metals in the treatment products.

Equilibrium Speciation of Select Lanthanides in the Presence of Acidic Ligands in Homo- and Heterogeneous Solutions

Energy Technology Data Exchange (ETDEWEB)

Robinson, Troy A [Univ. of Nevada, Las Vegas, NV (United States)

2011-08-01

This dissertation explores lanthanide speciation in liquid solution systems related to separation schemes involving the acidic ligands: bis(2-ethylhexyl) phosphoric acid (HDEHP), lactate, and 8-hydroxyquinoline. Equilibrium speciation of neodymium (Nd³⁺), sodium (Na+), HDEHP, water, and lactate in the TALSPEAK liquid-liquid extraction system was explored under varied Nd³⁺ loading of HDEHP in the organic phase and through extraction from aqueous HCl and lactate media. System speciation was probed through vapor pressure osmometry, visible and Fourier Transform Infrared (FTIR) spectroscopy, ²²Na and ¹³C labeled lactate radiotracer distribution measurements, Karl Fischer titrations, and equilibrium pH measurements. Distribution of Nd³⁺, Na⁺, lactate, and equilibrium pH were modeled using the SXLSQI software to obtain logKNd and logKNa extraction constants under selected conditions. Results showed that high Nd³⁺ loading of the HDEHP led to Nd³⁺ speciation that departs from the ion exchange mechanism and includes formation of highly aggregated, polynuclear [NdLactate(DEHP)₂]_x; (with x > 1). By substituting lanthanum (La³⁺) for Nd³⁺ in this system, NMR scoping experiments using ²³Na, ³¹P nuclei and ¹³C labeled lactate were performed. Results indicated that this technique is sensitive to changes in system speciation, and that further experiments are warranted. In a homogeneous system representing the TALSPEAK aqueous phase, Lactate protonation behavior at various temperatures was characterized using a combination of potentiometric titration and modeling with the Hyperquad computer program. The temperature dependent deprotonation behavior of lactate showed little change with temperature at 2.0 M NaCl ionic strength. Cloud point extraction is a non-traditional separation technique that starts with a homogeneous

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.

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.

Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae).

Science.gov (United States)

Takayama, Koji; Sun, Byung-Yun; Stuessy, Tod F

2013-05-01

Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis.

Arsenic, Antimony, Chromium, and Thallium Speciation in Water and Sediment Samples with the LC-ICP-MS Technique

Directory of Open Access Journals (Sweden)

Magdalena Jabłońska-Czapla

2015-01-01

Full Text Available Chemical speciation is a very important subject in the environmental protection, toxicology, and chemical analytics due to the fact that toxicity, availability, and reactivity of trace elements depend on the chemical forms in which these elements occur. Research on low analyte levels, particularly in complex matrix samples, requires more and more advanced and sophisticated analytical methods and techniques. The latest trends in this field concern the so-called hyphenated techniques. Arsenic, antimony, chromium, and (underestimated thallium attract the closest attention of toxicologists and analysts. The properties of those elements depend on the oxidation state in which they occur. The aim of the following paper is to answer the question why the speciation analytics is so important. The paper also provides numerous examples of the hyphenated technique usage (e.g., the LC-ICP-MS application in the speciation analysis of chromium, antimony, arsenic, or thallium in water and bottom sediment samples. An important issue addressed is the preparation of environmental samples for speciation analysis.

Phosphorus Speciation of Forest-soil Organic Surface Layers using P K-edge XANES Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

J Prietzel; J Thieme; D Paterson

2011-12-31

The phosphorus (P) speciation of organic surface layers from two adjacent German forest soils with different degree of water-logging (Stagnosol, Rheic Histosol) was analyzed by P K-edge XANES and subsequent Linear Combination Fitting. In both soils, {approx}70% of the P was inorganic phosphate and {approx}30% organic phosphate; reduced P forms such as phosphonate were absent. The increased degree of water-logging in the Histosol compared to the Stagnosol did not affect P speciation.

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...

Characteristics of PM2.5 speciation in representative megacities and across China

Science.gov (United States)

Yang, F.; Tan, J.; Zhao, Q.; Du, Z.; He, K.; Ma, Y.; Duan, F.; Chen, G.; Zhao, Q.

2011-06-01

Based on PM2.5 chemical data sets from literature and from our surface observations, chemical species and reconstructed speciation of PM2.5 in representative Chinese megacities and across China were compared to draw insights into the characteristics of PM2.5 speciation. PM2.5 mass concentrations and speciation compositions varied substantially over geographical regions in China. Near six-fold variations in average PM2.5 concentrations (34.0-193.4 μg m-3) across China were found with high PM2.5 levels (>100 μg m-3) appearing in the cities in the northern and western regions and low levels (transport of the secondary aerosols, thus more intensive characteristic of "complex atmospheric pollution" compared to the western region. Organic matter had significant contribution to PM2.5 over all the sites. Organic matter plus sulfate, nitrate, and ammonia accounted for 53-90 % of PM2.5 mass across China. PM2.5 speciation across China was also characterized by high content of crustal material, which was usually at more than ~10 μg m-3 level or shared ~10 % of PM2.5 mass in urban areas, due to transported desert dust and locally induced dust. In four representative megacities (i.e. Beijing, Chongqing, Shanghai, and Guangzhou), PM2.5 mass and major components (except sulfate) were at higher levels than those in US continental east by one order of magnitude. Distinct differences in nitrate and sulfate levels and their mass ratio [NO3-]/[SO42-] imply that mobile sources are likely more important in Guangzhou, whereas in Chongqing it is stationary (coal combustion) sources. The observed intra-city variations in PM2.5 mass and speciation indicate that both local emissions and regional transportation contributed significantly to high fine particle loadings in Beijing, while local contribution likely played a predominant role in Chongqing. During the ten-year period from 1999 through 2008 in urban Beijing, both the sum of sulfate, nitrate, and ammonia and [NO3-]/[SO42-] ratio

The genetic signature of recent speciation in manta rays (Manta alfredi and M. birostris).

Science.gov (United States)

Kashiwagi, Tom; Marshall, Andrea D; Bennett, Michael B; Ovenden, Jennifer R

2012-07-01

Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays. Copyright © 2012 Elsevier Inc. All rights reserved.

Measurement of elemental speciation by liquid chromatography -- inductively coupled plasma mass spectrometry (LC-ICP-MS) with the direct injection nebulizer (DIN)

Energy Technology Data Exchange (ETDEWEB)

Shum, Sam [Iowa State Univ., Ames, IA (United States)

1993-05-01

This thesis is divided into 4 parts: elemental speciation, speciation of mercury and lead compounds by microbore column LC-ICP-MS with direct injection nebulization, spatially resolved measurements of size and velocity distributions of aerosol droplets from a direct injection nebulizer, and elemental speciation by anion exchange and size exclusion chromatography with detection by ICP-MS with direct injection nebulization.

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].

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

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.

Male-male competition and speciation : aggression bias towards differently coloured rivals varies between stages of speciation in a Lake Victoria cichlid species complex

NARCIS (Netherlands)

Dijkstra, P. D.; Seehausen, O.; Pierotti, M. E. R.; Groothuis, T. G. G.

Sympatric speciation driven by sexual selection by female mate choice on a male trait is a much debated topic. The process is problematic because of the lack of negative frequency-dependent selection that can facilitate the invasion of a novel colour phenotype and stabilize trait polymorphism. It

Factors Controlling Redox Speciation of Plutonium and Neptunium in Extraction Separation Processes

Energy Technology Data Exchange (ETDEWEB)

Paulenova, Alena [Principal Investigator; Vandegrift, III, George F. [Collaborator

2013-09-24

The objective of the project was to examine the factors controlling redox speciation of plutonium and neptunium in UREX+ extraction in terms of redox potentials, redox mechanism, kinetics and thermodynamics. Researchers employed redox-speciation extractions schemes in parallel to the spectroscopic experiments. The resulting distribution of redox species w studied uring spectroscopic, electrochemical, and spectro-electrochemical methods. This work reulted in collection of data on redox stability and distribution of redox couples in the nitric acid/nitrate electrolyte and the development of redox buffers to stabilize the desired oxidation state of separated radionuclides. The effects of temperature and concentrations on the redox behavior of neptunium were evaluated.

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

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...

Solving mercury (Hg) speciation in soil samples by synchrotron X-ray microspectroscopic techniques

International Nuclear Information System (INIS)

Terzano, Roberto; Santoro, Anna; Spagnuolo, Matteo; Vekemans, Bart; Medici, Luca; Janssens, Koen; Goettlicher, Joerg; Denecke, Melissa A.; Mangold, Stefan; Ruggiero, Pacifico

2010-01-01

Direct mercury (Hg) speciation was assessed for soil samples with a Hg concentration ranging from 7 up to 240 mg kg -1 . Hg chemical forms were identified and quantified by sequential extractions and bulk- and micro-analytical techniques exploiting synchrotron generated X-rays. In particular, microspectroscopic techniques such as μ-XRF, μ-XRD and μ-XANES were necessary to solve bulk Hg speciation, in both soil fractions 3 S 2 Cl 2 ), and an amorphous phase containing Hg bound to chlorine and sulfur. The amount of metacinnabar and amorphous phases increased in the fraction <2 μm. No interaction among Hg-species and soil components was observed. All the observed Hg-species originated from the slow weathering of an inert Hg-containing waste material (K106, U.S. EPA) dumped in the area several years ago, which is changing into a relatively more dangerous source of pollution. - Direct mercury (Hg) speciation in chlor-alkali plant contaminated soils enabled the identification of potentially dangerous Hg-S/Cl amorphous species.

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, ...

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

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.

Detecting cryptic speciation in the widespread and morphologically conservative carpet chameleon (Furcifer lateralis) of Madagascar.

Science.gov (United States)

Florio, A M; Ingram, C M; Rakotondravony, H A; Louis, E E; Raxworthy, C J

2012-07-01

Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Speciation of the plutonium at trace levels by capillary electrophoresis-ICP-MS coupling

International Nuclear Information System (INIS)

Ambard, Ch.

2007-01-01

The CE-ICP-MS coupling allowed the development of new analytical methods for the study of plutonium speciation at trace levels including complexation studies of this element by organic and inorganic ligands. First, a method, called dual detection, based on the simultaneous use of the UV-Visible spectrophotometer integrated in the capillary electrophoresis and the ICPMS was developed and validated. It allows the unambiguous determination of electrophoretic mobilities for separated chemical species and gives a powerful tool for speciation studies. Then, the influence on plutonium redox speciation of the buffer from the background electrolyte was evaluated. This study showed the implications of the electrolyte constituents' choice on plutonium redox equilibrium in the sample. Furthermore, the CE-ICP-MS coupling was used for studying the plutonium complexation at trace levels by some organic (NTA and DTPA) and inorganic ligands (carbonates). The behaviour of plutonium valence +III, +IV and +VI was studied in the presence of buffer at near neutral pH. Different species of plutonium were observed depending on the initial oxidation state of the plutonium. This study showed the potential of poly-amino-carboxylic acids, such as NTA and DTPA, for dissolving plutonium precipitates, regardless its initial speciation. Finally, the carbonation of pentavalent neptunium, as an analogue of Pu(V), was achieved at very low concentration of Np (10 -8 mol.L -1 ). The formation constant of NpO 2 (CO 3 )- at 25 deg. C and 2,5 x 10 -2 mol.L -1 ionic strength was measured by CE-ICP-MS and found to be consistent with literature data. (author)

Speciation of the plutonium at trace levels by capillary electrophoresis-ICP-MS coupling

International Nuclear Information System (INIS)

Ambard, Ch.

2007-01-01

The CE-ICP-MS coupling allowed the development of new analytical methods for the study of plutonium (Pu) speciation at trace levels including complexation studies of this element by organic and inorganic ligands. First, a method, called dual detection, based on the simultaneous use of the UV-Visible spectrophotometer integrated in the capillary electrophoresis and the ICP-MS was developed and validated. It allows the unambiguous determination of electrophoretic mobilities for separated chemical species and gives a powerful tool for speciation studies. Then, the influence on Pu redox speciation of the buffer from the background electrolyte was evaluated. This study showed the implications of the electrolyte constituents' choice on Pu redox equilibrium in the sample. Furthermore, the CE-ICP-MS coupling was used for studying the Pu complexation at trace levels by some organic (NTA and DTPA) and inorganic ligands (carbonates). The behaviour of Pu valence +III, +IV and +VI was studied in the presence of buffer at near neutral pH. Different species of Pu were observed depending on the initial oxidation state of the plutonium. The study showed the potential of poly-amino-carboxylic acids, such as NTA and DTPA, for dissolving Pu precipitates, regardless its initial speciation. Finally, the carbonation of pentavalent neptunium, as an analogue of Pu(V), was achieved at very low concentration of Np (10 -8 mol.L -1 ). The formation of NpO 2 (CO 3 ) - at 25 C and 2,5*10 -2 mol.L -1 ionic strength was measured by CE-ICP-MS and found to consistent with literature data. (author)

Sampling genetic diversity in the sympatrically and allopatrically speciating Midas cichlid species complex over a 16 year time series

Directory of Open Access Journals (Sweden)

Bunje Paul ME

2007-02-01

Full Text Available Abstract Background Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an important case study for understanding the processes of speciation. Previous analyses have demonstrated that allopatric processes led to species formation among the lakes of Nicaragua as well as sympatric speciation that is occurring within at least one crater lake. However, since speciation is an ongoing process and sampling genetic diversity of such lineages can be biased by collection scheme or random factors, it is important to evaluate the robustness of conclusions drawn on individual time samples. Results In order to assess the validity and reliability of inferences based on different genetic samples, we have analyzed fish from several lakes in Nicaragua sampled at three different times over 16 years. In addition, this time series allows us to analyze the population genetic changes that have occurred between lakes, where allopatric speciation has operated, as well as between different species within lakes, some of which have originated by sympatric speciation. Focusing on commonly used genetic markers, we have analyzed both DNA sequences from the complete mitochondrial control region as well as nuclear DNA variation at ten microsatellite loci from these populations, sampled thrice in a 16 year time period, to develop a robust estimate of the population genetic history of these diversifying lineages. Conclusion The conclusions from previous work are well supported by our comprehensive analysis. In particular, we find that the genetic diversity of derived crater lake populations is lower than that of the source population regardless of when and how each population was sampled. Furthermore, changes in various estimates of

Selenium Speciation and Management in Wet FGD Systems

Energy Technology Data Exchange (ETDEWEB)

Searcy, K; Richardson, M; Blythe, G; Wallschlaeger, D; Chu, P; Dene, C

2012-02-29

This report discusses results from bench- and pilot-scale simulation tests conducted to determine the factors that impact selenium speciation and phase partitioning in wet FGD systems. The selenium chemistry in wet FGD systems is highly complex and not completely understood, thus extrapolation and scale-up of these results may be uncertain. Control of operating parameters and application of scrubber additives have successfully demonstrated the avoidance or decrease of selenite oxidation at the bench and pilot scale. Ongoing efforts to improve sample handling methods for selenium speciation measurements are also discussed. Bench-scale scrubber tests explored the impacts of oxidation air rate, trace metals, scrubber additives, and natural limestone on selenium speciation in synthetic and field-generated full-scale FGD liquors. The presence and concentration of redox-active chemical species as well as the oxidation air rate contribute to the oxidation-reduction potential (ORP) conditions in FGD scrubbers. Selenite oxidation to the undesirable selenate form increases with increasing ORP conditions, and decreases with decreasing ORP conditions. Solid-phase manganese [Mn(IV)] appeared to be the significant metal impacting the oxidation of selenite to selenate. Scrubber additives were tested for their ability to inhibit selenite oxidation. Although dibasic acid and other scrubber additives showed promise in early clear liquor (sodium based and without calcium solids) bench-scale tests, these additives did not show strong inhibition of selenite oxidation in tests with higher manganese concentrations and with slurries from full-scale wet FGD systems. In bench-tests with field liquors, addition of ferric chloride at a 250:1 iron-to-selenium mass ratio sorbed all incoming selenite to the solid phase, although addition of ferric salts had no impact on native selenate that already existed in the field slurry liquor sample. As ORP increases, selenite may oxidize to selenate more

Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and and pyrosequencing for the characterisation of the caries-associated microbiome

Directory of Open Access Journals (Sweden)

Kathrin eSchulze-Schweifing

2014-11-01

Full Text Available Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture.

On the use of time-resolved laser-induced fluorescence (TRLIF) and electrospray mass spectrometry (ES-MS) for speciation studies

International Nuclear Information System (INIS)

Moulin, C.

2003-01-01

Time-resolved laser induced fluorescence (TRLIF) and electrospray mass spectrometry (ES-MS) are used for speciation studies. While the former has been used for long time, the latter is rather new in the field of speciation. These two techniques have different advantages such as sensitivity (especially for TRLIF), selectivity and multielement capabilities (in case of ES-MS). Examples obtained from studies carried out within the CEA are presented. Concerning TRLIF, emphasis is put on uranyl ion speciation in nitric acid to phosphoric acid going through hydroxo complexes. Concerning ES-MS, humic substances identification as well as speciation of cesium, zirconium, thorium and uranyl ions in various complexing media are presented. Comparisons of TRLIF and ES-MS results are made in the case of uranyl hydroxo complexes and favourably compared with OECD data. Trends for these two techniques are also discussed. (orig.)

A review of recent developments in the speciation and location of arsenic and selenium in rice grain

Energy Technology Data Exchange (ETDEWEB)

Carey, Anne-Marie; Price, Adam H.; Meharg, Andrew A. [University of Aberdeen, Institute of Biological and Environmental Sciences, Aberdeen (United Kingdom); Lombi, Enzo; Donner, Erica [University of South Australia, Centre for Environmental Risk Assessment and Remediation, Mawson Lakes, South Australia (Australia); Jonge, Martin D. de [Australian Synchrotron, X-ray Fluorescence Microscopy, Clayton, Victoria (Australia); Punshon, Tracy; Jackson, Brian P.; Guerinot, Mary Lou [Dartmouth College, Department of Biological Sciences, Hanover, NH (United States)

2012-04-15

Rice is a staple food yet is a significant dietary source of inorganic arsenic, a class 1, nonthreshold carcinogen. Establishing the location and speciation of arsenic within the edible rice grain is essential for understanding the risk and for developing effective strategies to reduce grain arsenic concentrations. Conversely, selenium is an essential micronutrient and up to 1 billion people worldwide are selenium-deficient. Several studies have suggested that selenium supplementation can reduce the risk of some cancers, generating substantial interest in biofortifying rice. Knowledge of selenium location and speciation is important, because the anti-cancer effects of selenium depend on its speciation. Germanic acid is an arsenite/silicic acid analogue, and location of germanium may help elucidate the mechanisms of arsenite transport into grain. This review summarises recent discoveries in the location and speciation of arsenic, germanium, and selenium in rice grain using state-of-the-art mass spectrometry and synchrotron techniques, and illustrates both the importance of high-sensitivity and high-resolution techniques and the advantages of combining techniques in an integrated quantitative and spatial approach. (orig.)

A review of recent developments in the speciation and location of arsenic and selenium in rice grain

Science.gov (United States)

Carey, Anne-Marie; Lombi, Enzo; Donner, Erica; de Jonge, Martin D.; Punshon, Tracy; Jackson, Brian P.; Guerinot, Mary Lou; Price, Adam H.; Meharg, Andrew A.

2014-01-01

Rice is a staple food yet is a significant dietary source of inorganic arsenic, a class 1, nonthreshold carcinogen. Establishing the location and speciation of arsenic within the edible rice grain is essential for understanding the risk and for developing effective strategies to reduce grain arsenic concentrations. Conversely, selenium is an essential micronutrient and up to 1 billion people worldwide are selenium-deficient. Several studies have suggested that selenium supplementation can reduce the risk of some cancers, generating substantial interest in biofortifying rice. Knowledge of selenium location and speciation is important, because the anti-cancer effects of selenium depend on its speciation. Germanic acid is an arsenite/silicic acid analogue, and location of germanium may help elucidate the mechanisms of arsenite transport into grain. This review summarises recent discoveries in the location and speciation of arsenic, germanium, and selenium in rice grain using state-of-the-art mass spectrometry and synchrotron techniques, and illustrates both the importance of high-sensitivity and high-resolution techniques and the advantages of combining techniques in an integrated quantitative and spatial approach. PMID:22159463

Research on chromium and arsenic speciation in atmospheric particulate matter: short review

Science.gov (United States)

Nocoń, Katarzyna; Rogula-Kozłowska, Wioletta; Widziewicz, Kamila

2018-01-01

Atmospheric particulate matter (PM) plays an important role in the distribution of elements in the environment. The PM-bound elements penetrates into the other elements of the environment, in two basic forms - those dissolved in the atmospheric precipitation and those permanently bound to PM particles. Those forms differs greatly in their mobility, thus posing a potential threat to living organisms. They can also be an immediate threat, while being inhaled. Chromium (Cr) and arsenic (As) belong to the group of elements whose certain chemical states exhibit toxic properties, that is Cr(VI) and As(III). Thus, recognition of the actual threat posed by Cr and As in the environment, including those present in PM, is possible only through the in depth speciation analysis. Research on the Cr and As speciation in PM, more than the analogous studies of their presence in other compartments of the environment, have been undertaken quite rarely. Hence the knowledge on the speciation of PM-bound As and Cr is still limited. The state of knowledge in the field of PM-bound Cr and As is presented in the paper. The issues related to the characterization and occurrence of Cr and As species in PM, the share of Cr and As species mass in different PM size fractions, and in PM of different origin is also summarized. The analytical techniques used in the speciation analysis of PM-bound Cr and As are also discussed. In the existing literature there is no data on the physical characteristics of Cr and As (bound to a different PM size fractions), and thus it still lack of data needed for a comprehensive assessment of the actual environmental and health threat posed by airborne Cr and As.

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.

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...

Speciation of organic carbon in Hanford waste storage tanks: Part 1

International Nuclear Information System (INIS)

Carlson, C.D.

1997-02-01

This report is the first in a series to report on speciation of organic carbon in Hanford waste storage tanks. The comparison of the existing total organic carbon with oxalate and limited analyses of other organic species (acetate, formate, and normal paraffin hydrocarbons [NPH]) are reported. All of the data have been previously reported by the Grout and Characterization programs; the information includes all of the publicly available data through October 1996. Oxalate data were reported for 33 tanks, TOC data were reported for 82 tanks, and both oxalate and TOC data were available for 27 tanks. Of these 27 tanks, seven were found to have greater than 80% of the TOC identified as oxalate: 241-BY-104, 241-BY-105, 241-BY-106, 241-BY-110, 241-S-109, and 241-SX-108. Eighty percent accountability has been tentatively established as a minimum goal of the Organic Safety Program for speciation of TOC. Accountability of TOC through speciation will allow more accurate estimate of the potential energy content of the wastes as currently stored. Of the remaining 19 tanks, seven had between 40 and 80% of the TOC identified as oxalate, and eleven had less than 35% of the TOC identified. Of these, only five tanks had segment results that were greater than 1% TOC, and none was above 2%. Since the cur-rent safety criterion outlined in the Safety Analysis is 4.5% TOC, it may be determined that the further analyses of these tank wastes are not necessary. If additional analyses are deemed necessary, minimal work may be required, possibly limited to ion chromatography (IC), ion pair chromatography and capillary zone electrophoresis (CZE). Additional speciation work is planned for this fiscal year in both the Organic Tanks Safety and Characterization programs. The Characterization program reports acetate and formate data in addition to the oxalate data for all the tank cores it processes

Use of imidazole 4,5-dicarboxylic acid in vanadium speciation

International Nuclear Information System (INIS)

Banerjee, D.; Mondal, B.C.; Das, D.; Das, A.K.

2003-01-01

A new resin has been synthesized by fictionalization of polystyrene-divinylbenzene (8 %) with imidazole 4,5-dicarboxylic acid through -N=N- bonding. The resulting resin has been characterized by elemental analysis, thermogravimetric analysis, infrared spectroscopy, hydrogen ion capacity and metal ion capacity. The speciation study of vanadium has been studied by using this resin and the maximum exchange capacity was found to be 0.45 mmol g -1 for V 4+ and that for V 5+ was 1.57 mmol g -1 at pH 3 for both. The eluents malonic acid and sodium hydroxide have been used for the selective separation of vanadium(IV) and vanadium(V) species respectively. The effects of diverse ions on the sorption and recovery of each species have been studied. Finally, the developed method has been applied for the speciation and determination of these two species in natural water samples. (author)

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

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

[Speciation and Risk Characteristics of Heavy Metals in the Sediments of the Yangtze Estuary].

Science.gov (United States)

Yin, Su; Feng, Cheng-hong; Li, Yang-yang; Yin, Li-feng; Shen, Zhen-yao

2016-03-15

Based on the investigation on the distribution of total contents and speciation of 8 heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb, Zn) in the surface sediments at 14 typical sites of the Yangtze Estuary during three hydrological seasons ( wet, normal, and dry seasons) , this study applied equilibrium partitioning approach to build the sediment quality guidelines (SQGs) of the Yangtze Estuary, and assessed ecological risks of the heavy metals. The relationship between ecological risk and speciation of heavy metals was also revealed. The results showed that, except for Cd, the residual fraction was the main speciation of heavy metals, especially for As, Cr and Hg, their residual fraction proportions were all over 90%. The sediment quality guidelines of the Yangtze Estuary for As, Cd, Cr, Cu, Hg, Ni, Pb, Zn were 43.29, 0.672, 79.65, 19.08, 0.569, 339.09, 30.87, 411.36 µg · g⁻¹, respectively. Cu had the highest ecological risk to aquatic organisms. The upstream of Yangtze Estuary was mainly affected by Yangtze River runoff, where the risks were relatively high in wet season and relatively low in normal and dry seasons. However, the downstream of the estuary was mainly affected by municipal sewage of cities like Shanghai, where the risks were relatively high, especially in normal and dry seasons. There were three different relationships between the ecological risks and speciation of the eight heavy metals.

Speciation of Co(II) and Ni(II) in anaerobic bioreactors measured by competitive ligand exchange - adsorptive stripping voltammetry

NARCIS (Netherlands)

Jansen, S.; Steffen, F.; Threels, W.F.; Leeuwen, van H.P.

2005-01-01

Competitive ligand exchange-adsorptive stripping voltammetry is applied to speciation analysis of dissolved Ni(II) and Co(II) in an anaerobic bioreactor and similar batch media. Co and Ni speciation in these media can be measured down to concentration levels of ca. 1 nM. Sulfide interference is

Moving Speciation Genetics Forward: Modern Techniques Build on Foundational Studies in Drosophila.

Science.gov (United States)

Castillo, Dean M; Barbash, Daniel A

2017-11-01

The question of how new species evolve has been examined at every level, from macroevolutionary patterns of diversification to molecular population genetic analyses of specific genomic regions between species pairs. Drosophila has been at the center of many of these research efforts. Though our understanding of the speciation process has grown considerably over the past few decades, very few genes have been identified that contribute to barriers to reproduction. The development of advanced molecular genetic and genomic methods provides promising avenues for the rapid discovery of more genes that contribute to speciation, particularly those involving prezygotic isolation. The continued expansion of tools and resources, especially for species other than Drosophila melanogaster , will be most effective when coupled with comparative approaches that reveal the genetic basis of reproductive isolation across a range of divergence times. Future research programs in Drosophila have high potential to answer long-standing questions in speciation. These include identifying the selective forces that contribute to divergence between populations and the genetic basis of traits that cause reproductive isolation. The latter can be expanded upon to understand how the genetic basis of reproductive isolation changes over time and whether certain pathways and genes are more commonly involved. Copyright © 2017 by the Genetics Society of America.

Application of Hyphenated Techniques in Speciation Analysis of Arsenic, Antimony, and Thallium

Directory of Open Access Journals (Sweden)

Rajmund Michalski

2012-01-01

Full Text Available Due to the fact that metals and metalloids have a strong impact on the environment, the methods of their determination and speciation have received special attention in recent years. Arsenic, antimony, and thallium are important examples of such toxic elements. Their speciation is especially important in the environmental and biomedical fields because of their toxicity, bioavailability, and reactivity. Recently, speciation analytics has been playing a unique role in the studies of biogeochemical cycles of chemical compounds, determination of toxicity and ecotoxicity of selected elements, quality control of food products, control of medicines and pharmaceutical products, technological process control, research on the impact of technological installation on the environment, examination of occupational exposure, and clinical analysis. Conventional methods are usually labor intensive, time consuming, and susceptible to interferences. The hyphenated techniques, in which separation method is coupled with multidimensional detectors, have become useful alternatives. The main advantages of those techniques consist in extremely low detection and quantification limits, insignificant interference, influence as well as high precision and repeatability of the determinations. In view of their importance, the present work overviews and discusses different hyphenated techniques used for arsenic, antimony, and thallium species analysis, in different clinical, environmental and food matrices.

Application of Hyphenated Techniques in Speciation Analysis of Arsenic, Antimony, and Thallium

Science.gov (United States)

Michalski, Rajmund; Szopa, Sebastian; Jabłońska, Magdalena; Łyko, Aleksandra

2012-01-01

Due to the fact that metals and metalloids have a strong impact on the environment, the methods of their determination and speciation have received special attention in recent years. Arsenic, antimony, and thallium are important examples of such toxic elements. Their speciation is especially important in the environmental and biomedical fields because of their toxicity, bioavailability, and reactivity. Recently, speciation analytics has been playing a unique role in the studies of biogeochemical cycles of chemical compounds, determination of toxicity and ecotoxicity of selected elements, quality control of food products, control of medicines and pharmaceutical products, technological process control, research on the impact of technological installation on the environment, examination of occupational exposure, and clinical analysis. Conventional methods are usually labor intensive, time consuming, and susceptible to interferences. The hyphenated techniques, in which separation method is coupled with multidimensional detectors, have become useful alternatives. The main advantages of those techniques consist in extremely low detection and quantification limits, insignificant interference, influence as well as high precision and repeatability of the determinations. In view of their importance, the present work overviews and discusses different hyphenated techniques used for arsenic, antimony, and thallium species analysis, in different clinical, environmental and food matrices. PMID:22654649

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.

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

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.

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

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

FUNDAMENTALS OF MERCURY SPECIATION AND CONTROL IN COAL-FIRED BOILERS

Science.gov (United States)

The report describes the progress of an experimental investigation of the speciation of mercury in simulated coal combustion flue gasses. The effects of flue gas parameters and coal fly ash on the oxidation of elemental mercury (Hgo) in the presence of hydrogen chloride (HCl) in ...

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 ...

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.

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.

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.

Co-Speciation of the Ectoparasite Gyrodactylus teuchis (Monogenea, Platyhelminthes and Its Salmonid Hosts.

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Christoph Hahn

Full Text Available Co-speciation is a fundamental concept of evolutionary biology and intuitively appealing, yet in practice hard to demonstrate as it is often blurred by other evolutionary processes. We investigate the phylogeographic history of the monogenean ectoparasites Gyrodactylus teuchis and G. truttae on European salmonids of the genus Salmo. Mitochondrial cytochrome oxidase subunit 1 and the nuclear ribosomal internal transcribed spacer 2 were sequenced for 189 Gyrodactylus individuals collected from 50 localities, distributed across most major European river systems, from the Iberian- to the Balkan Peninsula. Despite both anthropogenic and naturally caused admixture of the principal host lineages among major river basins, co-phylogenetic analyses revealed significant global congruence for host and parasite phylogenies, providing firm support for co-speciation of G. teuchis and its salmonid hosts brown trout (S. trutta and Atlantic salmon (S. salar. The major split within G. teuchis, coinciding with the initial divergence of the hosts was dated to ~1.5 My BP, using a Bayesian framework based on an indirect calibration point obtained from the host phylogeny. The presence of G. teuchis in Europe thus predates some of the major Pleistocene glaciations. In contrast, G. truttae exhibited remarkably low intraspecific genetic diversity. Given the direct life cycle and potentially high transmission potential of gyrodactylids, this finding is interpreted as indication for a recent emergence (<60 ky BP of G. truttae via a host-switch. Our study thus suggests that instances of two fundamentally different mechanisms of speciation (co-speciation vs. host-switching may have occurred on the same hosts in Europe within a time span of less than 1.5 My in two gyrodactylid ectoparasite species.

Something's Fishy in Paxton Lake: A Case on Speciation in Sticklebacks.

Science.gov (United States)

Sharp, Joan

2002-01-01

Introduces a case study on speciation and evolutionary mechanisms. Teaches science process skills as well as natural selection, biological species concepts, basic genetic terminology, and classification. Includes teaching notes and classroom management strategies. (Contains 14 references.) (YDS)

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...

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.

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

Cadmium speciation and accumulation in periphyton in a small stream with dynamic concentration variations

Energy Technology Data Exchange (ETDEWEB)

Bradac, Philippe [Eawag, Swiss Federal Institute of Aquatic Science and Technology, P.O. Box 611, CH-8600 Duebendorf (Switzerland); ETH, Swiss Federal Institute of Technology, Department of Environmental Sciences, CH-8092 Zurich (Switzerland); Wagner, Bettina; Kistler, David; Traber, Jacqueline; Behra, Renata [Eawag, Swiss Federal Institute of Aquatic Science and Technology, P.O. Box 611, CH-8600 Duebendorf (Switzerland); Sigg, Laura, E-mail: laura.sigg@eawag.c [Eawag, Swiss Federal Institute of Aquatic Science and Technology, P.O. Box 611, CH-8600 Duebendorf (Switzerland); ETH, Swiss Federal Institute of Technology, Department of Environmental Sciences, CH-8092 Zurich (Switzerland)

2010-03-15

Accumulation of cadmium in periphyton was investigated under field conditions while Cd concentration and speciation were dynamically varying in a small stream during rain events. Speciation in water was determined in situ by diffusion gradient in thin-films (DGT) and by modeling of complexation with fulvic acids. During the rain events, dissolved Cd concentrations increased from 0.17 nM to 0.27-0.36 nM, and 70-97% were DGT-labile. Cd content in periphyton closely followed Cd concentrations in water, despite higher concentrations of Zn and Mn, and may be controlled by either free or DGT-labile Cd concentrations. Decrease of Cd content in periphyton after the rain events was slower than the decrease of Cd concentration in water. Concentrations of Zn, Mn, Cu, Pb and Fe in periphyton also followed the dynamic variations of metal concentrations in water. Repeated exposure of periphyton to elevated dissolved Cd may lead to Cd accumulation. - Cadmium accumulation in periphyton was examined in a small stream during rain events in relation to Cd speciation.

Mechanisms of rapid sympatric speciation by sex reversal and sexual selection in cichlid fish.

Science.gov (United States)

Lande, R; Seehausen, O; van Alphen, J J

2001-01-01

Mechanisms of speciation in cichlid fish were investigated by analyzing population genetic models of sexual selection on sex-determining genes associated with color polymorphisms. The models are based on a combination of laboratory experiments and field observations on the ecology, male and female mating behavior, and inheritance of sex-determination and color polymorphisms. The models explain why sex-reversal genes that change males into females tend to be X-linked and associated with novel colors, using the hypothesis of restricted recombination on the sex chromosomes, as suggested by previous theory on the evolution of recombination. The models reveal multiple pathways for rapid sympatric speciation through the origin of novel color morphs with strong assortative mating that incorporate both sex-reversal and suppressor genes. Despite the lack of geographic isolation or ecological differentiation, the new species coexists with the ancestral species either temporarily or indefinitely. These results may help to explain different patterns and rates of speciation among groups of cichlids, in particular the explosive diversification of rock-dwelling haplochromine cichlids.

Cadmium speciation and accumulation in periphyton in a small stream with dynamic concentration variations

International Nuclear Information System (INIS)

Bradac, Philippe; Wagner, Bettina; Kistler, David; Traber, Jacqueline; Behra, Renata; Sigg, Laura

2010-01-01

Accumulation of cadmium in periphyton was investigated under field conditions while Cd concentration and speciation were dynamically varying in a small stream during rain events. Speciation in water was determined in situ by diffusion gradient in thin-films (DGT) and by modeling of complexation with fulvic acids. During the rain events, dissolved Cd concentrations increased from 0.17 nM to 0.27-0.36 nM, and 70-97% were DGT-labile. Cd content in periphyton closely followed Cd concentrations in water, despite higher concentrations of Zn and Mn, and may be controlled by either free or DGT-labile Cd concentrations. Decrease of Cd content in periphyton after the rain events was slower than the decrease of Cd concentration in water. Concentrations of Zn, Mn, Cu, Pb and Fe in periphyton also followed the dynamic variations of metal concentrations in water. Repeated exposure of periphyton to elevated dissolved Cd may lead to Cd accumulation. - Cadmium accumulation in periphyton was examined in a small stream during rain events in relation to Cd speciation.

Arsenic in cooked rice: Effect of chemical, enzymatic and microbial processes on bioaccessibility and speciation in the human gastrointestinal tract

International Nuclear Information System (INIS)

Sun Guoxin; Van de Wiele, Tom; Alava, Pradeep; Tack, Filip; Du Laing, Gijs

2012-01-01

Rice, used as staple food for half of the world population, can easily accumulate arsenic (As) into its grain, which often leads to As contamination. The health risk induced by presence of As in food depends on its release from the food matrix, i.e., its bioaccessibility. Using an in vitro gastrointestinal simulator, we incubated two types of cooked rice (total As: 0.389 and 0.314 mg/kg). Arsenic bioaccessibility and speciation changes were determined upon gastrointestinal digestion. Washing with deionized water and cooking did not result in changes of As speciation in the rice although the arsenic content dropped by 7.1–20.6%. Arsenic bioaccessibility of the cooked rice in the small intestine ranged between 38 and 57%. Bioaccessibility slightly increased during digestion in the simulated small intestine and decreased with time in the simulated colon. Significant speciation changes were noted in the simulated colon, with trivalent monomethylarsonate (MMA III ) becoming an important species. - Highlights: ► We studied arsenic bioaccessibility and speciation in rice during in vitro digestion. ► Bioaccessibility in cooked rice ranged between 38 and 57%. ► Bioaccessibility increased in the small intestine and dropped in the colon. ► Significant speciation changes were observed in the colon. ► Toxic trivalent monomethylarsonate (MMA III ) was produced in the colon. - Arsenic bioaccessibility and speciation changes were studied upon in vitro gastrointestinal digestion of As-polluted rice with specific attention to the role of colon micro-organisms.

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.

Synergy between Allopatry and Ecology in Population Differentiation and Speciation

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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.

Speciation and bioavailability of Americium-241 in the fresh water environment

International Nuclear Information System (INIS)

Bierkens, J.

1986-01-01

Due to its anthropogenic origin, the transuranic americium 241 confronts physiologists with the intriguing question, which mechanisms are involved in the incorporation or elimination of such artificial elements in biological cycles. The investigations on the speciation and bioavailability of 241 Am in the freshwater environment aim to establish a relation between the behavior of 241 Am in freshwater ecosystems and its availability for biota. In the limnic environment, most often characterized by a high organic load and a low conductivity, the effect of complexation of 241 Am with humic acids and competition with trivalent cations such as A1 and Fe, were proven to be significant on the speciation of 241 Am. Based on the registration of the 241 Am uptake by a large number of freshwater organisms, the crayfish Astacus leptodactylus Eschscholtz was chosen to study the whole-body uptake of 241 Am, its corresponding organ distribution and its retention in the animal. The share of external fixation and ingestion in the global uptake, and the effect of speciation on it, were studied more carefully. Other aspects in this physiological part were: the kinetics of 241 Am in the hemolymph and the hepatopancreas, and its subcellular distribution in the digestive gland. Finally, by comparing the physiology of 241 Am with some other metals ( 240 Pu, 64 Cu, 198 Au) with analogous or contradictional properties, we tried to find out whether the behavior of 241 Am in organisms can be explained from its chemical characteristics

Speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry

Energy Technology Data Exchange (ETDEWEB)

Li Xun [Department of Chemistry, Beijing Normal University, Beijing 100875 (China); Department of Chemistry and Life Science, Gannan Teachers College, Ganzhou 341000 (China); Jia Jing [Department of Chemistry, Beijing Normal University, Beijing 100875 (China); Wang Zhenghao [Department of Chemistry, Beijing Normal University, Beijing 100875 (China)]. E-mail: zhwang@bnu.edu.cn

2006-02-23

A simple procedure was developed for the speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry (EcHG-AAS), without pre-reduction of As(V). Glassy carbon was selected as cathode material in the flow cell. An optimum catholyte concentration for simultaneous generation of arsine from As(III) and As(V) was 0.06 mol l{sup -1} H{sub 2}SO{sub 4}. Under the optimized conditions, adequate sensitivity and difference in ratio of slopes of the calibration curves for As(III) and As(V) can be achieved at the electrolytic currents of 0.6 and 1 A. The speciation of inorganic arsenic can be performed by controlling the electrolytic currents, and the concentration of As(III) and As(V) in the sample can be calculated according to the equations of absorbance additivity obtained at two selected electrolytic currents. The calibration curves were linear up to 50 ng ml{sup -1} for both As(III) and As(V) at 0.6 and 1 A. The detection limits of the method were 0.2 and 0.5 ng ml{sup -1} for As(III) and As(V) at 0.6 A, respectively. The relative standard deviations were of 2.1% for 20 ng ml{sup -1} As(III) and 2.5% for 20 ng ml{sup -1} As(V). The method was validated by the analysis of human hair certified reference material and successfully applied to speciation of soluble inorganic arsenic in Chinese medicine.

Speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry

International Nuclear Information System (INIS)

Li Xun; Jia Jing; Wang Zhenghao

2006-01-01

A simple procedure was developed for the speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry (EcHG-AAS), without pre-reduction of As(V). Glassy carbon was selected as cathode material in the flow cell. An optimum catholyte concentration for simultaneous generation of arsine from As(III) and As(V) was 0.06 mol l -1 H 2 SO 4 . Under the optimized conditions, adequate sensitivity and difference in ratio of slopes of the calibration curves for As(III) and As(V) can be achieved at the electrolytic currents of 0.6 and 1 A. The speciation of inorganic arsenic can be performed by controlling the electrolytic currents, and the concentration of As(III) and As(V) in the sample can be calculated according to the equations of absorbance additivity obtained at two selected electrolytic currents. The calibration curves were linear up to 50 ng ml -1 for both As(III) and As(V) at 0.6 and 1 A. The detection limits of the method were 0.2 and 0.5 ng ml -1 for As(III) and As(V) at 0.6 A, respectively. The relative standard deviations were of 2.1% for 20 ng ml -1 As(III) and 2.5% for 20 ng ml -1 As(V). The method was validated by the analysis of human hair certified reference material and successfully applied to speciation of soluble inorganic arsenic in Chinese medicine

Arsenic speciation for the phytoremediation by the Chinese brake fern, Pteris vittata.

Science.gov (United States)

Shoji, R; Yajima, R; Yano, Y

2008-01-01

Arsenic (As) speciation for the phytoremediation by the Chinese brake fern was studied. In particular, the mechanism of how plants induce compounds containing thiol (SH) and proteins by As exposure in terms of the relationship between As and phosphate uptaken into plant cells was examined. Pteris vittata callus could efficiently reduce As(V) to As(III) by the rapid introduction of reductase and synthesize thiols leading to phytochelatins production. Furthermore, Pteris vittata could control phosphate concentration in the cells corresponding to the concentration of arsenite and arsenate. To our best knowledge, this is the first report to show the mechanisms of such high As tolerance of Pteris vittata using their callus in terms of in vitro approach for the analysis of As speciation and metabolism route.

Speciation, Divergence, and the Origin of Gryllus rubens: Behavior, Morphology, and Molecules

Directory of Open Access Journals (Sweden)

David A. Gray

2011-05-01

Full Text Available The last 25 years or so has seen a huge resurgence of interest in speciation research. This has coincided with the development and widespread use of new tools in molecular genetics, especially DNA sequencing, to inform ecological and evolutionary questions. Here I review about a decade of work on the sister species of field crickets Gryllus texensis and G. rubens. This work has included analysis of morphology, behavior, and the mitochondrial DNA molecule. The molecular work in particular has dramatically re-shaped my interpretation of the speciational history of these taxa, suggesting that rather than ‘sister’ species we should consider these taxa as ‘mother-daughter’ species with G. rubens derived from within a subset of ancestral G. texensis.

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.

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

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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.

Chemical speciation analysis and environmental behaviour of 127I and 12

International Nuclear Information System (INIS)

Hansen, Violeta

2011-10-01

Chemical speciation analysis of 129 I and 127 I as iodide, iodate and total inorganic iodine in seawater samples from the Baltic Proper, Skagerrak and Kattegat has been carried out. The important findings of this study are that the reduction of iodate and oxidation of iodide in Skagerrak and Kattegat may be a slow process while along the Baltic Sea surface water reduction of iodate is a relatively fast process. Although suboxic or anoxic condition are encountered in some of the Baltic Sea deep basins, the concentration of 129 IO 3 - increases with water depth indicating that the reduction of iodate in the oxygen deficient bottom water of the Baltic Sea is a slow process. Iodine chemical speciation analysis (as iodide, iodate and total iodine including inorganic and organic iodine species) in lake water samples collected from Denmark and southern Sweden has been carried out. Destruction of organic iodine was performed by alkaline oxidation using NaOH - NaClO at 100 deg. C and anion exchange chromatography was used for separation of iodide and iodate. Iodine-129 concentrations in the lakes ranged from 1.3 - 12.8 x10 9 at/L and show elevated concentrations in lakes located in southwest Jutland (Denmark), near the North Sea. Except the Skaersoe Lake, were the organic iodine - 127 accounts for 50% of the total iodine, iodide (both 129 I and 127 I) is the predominant species form in surface water of the studied lakes. An investigation was conducted in order to quantify the total aquatic iodine ( 129 I and 127 I as inorganic and organic iodine) from fresh water and seawater samples by adsorption onto activated charcoal and DEAE 32 cellulose followed by alkaline digestion or combustion. The results show that iodide from freshwater samples can easily be adsorbed onto activated charcoal. The sorption was not affected by the pH. The absorption capacity of iodate is low and reduces quickly when its concentration increases. Compared with activated charcoal, DEAE 32 cellulose

Signals of speciation within Arabidopsis thaliana in comparison with its relatives

NARCIS (Netherlands)

Alcazar, R.; Pecinka, A.; Aarts, M.G.M.; Fransz, P.F.; Koornneef, M.

2012-01-01

The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to

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 ...

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.

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.

Allochronic speciation, secondary contact, and reproductive character displacement in periodical cicadas (Hemiptera: Magicicada spp.): genetic, morphological, and behavioural evidence.

Science.gov (United States)

Cooley, J R; Simon, C; Marshall, D C; Slon, K; Ehrhardt, C

2001-03-01

Periodical cicadas have proven useful in testing a variety of ecological and evolutionary hypotheses because of their unusual life history, extraordinary abundance, and wide geographical range. Periodical cicadas provide the best examples of synchronous periodicity and predator satiation in the animal kingdom, and are excellent illustrations of habitat partitioning (by the three morphologically distinct species groups), incipient species (the year classes or broods), and cryptic species (a newly discovered 13-year species, Magicicada neotredecim). They are particularly useful for exploring questions regarding speciation via temporal isolation, or allochronic speciation. Recently, data were presented that provided strong support for an instance of allochronic speciation by life-cycle switching. This speciation event resulted in the formation of a new 13-year species from a 17-year species and led to secondary contact between two formerly separated lineages, one represented by the new 13-year cicadas (and their 17-year ancestors), and the other represented by the pre-existing 13-year cicadas. Allozyme frequency data, mitochondrial DNA (mtDNA), and abdominal colour were shown to be correlated genetic markers supporting the life-cycle switching/allochronic speciation hypothesis. In addition, a striking pattern of reproductive character displacement in male call pitch and female pitch preference between the two 13-year species was discovered. In this paper we report a strong association between calling song pitch and mtDNA haplotype for 101 individuals from a single locality within the M. tredecim/M. neotredecim contact zone and a strong association between abdomen colour and mtDNA haplotype. We conclude by reviewing proposed mechanisms for allochronic speciation and reproductive character displacement.

A modelling exercise on the importance of ternary alkaline earth carbonate species of uranium(VI) in the inorganic speciation of natural waters

International Nuclear Information System (INIS)

Vercouter, Thomas; Reiller, Pascal E.; Ansoborlo, Eric; Février, Laureline; Gilbin, Rodolphe; Lomenech, Claire; Philippini, Violaine

2015-01-01

Highlights: • The U(VI) speciation in natural waters has been modelled through a modelling exercise. • The results evidence the importance of alkaline earth U(VI) carbonate complexes. • Possible solubility-controlling phases were reported and discussed. • The differences were related to the choice and reliability of thermodynamic data. • Databases need to be improved for reliable U(VI) speciation calculations. - Abstract: Predictive modelling of uranium speciation in natural waters can be achieved using equilibrium thermodynamic data and adequate speciation software. The reliability of such calculations is highly dependent on the equilibrium reactions that are considered as entry data, and the values chosen for the equilibrium constants. The working group “Speciation” of the CETAMA (Analytical methods establishment committee of the French Atomic Energy commission, CEA) has organized a modelling exercise, including four participants, in order to compare modellers’ selections of data and test thermodynamic data bases regarding the calculation of U(VI) inorganic speciation. Six different compositions of model waters were chosen so that to check the importance of ternary alkaline earth carbonate species of U(VI) on the aqueous speciation, and the possible uranium solid phases as solubility-limiting phases. The comparison of the results from the participants suggests (i) that it would be highly valuable for end-users to review thermodynamic constants of ternary carbonate species of U(VI) in a consistent way and implement them in available speciation data bases, and (ii) stresses the necessary care when using data bases to avoid biases and possible erroneous calculations

AQUATIC PLANT SPECIATION AFFECTED BY DIVERSIFYING SELECTION OF ORGANELLE DNA REGIONS(1).

Science.gov (United States)

Kato, Syou; Misawa, Kazuharu; Takahashi, Fumio; Sakayama, Hidetoshi; Sano, Satomi; Kosuge, Keiko; Kasai, Fumie; Watanabe, Makoto M; Tanaka, Jiro; Nozaki, Hisayoshi

2011-10-01

Many of the genes that control photosynthesis are carried in the chloroplast. These genes differ among species. However, evidence has yet to be reported revealing the involvement of organelle genes in the initial stages of plant speciation. To elucidate the molecular basis of aquatic plant speciation, we focused on the unique plant species Chara braunii C. C. Gmel. that inhabits both shallow and deep freshwater habitats and exhibits habitat-based dimorphism of chloroplast DNA (cpDNA). Here, we examined the "shallow" and "deep" subpopulations of C. braunii using two nuclear DNA (nDNA) markers and cpDNA. Genetic differentiation between the two subpopulations was measured in both nDNA and cpDNA regions, although phylogenetic analyses suggested nuclear gene flow between subpopulations. Neutrality tests based on Tajima's D demonstrated diversifying selection acting on organelle DNA regions. Furthermore, both "shallow" and "deep" haplotypes of cpDNA detected in cultures originating from bottom soils of three deep environments suggested that migration of oospores (dormant zygotes) between the two habitats occurs irrespective of the complete habitat-based dimorphism of cpDNA from field-collected vegetative thalli. Therefore, the two subpopulations are highly selected by their different aquatic habitats and show prezygotic isolation, which represents an initial process of speciation affected by ecologically based divergent selection of organelle genes. © 2011 Phycological Society of America.

How does male–male competition generate negative frequency-dependent selection and disruptive selection during speciation?

Science.gov (United States)

Border, Shana E

2018-01-01

Abstract Natural selection has been shown to drive population differentiation and speciation. The role of sexual selection in this process is controversial; however, most of the work has centered on mate choice while the role of male–male competition in speciation is relatively understudied. Here, we outline how male–male competition can be a source of diversifying selection on male competitive phenotypes, and how this can contribute to the evolution of reproductive isolation. We highlight how negative frequency-dependent selection (advantage of rare phenotype arising from stronger male–male competition between similar male phenotypes compared with dissimilar male phenotypes) and disruptive selection (advantage of extreme phenotypes) drives the evolution of diversity in competitive traits such as weapon size, nuptial coloration, or aggressiveness. We underscore that male–male competition interacts with other life-history functions and that variable male competitive phenotypes may represent alternative adaptive options. In addition to competition for mates, aggressive interference competition for ecological resources can exert selection on competitor signals. We call for a better integration of male–male competition with ecological interference competition since both can influence the process of speciation via comparable but distinct mechanisms. Altogether, we present a more comprehensive framework for studying the role of male–male competition in speciation, and emphasize the need for better integration of insights gained from other fields studying the evolutionary, behavioral, and physiological consequences of agonistic interactions. PMID:29492042

Infectious speciation revisited: impact of symbiont-depletion on female fitness and mating behavior of Drosophila paulistorum.

Directory of Open Access Journals (Sweden)

Wolfgang J Miller

2010-12-01

Full Text Available The neotropical Drosophila paulistorum superspecies, consisting of at least six geographically overlapping but reproductively isolated semispecies, has been the object of extensive research since at least 1955, when it was initially trapped mid-evolution in flagrant statu nascendi. In this classic system females express strong premating isolation patterns against mates belonging to any other semispecies, and yet uncharacterized microbial reproductive tract symbionts were described triggering hybrid inviability and male sterility. Based on theoretical models and limited experimental data, prime candidates fostering symbiont-driven speciation in arthropods are intracellular bacteria belonging to the genus Wolbachia. They are maternally inherited symbionts of many arthropods capable of manipulating host reproductive biology for their own benefits. However, it is an ongoing debate as to whether or not reproductive symbionts are capable of driving host speciation in nature and if so, to what extent. Here we have reevaluated this classic case of infectious speciation by means of present day molecular approaches and artificial symbiont depletion experiments. We have isolated the α-proteobacteria Wolbachia as the maternally transmitted core endosymbionts of all D. paulistorum semispecies that have coevolved towards obligate mutualism with their respective native hosts. In hybrids, however, these mutualists transform into pathogens by overreplication causing embryonic inviability and male sterility. We show that experimental reduction in native Wolbachia titer causes alterations in sex ratio, fecundity, and mate discrimination. Our results indicate that formerly designated Mycoplasma-like organisms are most likely Wolbachia that have evolved by becoming essential mutualistic symbionts in their respective natural hosts; they have the potential to trigger pre- and postmating isolation. Furthermore, in light of our new findings, we revisit the concept of

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

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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.

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.

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.

Influence of uranyl speciation and iron oxides on uranium biogeochemical redox reactions

Energy Technology Data Exchange (ETDEWEB)

Stewart, B.D.; Amos, R.T.; Nico, P.S.; Fendorf, S.

2010-03-15

Uranium is a pollutant of concern to both human and ecosystem health. Uranium's redox state often dictates its partitioning between the aqueous- and solid-phases, and thus controls its dissolved concentration and, coupled with groundwater flow, its migration within the environment. In anaerobic environments, the more oxidized and mobile form of uranium (UO{sub 2}{sup 2+} and associated species) may be reduced, directly or indirectly, by microorganisms to U(IV) with subsequent precipitation of UO{sub 2}. However, various factors within soils and sediments may limit biological reduction of U(VI), inclusive of alterations in U(VI) speciation and competitive electron acceptors. Here we elucidate the impact of U(VI) speciation on the extent and rate of reduction with specific emphasis on speciation changes induced by dissolved Ca, and we examine the impact of Fe(III) (hydr)oxides (ferrihydrite, goethite and hematite) varying in free energies of formation on U reduction. The amount of uranium removed from solution during 100 h of incubation with S. putrefaciens was 77% with no Ca or ferrihydrite present but only 24% (with ferrihydrite) and 14% (no ferrihydrite) were removed for systems with 0.8 mM Ca. Imparting an important criterion on uranium reduction, goethite and hematite decrease the dissolved concentration of calcium through adsorption and thus tend to diminish the effect of calcium on uranium reduction. Dissimilatory reduction of Fe(III) and U(VI) can proceed through different enzyme pathways, even within a single organism, thus providing a potential second means by which Fe(III) bearing minerals may impact U(VI) reduction. We quantify rate coefficients for simultaneous dissimilatory reduction of Fe(III) and U(VI) in systems varying in Ca concentration (0 to 0.8 mM), and using a mathematical construct implemented with the reactive transport code MIN3P, we reveal the predominant influence of uranyl speciation, specifically the formation of uranyl

A study of copper, lead and cadmium speciation in some estuarine and coastal marine waters

Energy Technology Data Exchange (ETDEWEB)

Batley, G E; Gardner, D

1978-07-01

The significance of the measured changes in heavy metal distribution for different sampled environments was ascertained. The potential of a heavy metal speciation scheme to reflect differences in marine metal distributions was evaluated in a study of soluble copper, lead, and cadmium speciation in water samples from Port Hacking Estuary and one coastal Pacific station in Australia. In all samples, the percentages of metals associated with colloidal matter were high40-60% of total copper, 45-75% of total lead, and 15-35% of total cadmium. (1 map, 26 references, 4 tables)

454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology

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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.

Investigating arsenic speciation and mobilization in sediments with DGT and DET

DEFF Research Database (Denmark)

Bennett, William W.; Teasdale, Peter R.; Panther, Jared G.

2012-01-01

Mobilization of arsenic from freshwater and estuarine sediments during the transition from oxic to anoxic conditions was investigated using recently developed diffusive sampling techniques. Arsenic speciation and Fe(II) concentrations were measured at high resolution (1-3 mm) with in situ diffusi...

Speciation of iron and manganese in the sediments of Mandovi Estuary

Digital Repository Service at National Institute of Oceanography (India)

Jayakumar, D.A.; Rajendran, A.

Several attempts have been made to study the distribution of iron and manganese in Mandovi Estuary, Goa, India. But this is the first report of its kind on the speciation of these metals in sediments from Indian waters. This study would be useful...

Dispersal and speciation: The cross Atlantic relationship of two parasitic cnidarians

DEFF Research Database (Denmark)

Dnyansagar, Rohit; Zimmermann, Bob; Moran, Yehu

2018-01-01

How dispersal strategies impact the distribution of species and subsequent speciation events is a fundamental question in evolutionary biology. Sedentary benthic marine organisms, such as corals or sea anemones usually rely on motile larval stages for dispersal and therefore have a relatively res...

Speciation and bioaccumulation in a model organism of U, Np and Am in the marine environment

International Nuclear Information System (INIS)

Maloubier, Melody

2015-01-01

The fate of natural and anthropogenic radionuclides in the environment remains a major concern in our modern nuclearized societies. Among the environmental compartments, the hydrosphere is ubiquitous and can transport compounds or elements over very long distances. The recent event of Fukushima demonstrated that the marine environment could be directly affected and this raises both scientific and societal questions. Moreover, some studies have already shown that radionuclides present in seawater can be strongly accumulated by marine organisms although their speciation is most of the time unknown. Yet this knowledge is essential to better understand the transfer mechanisms from the hydrosphere to the biosphere and to evaluate their global impact on humans. In this work, we chose to experimentally determine the speciation of three actinides in doped seawater: uranium(VI), neptunium(V) and americium(III) (and the chemical surrogate europium(III)) by coupling speciation modeling with spectroscopic tools among which Time-Resolved Laser-Induced Fluorescence (TRLIF) and X-ray Absorption Spectroscopy (XAS). Then, we have studied the accumulation process in the sponge A. cavernicola, chosen here because it is considered as a bio-monitor of heavy metal pollution. The accumulation of europium(III), americium(III) and uranium(VI) in A. cavernicola were investigated at trace and ultra-trace levels. Besides, for europium, X-ray and electronic imaging permit to localize the accumulated element in the sponge and to specify its speciation [fr

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 ...

Composition of COH fluids at 1 GPa: an experimental study on speciation and solubility

Science.gov (United States)

Tiraboschi, Carla; Tumiati, Simone; Recchia, Sandro; Ulmer, Peter; Pettke, Thomas; Fumagalli, Patrizia; Poli, Stefano

2014-05-01

COH fluids play a fundamental role in many geological processes, controlling the location of melting in subduction zones and promoting mass transfer from the subducting litosphere to the overlying mantle wedge. The properties of COH fluids are strictly dependent on the composition of the fluid in subduction systems, i.e., the speciation of the volatile components of the fluid itself and the presence of solutes deriving from the dissolution of rock-forming minerals. In the scientific literature, the speciation of COH fluids has been generally determined through thermodynamic calculations using equations of state of simple H2O-non-polar gas systems (e.g., H2O-CO2-CH4), equations that do not consider the complexity related to dissolution processes, which are substantially unexplored in COH fluids and limited so far to aqueous fluids (Newton & Manning, 2002). The aim of this work is to investigate experimentally the speciation and the dissolution of mantle minerals in carbon-saturated COH fluids at buffered fO2 conditions. Our experimental approach relies on two different techniques: 1) analysis by means of quadrupole mass spectrometer (QMS) of the fluids from pierced run capsules to retrieve speciation of volatile components and 2) analysis of frozen COH fluid with laser-ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS) to measure the amount of solutes. Experiments were conducted at pressure of 1 GPa and temperatures from 800 to 900° C using a rocking piston cylinder apparatus. Mantle minerals in equilibrium with COH fluid are represented by synthetic forsterite. fO2 conditions were controlled using the double capsule technique and NNO buffer (ΔFMQ=-0.61 at 800° C; ΔFMQ =-0.98 at 900° C). For the speciation experiments, oxalic acid dihydrate and graphite have been used to generate carbon-saturated COH fluid. The speciation was determined by analyzing the quenched COH fluid, retrieved by piercing the capsule in a gas-tight vessel at T =80° C and

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.

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.

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.

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)

Influence of dissolved organic matter and manganese oxides on metal speciation in soil solution: A modelling approach.

Science.gov (United States)

Schneider, Arnaud R; Ponthieu, Marie; Cancès, Benjamin; Conreux, Alexandra; Morvan, Xavier; Gommeaux, Maxime; Marin, Béatrice; Benedetti, Marc F

2016-06-01

Trace element (TE) speciation modelling in soil solution is controlled by the assumptions made about the soil solution composition. To evaluate this influence, different assumptions using Visual MINTEQ were tested and compared to measurements of free TE concentrations. The soil column Donnan membrane technique (SC-DMT) was used to estimate the free TE (Cd, Cu, Ni, Pb and Zn) concentrations in six acidic soil solutions. A batch technique using DAX-8 resin was used to fractionate the dissolved organic matter (DOM) into four fractions: humic acids (HA), fulvic acids (FA), hydrophilic acids (Hy) and hydrophobic neutral organic matter (HON). To model TE speciation, particular attention was focused on the hydrous manganese oxides (HMO) and the Hy fraction, ligands not considered in most of the TE speciation modelling studies in soil solution. In this work, the model predictions of free ion activities agree with the experimental results. The knowledge of the FA fraction seems to be very useful, especially in the case of high DOM content, for more accurately representing experimental data. Finally, the role of the manganese oxides and of the Hy fraction on TE speciation was identified and, depending on the physicochemical conditions of the soil solution, should be considered in future studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826.

Directory of Open Access Journals (Sweden)

Carola Greve

Full Text Available Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.

Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826).

Science.gov (United States)

Greve, Carola; Gimnich, France; Hutterer, Rainer; Misof, Bernhard; Haase, Martin

2012-01-01

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.

Migration and speciation of heavy metal in salinized mine tailings affected by iron mining.

Science.gov (United States)

Zhang, Xu; Yang, Huanhuan; Cui, Zhaojie

2017-10-01

The negative effects of heavy metals have aroused much attention due to their high toxicity to human beings. Migration and transformation trend of heavy metals have a close relationship with soil safety. Researching on migration and transformation of heavy metals in tailings can provide a reliable basis for pollution management and ecosystem restoration. Heavy metal speciation plays an important role in risk assessment. We chose Anshan tailings for our study, including field investigations and laboratory research. Four typical heavy metal elements of mine tailings {Fe (373.89 g/kg), Mn (2,303.80 mg/kg), Pb (40.99 mg/kg) and Cr (199.92 mg/kg)} were studied via Tessier test in vertical and horizontal direction. The main speciation of heavy metals in Anshan tailings was the residual. However, heavy metals have a strong ability for migration and transformation in vertical and horizontal directions. Its tendency to change from stable to unstable speciation results in increasing bioavailability and potential bioavailability. Fe, Mn, Pb and Cr showed different ability in the migration and transformation process (Mn > Pb > Fe > Cr) depending on the characteristics of heavy metals and physicochemical properties of the environment.

Recent Studies on the Speciation and Determination of Mercury in Different Environmental Matrices Using Various Analytical Techniques

Directory of Open Access Journals (Sweden)

Lakshmi Narayana Suvarapu

2017-01-01

Full Text Available This paper reviews the current research on the speciation and determination of mercury by various analytical techniques, including the atomic absorption spectrometry (AAS, voltammetry, inductively coupled plasma optical emission spectrometry (ICP-OES, ICP-mass spectrometry (MS, atomic fluorescence spectrometry (AFS, spectrophotometry, spectrofluorometry, and high performance liquid chromatography (HPLC. Approximately 96 research papers on the speciation and determination of mercury by various analytical instruments published in international journals since 2015 were reviewed. All analytical parameters, including the limits of detection, linearity range, quality assurance and control, applicability, and interfering ions, evaluated in the reviewed articles were tabulated. In this review, we found a lack of information in speciation studies of mercury in recent years. Another important conclusion from this review was that there were few studies regarding the concentration of mercury in the atmosphere.

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

Methylmercury speciation in the dissolved phase of a stratified lake using the diffusive gradient in thin film technique

Energy Technology Data Exchange (ETDEWEB)

Clarisse, Olivier [Trent University, Department of Chemistry, 1600 West Bank Drive, Peterborough, Ontario K9J 7B8 (Canada)], E-mail: olivier.clarisse@umoncton.ca; Foucher, Delphine; Hintelmann, Holger [Trent University, Department of Chemistry, 1600 West Bank Drive, Peterborough, Ontario K9J 7B8 (Canada)

2009-03-15

The diffusive gradient in thin film (DGT) technique was successfully used to monitor methylmercury (MeHg) speciation in the dissolved phase of a stratified boreal lake, Lake 658 of the Experimental Lakes Area (ELA) in Ontario, Canada. Water samples were conventionally analysed for MeHg, sulfides, and dissolved organic matter (DOM). MeHg accumulated by DGT devices was compared to MeHg concentration measured conventionally in water samples to establish MeHg speciation. In the epilimnion, MeHg was almost entirely bound to DOM. In the top of the hypolimnion an additional labile fraction was identified, and at the bottom of the lake a significant fraction of MeHg was potentially associated to colloidal material. As part of the METAALICUS project, isotope enriched inorganic mercury was applied to Lake 658 and its watershed for several years to establish the relationship between atmospheric Hg deposition and Hg in fish. Little or no difference in MeHg speciation in the dissolved phase was detected between ambient and spike MeHg. - Methylmercury speciation was determined in the dissolved phase of a stratified lake using the diffusive gradient in thin film technique.

Methylmercury speciation in the dissolved phase of a stratified lake using the diffusive gradient in thin film technique

International Nuclear Information System (INIS)

Clarisse, Olivier; Foucher, Delphine; Hintelmann, Holger

2009-01-01

The diffusive gradient in thin film (DGT) technique was successfully used to monitor methylmercury (MeHg) speciation in the dissolved phase of a stratified boreal lake, Lake 658 of the Experimental Lakes Area (ELA) in Ontario, Canada. Water samples were conventionally analysed for MeHg, sulfides, and dissolved organic matter (DOM). MeHg accumulated by DGT devices was compared to MeHg concentration measured conventionally in water samples to establish MeHg speciation. In the epilimnion, MeHg was almost entirely bound to DOM. In the top of the hypolimnion an additional labile fraction was identified, and at the bottom of the lake a significant fraction of MeHg was potentially associated to colloidal material. As part of the METAALICUS project, isotope enriched inorganic mercury was applied to Lake 658 and its watershed for several years to establish the relationship between atmospheric Hg deposition and Hg in fish. Little or no difference in MeHg speciation in the dissolved phase was detected between ambient and spike MeHg. - Methylmercury speciation was determined in the dissolved phase of a stratified lake using the diffusive gradient in thin film technique

Significance of wave form parameters in stripping chronopotentiometric metal speciation analysis

NARCIS (Netherlands)

Town, R.M.; Leeuwen, van H.P.

2002-01-01

An analysis is presented of the significance of stripping chronopotentiometric (SCP) stripping peak parameters (peak potential, Ep, and peak half-width, w1/2) for determination of metal ion speciation. This study focuses on depletive SCP (low stripping current, I¿ constant), and considers the change

The use of L-ascorbic acid in speciation of arsenic compounds in drinking water

Directory of Open Access Journals (Sweden)

Marjanović Nikola J.

2009-01-01

Full Text Available Arsenic speciation, besides total arsenic content determination, is very important in analysis of water, foodstuffs, and environmental samples, because of varying degrees of toxicity of different species. For such purpose hydride generation atomic absorption spectrometry can be used based on the generation of certain types of hydride, depending on the pH value and pretreatment in different reaction media. In this study, we have investigated the effect of L-ascorbic acid as the reaction medium as well as the pre-reducing agent in speciation of arsenic by hydride generation-atomic absorption spectrometry in order to determine monomethyl arsonic acid (MMA in the presence of inorganic forms of arsenic.

Mercury speciation modeling using site specific chemical and redox data from the TNXOD OU

International Nuclear Information System (INIS)

Kaplan, D.I.

2000-01-01

The objective of this study was to evaluate mercury speciation under reducing conditions expected in sediments at the TNX Outfall Delta Operable Unit. These changes in speciation would then be used to infer whether mercury toxicity and mobility would be expected to be significantly altered under reducing conditions. The results from this work suggest that mercury would likely become more strongly retained by the solid phase under reducing conditions than under oxidizing conditions at the TNX Outfall Delta Site. Considering that experimental results indicate that mercury is extremely tightly bound to the solid phase under oxidizing conditions, little mercury mobility would therefore be expected under reducing conditions

Influence of hydrology on heavy metal speciation and mobility in a Pb-Zn mine tailing

International Nuclear Information System (INIS)

Kovacs, Elza; Dubbin, William E.; Tamas, Janos

2006-01-01

Among the inorganic toxicants of greatest concern in mine tailings, Pb, Zn, Cu, Cd and As figure prominently due to their abundance and potential toxicity. Here we report on their biolability and solid-phase speciation in two sediment cores subject to variable hydrological regimes at an abandoned pyritic mine tailing. The oxic conditions of well-drained sediments induced pyrite oxidation and the subsequent liberation of H + , SO 4 2- and considerable quantities of Fe(III), which precipitated as goethite. Solubility of Pb, Zn, Cu and Cd was closely coupled to pH and goethite presence. Metal lability was particularly low in zones of neutralization, formed by the accumulation of calcite, first carried then deposited by percolating waters in both saturated and unsaturated cores. We conclude that differential hydrology induces variable heavy metal speciation and biolability in Pb-Zn mine tailings, and suggest that site-specific risk assessments must account for past and present hydrological regimes. - Variable hydrology influences heavy metal speciation and mobility, and the formation of neutralization zones, in a Pb-Zn mine tailing

Sorption Speciation of Lanthanides/Actinides on Minerals by TRLFS, EXAFS and DFT Studies: A Review

Directory of Open Access Journals (Sweden)

Xiaoli Tan

2010-11-01

Full Text Available Lanthanides/actinides sorption speciation on minerals and oxides by means of time resolved laser fluorescence spectroscopy (TRLFS, extended X-ray absorption fine structure spectroscopy (EXAFS and density functional theory (DFT is reviewed in the field of nuclear disposal safety research. The theoretical aspects of the methods are concisely presented. Examples of recent research results of lanthanide/actinide speciation and local atomic structures using TRLFS, EXAFS and DFT are discussed. The interaction of lanthanides/actinides with oxides and minerals as well as their uptake are also of common interest in radionuclide chemistry. Especially the sorption and inclusion of radionuclides into several minerals lead to an improvement in knowledge of minor components in solids. In the solid-liquid interface, the speciation and local atomic structures of Eu(III, Cm(III, U(VI, and Np(IV/VI in several natural and synthetic minerals and oxides are also reviewed and discussed. The review is important to understand the physicochemical behavior of lanthanides/actinides at a molecular level in the natural environment.

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.

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)

Impact of Eu(III) on mammalian cells as a function of its speciation

Energy Technology Data Exchange (ETDEWEB)

Sachs, Susanne; Heller, Anne; Geipel, Gerhard; Bernhard, Gert [Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstr. 400, 01328 Dresden (Germany)

2014-07-01

In the case of the accidental release of long-lived radionuclides, e.g., actinides, into the environment, knowledge of their behavior in bio-systems is necessary to asses and to prevent radiological and chemical induced adverse health effects. This includes knowledge of the bioavailability and chemo-/radio-toxicity of these elements for/onto cells, which are governed to a large extent by their speciation [1,2]. In order to gain a better process understanding, we study the interaction of trivalent actinides/lanthanides with mammalian cells on a cellular level combining biochemical and analytical methods. Results of these studies can contribute to the estimation of low dose effects and the development of new decontamination strategies. The cellular tolerance of FaDu cells (human squamous cell carcinoma cell line) toward Eu(III) as an analog for trivalent actinides as well as its uptake into the cells has been studied as a function of the Eu(III) concentration and nutrient composition. To differentiate between chemo-toxic and radio-toxic effects of Eu(III), {sup 152}Eu (β{sup -}, ε) was applied as radioactive tracer besides europium with natural isotope composition. The Eu(III) speciation in the cell culture media has been investigated by time-resolved laser-induced fluorescence spectroscopy as well as by solubility studies in combination with ultrafiltration, ultracentrifugation, cation and anion analysis. These results are used to correlate cytotoxicity and uptake of Eu(III) on/into the cells with its chemical speciation in the nutrient. Presently, we are studying the interaction of Eu(III) with NRK-52E cells (rat kidney epithelial-like cells). The results of these studies will be discussed and compared to those obtained with FaDu cells. From the studies with FaDu cells it was concluded that the Eu(III) cytotoxicity onto these cells depends on the Eu(III) concentration and is influenced by its chemical speciation. This was also reported, for instance, for the

The use of genus-specific amplicon pyrosequencing to assess phytophthora species diversity using eDNA from soil and water in Northern Spain.

Science.gov (United States)

Català, Santiago; Pérez-Sierra, Ana; Abad-Campos, Paloma

2015-01-01

Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.

Use of Moessbauer spectroscopy to determine the effect of salinity on the speciation of triorganotins in Anacostia River sediments

Energy Technology Data Exchange (ETDEWEB)

Eng, George; Song Xueqing [University of the District of Columbia, Department of Chemistry and Physics and Agricultural Experimental Station (United States); May, Leopold, E-mail: may@cua.edu [Catholic University of America, Department of Chemistry (United States)

2006-06-15

The speciation of several tributyltin and triphenyltin compounds under varying salinity conditions (0, 20, 40 and 60%) was studied by Moessbauer spectroscopy in both anaerobic and aerobic Anacostia River sediments. The Moessbauer spectral parameters of the spiked sediments indicated that changes in the salinity did not affect the speciation of the tin compounds in either aerobic or anaerobic sediments.

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

Faster speciation and reduced extinction in the tropics contribute to the Mammalian latitudinal diversity gradient.

Directory of Open Access Journals (Sweden)

Jonathan Rolland

2014-01-01

Full Text Available The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha, high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha, or both (Chiroptera and Rodentia. Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the "out of the tropics" hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern.

Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles.

Science.gov (United States)

Andújar, Carmelo; Pérez-González, Sergio; Arribas, Paula; Zaballos, Juan P; Vogler, Alfried P; Ribera, Ignacio

2017-11-01

Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species' habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below-ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species-rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil. A time-calibrated molecular phylogeny generated from >400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species-area-age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long-term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area- and age-dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna. © 2017 John Wiley & Sons Ltd.

Influence of Organic Matter - Mineral Interfacial Reactions on Metal(loid) Speciation and Bioaccessibility

Science.gov (United States)

Chorover, J.; Kong, S.; Root, R. A.; Thomas, A.

2015-12-01

Bioaccessibility of contaminant metals in geomedia is often measured on the basis of kinetic release to solution during in vitro reaction with biofluid simulants. We postulate that development of a predictive-mechanistic understanding of bioaccessibility requires knowledge of metal(loid) molecular speciation upon sample introduction, as well as its change over the course of the in vitro reaction. Our results - including data from batch, column, mesocosm and field studies pertaining to arsenic, lead, and zinc contaminated materials - indicate the strong influence of organic matter and associated biological activity on metal(loid) speciation in mine tailings and related model systems. Furthermore, presence/absence of organic matter during bioassays affects the kinetics of metal(loid) release into biofluid simulants through multiple mechanisms.

Hybridization and genome evolution I: The role of contingency during hybrid speciation

Directory of Open Access Journals (Sweden)

Fabrice EROUKHMANOFF, Richard I. BAILEY, Glenn-Peter SæTRE

2013-10-01

Full Text Available Homoploid hybrid speciation (HHS involves the recombination of two differentiated genomes into a novel, functional one without a change in chromosome number. Theoretically, there are numerous ways for two parental genomes to recombine. Hence, chance may play a large role in the formation of a hybrid species. If these genome combinations can evolve rapidly following hybridization and sympatric situations are numerous, recurrent homoploid hybrid speciation is a possibility. We argue that three different, but not mutually exclusive, types of contingencies could influence this process. First, many of these “hopeful monsters” of recombinant parent genotypes would likely have low fitness. Only specific combinations of parental genomic contributions may produce viable, intra-fertile hybrid species able to accommodate potential constraints arising from intragenomic conflict. Second, ecological conditions (competition, geography of the contact zones or the initial frequency of both parent species might favor different outcomes ranging from sympatric coexistence to the formation of hybrid swarms and ultimately hybrid speciation. Finally, history may also play an important role in promoting or constraining recurrent HHS if multiple hybridization events occur sequentially and parental divergence or isolation differs along this continuum. We discuss under which conditions HHS may occur multiple times in parallel and to what extent recombination and selection may fuse the parent genomes in the same or different ways. We conclude by examining different approaches that might help to solve this intriguing evolutionary puzzle [Current Zoology 59 (5: 667-674, 2013].　

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.

Speciation of major and selected trace elements in IGCC fly ash

Energy Technology Data Exchange (ETDEWEB)

Oriol Font; Xavier Querol; Frank E. Huggins; Jose M. Chimenos; Ana I. Fernandez; Silvia Burgos; Francisco Garcia Pena [Institute of Earth Sciences ' Jaume Almera' , Barcelona (Spain)

2005-08-01

The speciation of Ga, Ge, Ni, V, S and Fe in fly ash from IGCC power plant were investigated for possible further extraction process by combining conventional mineral and chemical analysis, leaching tests, wet sequential extraction, Moessbauer and XAFS spectroscopies. The results shown that Ge occurs mainly as water-soluble species, GeS and/or GeS{sub 2} and hexagonal GeO{sub 2}. Ga is present as an oxide, Ni occurs mainly as nickeline (NiAs), with minor proportions of Ni arsenates and vanadium as V(III) with minor amounts of V(IV) in the aluminosilicate glass matrix. Pyrrhotite and wurtzite-sphalerite are sulfide species containing Fe and Zn, but an important fraction of iron is also present in the aluminosilicate glass. These clear differences between the speciation of the above elements in this material and those reported for fly ash from conventional PC combustion. 15 refs., 8 figs., 5 tabs.

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.

Geochemical modelling. Whatif-AQ: a computer programme for speciation calculations

International Nuclear Information System (INIS)

Skytte-Jensen, B.; Jensen, H.; Nielsen, O.J.

1985-01-01

WHATIF-AQ is part of a family of programmes for calculations of geochemistry in the near-field of radioactive waste with temperature gradients. The computer programme presented in this report calculates speciation and saturation indices for an aqueous solution at temperatures between 0-125 0 C. This report also serves as a manual to the programme

Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

Science.gov (United States)

Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L

2012-08-20

Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters

Foliar or root exposures to smelter particles: Consequences for lead compartmentalization and speciation in plant leaves

International Nuclear Information System (INIS)

Schreck, Eva; Dappe, Vincent; Sarret, Géraldine; Sobanska, Sophie; Nowak, Dorota; Nowak, Jakub; Stefaniak, Elżbieta Anna; Magnin, Valérie; Ranieri, Vincent; Dumat, Camille

2014-01-01

In urban areas with high fallout of airborne particles, metal uptake by plants mainly occurs by foliar pathways and can strongly impact crop quality. However, there is a lack of knowledge on metal localization and speciation in plants after pollution exposure, especially in the case of foliar uptake. In this study, two contrasting crops, lettuce (Lactuca sativa L.) and rye-grass (Lolium perenne L.), were exposed to Pb-rich particles emitted by a Pb-recycling factory via either atmospheric or soil application. Pb accumulation in plant leaves was observed for both ways of exposure. The mechanisms involved in Pb uptake were investigated using a combination of microscopic and spectroscopic techniques (electron microscopy, laser ablation, Raman microspectroscopy, and X-ray absorption spectroscopy). The results show that Pb localization and speciation are strongly influenced by the type of exposure (root or shoot pathway) and the plant species. Foliar exposure is the main pathway of uptake, involving the highest concentrations in plant tissues. Under atmospheric fallouts, Pb-rich particles were strongly adsorbed on the leaf surface of both plant species. In lettuce, stomata contained Pb-rich particles in their apertures, with some deformations of guard cells. In addition to PbO and PbSO 4 , chemical forms that were also observed in pristine particles, new species were identified: organic compounds (minimum 20%) and hexagonal platy crystals of PbCO 3 . In rye-grass, the changes in Pb speciation were even more egregious: Pb–cell wall and Pb–organic acid complexes were the major species observed. For root exposure, identified here as a minor pathway of Pb transfer compared to foliar uptake, another secondary species, pyromorphite, was identified in rye-grass leaves. Finally, combining bulk and spatially resolved spectroscopic techniques permitted both the overall speciation and the minor but possibly highly reactive lead species to be determined in order to better

Foliar or root exposures to smelter particles: Consequences for lead compartmentalization and speciation in plant leaves

Energy Technology Data Exchange (ETDEWEB)

Schreck, Eva [Université de Toulouse, INP, UPS, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), ENSAT, Avenue de l' Agrobiopole, 31326 Castanet-Tolosan (France); CNRS, EcoLab, 31326 Castanet-Tolosan (France); Géosciences Environnement Toulouse (GET), Observatoire Midi Pyrénées, Université de Toulouse, CNRS, IRD, 14 Avenue E. Belin, F-31400 Toulouse (France); Dappe, Vincent [LASIR (UMR CNRS 8516), Université de Lille 1, Bât. C5, 59655 Villeneuve d' Ascq Cedex (France); Sarret, Géraldine [ISTerre, UMR 5275, Université Grenoble I, CNRS, F-38041 Grenoble (France); Sobanska, Sophie [LASIR (UMR CNRS 8516), Université de Lille 1, Bât. C5, 59655 Villeneuve d' Ascq Cedex (France); Nowak, Dorota; Nowak, Jakub; Stefaniak, Elżbieta Anna [Department of Chemistry, John Paul II Catholic University of Lublin, Al. Kraśnicka 102, 20-718 Lublin (Poland); Magnin, Valérie [ISTerre, UMR 5275, Université Grenoble I, CNRS, F-38041 Grenoble (France); Ranieri, Vincent [CEA-INAC, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Dumat, Camille, E-mail: camille.dumat@ensat.fr [Université de Toulouse, INP, UPS, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), ENSAT, Avenue de l' Agrobiopole, 31326 Castanet-Tolosan (France); CNRS, EcoLab, 31326 Castanet-Tolosan (France)

2014-04-01

In urban areas with high fallout of airborne particles, metal uptake by plants mainly occurs by foliar pathways and can strongly impact crop quality. However, there is a lack of knowledge on metal localization and speciation in plants after pollution exposure, especially in the case of foliar uptake. In this study, two contrasting crops, lettuce (Lactuca sativa L.) and rye-grass (Lolium perenne L.), were exposed to Pb-rich particles emitted by a Pb-recycling factory via either atmospheric or soil application. Pb accumulation in plant leaves was observed for both ways of exposure. The mechanisms involved in Pb uptake were investigated using a combination of microscopic and spectroscopic techniques (electron microscopy, laser ablation, Raman microspectroscopy, and X-ray absorption spectroscopy). The results show that Pb localization and speciation are strongly influenced by the type of exposure (root or shoot pathway) and the plant species. Foliar exposure is the main pathway of uptake, involving the highest concentrations in plant tissues. Under atmospheric fallouts, Pb-rich particles were strongly adsorbed on the leaf surface of both plant species. In lettuce, stomata contained Pb-rich particles in their apertures, with some deformations of guard cells. In addition to PbO and PbSO{sub 4}, chemical forms that were also observed in pristine particles, new species were identified: organic compounds (minimum 20%) and hexagonal platy crystals of PbCO{sub 3}. In rye-grass, the changes in Pb speciation were even more egregious: Pb–cell wall and Pb–organic acid complexes were the major species observed. For root exposure, identified here as a minor pathway of Pb transfer compared to foliar uptake, another secondary species, pyromorphite, was identified in rye-grass leaves. Finally, combining bulk and spatially resolved spectroscopic techniques permitted both the overall speciation and the minor but possibly highly reactive lead species to be determined in order to

Tempo-spatial variation of emission inventories of speciated volatile organic compounds from on-road vehicles in China

Directory of Open Access Journals (Sweden)

H. Cai

2009-09-01

Full Text Available Emission inventories of sixty-seven speciated non-methane volatile organic compounds (NMVOC from on-road vehicles in China were estimated for the period of 1980–2005, using seven NMVOC emission profiles, which were summarized based on local and international measurements from published literatures dealing with specific vehicle categories running under particular modes.

Results show an exponential growth trend of China's historical emissions of alkanes, alkenes, alkines, aromatics and carbonyls during the period of 1980–2005, increasing from 63.9, 39.3, 6.9, 36.8 and 24.1 thousand tons, respectively, in 1980 to 2778.2, 1244.5, 178.7, 1351.7 and 406.0 thousand tons, respectively, in 2005, which coincided well with China's economic growth. Emission inventories of alkenes, aromatics and carbonyls were gridded at a high resolution of 40 km×40 km for air quality simulation and health risk evaluation, using the geographic information system (GIS methodology. Spatial distribution of speciated NMVOC emissions shows a clear difference in emission densities between developed eastern and relatively underdeveloped western and inland China. Besides, the appearance and expansion of high-emission areas was another notable characteristic of spatial distribution of speciated NMVOC emissions during the period.

Emission contributions of vehicle categories to speciated NMVOC groups showed annual variation, due to the variance in the provincial emissions and in the relative fractions of the seven emission profiles adopted at the provincial level. Highly reactive and toxic compounds accounted for high proportions of emissions of speciated NMVOC groups. The most abundant compounds were isopentane, pentane and butane from alkanes; ethene, propene, 2-methyl-2-butene and ethyne from alkenes and alkines; benzene, toluene, ethylbenzene, o-xylene, and m,p-xylene (BTEX and 1,2,4-trimethylbenzene from aromatics and formaldehyde, acetaldehyde

Relationship between metal speciation in soil solution and metal adsorption at the root surface of ryegrass.

Science.gov (United States)

Kalis, Erwin J J; Temminghoff, Erwin J M; Town, Raewyn M; Unsworth, Emily R; van Riemsdijk, Willem H

2008-01-01

The total metal content of the soil or total metal concentration in the soil solution is not always a good indicator for metal availability to plants. Therefore, several speciation techniques have been developed that measure a defined fraction of the total metal concentration in the soil solution. In this study the Donnan Membrane Technique (DMT) was used to measure free metal ion concentrations in CaCl(2) extractions (to mimic the soil solution, and to work under standardized conditions) of 10 different soils, whereas diffusive gradients in thin-films (DGT) and scanning chronopotentiometry (SCP) were used to measure the sum of free and labile metal concentrations in the CaCl(2) extracts. The DGT device was also exposed directly to the (wetted) soil (soil-DGT). The metal concentrations measured with the speciation techniques are related to the metal adsorption at the root surface of ryegrass (Lolium perenne L.), to be able to subsequently predict metal uptake. In most cases the metal adsorption related pH-dependently to the metal concentrations measured by DMT, SCP, and DGT in the CaCl(2) extract. However, the relationship between metal adsorption at the root surface and the metal concentrations measured by the soil-DGT was not-or only slightly-pH dependent. The correlations between metal adsorption at the root surface and metal speciation detected by different speciation techniques allow discussion about rate limiting steps in biouptake and the contribution of metal complexes to metal bioavailability.

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...

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.

Geological and anthropogenic factors influencing mercury speciation in mine wastes: An EXAFS spectroscopy study

Science.gov (United States)

Kim, C.S.; Rytuba, J.J.; Brown, Gordon E.

2004-01-01

The speciation of Hg is a critical determinant of its mobility, reactivity, and potential bioavailability in mine-impacted regions. Furthermore, Hg speciation in these complex natural systems is influenced by a number of physical, geological, and anthropogenic variables. In order to investigate the degree to which several of these variables may affect Hg speciation, extended X-ray absorption fine structure (EXAFS) spectroscopy was used to determine the Hg phases and relative proportions of these phases present in Hg-bearing wastes from selected mine-impacted regions in California and Nevada. The geological origin of Hg ore has a significant effect on Hg speciation in mine wastes. Specifically, samples collected from hot-spring Hg deposits were found to contain soluble Hg-chloride phases, while such phases were largely absent in samples from silica-carbonate Hg deposits; in both deposit types, however, Hg-sulfides in the form of cinnabar (HgS, hex.) and metacinnabar (HgS, cub.) dominate. Calcined wastes in which Hg ore was crushed and roasted in excess of 600??C, contain high proportions of metacinnabar while the main Hg-containing phase in unroasted waste rock samples from the same mines is cinnabar. The calcining process is thought to promote the reconstructive phase transformation of cinnabar to metacinnabar, which typically occurs at 345??C. The total Hg concentration in calcines is strongly correlated with particle size, with increases of nearly an order of magnitude in total Hg concentration between the 500-2000 ??m and process, identified the presence of Hg-sulfides and schuetteite (Hg3O2SO4), which may have formed as a result of long-term Hg(0) burial in reducing high-sulfide sediments. ?? 2003 Elsevier Ltd. All rights reserved.

Modeling bromide effects on yields and speciation of dihaloacetonitriles formed in chlorinated drinking water.

Science.gov (United States)

Roccaro, Paolo; Chang, Hyun-shik; Vagliasindi, Federico G A; Korshin, Gregory V

2013-10-15

This study examined effects of bromide on yields and speciation of dihaloacetonitrile (DHAN) species that included dichloro-, bromochloro- and dibromoacetonitriles generated in chlorinated water. Experimental data obtained using two water sources, varying concentrations and characters of Natural Organic Matter (NOM), bromide concentrations, reaction times, chlorine doses, temperatures and pHs were interpreted using a semi-phenomenological model that assumed the presence of three kinetically distinct sites in NOM (denoted as sites S1, S2 and S3) and the occurrence of sequential incorporation of bromine and chlorine into them. One site was found to react very fast with the chlorine and bromine but its contribution in the DHAN generation was very low. The site with the highest contribution to the yield of DHAN (>70%) has the lowest reaction rates. The model introduced dimensionless coefficients (denoted as φ1(DHAN), φ2(DHAN) and φ3(DHAN)) applicable to the initial DHAN generation sites and their monochlorinated and monobrominated products, respectively. These parameters were used to quantify the kinetic preference to bromine incorporation over that of chlorine. Values of these coefficients optimized for DHAN formation were indicative of the strongly preferential incorporation of bromine into the engaged NOM sites. The same set of φ(i)(DHAN) coefficients could be used to model the speciation of DHAN released from their kinetically different precursors. The dimensionless speciation coefficients φ(i)(DHAN) were determined to be site specific and dependent on the NOM content and character as well as pH. The presented model of DHAN formation and speciation can help quantify in more detail the generation of DHAN and provide more insight necessary for further assessment of their potential health effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Glacial cycles as an allopatric speciation pump in north-eastern American freshwater fishes.

Science.gov (United States)

April, Julien; Hanner, Robert H; Dion-Côté, Anne-Marie; Bernatchez, Louis

2013-01-01

Allopatric speciation may be the principal mechanism generating new species. Yet, it remains difficult to judge the generality of this process because few studies have provided evidence that geographic isolation has triggered the development of reproductive isolation over multiple species of a regional fauna. Here, we first combine results from new empirical data sets (7 taxa) and published literature (9 taxa) to show that the eastern Great Lakes drainage represents a multispecies suture zone for glacial lineages of freshwater fishes with variable levels of genetic divergence. Second, we performed amplified fragment length polymorphism analyses among four pairs of lineages. Results indicate that lineages with relatively deep levels of mtDNA 5' COI (barcode) sequence divergence (>2%) developed strong reproductive barriers, while lineages with lower levels of divergence show weaker reproductive isolation when found in sympatry. This suggests that a threshold of 2% sequence divergence at mtDNA could be used as a first step to flag cryptic species in North American freshwater fishes. By describing different levels of divergence and reproductive isolation in different co-occurring fishes, we offer strong evidence that allopatric speciation has contributed significantly to the diversification of north-eastern American freshwater fishes and confirm that Pleistocene glacial cycles can be viewed as a 'speciation pump' that played a predominant role in generating biodiversity. © 2012 Blackwell Publishing Ltd.

ESTIMATING SPECIATION AND EXTINCTION RATES FROM DIVERSITY DATA AND THE FOSSIL RECORD

NARCIS (Netherlands)

Etienne, Rampal S.; Apol, M. Emile F.

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth-death model of

Nickel speciation and complexation kinetics in freshwater by ligand exchange and DPCSV

NARCIS (Netherlands)

Han Bin Xue,; Jansen, S.; Prasch, A.; Sigg, L.

2001-01-01

A technique of ligand exchange with DMG (dimethylglyoxime) and DPCSV was applied to determine Ni speciation in lake, river, and groundwater samples. The working conditions related to ligand-exchange equilibrium were optimized, and the ligand-exchange kinetics were examined. The observed

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)

Environmental controls on the speciation and distribution of mercury in surface sediments of a tropical estuary, India

International Nuclear Information System (INIS)

Chakraborty, Parthasarathi; Babu, P.V. Raghunadh

2015-01-01

Highlights: • Physico-chemical parameters of water column control Hg speciation in sediments. • Sediments from the middle of the estuary were contaminated by Hg. • Concentrations of Hg were less during the monsoon and post monsoon period. • Salinity, pH of water column may change Hg speciation of the bottom sediments. • TOC in sediments control Hg partitioning in the system. - Abstract: Distribution and speciation of mercury (Hg) in the sediments from a tropical estuary (Godavari estuary) was influenced by the changing physico-chemical parameters of the overlying water column. The sediments from the upstream and downstream of the estuary were uncontaminated but the sediments from the middle of the estuary were contaminated by Hg. The concentrations of Hg became considerably less during the monsoon and post monsoon period. Total Hg concentrations and its speciation (at the middle of the estuary) were dependent on the salinity of the overlying water column. However, salinity had little or no effect on Hg association with organic phases in the sediments at downstream. Increasing pH of the overlying water column corresponded with an increase in the total Hg content in the sediments. Total organic carbon in the sediments played an important role in controlling Hg partitioning in the system. Uncomplexed Hg binding ligands were available in the sediments

Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

Science.gov (United States)

Aleixandre, Pau; Hernández Montoya, Julio; Milá, Borja

2013-01-01

The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving

Aluminium (Al) fractionation and speciation: getting closer to describing the factors influencing Al(sup3+) in water impacted by acid mine drainage

CSIR Research Space (South Africa)

Chamier, J

2015-07-01

Full Text Available Acid mine drainage (AMD) severely impacts the water chemistry of a receiving resource, changing the occurrence, speciation and toxicity of metals such as Aluminium (Al). The toxicity of Al is determined by its speciation represented by the labile...

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

Directory of Open Access Journals (Sweden)

Mark Ravinet

2018-05-01

Full Text Available Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus and the Japan Sea stickleback (G. nipponicus, which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

Science.gov (United States)

Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

2018-05-01

Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

Equilibrium Measurements of the NH3-CO2-H2O System: Speciation Based on Raman Spectroscopy and Multivariate Modeling

Directory of Open Access Journals (Sweden)

Maths Halstensen

2017-01-01

Full Text Available Liquid speciation is important for reliable process design and optimization of gas-liquid absorption process. Liquid-phase speciation methods are currently available, although they involve tedious and time-consuming laboratory work. Raman spectroscopy is well suited for in situ monitoring of aqueous chemical reactions. Here, we report on the development of a method for speciation of the CO2-NH3-H2O equilibrium using Raman spectroscopy and PLS-R modeling. The quantification methodology presented here offers a novel approach to provide rapid and reliable predictions of the carbon distribution of the CO2-NH3-H2O system, which may be used for process control and optimization. Validation of the reported speciation method which is based on independent, known, NH3-CO2-H2O solutions shows estimated prediction uncertainties for carbonate, bicarbonate, and carbamate of 6.45 mmol/kg H2O, 34.39 mmol/kg H2O, and 100.9 mmol/kg H2O, respectively.

Metal Speciation in Landfill Leachates with a Focus on the Influence of Organic Matter

Energy Technology Data Exchange (ETDEWEB)

F Claret; C Tournassat; C Crouzet; E Gaucher; T Schäfer; G Braibant; D Guyonnet

2011-12-31

This study characterizes the heavy-metal content in leachates collected from eight landfills in France. In order to identify heavy metal occurrence in the different size fractions of leachates, a cascade filtration protocol was applied directly in the field, under a nitrogen gas atmosphere to avoid metal oxidation. The results of analyses performed on the leachates suggest that most of the metals are concentrated in the <30 kDa fraction, while lead, copper and cadmium show an association with larger particles. Initial speciation calculations, without considering metal association with organic matter, suggest that leachate concentrations in lead, copper, nickel and zinc are super-saturated with respect to sulphur phases. Speciation calculations that account for metal complexation with organic matter, considered as fulvic acids based on C1(s) NEXAFS spectroscopy, show that this mechanism is not sufficient to explain such deviation from equilibrium conditions. It is therefore hypothesized that the deviation results also from the influence of biological activity on the kinetics of mineral phase precipitation and dissolution, thus providing a dynamic system. The results of chemical analyses of sampled fluids are compared with speciation calculations and some implications for the assessment of metal mobility and natural attenuation in a context of landfill risk assessment are discussed.

Carbon speciation in ash, residual waste and contaminated soil by thermal and chemical analyses.

Science.gov (United States)

Kumpiene, Jurate; Robinson, Ryan; Brännvall, Evelina; Nordmark, Désirée; Bjurström, Henrik; Andreas, Lale; Lagerkvist, Anders; Ecke, Holger

2011-01-01

Carbon in waste can occur as inorganic (IC), organic (OC) and elemental carbon (EC) each having distinct chemical properties and possible environmental effects. In this study, carbon speciation was performed using thermogravimetric analysis (TGA), chemical degradation tests and the standard total organic carbon (TOC) measurement procedures in three types of waste materials (bottom ash, residual waste and contaminated soil). Over 50% of the total carbon (TC) in all studied materials (72% in ash and residual waste, and 59% in soil) was biologically non-reactive or EC as determined by thermogravimetric analyses. The speciation of TOC by chemical degradation also showed a presence of a non-degradable C fraction in all materials (60% of TOC in ash, 30% in residual waste and 13% in soil), though in smaller amounts than those determined by TGA. In principle, chemical degradation method can give an indication of the presence of potentially inert C in various waste materials, while TGA is a more precise technique for C speciation, given that waste-specific method adjustments are made. The standard TOC measurement yields exaggerated estimates of organic carbon and may therefore overestimate the potential environmental impacts (e.g. landfill gas generation) of waste materials in a landfill environment. Copyright © 2010 Elsevier Ltd. All rights reserved.

Data Fusion approach for spatial analysis of speciated PM2.5 across time

Data.gov (United States)

U.S. Environmental Protection Agency — speciated pm2.5 monitoring data and total pm2.5 monitoring data. This dataset is associated with the following publication: Rundel, C., E. Schliep, A. Gelfand, and...

Particulate matter speciation profiles for light-duty gasoline vehicles in the United States.

Science.gov (United States)

Sonntag, Darrell B; Baldauf, Richard W; Yanca, Catherine A; Fulper, Carl R

2014-05-01

Representative profiles for particulate matter particles less than or equal to 2.5 microm (PM2.5) are developed from the Kansas City Light-Duty Vehicle Emissions Study for use in the US. Environmental Protection Agency (EPA) vehicle emission model, the Motor Vehicle Emission Simulator (MOVES), and for inclusion in the EPA SPECIATE database for speciation profiles. The profiles are compatible with the inputs of current photochemical air quality models, including the Community Multiscale Air Quality Aerosol Module Version 6 (AE6). The composition of light-duty gasoline PM2.5 emissions differs significantly between cold start and hot stabilized running emissions, and between older and newer vehicles, reflecting both impacts of aging/deterioration and changes in vehicle technology. Fleet-average PM2.5 profiles are estimated for cold start and hot stabilized running emission processes. Fleet-average profiles are calculated to include emissions from deteriorated high-emitting vehicles that are expected to continue to contribute disproportionately to the fleet-wide PM2.5 emissions into the future. The profiles are calculated using a weighted average of the PM2.5 composition according to the contribution of PM2.5 emissions from each class of vehicles in the on-road gasoline fleet in the Kansas City Metropolitan Statistical Area. The paper introduces methods to exclude insignificant measurements, correct for organic carbon positive artifact, and control for contamination from the testing infrastructure in developing speciation profiles. The uncertainty of the PM2.5 species fraction in each profile is quantified using sampling survey analysis methods. The primary use of the profiles is to develop PM2.5 emissions inventories for the United States, but the profiles may also be used in source apportionment, atmospheric modeling, and exposure assessment, and as a basis for light-duty gasoline emission profiles for countries with limited data. PM2.5 speciation profiles were

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, ...

Origin and speciation of Picea schrenkiana and Piceasmithiana in the Center Asian Highlands and Himalayas.

Science.gov (United States)

Li, Lili; Sun, Yongshuai; Zou, Jiabin; Yue, Wei; Wang, Xi; Liu, Jianquan

Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with Picea likiangensis or Picea wilsonii which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, P. schrenkiana appeared to be closely related to P. likiangensis , although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that P. schrenkiana and P. smithiana are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the P. likiangensis - P. wilsonii clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands.

Integration of the metal ion charge neutralization model for humic acid complexation into the geochemical speciation code EQ3/6

International Nuclear Information System (INIS)

Brendler, V.

2002-01-01

Geochemical modeling often requires the consideration of humics as major complexing agent and colloid. The metal ion charge neutralization model can handle respective interactions and has therefore been integrated into the speciation software EQ3/6. An application showing the influence of the pH-dependence of the loading capacity on actinide speciation is given. (orig.)

Actinide, lanthanide and fission product speciation and electrochemistry in high and low temperature ionic melts

Energy Technology Data Exchange (ETDEWEB)

Bhatt, Anand I.; Kinoshita, Hajime; Koster, Anne L.; May, Iain; Sharrad, Clint A.; Volkovich, Vladimir A.; Fox, O. Danny; Jones, Chris J.; Lewin, Bob G.; Charnock, John M.; Hennig, Christoph

2004-07-01

There is currently a great deal of research interest in the development of molten salt technology, both classical high temperature melts and low temperature ionic liquids, for the electrochemical separation of the actinides from spent nuclear fuel. We are interested in gaining a better understanding of actinide and key fission product speciation and electrochemical properties in a range of melts. Our studies in high temperature alkali metal melts (including LiCl and LiCl-KCl and CsCl-NaCl eutectics) have focussed on in-situ species of U, Th, Tc and Ru using X-ray absorption spectroscopy (XAS, both EXAFS and XANES) and electronic absorption spectroscopy (EAS). We report unusual actinide speciation in high temperature melts and an evaluation of the likelihood of Ru or Tc volatilization during plant operation. Our studies in lower temperature melts (ionic liquids) have focussed on salts containing tertiary alkyl group 15 cations and the bis(tri-fluor-methyl)sulfonyl)imide anion, melts which we have shown to have exceptionally wide electrochemical windows. We report Ln, Th, U and Np speciation (XAS, EAS and vibrational spectroscopy) and electrochemistry in these melts and relate the solution studies to crystallographic characterised benchmark species. (authors)

Actinide, lanthanide and fission product speciation and electrochemistry in high and low temperature ionic melts

International Nuclear Information System (INIS)

Bhatt, Anand I.; Kinoshita, Hajime; Koster, Anne L.; May, Iain; Sharrad, Clint A.; Volkovich, Vladimir A.; Fox, O. Danny; Jones, Chris J.; Lewin, Bob G.; Charnock, John M.; Hennig, Christoph

2004-01-01

There is currently a great deal of research interest in the development of molten salt technology, both classical high temperature melts and low temperature ionic liquids, for the electrochemical separation of the actinides from spent nuclear fuel. We are interested in gaining a better understanding of actinide and key fission product speciation and electrochemical properties in a range of melts. Our studies in high temperature alkali metal melts (including LiCl and LiCl-KCl and CsCl-NaCl eutectics) have focussed on in-situ species of U, Th, Tc and Ru using X-ray absorption spectroscopy (XAS, both EXAFS and XANES) and electronic absorption spectroscopy (EAS). We report unusual actinide speciation in high temperature melts and an evaluation of the likelihood of Ru or Tc volatilization during plant operation. Our studies in lower temperature melts (ionic liquids) have focussed on salts containing tertiary alkyl group 15 cations and the bis(tri-fluor-methyl)sulfonyl)imide anion, melts which we have shown to have exceptionally wide electrochemical windows. We report Ln, Th, U and Np speciation (XAS, EAS and vibrational spectroscopy) and electrochemistry in these melts and relate the solution studies to crystallographic characterised benchmark species. (authors)

Speciation and leachability of copper in mine tailings from porphyry copper mining

DEFF Research Database (Denmark)

Hansen, Henrik K.; Yianatos, Juan B; Ottosen, Lisbeth M.

2005-01-01

Mine tailing from the El Teniente-Codelco copper mine situated in VI Region of Chile was analysed in order to evaluate the mobility and speciation of copper in the solid material. Mine tailing was sampled after the rougher flotation circuits, and the copper content was measured to 1150mgkg^-^1 dry...... matter. This tailing was segmented into fractions of different size intervals: 0-38, 38-45, 45-53, 53-75, 75-106, 106-150, 150-212, and >212@mm, respectively. Copper content determination, sequential chemical extraction, and desorption experiments were carried out for each size interval in order...... to evaluate the speciation of copper. It was found that the particles of smallest size contained 50-60% weak acid leachable copper, whereas only 32% of the copper found in largest particles could be leached in weak acid. Copper oxides and carbonates were the dominating species in the smaller particles...

Solid phase extraction for the speciation and preconcentration of inorganic selenium in water samples: a review.

Science.gov (United States)

Herrero Latorre, C; Barciela García, J; García Martín, S; Peña Crecente, R M

2013-12-04

Selenium is an essential element for the normal cellular function of living organisms. However, selenium is toxic at concentrations of only three to five times higher than the essential concentration. The inorganic forms (mainly selenite and selenate) present in environmental water generally exhibit higher toxicity (up to 40 times) than organic forms. Therefore, the determination of low levels of different inorganic selenium species in water is an analytical challenge. Solid-phase extraction has been used as a separation and/or preconcentration technique prior to the determination of selenium species due to the need for accurate measurements for Se species in water at extremely low levels. The present paper provides a critical review of the published methods for inorganic selenium speciation in water samples using solid phase extraction as a preconcentration procedure. On the basis of more than 75 references, the different speciation strategies used for this task have been highlighted and classified. The solid-phase extraction sorbents and the performance and analytical characteristics of the developed methods for Se speciation are also discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

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

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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

Quantitative uranium speciation with U M{sub 4,5}-edge HERFD absorption spectra

Energy Technology Data Exchange (ETDEWEB)

Kvashnina, Kristina O.; Rossberg, Andre [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Molecular Structures

2017-06-01

This report gives a brief description of the quantitative uranium speciation performed by iterative transformation factor analysis (ITFA) of High Energy Resolution X-ray Fluorescence Detection (HERFD) data collected at the M{sub 4,5} edge.

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.

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.)

AN ANALYTICAL METHOD FOR CHEMICAL SPECIATION OF SELENIUM IN SOIL

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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.

The long term tsunami impact: Evolution of iron speciation and major elements concentration in tsunami deposits from Thailand.

Science.gov (United States)

Kozak, Lidia; Niedzielski, Przemyslaw

2017-08-01

The article describes the unique studies of the chemical composition changes of new geological object (tsunami deposits in south Thailand - Andaman Sea Coast) during four years (2005-2008) from the beginning of formation of it (deposition of tsunami transported material, 26 December 2004). The chemical composition of the acid leachable fraction of the tsunami deposits has been studied in the scope of concentration macrocompounds - concentration of calcium, magnesium, iron, manganese and iron speciation - the occurrence of Fe(II), Fe(III) and non-ionic iron species described as complexed iron (Fe complex). The changes of chemical composition and iron speciation in the acid leachable fraction of tsunami deposits have been observed with not clear tendencies of changes direction. For iron speciation changes the transformation of the Fe complex to Fe(III) has been recorded with no significant changes of the level of Fe(II). Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient

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Rossetto Maurizio

2012-08-01

Full Text Available Abstract Background Four of the five species of Telopea (Proteaceae are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation. Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Results Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR and six chloroplast microsatellites (cpSSR were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM. The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed

Speciation and detection of arsenic in aqueous samples: A review of recent progress in non-atomic spectrometric methods

Energy Technology Data Exchange (ETDEWEB)

Ma, Jian [State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102 (China); Department of Chemistry and Biochemistry, University of Texas, 700 Planetarium Place, Arlington, TX 76019 (United States); Sengupta, Mrinal K. [Department of Chemistry and Biochemistry, University of Texas, 700 Planetarium Place, Arlington, TX 76019 (United States); Thermo Fisher Scientific, Dionex Products, 445 Lakeside Drive, Sunnyvale, CA, 94085 (United States); Yuan, Dongxing [State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102 (China); Dasgupta, Purnendu K., E-mail: Dasgupta@uta.edu [Department of Chemistry and Biochemistry, University of Texas, 700 Planetarium Place, Arlington, TX 76019 (United States)

2014-06-01

Highlights: • Compilation of principal official documents and major review articles, including the toxicology and chemistry of As. • Review of non-atomic spectrometric methods for speciation and detection of arsenic in aqueous samples (2005–2013) of the performance of field-usable methods. - Abstract: Inorganic arsenic (As) displays extreme toxicity and is a class A human carcinogen. It is of interest to both analytical chemists and environmental scientists. Facile and sensitive determination of As and knowledge of the speciation of forms of As in aqueous samples are vitally important. Nearly every nation has relevant official regulations on permissible limits of drinking water As content. The size of the literature on As is therefore formidable. The heart of this review consists of two tables: one is a compilation of principal official documents and major review articles, including the toxicology and chemistry of As. This includes comprehensive official compendia on As speciation, sample treatment, recommended procedures for the determination of As in specific sample matrices with specific analytical instrument(s), procedures for multi-element (including As) speciation and analysis, and prior comprehensive reviews on arsenic analysis. The second table focuses on the recent literature (2005–2013, the coverage for 2013 is incomplete) on As measurement in aqueous matrices. Recent As speciation and analysis methods based on spectrometric and electrochemical methods, inductively coupled plasma-mass spectrometry, neutron activation analysis and biosensors are summarized. We have deliberately excluded atomic optical spectrometric techniques (atomic absorption, atomic fluorescence, inductively coupled plasma-optical emission spectrometry) not because they are not important (in fact the majority of arsenic determinations are possibly carried out by one of these techniques) but because these methods are sufficiently mature and little meaningful innovation has been

Speciation and detection of arsenic in aqueous samples: A review of recent progress in non-atomic spectrometric methods

International Nuclear Information System (INIS)

Ma, Jian; Sengupta, Mrinal K.; Yuan, Dongxing; Dasgupta, Purnendu K.

2014-01-01

Highlights: • Compilation of principal official documents and major review articles, including the toxicology and chemistry of As. • Review of non-atomic spectrometric methods for speciation and detection of arsenic in aqueous samples (2005–2013) of the performance of field-usable methods. - Abstract: Inorganic arsenic (As) displays extreme toxicity and is a class A human carcinogen. It is of interest to both analytical chemists and environmental scientists. Facile and sensitive determination of As and knowledge of the speciation of forms of As in aqueous samples are vitally important. Nearly every nation has relevant official regulations on permissible limits of drinking water As content. The size of the literature on As is therefore formidable. The heart of this review consists of two tables: one is a compilation of principal official documents and major review articles, including the toxicology and chemistry of As. This includes comprehensive official compendia on As speciation, sample treatment, recommended procedures for the determination of As in specific sample matrices with specific analytical instrument(s), procedures for multi-element (including As) speciation and analysis, and prior comprehensive reviews on arsenic analysis. The second table focuses on the recent literature (2005–2013, the coverage for 2013 is incomplete) on As measurement in aqueous matrices. Recent As speciation and analysis methods based on spectrometric and electrochemical methods, inductively coupled plasma-mass spectrometry, neutron activation analysis and biosensors are summarized. We have deliberately excluded atomic optical spectrometric techniques (atomic absorption, atomic fluorescence, inductively coupled plasma-optical emission spectrometry) not because they are not important (in fact the majority of arsenic determinations are possibly carried out by one of these techniques) but because these methods are sufficiently mature and little meaningful innovation has been

Coupling pervaporation to AAS for inorganic and organic mercury determination. A new approach to speciation of Hg in environmental samples.

Science.gov (United States)

Fernandez-Rivas, C; Muñoz-Olivas, R; Camara, C

2001-12-01

The design and development of a new approach for Hg speciation in environmental samples is described in detail. This method, consisting of the coupling of pervaporation and atomic absorption spectrometry, is based on a membrane phenomenon that combines the evaporation of volatile analytes and their diffusion through a polymeric membrane. It is proposed here as an alternative to gas chromatography for speciation of inorganic and organic Hg compounds, as the latter compounds are volatile and can be separated by applying the principles mentioned above. The interest of this method lies in its easy handling, low cost, and rapidity for the analysis of liquid and solid samples. This method has been applied to Hg speciation in a compost sample provided by a waste water treatment plant.

Chromium speciation in environmental samples using a solid phase spectrophotometric method

Science.gov (United States)

Amin, Alaa S.; Kassem, Mohammed A.

2012-10-01

A solid phase extraction technique is proposed for preconcentration and speciation of chromium in natural waters using spectrophotometric analysis. The procedure is based on sorption of chromium(III) as 4-(2-benzothiazolylazo)2,2'-biphenyldiol complex on dextran-type anion-exchange gel (Sephadex DEAE A-25). After reduction of Cr(VI) by 0.5 ml of 96% concentrated H2SO4 and ethanol, the system was applied to the total chromium. The concentration of Cr(VI) was calculated as the difference between the total Cr and the Cr(III) content. The influences of some analytical parameters such as: pH of the aqueous solution, amounts of 4-(2-benzothiazolylazo)2,2'-biphenyldiol (BTABD), and sample volumes were investigated. The absorbance of the gel, at 628 and 750 nm, packed in a 1.0 mm cell, is measured directly. The molar absorptivities were found to be 2.11 × 107 and 3.90 × 107 L mol-1 cm-1 for 500 and 1000 ml, respectively. Calibration is linear over the range 0.05-1.45 μg L-1 with RSD of <1.85% (n = 8.0). Using 35 mg exchanger, the detection and quantification limits were 13 and 44 ng L-1 for 500 ml sample, whereas for 1000 ml sample were 8.0 and 27 ng L-1, respectively. Increasing the sample volume can enhance the sensitivity. No considerable interferences have been observed from other investigated anions and cations on the chromium speciation. The proposed method was applied to the speciation of chromium in natural waters and total chromium preconcentration in microwave digested tobacco, coffee, tea, and soil samples. The results were simultaneously compared with those obtained using an ET AAS method, whereby the validity of the method has been tested.

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

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.

Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation.

Science.gov (United States)

Bay, Rachael A; Arnegard, Matthew E; Conte, Gina L; Best, Jacob; Bedford, Nicole L; McCann, Shaugnessy R; Dubin, Matthew E; Chan, Yingguang Frank; Jones, Felicity C; Kingsley, David M; Schluter, Dolph; Peichel, Catherine L

2017-11-06

Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of a soil enzyme on iron-cyanide complex speciation and mineral adsorption.

Science.gov (United States)

Zimmerman, Andrew R; Kang, Dong-Hee; Ahn, Mi-Youn; Hyun, Seunghun; Banks, M Katherine

2008-01-01

Cyanide is commonly found as ferrocyanide [Fe(II)(CN)(6)](-4) and in the more mobile form, ferricyanide [Fe(III)(CN)(6)](-3) in contaminated soils and sediments. Although soil minerals may influence ferrocyanide speciation, and thus mobility, the possible influence of soil enzymes has not been examined. In a series of experiments conducted under a range of soil-like conditions, laccase, a phenoloxidase enzyme derived from the fungi Trametes versicolor, was found to exert a large influence on iron-cyanide speciation and mobility. In the presence of laccase, up to 93% of ferrocyanide (36-362ppm) was oxidized to ferricyanide within 4h. No significant effect of pH (3.6 and 6.2) or initial ferrocyanide concentration on the extent or rate of oxidation was found and ferrocyanide oxidation did not occur in the absence of laccase. Relative to iron-cyanide-mineral systems without laccase, ferrocyanide adsorption to aluminum hydroxide and montmorillonite decreased in the presence of laccase and was similar to or somewhat greater than that of ferricyanide without laccase. Laccase-catalyzed conversion of ferrocyanide to ferricyanide was extensive though up to 33% of the enzyme was mineral-bound. These results demonstrate that soil enzymes can play a major role in ferrocyanide speciation and mobility. Biotic soil components must be considered as highly effective oxidation catalysts that may alter the mobility of metals and metal complexes in soil. Immobilized enzymes should also be considered for use in soil metal remediation efforts.

Q-Speciation and Network Structure Evolution in Invert Calcium Silicate Glasses.

Science.gov (United States)

Kaseman, Derrick C; Retsinas, A; Kalampounias, A G; Papatheodorou, G N; Sen, S

2015-07-02

Binary silicate glasses in the system CaO-SiO2 are synthesized over an extended composition range (42 mol % ≤ CaO ≤ 61 mol %), using container-less aerodynamic levitation techniques and CO2-laser heating. The compositional evolution of Q speciation in these glasses is quantified using (29)Si and (17)O magic angle spinning nuclear magnetic resonance spectroscopy. The results indicate progressive depolymerization of the silicate network upon addition of CaO and significant deviation of the Q speciation from the binary model. The equilibrium constants for the various Q species disproportionation reactions for these glasses are found to be similar to (much smaller than) those characteristic of Li (Mg)-silicate glasses, consistent with the corresponding trends in the field strengths of these modifier cations. Increasing CaO concentration results in an increase in the packing density and structural rigidity of these glasses and consequently in their glass transition temperature Tg. This apparent role reversal of conventional network-modifying cations in invert alkaline-earth silicate glasses are compared and contrasted with that in their alkali silicate counterparts.

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

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

Comparison of analytical techniques for dynamic trace metal speciation in natural freshwaters.

NARCIS (Netherlands)

Sigg, Laura; Black, Frank; Buffle, Jacques; Cao, Jun; Cleven, Rob; Davison, William; Galceran, Josep; Gunkel, Peggy; Kalis, Erwin; Kistler, David; Martin, Michel; Noël, Stéphane; Nur, Yusuf; Odzak, Niksa; Puy, Jaume; Riemsdijk, Willem van; Temminghoff, Erwin; Tercier-Waeber, Mary-Lou; Toepperwien, Stefanie; Town, Raewyn M; Unsworth, Emily R; Warnken, Kent W; Weng, Liping; Xue, Hanbin; Zhang, Hao

2006-01-01

Several techniques for speciation analysis of Cu, Zn, Cd, Pb, and Ni are used in freshwater systems and compared with respect to their performance and to the metal species detected. The analytical techniques comprise the following: (i) diffusion gradients in thin-film gels (DGT); (ii) gel integrated

First insights in the Eu(III) speciation in plant cell suspension cultures

International Nuclear Information System (INIS)

Moll, Henry; Sachs, Susanne

2017-01-01

More than 80 % of the initial Eu(III) amount was associated on Brassica napus cells after an incubation time of 24 h. The spectroscopic speciation of the cell-bound Eu(III) is characterized by an increased intensity of the "7F_2 transition and prolonged luminescence lifetimes.

Solid phase microextraction speciation analysis of triclosan in aqueous mediacontaining sorbing nanoparticles

NARCIS (Netherlands)

Zielinska, K.

2014-01-01

Solid phase microextraction (SPME) is applied in the speciation analysis of the hydrophobic compound triclosan in an aqueous medium containing sorbing SiO2 nanoparticles (NPs). It is found that these NPs, as well as their complexes with triclosan, partition between the bulk medium and the solid

The aqueous solubility and speciation analysis for uranium, neptunium and selenium by the geochemical code(EQ3/6)

International Nuclear Information System (INIS)

Takeda, Seiji; Shima, Shigeki; Kimura, Hideo; Matsuzuru, Hideo

1995-11-01

The geochemical condition of a geologic disposal system of HLW controls the solubility and physicochemical forms of dominant aqueous species for elements, which are one of essential information required for safety assessment. Based on the measured compositions of groundwater, the compositions of groundwater in the disposal system were calculated. The solubility and speciation analyses for the polyvalent elements, uranium, neptunium, and selenium, were performed by the geochemical code EQ3/6. The results obtained were compared with the data appeared in the literatures on the solubilities and speciations. The geochemical behaviors of the elements with respect to the solubility and speciation could quantitatively be elucidated for the compositions of the interstitial waters in an engineered barrier and ground water in a natural barrier. In the pH range of neutral to alkali, the solubilities of U and Np tend to increase with an increase of the carbonate concentration in groundwater. This carbonate concentration dependence of the solubility was also estimated. In the engineered barrier the predominant aqueous species were specified, and in the natural barrier the change of aqueous species was also predicted while the chemical compositions changed from the reducing to oxidizing conditions. The dominant aqueous species for the elements, which migrate in and through the disposal system, were determined by the speciation analysis. (author)

Intraparticulate Metal Speciation Analysis of Soft Complexing Nanoparticles. The Intrinsic Chemical Heterogeneity of Metal-Humic Acid Complexes

DEFF Research Database (Denmark)

Town, R. M.; van Leeuwen, Herman P.

2016-01-01

ion condensation potential for higher valency counterions within the intraparticulate double layer zone of the soft NP. The approach offers new insights into the intrinsic heterogeneity of the HA. complexes, as revealed by the intraparticulate speciation as a function of the true degree of inner......-sphere complexation, theta(M). The ensuing intrinsic heterogeneity parameters, Gamma, for CdHA and CuHA complexes are in very good agreement with those obtained from dynamic electrochemical stripping chronopotentiometric measurements. The overall intraparticulate metal ion speciation is found to depend on theta...

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

The contribution of post-copulatory mechanisms to incipient ecological speciation in sticklebacks.

Science.gov (United States)

Kaufmann, Joshka; Eizaguirre, Christophe; Milinski, Manfred; Lenz, Tobias L

2015-01-01

Ecology can play a major role in species diversification. As individuals are adapting to contrasting habitats, reproductive barriers may evolve at multiple levels. While pre-mating barriers have been extensively studied, the evolution of post-mating reproductive isolation during early stages of ecological speciation remains poorly understood. In diverging three-spined stickleback ecotypes from two lakes and two rivers, we observed differences in sperm traits between lake and river males. Interestingly, these differences did not translate into ecotype-specific gamete precedence for sympatric males in competitive in vitro fertilization experiments, potentially owing to antagonistic compensatory effects. However, we observed indirect evidence for impeded development of inter-ecotype zygotes, possibly suggesting an early stage of genetic incompatibility between ecotypes. Our results show that pre-zygotic post-copulatory mechanisms play a minor role during this first stage of ecotype divergence, but suggest that genetic incompatibilities may arise at early stages of ecological speciation. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models.

Science.gov (United States)

McCormack, John E; Zellmer, Amanda J; Knowles, L Lacey

2010-05-01

The role of ecology in the origin of species has been the subject of long-standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large-scale tests of whether speciation is associated with niche divergence or whether closely related species tend to be similar ecologically (niche conservatism). Because of the confounding effects of spatial autocorrelation of environmental variables, we generate null expectations for niche divergence for both an ecological-niche modeling and a multivariate approach to address the question: do allopatrically distributed taxa occupy similar niches? In a classic system for the study of niche evolution--the Aphelocoma jays--we show that there is little evidence for niche divergence among Mexican Jay (A. ultramarina) lineages in the process of speciation, contrary to previous results. In contrast, Aphelocoma species that exist in partial sympatry in some regions show evidence for niche divergence. Our approach is widely applicable to the many cases of allopatric lineages in the beginning stages of speciation. These results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model.

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.

Mercury distribution and speciation in soils affected by historic mercury mining

Czech Academy of Sciences Publication Activity Database

Hojdová, Maria; Navrátil, Tomáš; Rohovec, Jan; Penížek, V.; Grygar, Tomáš

2009-01-01

Roč. 200, 1/4 (2009), s. 89-99 ISSN 0049-6979 R&D Projects: GA AV ČR(CZ) KJB300130615 Institutional research plan: CEZ:AV0Z30130516; CEZ:AV0Z40320502 Keywords : mercury speciation * thermo-desorption analysis * forest soil * contamination * mining * contamination (Czech Republic ) Subject RIV: DD - Geochemistry Impact factor: 1.676, year: 2009

SPECIATION OF BINARY COMPLEXES OF Pb(II) AND Cd(II) WITH ...

African Journals Online (AJOL)

ABSTRACT. Chemical speciation of L-Asparagine complexes of Pb(II) and Cd(II) in presence of (0-50% v/v) dimethyl sulfoxide(DMSO)-water mixtures has been studied potentiometrically at 303.0 K and at an ionic strength of 0.16 mol L-1. The models containing different number of species were refined by using the ...